WORKLIST ENTRIES (1):
DNAPOLXTDT View alignment View Structure DNA nucleotidylexotransferase (TDT) signature
Type of fingerprint: COMPOUND with 10 elements
Links:
PRINTS; PR00106 DNAPOLB; PR00867 DNAPOLG; PR00868 DNAPOLI
PRINTS; PR00869 DNAPOLX; PR00870 DNAPOLXBETA; PR00866 RNADNAPOLMS
INTERPRO; IPR001726
PDB; 1BPY 3Dinfo; 1BPX 3Dinfo
SCOP; 1BPY; 1BPX
CATH; 1BPY; 1BPX
Creation date 29-JUN-1998; UPDATE 07-JUN-1999
1. JUNG, G., LEAVITT, M.C., HSIEH, J-C. AND ITO, J.
Bacteriophage PRD1 DNA polymerase: Evolution of DNA polymerases.
PROC.NATL.ACAD.SCI.U.S.A. 84 8287-8291 (1987).
2. DELARUE, M., POCH, O., TORDO, N., MORAS, D. AND ARGOS, P.
An attempt to unify the structure of polymerases.
PROTEIN ENG. 3(6) 461-467 (1990).
DNA carries the biological information that instructs cells how to exist
in an ordered fashion: accurate replication is thus one of the most
important events in the cell life cycle. This function is mediated by
DNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP)
residues to the 5'-end of the growing DNA chain, using a complementary
DNA as template. Small RNA molecules are generally used as primers for
chain elongation, although terminal proteins may also be used.
DNA-dependent DNA-polymerases have been grouped into families, denoted A, B
and X, on the basis of sequence similarities [1,2]. Members of family X
encompass two distinct polymerase enzymes that have similar functionality:
vertebrate polymerase beta (yeast pol 4), and terminal deoxynucleotidyl-
transferase (TdT) (EC 2.7.7.31). The former functions in DNA repair, while
the latter terminally adds single nucleotides to polydeoxynucleotide chains.
Both enzymes catalyse addition of nucleotides in a distributive manner,
i.e. they dissociate after the addition of a single nucleotide.
Three motifs, A, B and C, as defined by Delarue et al. [2], are seen to be
conserved across all DNA-polymerases, with motifs A and C also seen in RNA-
polymerases. They are centered on invariant residues, and their structural
significance was implied from the Klenlow (E.coli) structure: motif A
contains a strictly-conserved aspartate at the junction of a beta-strand
and an alpha-helix; motif B contains an alpha-helix with positive charges;
and motif C has a doublet of negative charges, located in a beta-turn-beta
secondary structure [2].
DNAPOLXTDT is a 10-element fingerprint that provides a signature for the DNA
nucleotidylexotransferase (TDT) family. The fingerprint was derived from an
initial alignment of 7 sequences: the motifs were drawn from conserved
sections spanning the full alignment length, focusing on those regions that
characterise the TDT proteins but distinguish them from the polymerase X
and beta-like families - motif 8, which corresponds to "motif C", encodes
strand 7, which contains an active site Asp. Two iterations on OWL30.1 were
required to reach convergence, at which point a true set comprising 9
sequences was identified.
An update on SPTR37_9f identified a true set of 8 sequences.
SUMMARY INFORMATION
8 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
10| 8 8 8 8 8 8 8 8 8 8
9| 0 0 0 0 0 0 0 0 0 0
8| 0 0 0 0 0 0 0 0 0 0
7| 0 0 0 0 0 0 0 0 0 0
6| 0 0 0 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0 0 0 0
--+---------------------------------------------------
| 1 2 3 4 5 6 7 8 9 10
True positives..
