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InBase, The Intein Database:
DOD Homing Endonuclease Motifs

InBase Reference: Perler, F. B. (2002). InBase, the Intein Database. Nucleic Acids Res. 30, 383-384.

 

The Endonuclease Motifs Page will not be updated after July 7, 2003

 

Please note: Finding DOD homing endonuclease motifs is not sufficient evidence that the gene contains an intein since DOD homing endonucleases are also present in introns and as free standing genes.


DOD (LAGLIDADG) Homing Endonuclease Motifs


The entire intein sequence is present in the individual intein files.
Central intein motifs C, D, E & H are in the DOD family core homing endonuclease domain (Duan 1997, Hall 1997, Klabunde 1998, Perler 1998, Perler 1997, Pietrokovski 1998, Dalgaard 1997, Belfort 1997, Jurica 1999 and Mueller 1994). These motifs form 4 conserved helices (Duan 1997 and Heath 1997). Blocks C and E are the original LAGLIDADG motifs and each contains an endonuclease active site Asp (D) or Glu (E). Block D contains a putative active site Lys (K), as observed in the Sce VMA intein (Duan 1997). Several inteins have mutations in these active site residues and therefore may not be active endonucleases although the remainder of the motif is present.
Mini-inteins are indicated as 'none' in Blocks C, D, E & H.
Dashes indicate that the individual motif ihas not been found.
The Ssp GyrB intein has an HNH family homing endonuclease between intein Blocks B and F.
The Ssp DnaX and Cau RIR1 inteins have a DOD homing endonuclease present in a different reading frame than the intein.
The position of the last amino acid in each block is listed to the right of the block.
An individual or amino acid group designation (see The Consensus Key below) in the consensus line indicates that the amino acid (upper case letter) or group (lower case letter) is present in a majority of the first 38 inteins sequenced, excluding the highly similar allelic inteins Perler 1997.
Dots in the consensus motifs indicate the position of non-conserved amino acids.

Please note: the absence of motif annotation indicates that the record was submitted without this information and it has yet to be added by the curator.


Intein                     Block C        Block D       Block E         Block H                  
Consensus                  LhG..hhaG      .K.IP..h      .L.GhFahDG      p.S..hh..h..LL..hGI      
Eucarya
Intein                     Block C        Block D       Block E         Block H                  
APMV Pol                                                                                         
Abr PRP8                   None           None          None            None                     
Aca-G186AR PRP8            FVGFWLCDGI 141 NKRIPFMY 393  LLAGLIDSDG 413  RISPTLFWDIVTLARSLGL 447  
Aca-H143 PRP8              FVGFWLCDG 140                LLAGLIDSDV 389  RISPTLFWDIVTLARSLGL 423  
Aca-JER2004 PRP8           FVGFWLCDG140   NKRIPLMY 394  LLAGLIDSDG 414  RISPTLFWDIVTLARSLGL 448  
Aca-NAm1 PRP8              FLGFWLCDG 140                LLAGLIDSDG 373  RISPTLFWDIVTLARSLGL 407  
Ade-ER3 PRP8               YLALWLCDG 141                LLAGLIDGDG 405  RIAPSLFWDIVVLARSLGL 439  
Ade-SLH14081 PRP8          YLALWLCDG 141                LLAGLIDGDG 405  RIAPSLFWDIVVLARSLGL 439  
Afu-Af293 PRP8             YFLGLWLGD 357  RKHIPSIY 678  VLAGLIDSDG 698  RWHSKLFWDVVALARSLGL 732  
Afu-FRR0163 PRP8           YFLGLWLGD 357  RKHIPSIY 678  VLAGLIDSDG 698  RWHSKLFWDVVALARSLGL 732  
Afu-NRRL5109 PRP8          YFLGLWLGD 357  RKHIPSIY 678  VLAGLIDSDG 698  RWHSKLFWDVVALARSLGL 732  
Agi-NRRL6136 PRP8          None           None          None            None                     
Ani-FGSCA4 PRP8            YFLGLWLGD 155  KKRIPQVF 464  VLAGLLDSDG 484  LCHKELFWDVVTLARSLGF 518  
Avi PRP8                   None           None          None            None                     
Bci PRP8                   FLGLWLGDG 391  KKHIPSIY 697  VLAGLIDSDG 717  IWHKTLFWDVVALARSLGL 751  
Bde-JEL197 RPB2            LFGLVLSAG 166  YCLLPKWL 251  FLGALFGGNG 271  ESTVVYLKQVATLLGMLNI 318  
Bde-JEL423 PRP8-1          SFGYLLGAW 233                                                         
Bde-JEL423 PRP8-2          FVGLWLGEY 186  IPRIPSAY 341  LLAGYASCFV 361  TDLAPLFGDLETVSRGCGL 395  
Bde-JEL423 RPC2            LFGLVLSAG 166  YCLLPKWL 251  FLGALFGGNG 271  ESTVVYLKQVATLLGMLNI 318  
Bde-JEL423 eIF-5B          CIGLWILLG 195                                CKNNMIFENIKRLSSSLGL 326  
Bfu-B05 PRP8               FLGLWLGDG 391  KKHIPSIY 670  VLAGLIDSDG 690  IWHKTLFWDVVALARSLGL 724  
CIV RIR1                   THGFFCGDG 131  --------      WLAGYLDADG 204  CIHLDFLKRIQLLLIGMGV 237  
CV-NY2A ORF212392          ILGAWLGDG 171  NKHIPDDI 253  ILAGLLDTDG 273  QKNKRLSEDIAFVARSLGY 302  
CV-NY2A RIR1               TKGFFSADG 124                WLAGFMDGDG 200  SINKSFLQDIRLMLQTIGI 233  
CZIV RIR1                  None           None          None            None                     
Cba-WM02.98 PRP8           None           None          None            None                     
Cba-WM728 PRP8             None           None          None            None                     
Ceu ClpP                   FFGLWIANG 151  NKYLPDWV 230  ----------      STSERFANDVSRLALHAGT 281  
Cga PRP8                   None           None          None            None                     
Cgl VMA                    LLGTWIASK 187  VTNHSSKL 273  LALSMINQDG 286  VEIDSSINGLAKLSRSLGL 339  
Cla PRP8                   FLGLWLGDD 150  SKHIPQVY 382  VLAGLLDSHG 402  ETDGRLFWDAVHLARSLGF 435  
Cmo ClpP                   FFGLWIANG 151  NKYLPDWV 230                  STSERFANDVSRLALHAGT 281  
Cmo RPB2 (RpoBb)           FFALWLTGT 288  KKSLPSWV 517                  TNSLNLSDDIMRLALHAGW 575  
Cne-A PRP8 (Fne-A PRP8)    None           None          None            None                     
Cne-AD PRP8 (Fne-AD PRP8)  None           None          None            None                     
Cne-JEC21 PRP8             None           None          None            None                     
Cpa ThrRS                  None           None          None            None                     
Cre RPB2                   LYGYWLGDG 167  AKWFAGWV 290  ILVGLSFADG 310  TSSARFRDDTVRLALHAGY 339  
CroV Pol                                  EKKVPQCI 232  FLIGLYPEYK 252  CKNNEFSLGIYYLIKKLGY 280  
CroV RIR1                  LLGLILGKG 136                LIKGLIDSNG 230                           
CroV RPB2                  None           None          None            None                     
CroV Top2                  LLGLWIGED 214  SKGIPDDY 243  VLAGIIDKKG 263  LSNKELINDIIYLAQSLGF 296  
Cst RPB2                   LFGLFLSES 154  RKNLPDFI 229                  LPNSSFADDFQRLALHAGY 281  
Ctr ThrRS                                                                                        
Ctr VMA                    LLGTWAGIG 210  VKSIPQHI 325  LIAGLVDAAG 345  TSFRHVARGLVKIAHSLGI 379  
Ctr-MYA3404 VMA            LLGTWAGIG 210  VKSIPQHI 325  LIAGLVDAAG 345  TSFRHVARGLAKIAHSLGI 379  
Ddi RPC2                                                                                         
Dhan GLT1                  LGLWLGDGD 363  NQNKPEGC 395  VIAGLMDSDG 484  EDHKKIVYDLKELALSCGI 518  
Dhan VMA                                                                                         
Eni PRP8                                                                                         
Eni-FGSCA4 PRP8            YFLGLWLGD 155  KKRIPQVF 464  VLAGLLDSDG 484  LCHKELFWDVVTLARSLGF 518  
Fte RPB2 (RpoB)            FFGLWVTKG 147  KKSLPPWA 233                  TKSIKLADDVMRLALHAGW 290  
Gth DnaB                   None           None          None            None                     
HaV01 Pol                                                                                        
Hca PRP8                   FVGFWLCDG 140  NKRIPLMY 393  LLAGLIDSDG 413  RISPTLFWDIVTLARSLGL 447  
IIV6 RIR1                  THGFFCGDG 131  --------      WLAGYLDADG 204  CIHLDFLKRIQLLLIGMGV 237  
Kex-CBS379 VMA             LIGFWVGNG 208  VSKIAHEL 344  FVAGLVDATG 364  IESKSTVLGLVKIARSLGI 399  
Kla-CBS683 VMA             LLGAFVGSS 206  SSGIPSFM 282  FLAGIVDSQN 302  TLSVKTHDGIARLARSLGI 330  
Kla-IFO1267 VMA            LLGAFVGSS 206  SSGIPSFM 282  FLAGIVDSQN 302  TLSVKTHDGIARLARSLGI 331  
Kla-NRRLY1140 VMA          LLGAFVGSS 206  SSGIPSFM 282  FLAGIVDSQN 302  TLSVKTHDGIARLARSLGI 331  
Lel VMA                                                                                          
Mca-CBS113480 PRP8         FLGLWLGDG 133  RKRIPAVF 421  VLAGLIDSDG 441  RWHSALFWDTVALARSLGF 464  
Nau PRP8                   None           None          None            None                     
Nfe-NRRL5534 PRP8          None           None          None            None                     
Nfi PRP8                   FLGLWLGDG 156  RKHIPSIY 378  VLAGLIDSDG 396  RCHSKLFWDVVALARSLGL 430  
Ngl-FR2163 PRP8            None           None          None            None                     
Ngl-FRR1833 PRP8           None           None          None            None                     
Nqu PRP8                   None           None          None            None                     
Nspi PRP8                  None           None          None            None                     
Pabr-Pb01 PRP8             YFLGLWLGD 156  KKRIPSVY 429  LLAGLIDSSG 449  DSNSTLIWDVVTLARSLGF 472  
Pabr-Pb03 PRP8             YFLGLWLGD 159  KKRIPSVY 432  LLAGLIDSGG 452  DSNSTLIWDVVTLARSLGF 486  
Pan CHS2                   WFGFWLGNG 405                VLAGLIESDG 529  YELKKLVEDARKLALSCGI 563  
Pan GLT1                   LLGFWLGDG 435  NASRPAGA 468  VIAGLIDSDG 557  DEHRKIVEDLRDLALSCGI 590  
Pbl PRP8-a                 None           None          None            None                     
Pbl PRP8-b                 None           None          None            None                     
Pbr-Pb18 PRP8              YFLGLWLGD159   KKRIPSVY 432  LLAGLIDSGG 452  DSNSTLIWDVVTLARSLGF 486  
Pch PRP8                   None           None          None            None                     
Pex PRP8                   None           None          None            None                     
Pgu GLT1                   FLGLWLGEG 311  NKDKPAEA 344  LLAGLVDSDG 431  ELHKKIVYDLKEMATSCGI 465  
Pgu-alt GLT1               FLGLWLGEG 311  NKDKPAEA 344  LLAGLVDSDG 431  ELHKKIVYDLKEMATSCGI 465  
Pno GLT1                   FLGIWMGDG 386  NRQCPDGA 419  FIAGLVESDG 507  DDHKKIIYDLKDLALSCGI 523  
Pno RPA2                                                                                         
Ppu DnaB                   None           None          None            None                     
Pst VMA                    LVGLWVGDG 211  FKLVPSFL 301  FISGLVDSDG 321  TIYPAVRDGLVSVARSLGI 356  
Ptr PRP8                   FLGLWLGDG 370  RKHIPTAY 703  VLAGLLDSDG 723  LWHKTLFWNTVALARSLGF 757  
Pvu PRP8                   None           None          None            None                     
Pye DnaB                   None           None          None            None                     
Sas RPB2                   IGGCLLGRG 140  ARQFPHWV 209                  VASKHLADDIQRLCLHAAS 265  
Sca-CBS4309 VMA            LLGFWVGNG 209  EKSVPLHL 372  FIAGLIDSDG 392  TIYKGVSEGLIRLARSLGI 415  
Sca-IFO1992 VMA            LLGFWVGNG 209  EKSVPLHL 372  FIAGLIDSDG 392  TIYKGVSEGLIRLARSLGI 415  
Scar VMA                   FLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSVARSLGL 359  
Sce VMA                    LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sce-DH1-1A VMA             LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sce-JAY291 VMA             LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sce-OUT7091 VMA            LLGLWIGDG 211  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sce-OUT7112 VMA            LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sce-YJM789 VMA             LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Sda VMA                    LLGFWVGNG 210  VKAIPMHL 353  FIAGLVDSIG 373  TAYKSVSEGLIRLARSLGI 408  
Sex-IFO1128 VMA            LIGFWVGNG 208  VTKIAHEL 344  FVAGLVDAAG 364  TESKSTVLGLVKIARSLGI 399  
She RPB2 (RpoB)            FFGIWIAEG 147  YRKLPIWV 230                  TSSVELADDISRLALHAGW 307  
Sja VMA                    LLGVWVGAG 217  VKSIPSHF 331  FLAGLIDADG 351  TTSPKVRDGTVRIARSLGI 383  
Spa VMA                    LLGLWIGDG 219  VKNIPSFL 307  FLAGLIDSDG 327  TIHTSVRDGLVSLARSLGL 359  
Spu PRP8                   FLGIWLGNG 221  AKHIPVGY 300  LLAGLIDANG 320                           
Sun VMA                    VMGSWVGAG 206  TKTIPKEL 267  FIAGLVDTQG 287  TVYERISNDLVKLARSLGI 322  
Tgl VMA                    LLGLWVGDG 221  VKHVPSYL 309  FLAGLIDSDG 329  TIHKTVMEGTVAVARSLGL 361  
Tpr VMA                    LLGLWAGDV 221  VKNVPTYL 309  FLAGLIDSDG 329  TTLKTVMAGTVAVARSLGL 361  
Ure-1704 PRP8              None           None          None            None                     
Vpo VMA                    LLGLWTGSG 219  NKTVPSFL 392  FLAGLIDSNG 302  LEDNKVMSGIVSLIRSLGL 295  
WIV RIR1                   None           None          None            None                     
Zba VMA                    LLGLWVGDG 221  VKHVPSYL 309  FLAGLIDSDG 329  TIHKTVMEGTVAVARSLGL 361  
Zbi VMA                    FLGLWIGGG 218  SKNVPAYL 306  FLAGLVDSEG 326  TCHHSVMTGVVAVARSLGI 355  
Zro VMA                    FLGLWIGDG 220  SKNVPGYI 309  FLAGIIDSTG 329  TIDQSVMTGTVAVARSLGI 358  
Eubacteria
Intein                     Block C        Block D       Block E         Block H                  
AP-APSE1 dpol              None           None          None            None                     
AP-APSE2 dpol              None           None          None            None                     
AP-APSE4 dpol              None           None          None            None                     
AP-APSE5 dpol              None           None          None            None                     
AP-Aaphi23 MupF                                                                                  
Aae RIR2                   LLIVLQADG 149  TKFFDEWV 223  FVEELVKWDG 245  STKEKRNKDFVQALCALGG 278  
Aave-AAC001 Aave1721       VLGWVVTEG 137                LVDRMIEGDG 238                           
Aave-AAC001 RIR1           LLGLLIGDG 125                LLRGLFDTDG 244  QSNPALLQTVQRMLLRLGI 278  
Aave-ATCC19860 RIR1        LLGLLIGDG 125                LLRGLFDTDG 244  QSDLELLQCAQRMLLRLGI 278  
Aba Hyp-02185              None           None          None            None                     
Ace RIR1                   None           None          None            None                     
Aeh DnaB-1                 LLAYFLGDG 121  EKAVPEVV 278  FLSRLFACDG 298  TSSRALARDVQHLLLRFGI 332  
Aeh DnaB-2                 LLAHLVGDG 120  EKHLPQEV 201  FLRHLWATDG 221  TASRHLIQDVAALLLRFGI 255  
Aeh RIR1                   LMGLLLGDG 125                FLRGLYDADG 233  QSDSDNLEAAQRMLLRLGI 267  
AgP-S1249 MupF                                                                                   