TDT_BOVIN TDT_HUMAN TDT_MOUSE TDT_CHICK
TDT_MONDO TDT_XENLA TDT_AMBME TDT_ONCMY
PROTEIN TITLES
TDT_BOVIN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_HUMAN DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_MOUSE DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_CHICK DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_MONDO DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_XENLA DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_AMBME DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
TDT_ONCMY DNA NUCLEOTIDYLEXOTRANSFERASE (EC 2.7.7.31) (TERMINAL ADDITI
SCAN HISTORY
OWL30_1 2 50 NSINGLE
SPTR37_9f 2 9 NSINGLE
INITIAL MOTIF SETS
DNAPOLXTDT1 Length of motif = 17 Motif number = 1
DNA nucleotidylexotransferase motif I - 1
PCODE ST INT
RRNFLTRLARSKGFRVE OMU53366 45 45
RRTFLMELARSKGFRVE TDT_CHICK 48 48
RRNFLMELARRKGFRVE TDT_BOVIN 59 59
RRAFLMELARRKGFRVE TDT_HUMAN 48 48
RRAFLMELARRKGFRVE TDT_MOUSE 48 48
RRTFLTDLARKKGFRVE MDU91571 48 48
RRYFLMELARKKGFRVE AF039209 48 48
DNAPOLXTDT2 Length of motif = 14 Motif number = 2
DNA nucleotidylexotransferase motif II - 1
PCODE ST INT
LSDDVTHVVAEDNQ OMU53366 64 2
LSDSVTHIVAENNS TDT_CHICK 67 2
LSDSVTHIVAENNS TDT_BOVIN 78 2
LSDSVTHIVAENNS TDT_HUMAN 67 2
LSDSVTHIVAENNS TDT_MOUSE 67 2
LSNSVTHIVAENNS MDU91571 67 2
LSEYVTHVVSEKNS AF039209 67 2
DNAPOLXTDT3 Length of motif = 16 Motif number = 3
DNA nucleotidylexotransferase motif III - 1
PCODE ST INT
LDISWFTDSMREGRPV OMU53366 99 21
LDISWLTACMEMGRPV TDT_CHICK 102 21
LDVSWLIESMGAGKPV TDT_BOVIN 113 21
LDVSWLIECIGAGKPV TDT_HUMAN 102 21
LDISWLIECMGAGKPV TDT_MOUSE 102 21
LDISWLIECMKVGKPV MDU91571 102 21
LDISWFTDRMGAGQPV AF039209 102 21
DNAPOLXTDT4 Length of motif = 16 Motif number = 4
DNA nucleotidylexotransferase motif IV - 1
PCODE ST INT
FTDVMEELAESSEFNE OMU53366 159 44
FTDAFEIMAENYEFKE TDT_CHICK 168 50
FTDAFEILAENSEFKE TDT_BOVIN 179 50
FTDAFDILAENCEFRE TDT_HUMAN 168 50
FTDALDILAENDELRE TDT_MOUSE 168 50
FTDAFEILAKNYEFKE MDU91571 170 52
FTDAFEILAENYEFRE AF039209 164 46
DNAPOLXTDT5 Length of motif = 13 Motif number = 5
DNA nucleotidylexotransferase motif V - 1
PCODE ST INT
FRQAASVLKSLPS OMU53366 182 7
FLRAASVLKSLPF TDT_CHICK 191 7
FMRAASVLKSLPF TDT_BOVIN 202 7
FMRAASVLKSLPF TDT_HUMAN 191 7
FMRASSVLKSLPF TDT_MOUSE 191 7
FMRAISVLKCLPF MDU91571 193 7
FRQAASVLKSLTF AF039209 187 7
DNAPOLXTDT6 Length of motif = 12 Motif number = 6
DNA nucleotidylexotransferase motif VI - 1
PCODE ST INT
PDAILALTGGFR OMU53366 315 120
PDALVTITGGFR TDT_CHICK 324 120
PDAFVTMTGGFR TDT_BOVIN 335 120
PDAFVTMTGGFR TDT_HUMAN 324 120
PDALVTMTGGFR TDT_MOUSE 324 120
PDALVTITGGFR MDU91571 326 120
PDAVVTLTGGFR AF039209 317 117