Aha DnaE-c                 None           None          None            None                     
Aha DnaE-n                 None           None          None            None                     
Alvi-DSM180 GyrA                                                                                 
Ama MADE823                VLGAWLGDG 133  NKHIPEVF 206  LLAGLIDTDG 226                           
Amax-CS328 DnaX            None           None          None            None                     
Aov DnaE-c                 None           None          None            None                     
Aov DnaE-n                 None           None          None            None                     
Apl-C1 DnaX                None           None          None            None                     
Arsp-FB24 DnaB             LLGYWLGDG 124  NKHIPEEY 200  LLQGLLDSDG 220                           
Asp DnaE-c                 None           None          None            None                     
Asp DnaE-n                 None           None          None            None                     
Ava DnaE-c                 None           None          None            None                     
Ava DnaE-n                 None           None          None            None                     
Avin RIR1 BIL                                                                                    
Bce-MCO3 DnaB              VLGALLGDG 126  DKFIPRLY 206  VLRGLLDTDG 226  TASAQLASDVRELARSLGA 256  
Bce-PC184 DnaB             VLGALLGDG 126  DKFIPRLY 206  VLRGLLDADG 226  TASAQLASDVRELARSLGA 256  
Bse-MLS10 TerA             LFGYWIGNG 130  DKRIPAAF 190  LLQGLMDSDG 210  TILPELAKDVQDVLGSLGI 241  
BsuP-M1918 RIR1            IMGIIAGDG 131  KTRVPEFI 219  YLSGLFQTDG 239  SIHYESLQDVQKLLLNMGV 274  
BsuP-SPBc2 RIR1            IMGIIAGDG 131  KTRVPEFI 219  YLSGLFQTDG 239  SIHYESLQDVQKLLLNMGV 274  
Bvi IcmO                   None           None          None            None                     
CP-P1201 Thy1              LVGFFAGDG 129                LLQGMIDSDG 226  STSKSLRDAFSQVALHAGF 258  
Cag RIR1                   LIGLLTGDG 114  TDKVFQLA 210  LLRGLFTADG 226  ATSLELLQQVQLLLFNFGI 260  
Cau SpoVR                                                                                        
CbP-C-St RNR               LIGAYLGDG 129                VLDGIYFTDG 228  TTSDSLKEDLEILIHSLGM 254  
CbP-D1873 RNR              LIGAYLGDG 129                VLDGIYFTDG 228  TTSDSLKEDLEILINSLGM 254  
Cbu-Dugway DnaB            None           None          None            None                     
Cbu-Goat DnaB              None           None          None            None                     
Cbu-RSA334 DnaB            None           None          None            None                     
Cbu-RSA493 DnaB            None           None          None            None                     
Cce Hyp1-Csp-2             LLGLILSDG 133                FLAGYLDGDG 254  VVKREIFSPLVCIFLSLGV 283  
Cch RIR1                   LIGLLTGDG 114  TDKVFQLA 210  LLRGLFTADG 226  ATSLELLQQVQLLLFNFGI 260  
Ccy Hyp1-Csp-1             None           None          None            None                     
Ccy Hyp1-Csp-2             LLGVILSDG 133                FLAGYLDGDG 254  IGKNKMFSPLVCAFLSLGI 283  
Cfl-DSM20109 DnaB          LLGVWLGDG 133  ELHIPADY 180  LLAGLLDTDG 200  VTHERLARDVRELVHSLGY 230  
Chy RIR1                   FLGYFLGDG 113  EKDIPSSL 188  LLRGLFSADG 208  STSYPLLRKVQILLLSLGI 241  
Ckl PTerm                  ILGVWIGNG 154  NKHIPEIY 264  LLKGLMDTDG 284  QKNKIIIDGFSNLLSSLGI 314  
Cra-CS505 DnaE-c           None           None          None            None                     
Cra-CS505 DnaE-n           None           None          None            None                     
Cra-CS505 GyrB             None           None          None            None                     
Csp-CCY0110 DnaE-c         None           None          None            None                     
Csp-CCY0110 DnaE-n         None           None          None            None                     
Csp-PCC7424 DnaE-c         None           None          None            None                     
Csp-PCC7424 DnaE-n         None           None          None            None                     
Csp-PCC7425 DnaB           LLGHLIGDG 122  EKFIPDQV 207  FLRHLWSTDG 227  TSSERLARDVQSLLLRLSI 263  
Csp-PCC7822 DnaE-n         None           None          None            None                     
Csp-PCC8801 DnaE-c         None           None          None            None                     
Csp-PCC8801 DnaE-n         None           None          None            None                     
Cth ATPase BIL             None           None          None            None                     
Cth-ATCC27405 TerA         LFGYWIGNG 131  EKRIPIEY 191  LLQGLIDSDG 211  TILFELAKDVQDLLWSLGI 242  
Cth-DSM2360 TerA           LYGYWLGNG 135  LKRIPYEV 160  LLQGLMDSDG 215  STEKQLALDVRELLWSLGI 246  
Cwa DnaB                                                                                         
Cwa DnaE-c                 None           None          None            None                     
Cwa DnaE-n                 None           None          None            None                     
Cwa PEP                    FLGGIITDG 132                FLGGVIDGDG 238  KNRLHIYISEENLLQAVII 260  
Cwa RIR1                                                                                         
Daud RIR1                  LLGLLVGDG 126                FLRGLFDADG 231  QSNRDLLGIVQRMLARLGI 265  
Dge DnaB                   LLAYLLAEG 122  NADPELVQ 140  FLRVLLSCDG 226  VASEGLARDVHHALVRFGI 259  
Dha-DCB2 RIR1              LLGLLLGDG 124  SKAITQEL 202  LLRGLYDTDG 222  TDLAGLKVVQRMLQRLGII 257  
Dha-Y51 RIR1               LLGLLLGDG 124  SKAITQEL 202  LLRGLYDTDG 222  TDLAGLKVVQRMLQRLGII 257  
Dpr-MLMS1 RIR1             LLGLLLGDG 125                FLRGLFDADG 232  QSELADLQAVQRMLLRLGI 266  
Dra RIR1                   LLGSLIGDG 124  HKTLTDKV 202  VLQGLFDADG 222  SDLSLLKRAQRMLSRLGIM 257  
Dra Snf2-c                                              VLQGLLDTDG C39  SVSEHLARGVVELVQSLGG C67  
Dra Snf2-n                 YTLGALLGD N129 YKFIPPDY N205                                          
Dra-ATCC13939 Snf2         YTLGALLGD 129  YKFIPPDY 205  VLQGLLDTDG 225  SVSEHLARGVVELVQSLGG 254  
Dth UDP GD                 FIGYYLSEG 239                LLKGLFRGDG 339                           
Dvul ParB                                                                                        
EP-Min27 Primase           VIGSLLGDG 128  NKFIPRVF 199  MLCGLLETDG 219  SASEELRNGVVQLVNSLGG 249  
Fal DnaB                   VLGSWLGDE 143  DRHIPAGY 270  LLAGLLDADG 290  TTNPRLAREVRELVLSLGC 321  
Fsp-CcI3 RIR1              None           None          None            None                     
Gob DnaE                                                                                         
Gob Hyp                                                                                          
Gvi DnaB                   None           None          None            None                     
Gvi RIR1-1                                                                                       
Gvi RIR1-2                                                                                       
Hhal DnaB                  LLGHLIGDG 120  EKTVPDCV 276  FLNRLFSSDG 295  FSSDGWVTHLASGQGQIGY 309  
Kfl-DSM17836 DnaB          None           None          None            None                     
Kra DnaB                   LLGHLIGDG 125                FLRHLWATDG 229  STSLQLIQDVSRLLLRFGI 264  