DNAPOLXTDT7 Length of motif = 23 Motif number = 7
DNA nucleotidylexotransferase motif VII - 1
PCODE ST INT
STFDVSKLPSCRFEDMDCFQKCF OMU53366 372 45
STFVKEQIPSRHVDAMDHFQKCF TDT_CHICK 373 37
STFEKFKLPSRQVDTLDHFQKCF TDT_BOVIN 393 46
STFEKLRLPSRKVDALDHFQKCF TDT_HUMAN 382 46
STFEKFKQPSRKVDALDHFQKCF TDT_MOUSE 383 47
STFEDLKLPSRKIDALDHFQKCF MDU91571 385 47
STMDEDNLPSKSVNLLDHFQKCF AF039209 374 45
DNAPOLXTDT8 Length of motif = 12 Motif number = 8
DNA nucleotidylexotransferase motif VIII - 1
PCODE ST INT
WRAVRVDLVAPP OMU53366 420 25
WKAIRVDLVITP TDT_CHICK 424 28
WKAIRVDLVMCP TDT_BOVIN 438 22
WKAIRVDLVLCP TDT_HUMAN 427 22
WKAIRVDLVMCP TDT_MOUSE 428 22
WKAIRVDLVVCP MDU91571 436 28
WKAIRVDLVFCP AF039209 425 28
DNAPOLXTDT9 Length of motif = 24 Motif number = 9
DNA nucleotidylexotransferase motif IX - 1
PCODE ST INT
DLRTFAQKERQMLLDNHALYDKTK OMU53366 450 18
DLRRYATHERKMMLDNHALYDKRK TDT_CHICK 455 19
DIRRYATHERKMMLDNHALYDKTK TDT_BOVIN 469 19
DLRRYATHERKMILDNHALYDKTK TDT_HUMAN 457 18
DLRRYATHERKMMLDNHALYDRTK TDT_MOUSE 458 18
DLRRYATHEKKMMLDNHALYDKTK MDU91571 467 19
DLRRYASHEKKMMIDNHALYDKTK AF039209 456 19
DNAPOLXTDT10 Length of motif = 20 Motif number = 10
DNA nucleotidylexotransferase motif X - 1
PCODE ST INT
EEDIFTHLGLEYVEPWQRNA OMU53366 482 8
EEEIFAHLGLDYVEPWERNA TDT_CHICK 487 8
EEEIFAHLGLDYIEPWERNA TDT_BOVIN 501 8
EEEIFAHLGLDYIEPWERNA TDT_HUMAN 489 8
EEEIFAHLGLDYIEPWERNA TDT_MOUSE 510 28
EEEIFAHLGLEYIQPSERNA MDU91571 499 8
GEEIFGHLGLEYIDPVERNA AF039209 488 8
FINAL MOTIF SETS
DNAPOLXTDT1 Length of motif = 17 Motif number = 1
DNA nucleotidylexotransferase motif I - 2
PCODE ST INT
RRNFLMELARRKGFRVE TDT_BOVIN 59 59
RRAFLMELARRKGFRVE TDT_HUMAN 48 48
RRAFLMELARRKGFRVE TDT_MOUSE 48 48
RRTFLMELARSKGFRVE TDT_CHICK 48 48
RRTFLTDLARKKGFRVE TDT_MONDO 48 48
RRTFLMELARKRGFQTE TDT_XENLA 48 48
RRYFLMELARKKGFRVE TDT_AMBME 48 48
RRNFLTRLARSKGFRVE TDT_ONCMY 45 45
DNAPOLXTDT2 Length of motif = 14 Motif number = 2
DNA nucleotidylexotransferase motif II - 2
PCODE ST INT
LSDSVTHIVAENNS TDT_BOVIN 78 2
LSDSVTHIVAENNS TDT_HUMAN 67 2
LSDSVTHIVAENNS TDT_MOUSE 67 2
LSDSVTHIVAENNS TDT_CHICK 67 2
LSNSVTHIVAENNS TDT_MONDO 67 2
LSDSVTHIVAENNS TDT_XENLA 67 2
LSEYVTHVVSEKNS TDT_AMBME 67 2
LSDDVTHVVAEDNQ TDT_ONCMY 64 2
DNAPOLXTDT3 Length of motif = 16 Motif number = 3
DNA nucleotidylexotransferase motif III - 2
PCODE ST INT
LDVSWLIESMGAGKPV TDT_BOVIN 113 21
LDVSWLIECIGAGKPV TDT_HUMAN 102 21
LDISWLIECMGAGKPV TDT_MOUSE 102 21
LDISWLTACMEMGRPV TDT_CHICK 102 21
LDISWLIECMKVGKPV TDT_MONDO 102 21
LDISWFTECMEAGRPV TDT_XENLA 102 21
LDISWFTDRMGAGQPV TDT_AMBME 102 21
LDISWFTDSMREGRPV TDT_ONCMY 99 21
DNAPOLXTDT4 Length of motif = 16 Motif number = 4
DNA nucleotidylexotransferase motif IV - 2