LLP-KSY1 PolA              None           None          None            None                     
LP-phiHSIC Helicase                                                                              
Lsp-PCC8106 GyrB                                                        HNH FAMILY ENDONUCLEASE  
MP-Be DnaB                 FLGLWLGDG 130  NKHIPAAY 208  LLRGLIDSDG 228  NANRNLVYQFQELVVGLGF 258  
MP-Be gp51                                                                                       
MP-Catera gp206            LLGAWLGDG 126  NKHIPDRY 190  LLAGLMDSDG 201  MKNERLMRQVLQLVRSLGY 239  
MP-KBG gp53                                                                                      
MP-Mcjw1 DnaB              ILGAWLGDG 126  AKHVPQDY 197  LLQGLMDTDG 207  NTNRDLAEAALFLARSLGW 240  
MP-Omega DnaB              LLGYWLGDG 135  NKHIPETY 200  LLAGIMDSDG 220  MKNEALMRQVLMLARSLGY 259  
MP-U2 gp50                                                                                       
Maer-NIES843 DnaB          None           None          None            None                     
Maer-NIES843 DnaE-c        None           None          None            None                     
Maer-NIES843 DnaE-n        None           None          None            None                     
Mau-ATCC27029 GyrA         LAGALVSEG 133  DKFVPEFV 211  FLQALFEGDG 231  TRSERLAREVQQLLLEFGV 265  
Mav-104 DnaB               TLGAWLGDG 147  NKHIPTEY 196  LLAGLLDTDG 216  VTNQRLARDVNELIVSLGY 246  
Mav-ATCC25291 DnaB         TLGAWLGDG 147  NKHIPTEY 196  LLAGLLDTDG 216  VTNQRLARDVNELIVSLGY 246  
Mav-ATCC35712 DnaB         TLGAWLGDG 147  NKHIPTEY 196  LLAGLLDTDG 216  VTNQRLARDVNELIVSLGY 246  
Mav-PT DnaB                TLGAWLGDG 147  NKHIPTEY 276  LLAGLLDTDG 298  VTNQRLARDVNELIVSLGY 326  
Mbo Pps1                   LAGYYLAEG 144  NKKLSDLL 223  LVDAYVNGDG 243  TTSRLWAFQLQSILARLGH 276  
Mbo RecA                   LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mbo SufB (Mbo Pps1)        LAGYYLAEG 144  NKKLSDLL 223  LVDAYVNGDG 243  TTSRLWAFQLQSILARLGH 276  
Mbo-1173P DnaB             SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mbo-AF2122 DnaB            SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mca MupF                                                                                         
Mca RIR1                   HRALPSWDG 108  RLTAPLET 218  LLRGMFDADG 236  QTDLGNLQTVQRMLLRLGV 270  
Mch RecA                   VLGSLMGDG 123  --------      LQRAVYLGDG 193  FLSEEYLKALTPLALAIWY 214  
Mcht-PCC7420 DnaE-1        None           None          None            None                     
Mcht-PCC7420 DnaE-2c       None           None          None            None                     
Mcht-PCC7420 DnaE-2n       None           None          None            None                     
Mcht-PCC7420 GyrB                                                                                
Mcht-PCC7420 RIR1-1        FLGYLQGDG 136                YLAGLADADG 234  SVHPDFLRQIQTLYASLGI 262  
Mcht-PCC7420 RIR1-2        LLGSLVGDG 125                FLQGLFDADG 220  QHNLELLQAVQRMLLRLGI 254  
Mex Helicase                                                                                     
Mex TrbC                                                                                         
Mfa RecA                   ILGSLMGGG 123  --------      LRRAVYLGDG 193  FLSEDYLKALTPLALAVWY 214  
Mfl GyrA                   HLGAFISEG 134  DKAVPEWL 212  FLQALFEGDG 232  TRSGRLAKDIQQMLLEFGV 266  
Mfl RecA                   VLGSLMGDG 123  --------      LQRAVYLGDG 193  FLSEENFKALTPLALVFWY 214  
Mfl-ATCC14474 RecA         VLGSLMGDG 123  --------      LQRAVYLGDG 193  FLSEEYLKALTPLALAIWY 214  
Mfl-PYR-GCK DnaB           TLGAWLGDG 147  AKHIPIDY 276  LLAGLLDTDG 296  GTNARLIGDVAELVVSLGY 326  
Mga GyrA                   LLGAFISEG 134  DKYVPEWM 212  FLRALFEGGG 232  TISKQLAMDVQQMLLEFGV 266  
Mga RecA                   VLGSLMGDG 126  --------      LRSAVYLGDG 197  FLSEEYLKGLTPLSLAIWY 218  
Mga SufB (Mga Pps1)        LLGLYVGDG 137  TKRVPDWV 213  FLGGWVDADG 230  CANQALIGQARELAELAGL 272  
Mgi-PYR-GCK DnaB           TLGAWLGDG 147  AKHIPIDY 276  LLAGLLDTDG 296  GTNARLIGDVAELVVSLGY 326  
Mgi-PYR-GCK GyrA           LLGAFISDG 134  AKTVPNWL 212  FLQALFEGDG 232  TRSGQLAKDVQNMLLEFGV 266  
Mgo GyrA                   LLGAFISEG 134  DKSVPEWL 212  FLQALFEGDG 232  TRSRQLAIDVQQMLLEFGV 266  
Min-1442 DnaB              TLGAWLGDG 147  NKHIPTEY 195  LLAGLLDTDG 215  VTNQRLACDVAELIVSLGY 245  
Min-ATCC13950 GyrA         LLGAFISEG 134  DKAVPEWL 212  FLQALFEGDG 232  TRSERLAKDVQQMLLEFGV 266  
Mkas GyrA                  LLGAFISEG 134  DTYVPEWM 212  FLQALFEGDG 232  TVSKQLAMDVQQMLLEFGV 266  
Mkas-ATCC12478 GyrA        LLGAFISEG 134  DTYVPEWM 212  FLQALFEGDG 232  TVSKQLAMDVQQMLLEFGV 266  
Mle-Br4923 GyrA            LFGAFISGG 134  DKLVPDWL 212  FLQALFEGEG 232  TPSERLAADVQQMLLEFGV 266  
Mle-TN DnaB                None           None          None            None                     
Mle-TN GyrA                LFGAFISGG 134  DKLVPDWL 212  FLQALFEGEG 232  TLSERLAADVQQMLLEFGV 266  
Mle-TN RecA                VLGSLMGDG 123  --------      LQRAVYLGDG 194  FSLEEYLKALTPLVLAIWY 215  
Mle-TN SufB (Mle Pps1)     LLGLWLGDG 151  TKRLPAWI 225  LIGGLVDADG 245  FASRELLEDVRQLAIGCGL 276  
Mma GyrA                   LLGAFISEG 134  DKSVPDWL 212  FLQALFEGGG 232  TRSRQLAVDVQQMLLEFGI 266  
Mmag Magn8951 BIL          None           None          None            None                     
Msh RecA                   VLGSLMGDG 123  --------      LQRAVYMGDG 193  FLSEEYLKALTPLALAIWY 214  
Msm DnaB-1                 None           None          None            None                     
Msm DnaB-2                 MLAHMIGDG 123  EKFVPAQV 207  FLRHLWATDG 227  TTSRQLADDVVQLLLRVGV 262  
Msp-KMS DnaB               TLGAWLGDG 134  DKHIPIEY 181  LLAGLLDTDG 201  VTNKRLAADVAELVVSLGY 231  
Msp-KMS GyrA               LAGAFISEG 134  DKFVPEWI 212  FLQALFEGDG 232  TRSERLAADVQQMLLEFGI 266  
Msp-MCS DnaB               TLGAWLGDG 134  DKHIPIEY 181  LLAGLLDTDG 201  VTNKRLAADVAELVVSLGY 231  
Msp-MCS GyrA               LAGAFISEG 134  DKFVPEWI 212  FLQALFEGDG 232  TRSERLAADVQQMLLEFGI 266  
Mthe RecA                  VLGSLMGDG 123  --------      LRRAVYLGDD 193  FISEEYLKALTPLALAIWY 215  
Mtu SufB (Mtu Pps1)        LAGYYLAEG 144  NKKLSDLL 223  LVDAYVNGDG 243  TTSRLWAFQLQSILARLGH 276  
Mtu-C RecA                 LLCYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-CDC1551 DnaB           SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mtu-CPHL RecA              LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-Canetti RecA           LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-EAS054 RecA            LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-F11 DnaB               SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mtu-H37Ra DnaB             SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mtu-H37Rv DnaB             SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mtu-H37Rv RecA             LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-Haarlem DnaB           SLARMIGDG 123  EKCVPEAV 206  FLRHLWSAGG 226  STSRRLIDDVAQLLLRVGI 261  
Mtu-K85 RecA               LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-R604 RecA-n            LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-So93 RecA              LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-T17 RecA-c             LLGYLIGDG C38  EKTIPNWF C116 LLFGLFESDG C138 TTSEQLAHQIHWLLLRFGV C172 
Mtu-T17 RecA-n                                                                                   
Mtu-T46 RecA               LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-T85 RecA               LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mtu-T92 RecA               LLGYLIGDG 123  EKTIPNWF 201  LLFGLFESDG 223  TTSEQLAHQIHWLLLRFGV 257  
Mvan DnaB                  TLGAWLGDG 147  NKHIPTEY 276  LLAGLLDTDG 296  VTSRRLAADVAELVVSLGY 326  
Mvan GyrA                  LLGAFISEG 134  AKMVPEWL 212  FLQALFEGDG 232  TRSGQLAKDVQQMLLEFGV 266  
Mxa RAD25                                                                                        
Mxe GyrA                   None           None          None            None                     
Naz-0708 RIR1-1                                                                                  
Naz-0708 RIR1-2            FIGALFGDG 153                FFCGLIDTDG 252  SASEKFLRNLQEIGEAVGL 282  
Nfa DnaB                   LLAHMIGDG 115  EKFIPRRV 207  FLRHLWATDG 227  STSRRLIDDVAQLLLRLGV 262  
Nfa Nfa15250                                                                                     
Nfa RIR1                                                                                         
Nosp-CCY9414 DnaE-n        None           None          None            None                     
Npu DnaB                   LLGHLIGDG 121  EKFVPREL 207  FLRHLWSTDG 227  SSSERLAFDVQTLLLRLGI 263  
Npu GyrB                   ---------      --------      ----------      HNH FAMILY ENDONUCLEASE  
Npu-PCC73102 DnaE-c        None           None          None            None                     
Npu-PCC73102 DnaE-n        None           None          None            None                     
Nsp-JS614 DnaB             VLGAWLGDG 146  DKHIPADY 211  LLAGLMDTDG 231  VTNKRLADDVYELVVSLGY 262  
Nsp-JS614 TOPRIM           AHGFTYGDG 122  FKELPDPD 173  WLAGYFAADG 191  SARRENLEFVRMVTTRLGI 221  
Nsp-PCC7120 DnaB           LLGHLIGDG 121  EKFVPQEL 207  FLRHLWSTDG 227  TSSYRLAVDVQTLLLKLGI 263  
Nsp-PCC7120 DnaE-c         None           None          None            None                     
Nsp-PCC7120 DnaE-n         None           None          None            None                     
Nsp-PCC7120 RIR1           LIGFTHGDG 140  QPNIPLTV 223  YLAGLMDSDG 247  SVYRSFIRQVSVVLSSLGI 277  
Oli DnaE-c                 None           None          None            None                     
Oli DnaE-n                 None           None          None            None                     
PP-PhiEL Helicase                                                                                
PP-PhiEL ORF11                                                                                   
PP-PhiEL ORF39             VLGVLLGDG 139  GKVIPEEY 224  LLQGLLDTDG 244  DKHKSVSFSSSSKLLSLGV 265  
PP-PhiEL ORF40                                                                                   
Pfl Fha BIL                None           None          None            None                     
Plut RIR1                  LIGLLVGDG 114                LLRGLFTADG 226  STSLDLLLQVQLLLLNFGI 260  
Pma-EXH1 GyrA              None           None          None            None                     
Pma-ExH1 DnaE              LLADGYLAK 127  EKFIPEFV 206  FLAYYWDCDG 226  TISKDLAYGLYYLLLRLGI 255  
Pna RIR1                   LIGLITGDG 125  KLEVPEVV 211  YLQGLFQTDG 231  SSHRPLLQDVQVLLANFGV 266  
Pnuc DnaB                  VLGALLGDG 126  DKYIPATY 211  LFQGLMDTDG 231  TASKQLSEDVASLARSLGG 261  
Posp-JS666 DnaB            VLGGLLGDG 126                VLRGLLDTDG 229  TASHQLAKDVQELVRSLGG 259  
Posp-JS666 RIR1            LLGLLIGDG 125  EMGMRPGH 211  LLRGLFDADG 236  QSDLSLLQTAQRMLLRLGI 270  
Pssp-A1-1 Fha              None           None          None            None                     
Psy Fha                    None           None          None            None                     
Rbr-D9 GyrB                None           None          None            None                     
Rce RIR1                   LLSLLVGDA 130                FLRGLFDADG 233  QSDLERLRAVQRMLLRLGI 267  
Rer-SK121 DnaB                                                                                   
Rma DnaB                   LLGHLIGDG 121  EKKVPALL 206  FLRHLWATDG 226  TSSYQLARDVQSLLLRLGI 263  
Rma-DSM4252 DnaB           LLGHLIGDG 121  EKKVPALL 206  FLRHLWATDG 226  TSSYQLARDVQSLLLRLGI 262  
Rma-DSM4252 DnaE           LLAYLLGDG 119  EKRVPEEV 204  LGRLWSTDGS 225  STSMELIEDIAHLLLRLGI 253  
Rsp RIR1                   LLGLLIGDG 124  RKTITPEI 207  VLRGLFDADG 228  QSDLALLQAAQRMLARLGM 262  
SaP-SETP12 dpol                                                                                  
SaP-SETP3 Helicase         LMGLWLGDG 137  NKHIPHNY 208  LLAGLLDSDG 228  SVSERLADDFCYLCRSLGF 259  
SaP-SETP3 dpol                                                                                   
SaP-SETP5 dpol                                                                                   
Sare DnaB                  LLARLVGGR 124                FLRHLWAAGG 172  SPSRRILDDVSRLLLRYGI 206  
Sav RecG Helicase          YLFGLLLGD 130  GKFIPEDF 208  LLQGLLDTDG 228  SVSLRSASLRLAEDVAWLV 254  
Sel-PC6301 RIR1            LLGNFIGDG 125  SFGLKQGL 199  FLRGLFDADG 226  QGSQEKGVSVRLAQSDLGL 247  
Sel-PC7942 DnaE-c          None           None          None            None                     
Sel-PC7942 DnaE-n          None           None          None            None                     
Sel-PC7942 RIR1            LLGNFIGDG 125  SFGLKQGL 199  FLRGLFDADG 226  QGSQEKGVSVRLAQSDLGL 247  
Sel-PCC6301 DnaE-c         None           None          None            None                     
Sel-PCC6301 DnaE-n         None           None          None            None                     
Sep RIR1                                                                                         
ShP-Sfv-2a-2457T-n Primase VIGSLLGDG 128  NKFIPRVF 199  MLCGLLETDG 219                           
ShP-Sfv-2a-301-n Primase   VIGSLLGDG 128  NKFIPRVF 199  MLCGLLETDG 219                           
ShP-Sfv-5 Primase          VIGSLLGDG 128  NKFIPRVF 199  MLCGLLETDG 219  SASEELRNGVVQLVNSLGG 249  
SoP-SO1 dpol                                                                                     
Spl DnaX                   None           None          None            None                     
Sru DnaB                   FLGLWLGDG 129  DKHIPHLY 206  LLAGLIDSDG 226                           
Sru PolBc                                                                                        
Sru RIR1                   ILGMWQSDG 120  KGTVPEWI 211  YVRGLLVADG 231  DVDRDFLQELQLLFNNLGL 267  
Ssp DnaB                   LLGHLIGDG 122  EKFVPNQV 207  FLRHLWSTDG 227  TSSEKLAKDVQSLLLKLGI 263  
Ssp DnaE-c                 None           None          None            None                     
Ssp DnaE-n                 None           None          None            None                     
Ssp DnaX                   DOD FAMILY     ENDONUCLEASE  IS IN A         DIFFERENT READING FRAME  
Ssp GyrB                   ---------      --------      ----------      HNH FAMILY ENDONUCLEASE  
Ssp-JA2 DnaB               None           None          None            None                     
Ssp-JA2 RIR1               LLGNLLGDG 125                FLCGLFDADG 225  QSHLGTLKAVQRMLARLGI 259  
Ssp-JA3 DnaB               None           None          None            None                     
Ssp-JA3 RIR1               LLGNLLGDG 125                FLCGLFDADG 225  QSNLDTLKAVQRMLARLGI 259  