PCODE ST INT
FTDAFEILAENSEFKE TDT_BOVIN 179 50
FTDAFDILAENCEFRE TDT_HUMAN 168 50
FTDALDILAENDELRE TDT_MOUSE 168 50
FTDAFEIMAENYEFKE TDT_CHICK 168 50
FTDAFEILAKNYEFKE TDT_MONDO 170 52
FTDAFDILAEHFEFCE TDT_XENLA 164 46
FTDAFEILAENYEFRE TDT_AMBME 164 46
FTDVMEELAESSEFNE TDT_ONCMY 159 44
DNAPOLXTDT5 Length of motif = 13 Motif number = 5
DNA nucleotidylexotransferase motif V - 2
PCODE ST INT
FMRAASVLKSLPF TDT_BOVIN 202 7
FMRAASVLKSLPF TDT_HUMAN 191 7
FMRASSVLKSLPF TDT_MOUSE 191 7
FLRAASVLKSLPF TDT_CHICK 191 7
FMRAISVLKCLPF TDT_MONDO 193 7
FLRASSLIKSLPF TDT_XENLA 187 7
FRQAASVLKSLTF TDT_AMBME 187 7
FRQAASVLKSLPS TDT_ONCMY 182 7
DNAPOLXTDT6 Length of motif = 12 Motif number = 6
DNA nucleotidylexotransferase motif VI - 2
PCODE ST INT
PDAFVTMTGGFR TDT_BOVIN 335 120
PDAFVTMTGGFR TDT_HUMAN 324 120
PDALVTMTGGFR TDT_MOUSE 324 120
PDALVTITGGFR TDT_CHICK 324 120
PDALVTITGGFR TDT_MONDO 326 120
PDAIVTLTGGFR TDT_XENLA 320 120
PDAVVTLTGGFR TDT_AMBME 317 117
PDAILALTGGFR TDT_ONCMY 315 120
DNAPOLXTDT7 Length of motif = 23 Motif number = 7
DNA nucleotidylexotransferase motif VII - 2
PCODE ST INT
STFEKFKLPSRQVDTLDHFQKCF TDT_BOVIN 393 46
STFEKLRLPSRKVDALDHFQKCF TDT_HUMAN 382 46
STFEKFKQPSRKVDALDHFQKCF TDT_MOUSE 383 47
STFVKEQIPSRHVDAMDHFQKCF TDT_CHICK 373 37
STFEDLKLPSRKIDALDHFQKCF TDT_MONDO 385 47
STFDETKLPSRHVDALDHFQKCF TDT_XENLA 377 45
STMDEDNLPSKSVNLLDHFQKCF TDT_AMBME 374 45
STFDVSKLPSCRFEDMDCFQKCF TDT_ONCMY 372 45
DNAPOLXTDT8 Length of motif = 12 Motif number = 8
DNA nucleotidylexotransferase motif VIII - 2
PCODE ST INT
WKAIRVDLVMCP TDT_BOVIN 438 22
WKAIRVDLVLCP TDT_HUMAN 427 22
WKAIRVDLVMCP TDT_MOUSE 428 22
WKAIRVDLVITP TDT_CHICK 424 28
WKAIRVDLVVCP TDT_MONDO 436 28
WKAVRLDLVITP TDT_XENLA 425 25
WKAIRVDLVFCP TDT_AMBME 425 28
WRAVRVDLVAPP TDT_ONCMY 420 25
DNAPOLXTDT9 Length of motif = 24 Motif number = 9
DNA nucleotidylexotransferase motif IX - 2
PCODE ST INT
DIRRYATHERKMMLDNHALYDKTK TDT_BOVIN 469 19
DLRRYATHERKMILDNHALYDKTK TDT_HUMAN 457 18
DLRRYATHERKMMLDNHALYDRTK TDT_MOUSE 458 18
DLRRYATHERKMMLDNHALYDKRK TDT_CHICK 455 19
DLRRYATHEKKMMLDNHALYDKTK TDT_MONDO 467 19
DLRRYATHEKRMMLDNHGLYDKTK TDT_XENLA 456 19
DLRRYASHEKKMMIDNHALYDKTK TDT_AMBME 456 19
DLRTFAQKERQMLLDNHALYDKTK TDT_ONCMY 450 18
DNAPOLXTDT10 Length of motif = 20 Motif number = 10
DNA nucleotidylexotransferase motif X - 2
PCODE ST INT
EEEIFAHLGLDYIEPWERNA TDT_BOVIN 501 8
EEEIFAHLGLDYIEPWERNA TDT_HUMAN 489 8
EEEIFAHLGLDYIEPWERNA TDT_MOUSE 510 28
EEEIFAHLGLDYVEPWERNA TDT_CHICK 487 8
EEEIFAHLGLEYIQPSERNA TDT_MONDO 499 8
EEDIFKQLGLDYLEPWERNA TDT_XENLA 488 8
GEEIFGHLGLEYIDPVERNA TDT_AMBME 488 8
EEDIFTHLGLEYVEPWQRNA TDT_ONCMY 482 8
User query: Display/Full Code "DNAPOLXTDT"