Ssp-PCC7002 DnaE-c         None           None          None            None                     
Ssp-PCC7002 DnaE-n         None           None          None            None                     
Ssp-PCC7335 RIR1           LIGFTHGDG 140  QPNRPLEV 225  YLAGLMDSDG 249  SVYRNFVRQVAAVLSSLGI 279  
StP-Twort ORF6                                                                                   
Susp-NBC371 DnaB intein    FLGLWLGDG 129  NKHIPRSY 207  LLAGLIDSDG 227  LGFRSSLVKKKASIKAIGY 274  
Taq-Y51MC23 DnaE                                                                                 
Taq-Y51MC23 RIR1                                                                                 
Tcu-DSM43183 RecA          GDGSLSPNR 123                LRRVVYFGDG 193  HLTWDYLKALTPLALAIWY 214  
Tel DnaE-c                 None           None          None            None                     
Tel DnaE-n                 None           None          None            None                     
Ter DnaB-1                                                                                       
Ter DnaB-2                 None           None          None            None                     
Ter DnaE-1                 None           None          None            None                     
Ter DnaE-2                                                                                       
Ter DnaE-3c                None           None          None            None                     
Ter DnaE-3n                None           None          None            None                     
Ter GyrB                                                                                         
Ter Ndse-1                                                                                       
Ter Ndse-2                                                                                       
Ter RIR1-1                 FLGYLSGNG 137                YLAGLVDADG 234  SVDQGFLRQVQALYASLGI 262  
Ter RIR1-2                 MLGWWYRDG 120                FLQGIFSADG 226  MVSEKLLQQIQLILSNLGI 259  
Ter RIR1-3                 TLGAALGNG 122                FIAGLADTDG 205  VSDYERAKRLQLLLTKCGI 235  
Ter RIR1-4                 FLGCLFGNG 153                FFCGLIDTNG 251  SASSDFIHNLQQIGESIGL 281  
Ter Snf2                   FVAWQVAEG 135  EKTIPLFI 220  FLSNYFDAEG 249  TASSQLIQELSILLRRFGV 271  
Ter ThyX                                                                                         
Tfus RecA-1                LLGYLTAAG 138  AARIPQCV 211  FLAALYTAAG 231  TASAPLAREVQYLLYGLGI 261  
Tfus RecA-2                VYGSLMGRG 123  --------      LHRVVDFGDG 193  HLTWEFLKQLTPLALAVWY 214  
Tfus Tfu2914                                                                                     
Thsp-K90 RIR1              LLGMLVGDG 125                FLRGMFDADG 234  QSDMSRLEAVQRMLLRLGI 268  
Tth-DSM571 RIR1            LLGLLVGDG 125                FIRGLFDCDA 230  QSDLDLLKAVQRMLLRLGI 264  
Tth-HB27 DnaE-1                                                                                  
Tth-HB27 DnaE-2                                                                                  
Tth-HB27 RIR1-1                                                                                  
Tth-HB27 RIR1-2                                                                                  
Tth-HB8 DnaE-1                                                                                   
Tth-HB8 DnaE-2                                                                                   
Tth-HB8 RIR1-1                                                                                   
Tth-HB8 RIR1-2                                                                                   
Tvu DnaE-c                 None           None          None            None                     
Tvu DnaE-n                 None           None          None            None                     
Tye RNR-1                  FFGFWLAEG 182  DKFIPSEI 264  MKGDGWSGDG 289  TKSKRLADDIQEIVLKLGM 313  
Tye RNR-2                  IFSWILSEG 126                FLETYLKGDG 222  VTEEEAKDFITAIAVLAGY 251  
Archaea
Intein                     Block C        Block D       Block E         Block H                  
Ape APE0745                                                                                      
Cme-boo Pol-II             None           None          None            None                     
Fac-Fer1 RIR1              VLGWLVGDG 119  KLNVPDKV 202  FLQALFEADG 222  SISLNLLKQVQMLLLNFGI 256  
Fac-Fer1 SufB (Fac Pps1)   ILGLYTAEG 140  MKLPPEKQ 229  LIDYYLKGDG 241  TASKILALQLQEMLSRNNT 274  
Fac-TypeI RIR1             VLGWLVGDG 119  KLNVPDKV 202  FLQALFEADG 222  SISLNLLKQVQMLLLNFGI 256  
Fac-typeI SufB (Fac Pps1)  ILGLYTAEG 140  MKLPPEKQ 229  LIDYYLKGDG 241  TASKILALQLQEMLSRNNT 274  
Hma CDC21                                                                                        
Hma Pol-II                 None           None          None            None                     
Hma PolB                                                                                         
Hma TopA                                                                                         
Hmu-DSM12286 MCM           None           None          None            None                     
Hmu-DSM12286 PolB                                                                                
Hsa-R1 MCM                 None           None          None            None                     
Hsp-NRC1 CDC21             None           None          None            None                     
Hsp-NRC1 Pol-II            None           None          None            None                     
Hut MCM-2                  None           None          None            None                     
Hut-DSM12940 MCM-1                                                                               
Hvo PolB                                                                                         
Hwa GyrB                                                                                         
Hwa MCM-1                  None           None          None            None                     
Hwa MCM-2                                                                                        
Hwa MCM-3                  None           None          None            None                     
Hwa MCM-4                                                                                        
Hwa Pol-II-1               LLGYYAAAG 264                                                         
Hwa Pol-II-2               LLGQFIAQR 239                FLQGFILAEN 343  ESETTVTLETPSVGVKDGL 378  
Hwa PolB-1                                              FLAGTLDGSE 272  TESASIARWYAQLYRRLGI 303  
Hwa PolB-2                                                                                       
Hwa PolB-3                                                                                       
Hwa RCF                                                                                          
Hwa RIR1-1                 LLGLWIDTG 190  IKEAPTNV 271  FLRGCFTAEG 284                           
Hwa RIR1-2                 FLGYFMGSG 152                FLRGVFEAIG 255  TTSTTLADQLQSLLLSLGH 283  
Hwa Top6B                                                                                        
Hwa rPol A''               None           None          None            None                     
Maeo Pol-II                IIGYYLAEG 256                MLSAYFTGDG 352                           
Maeo RFC                   LVGFIIGDG 306  GYKVPEWI 395  FIRGLFGADG 415                           
Maeo RNR                   FLGLFVAEG 178  NKNIPEFI 249  FLGGLISGDG 269  TTSEQLLGQLHILLSGLNM 297  
Maeo-N3 Helicase           FIGYFIGDG 122  FYILPLEK 203  FIAGLFDSDG 216  SISENLIKKLQLALLRFGI 247  
Maeo-N3 RtcB               LLGFALGDG 157  IKKSPLWV 262  FLAGLFGADG 275  DSLLNYLADIKKMLSEFGI 318  
Maeo-N3 UDP GD             LIGYYLAEG 225  NKQIPPQI 305  FLKGILRGDG 328  TVSKKLANSLMILLQSLGI 363  
Mein-ME PEP                LCGAILSDG 134  SKIMPSKI 148  FLAGYVDGDG 180  SKHVKKIEGLILSLYRVGI 212  
Mein-ME RFC                AFGLYTAEE 163  NKRVPSFM 249  YLKGLADGDI 269  SVSKDLLIDIAWLSRISGI 296  
Memar MCM2                 FLGYFLSEG 153  AKSLPPEQ 231  LLDALMLGDG 244  TSSRRLADDVTELLLKKGL 275  
Memar Pol-II               None           None          None            None                     
Mesp-FS406 PolB-1                                                                                
Mesp-FS406 PolB-2                                                                                
Mesp-FS406 PolB-3          FLGYYVSEG 245  NKQIPEII 322  FLEGYFIGDG 342  TKSEKLAYQLMFLLNSLGI 372  
Mesp-FS406-22 LHR          LLGFWMADG 215  KNGMFPEI 289  FLSGYFDGDG 310  TFNKRFAEGIRDLLLYFGI 345  
Mfe-AG86 Pol-1             FLGYFVARG 289  RKHIPEQL 364                  AKDEEYLNQLMLLFNLVGI 413  
Mfe-AG86 Pol-2             LVGLLIGDG 155  KKIIPKFM 232  FLRGLFSADG 252  NTNENIIENVRKLLYLVGI 285  
Mhu Pol-II                 None           None          None            None                     
Mja GF-6P                  IIGYIIGDG 215  NERTPEFV 291  YLRGIFDAEG 311  MTSKCFIKEIQFLLLRFGI 342  
Mja Helicase               FIGYFIGDG 122  NKNIDAFC 197  LIAGLFDSDG 216  SISEKLVEQLQFVLLRFGI 247  
Mja Hyp-1                  ---------      RSRIPEKI 156  RLVGYFLSEG 173  TTSEILMNQLRLISLRLGF 293  
Mja IF2                    FAGVMFGDG 215  NIKIPQIL 286  FIKGYFDADG 306  SASKEFIEGLSILLLRFEI 337  
Mja KlbA                   None           None          None            None                     
Mja PEP                    LGGAVLSDG 134  SRKIPSEI 196  LIAGFVDGDG 228  SSHIKKIEGLIVGLYRLGI 260  
Mja Pol-1                  LIGILLAEG 135  --------      ILRGFFEGDG 235  TNNYDKIKFIASLLDRLGI 268  
Mja Pol-2                  FLGFFVTRG 289  KKHIPEEL 364  ----------      AKDEKYLNQLMILFNLVGI 413  
Mja RFC-1                  WLGYFIGDG 134  KVRIPKEI 211  FLRAYFDCDG 229  TASKEMAEDLVYALLRFGI 258  
Mja RFC-2                  MLGLYVAEG 162  NKRIPDII 251  FLKGLADGDS 271  SKSDNLLIDTVWLARISGI 301  
Mja RFC-3                  LLGFIIGDG 232  GYNIPKWI 321  FLRGLFGADG 341  DKTLEFFEEVKKMLEEFEV 384  
Mja RNR-1                  FLGLFVAEG 178  NKNSPEFI 247  FLGGLISGDG 267  TTSEQLLGQLHLLLSDLGM 297  
Mja RNR-2                  LIGAFLSEG 236  NKEIPSIL 314  LIKGYIDGDG 333  TTSETLRDTLCLALKILGI 368  
Mja RtcB (Mja Hyp-2)       LLGFAFGDG 156  IYKIPEWI 254  FLAGLFGADG 274  ENILEFLNEIKLLLAEFDI 317  
Mja TFIIB                  ILGYIIAEG 147  NKRIPSII 216  FIDGIFNGKD 236  FVSKELAEDVIFLLLQIKE 258  
Mja UDP GD                 LIGYYLSEG 216  NKNIPPQM 299  FLKGLFRGDG 319  TVSKKMAHSLLILLQLLGI 354  
Mja r-Gyr                  FAGLVLGDG 212  IFSLPESY 281  LIAGYFDTDG 294  SKRRDVLEKIGIYLNSIGI 333  
Mja rPol A'                ---------      RKLIPLTY 146  RIVGHVMGDG 165  YSFEVRKKSLCILLKALGC 244  
Mja rPol A''               FIGIYLAEG 181  TKKIAEFV 254  LIRGYFDGDG 274  SNSKELIDGIAILLARFNI 305  
Mka CDC48                  LLGLYVAEG 136  KRLGPLLS 206  ALRGYYTGDG 224  TVSKRLADELLVALQILDI 259  
Mka EF2                                                                                          
Mka RFC                    ---------                    ELLRELADDG 159  EASEDVSVDLAWLARISGV 180  
Mka RtcB                   ILGFAMGDG 159  PYKVPDWI 252  FLAGLFAADG 272  ENLREFMNDVAKLLREFGI 305  
Mka VatB                   VAGLIASDG 239  VLKMPREL 312  YLAGYVDGDG 325  TADRERAGDLQLLLKRLGV 354  
Mth RIR1                   None           None          None            None                     
Mvu-M7 Helicase                                                         STSELFIKRLQVALLRFGI 157  
Mvu-M7 Pol-1                                                                                     
Mvu-M7 Pol-2               FLGYFVTRG 286  NKKHIPEE 360                  AKDEDYLNQLMILFNLVGI 410  
Mvu-M7 Pol-3               None           None          None            None                     
Mvu-M7 UDP GD              LMGYYLSEG 216  NKNIPPQI 299  FLKGLFRGDG 319  TVSKKMAHSLLILLQSLGI 354  
Neq Pol-c                  None           None          None            None                     
Neq Pol-n                  None           None          None            None                     
Nma-ATCC43099 MCM          ILGYIAGDG 158                                SSSYELLLGTKMLLLEFGI 290  
Nma-ATCC43099 PolB-1                                    FLAGAIDGDG 295  AENRSIGTWYVKLFKRLGI 324  
Nma-ATCC43099 PolB-2                                                                             
Nph CDC21                                                                                        
Nph PolB-1                 DLAGAVDDG 127                LLETLVDGDG 311  TDSGLGEFWTQSDRLKDDV 332  
Nph PolB-2                 LLAWYVTEG 214  DKRIPQLV 298  FMQTLISGDG 318                           
Nph rPol A''                                                                                     
Pab CDC21-1                None           None          None            None                     
Pab CDC21-2                                                                                      
Pab IF2                    LAGRKGNID 149                FLRGYFEERS 173  VEARELVEPLSLALLRFGI 200  
Pab KlbA                   None           None          None            None                     
Pab Lon                    LMGILFNGG 158  DLKMPWWV 231  PSLFLAFLEG?244  NKNLPFFQELSWYLGLFGI 276  
Pab Moaa                   LIGYFVSDG 227  VFKIPEGA 291  LLSGLFNGDG 320  STSKGLIRDILYLLASLGI 353  
Pab Pol-II                 None           None          None            None                     
Pab RFC-1                  WLGYFFGNG 133  KDSIPEQA 196  FLRAYFDCNA 212  TAGKEIAEQISYALAGLGI 240  
Pab RFC-2                  VVGFILGDG 301  GYTVPEWI 388  FLRGLFGADG 408  ERTVEFLNDVADLLREFDV 451  
Pab RIR1-1                 LAGFIAGNG 150  ENGIPPKI 176  FITGLFDAEG 196  MVNKKLIEAVTHYLNSLGI 226  
Pab RIR1-2                 LLGIIYADG 141  NIRVPEAI 227  FLAGFFDGDG 247  SISREFIKEAQLLFLALGI 277  
Pab RIR1-3                 VLGWFIGDG 157  EKRIPEIV 230  FLRGLFSADG 250  SKSRELLREVQDLLLLFGI 280  
Pab RtcB (Pab Hyp-2)       ILGFAFGDG 159  AYRVPGWI 249  FLAGLFAADG 269  ENLVEFLGDVAKLLAEFGI 312  
Pab VMA                    FLGYLIADG 164  KLGVPRNK 227  FIKAYIMCDG 258  TASEEAAYGFSYLLAKLFI 289  
Par RIR1                   LLGRVVGDG 156  DKLVPEVI 238  FLRGLFDADG 258  STSKRLLREVQQLLLLFGI 288  
Pfu CDC21                                 NO                                                     
Pfu IF2                    LAGASLDIP 158                FRKHVGFTDS 225  KAKESERYPILEELRRLGL 255  
Pfu KlbA                   LAGVILGDG 202  MWDIPDVV 279  FIAGLFDADG 298  TKSETVARKIWYVLQRLGI 329  
Pfu Lon                    IMGALFGSG 165  KLKLPWWV 243  PSLFLAFMDG 256  DNVETFFEEISWYLSFFGI 293  
Pfu RFC                    WLGYFMGSG 132  LTLIPREG 202  FLRAYSDCNG 218  TDNNDMAQQIAYALASFGI 247  
Pfu RIR1-1                 LAGFIAGDG 150  DNGIPPQI 231  FIAGLFDAEG 251  MVNKRLIEDVTHYLNALGI 281  
Pfu RIR1-2                 VLGWFIGDG 157  EKRIPEIV 230  FLRGLFSADG 250  SKSRELLREVQDLLLLFGI 280  
Pfu RtcB (Pfu Hyp-2)       ILGFALGDG 159  AYRIPVWI 252  FLAGFFGADG 272  ENIKEFLYDISRILEEFGV 314  
Pfu TopA                   LIGYLAGKG 176  --------      FLAGYYDATL 256  GLTLEALYKIKVYLQLLGI 277  
Pfu VMA                    FLGYVIGDG 160  KLGIPGNK 222  FINAYIACDG 253  TASEEGAYGLTYLLAKLGI 285  
Pho CDC21-1                None           None          None            None                     
Pho CDC21-2                                                                                      
Pho IF2                    FAGTIFGRE 159                FLRGFFDING 212  GAPHEVLEELSLILLRLGI 243  
Pho KlbA                   LAGVILGDG 202  EWDVPDIV 279  FIAGLFDADG 298  TKSENVARKIWYALQRLGI 327  
Pho LHR                    LLGFWMASG 214  KLEVPPII 283  FLAGYFDGNG 303  AFNRKFAEGIRDILLQLGI 337  
Pho Lon                    ILGALFSDG 215  KLELPWWI 297  FMDGLYSGDG 316  EKKLPFFEEIAWYLSFFGI 362  
Pho Pol I                  LLGYYISSG 289  GKRIPEFI 351  FLKGLNGNAE 371  TKSELLVNQLILLLNSIGV 395  
Pho Pol-II                 None           None          None            None                     
Pho RFC                    WLGYFLGGG 132  NAHIPKEC 202  FLRAYFDCNG 218  TASKEMSQEIAYALAGFGI 247  
Pho RIR1                   VLGWLIGDG 160  DKRVPEIV 233  FLRGLFTADG 253  SKSRELLRDVQDLLLLFGI 283  
Pho RadA                   None           None          None            None                     
Pho RtcB (Pho Hyp-2)       ILGFALANG 159  HDSIPEWI 223  FLAGLFGANG 243  THSRELLNDVSRILEGFKV 277  
Pho VMA                    FLGYLMANG 160  RLGVPEDK 224                  LASEEGAYELSYLFAKLGI 278  
Pho r-Gyr                  GKGTLKGDK 168  --------      MIAGYFDASG 241  SKRGDILRMLSVYLYQIGI 269  
Psp-GBD Pol                LLGYYVSEG 289  NKRVPEVI 364  FLEGYFIGDG 384  TKSELLVNGLVLLLNSLGV 414  
Pto VMA                    LLGLYASYG 141                                HDNEQNILKISYMLTGLGI 248  
Smar 1471                                                                                        
Smar MCM2                                                                                        
Tac-ATCC25905 VMA          None           None          None            None                     
Tac-DSM1728 VMA            None           None          None            None                     
Tag Pol-1 (Tsp-TY Pol-1)   LSGIILAEG 126  LKNIESLY 213  VLRGFFERDA 226  TNNKWKIDIVAKLLDSLGI 259  
Tag Pol-2 (Tsp-TY Pol-2)   FLGYYVSEG 290  NKRIPSII 365  FLRAYFVGDG 385  TKSELLANQLVFLLNSLGV 415  
Tag Pol-3 (Tsp-TY Pol-3)   None           None          None            None                     
Tba Pol-II                 LIGYYLAEG 229                RALRKAFGDG 324                           
Tfu Pol-1                  LAGIILAEG 126  VREIMDGI 209  VLRGFFEGDG 224  TNNEWKIEVVSKLLNKLGI 259  
Tfu Pol-2                  LIGLLVGDG 155  NKAIPSFM 233  FLRGLFSADG 253  SNSLFTETKPNRYLEKESG 305  
Thy Pol-1                  LLGYYVSEG 289  NKRVPEAI 364  FIEGYFIGDG 384  TKSELLVNGLVLLLNSLGV 414  
Thy Pol-2                  LIGLLVGDG 155  SKRIPEFM 234  FLRGLFSADG 253  SVNPELSSSVRKLLWLVGV 286  
Tko CDC21-1                None           None          None            None                     
Tko CDC21-2                                                                                      
Tko Helicase                                                                                     
Tko IF2                    FAGVMFGDG 220                FLRGYFDADG 302  SASQEFLEDLSLLLLRFGI 342  
Tko KlbA                   VAGVILGDG 202  IWDVPDVV 280  FIAGLFDADG 299  TKSESAARKIWYALQRLGI 330  
Tko LHR                    LLGFWMADG 215  KLGTFPSI 289  FLAGYFDGDG 309  TFNKRFAEGIRDILLQLGI 343  
Tko Pol-1 (Pko Pol-1)      LAGILLAEG 126  VKEIMDNI 209  VLRGFFEGDG 226  TKNEWKIKLVSKLLSQLGI 259  
Tko Pol-2 (Pko Pol-2)      LLGYYVSEG 289  NKRIPEFV 364  FLEGYFIGDG 384  NEKRALANQLVLLLNSVGV 413  
Tko Pol-II                                                                                       
Tko RFC                    WLGYFIGDG 132  KVYIPEKG 202  FLRAYFDCDA 225  TASREMAEQVTYALAGFGI 254  
Tko RIR1-1                 LAGFIAGDG 150  TNGIPQPI 231  FITGLFDAEG 251  SKPGVELGMVNRKLIEDIT 273  
Tko RIR1-2                 VLGWFIGDG 157  EKRVPEII 230  FLRGLFSADG 250  SKDRGLLRDVQDLLLLFGI 280  
Tko RadA                                                                                         
Tko TopA                   LFGLVAGDG 221                FLAGYYDADG 314  SKNRMAIYTVKQMWQLLGV 353  
Tko r-Gyr                  VFGLVLGDG 208  GKLHPLVF 271  MIAGYFDTDG 290  SKRGDVLRMLSVYLYQIGI 327  
Tli Pol-1                  LLGYYVSEG 290  NKRIPSVI 365  FLEAYFTGDG 385  TKSELLANQLVFLLNSLGI 415  
Tli Pol-2                  LVGLIVGDG 156  RRKIPEFM 234  FLRGLFSADG 254  NIDADFLREVRKLLWIVGI 287  
Tma Pol                    LLGYYVSEG 289  NKRVPEVI 364  FLEGYFIGDG 384  TKSELLANGLVLLLNSLGV 414  
Ton-NA1 LHR                LLGFWLADG 214  KFGVFPEI 287  FLSGYFDGDG 308  TFNPEFAEGIRNLLLQLGI 342  
Ton-NA1 Pol                LLGYYVSEG 287  NKRVPEVI 362  FLEGYFIGDG 382  TKSETLVNGLIILLNSLGI 412  
Tpe Pol                    LVGLLVGDG 156  NKKIPEFM 234  FLRGLFSADG 254  TISDRLASDVRKLLWLVGI 287  
Tsi-MM739 Lon              VMGILFSDG 215  KLELPWWI 297  PSLFLAFIDG 310  EKKLPFFEEIAWHLGLFGI 362  
Tsi-MM739 Pol-1            LLGYYVSEG 290  NKRIPPII 365  FLEAYFAGDG 385  TKSELLANQLIFFLNSLGV 415  
Tsi-MM739 Pol-2            None           None          None            None                     
Tsi-MM739 RFC              IFGLYAAEG 162  NKRLPGFV 251  FLKGLADGDG 271  SVSRDLLIDTVWLARVSGI 301  
Tsp AM4 RtcB               ILGFAFGDG 159  LYNVPEWI 252  FLAGLFAADG 272  ENLRGFMEEIAGLLAEFGI 315  
Tsp-AM4 LHR                LLGFWIADG 214  ELGIEGSI 248  FLSGYFDGDG 309  TFNPEFAEGIRNLLLQLGI 344  
Tsp-AM4 Lon                LVGALFSDG 215  RLELPWWV 297  PSLFLAFFDG 310  EDKLPFFEELAWHLGLFGI 362  
Tsp-AM4 RIR1               LAGFIAGDG 150  DTGIPPEI 231  FITGLFDAEG 251  MVNRKLIEDIAHYLSSLGI 281  
Tsp-GE8 Pol-1              LLGYYVSEG 287  NKRVPEVI 362  FFEGYFIGDG 382  TKSEELVNGLVVLLNSLGI 412  
Tsp-GE8 Pol-2              LIGLLVGDG 155  NKRIPSFM 233  FLRGLFSADG 254  SVNRELSNEVRKLLWLVGV 286  
Tsp-GT Pol-1               LLGYYVSEG 289  NKRVPEAI 364  FIEGYFIGDG 385  TKSELLVNGLVLLLNSLGV 414  
Tsp-GT Pol-2               LIGLLVGDG 155  SKRIPEFM 233  FLRGLFSADG 253  SVNPELSSSVRKLLWLVGV 286  
Tsp-OGL-20P Pol            LLGYYVSEG 289  NKRVPEVV 364  FLGGYFIGDG 384  TKSELLVNGLVLLLNSLGI 414  
Tthi Pol                   LLGYYVSEG 289  NKRVPEVV 364  FLGGYFIGDG 384  TKSELLVNGLVLLLNSLGI 414  
Tvo VMA                    None           None          None            None                     
Tzi Pol                    LLSYYVSEG 287  NKRVPEII 362  FLEGCFIGDG 382  TKSEELVNGLVILLNSLGV 412  
Unc-ERS PFL                LLGYYLSEG 215  NKKLPTEF 297  LIIGLFRGDG 317  ITSKLLRYQISLILLRLGI 352  
Unc-ERS RIR1                                                                                     
Unc-ERS RNR                WLGLLLSEG 249  NKSVPDFM 319  FIRGYHAGDG 339  TISEGILRFLRYAFLILGV 366  
Unc-MetRFS MCM2            None           None          None            None                     

CONSENSUS LINE KEY:
hhydrophobic residues (G,V,L,I,A,M)
aacidic residues (D,E)
raromatic residues (F,Y,W)
ppolar residues (S,T,C)
/to align block, 1 or more AA not shown
-motif absent
.non-conserved residue
*gap introduced into Block F
underlined residuesconserved in almost all inteins
capital letterssingle letter amino acid code


Last database update: 11/05/10

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