WORKLIST ENTRIES (1):
DNAPOLG View alignment DNA-polymerase gamma (family A) signature
Type of fingerprint: COMPOUND with 9 elements
Links:
PRINTS; PR00106 DNAPOLB; PR00868 DNAPOLI; PR00869 DNAPOLX
PRINTS; PR00870 DNAPOLXBETA; PR00871 DNAPOLXTDT; PR00866 RNADNAPOLMS
INTERPRO; IPR002297
PROSITE; PS00447 DNA_POLYMERASE_A
PDB; 1KFS 3Dinfo; 1KRP 3Dinfo
SCOP; 1KFS; 1KRP
CATH; 1KFS; 1KRP
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).
3. GENGA, A., BIANCHI, L. AND FOURY, F.
The nuclear gene MIP1 is strictly required for mitochondrial DNA
replication and mitochondrial DNA polymerase activity.
J.BIOL.CHEM. 261 9328-9332 (1986).
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 A,
which includes bacterial and bacteriophage polymerases, share significant
similarity to E.coli polymerase I; hence family A is also known as the pol I
family. The bacterial polymerases also contain an exonuclease activity,
which is coded for in the N-terminal portion. The yeast gamma polymerases
show some similarity to the prokaryotic nuclear polymerases of family A,
but their function is restricted to mitochondrial DNA replication and
repair [3].
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].
DNAPOLG is a 9-element fingerprint that provides a signature for the DNA-
polymerase gamma 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 gamma polymerases but distinguish them from the rest of
the pol I family - motif 5 includes part of the region encoded by PROSITE
pattern DNA_POLYMERASE_A (PS00447), which corresponds to "motif B". Two
iterations on OWL30.1 were required to reach convergence, at which point a
true set comprising 10 sequences was identified. A single partial match was
also found, DPOG_CHICK, a chicken gamma polymerase fragment that matches
motifs 4-9.
An update on SPTR37_9f identified a true set of 7 sequences.
SUMMARY INFORMATION
7 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
9| 7 7 7 7 7 7 7 7 7
8| 0 0 0 0 0 0 0 0 0
7| 0 0 0 0 0 0 0 0 0
6| 0 0 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0 0 0
--+----------------------------------------------
| 1 2 3 4 5 6 7 8 9
True positives..
DPOG_HUMAN DPOG_MOUSE DPOG_XENLA DPOG_PICPA
DPOG_SCHPO DPOG_YEAST DPOG_DROME
PROTEIN TITLES
DPOG_HUMAN DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_MOUSE DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_XENLA DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_PICPA DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_SCHPO DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_YEAST DNA POLYMERASE GAMMA (EC 2.7.7.7) (MITOCHONDRIAL DNA POLYMER
DPOG_DROME DNA POLYMERASE GAMMA PRECURSOR (EC 2.7.7.7) (MITOCHONDRIAL D
SCAN HISTORY
OWL30_1 2 100 NSINGLE
SPTR37_9f 2 10 NSINGLE
INITIAL MOTIF SETS
DNAPOLG1 Length of motif = 13 Motif number = 1
DNA-polymerase gamma motif I - 1
PCODE ST INT
LPRLFGGNLDQHF DPOG_MOUSE 110 110
LPPLYGDNLDQHF DPOG_HUMAN 127 127
LPKMYGNNIEEHF DPOG_XENLA 101 101
LPALRGANIEEHF DPOG_DROME 112 112
LPPLQGRSLDEHF DPOG_YEAST 101 101
LPSLQGNTLDEHF DPOG_PICPA 75 75
LPPLQGKTISEHF DPOG_SCHPO 100 100
DNAPOLG2 Length of motif = 15 Motif number = 2
DNA-polymerase gamma motif II - 1
PCODE ST INT
GHNVSFDRAHIREQY DPOG_MOUSE 251 128
GHNVSFDRAHIREQY DPOG_HUMAN 268 128
GHNVSFDRAHIKEQY DPOG_XENLA 242 128
GHNVSYDRARLKEQY DPOG_DROME 257 132
GHNVAYDRARVLEEY DPOG_YEAST 224 110
GHNVSYDRARALEEY DPOG_PICPA 200 112
GHNVSFDRQRIREEY DPOG_SCHPO 223 110
DNAPOLG3 Length of motif = 10 Motif number = 3
DNA-polymerase gamma motif III - 1
PCODE ST INT
PLFLERCPHP DPOG_MOUSE 394 128
PLFLERCPHP DPOG_HUMAN 412 129
PLFMERCPHP DPOG_XENLA 386 129
PLYAERFPHP DPOG_DROME 379 107
PVFLKKCPHP DPOG_YEAST 360 121
PKFKKLIPHP DPOG_PICPA 353 138
PQFLEVCPHP DPOG_SCHPO 368 130
DNAPOLG4 Length of motif = 27 Motif number = 4
DNA-polymerase gamma motif IV - 1
PCODE ST INT
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_MOUSE 826 422
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_HUMAN 848 426
GTITRRAVEPTWLTASNARADRVGSEL DPOG_XENLA 818 422
GTLTRRAMEPTWMTASNSRPDRLGSEL DPOG_DROME 766 377
GTITRRAVENAWLTASNAKANRIGSEL DPOG_YEAST 651 281
GTITRRAVENTWLTASNAKKNRLGSEL DPOG_PICPA 621 258
GTVTRRAVENTWLTASNSKKNRLGSEL DPOG_SCHPO 639 261
DNAPOLG5 Length of motif = 9 Motif number = 5
DNA-polymerase gamma motif V - 1
PCODE ST INT
NYGRIYGAG DPOG_MOUSE 928 75
NYGRIYGAG DPOG_HUMAN 950 75
NYGRIYGAG DPOG_XENLA 920 75
NYARIYGAG DPOG_DROME 868 75
NYGRIYGAG DPOG_YEAST 752 74
NYGRIYGAG DPOG_PICPA 722 74
NYGRLYGAG DPOG_SCHPO 740 74
DNAPOLG6 Length of motif = 14 Motif number = 6
DNA-polymerase gamma motif VI - 1
PCODE ST INT
WTGGTESEMFNKLE DPOG_MOUSE 1027 90
WKGGTESEMFNKLE DPOG_HUMAN 1049 90
WTGGTESQMFNKLE DPOG_XENLA 1018 89
WQGGTESAMFNRLE DPOG_DROME 953 76
WYGGSESILFNKLE DPOG_YEAST 805 44
WYGGSESIIFNRLE DPOG_PICPA 774 43
WSQGTESFVFNKLE DPOG_SCHPO 801 52
DNAPOLG7 Length of motif = 17 Motif number = 7
DNA-polymerase gamma motif VII - 1
PCODE ST INT
SRVNWVVQSSAVDYLHL DPOG_MOUSE 1073 32
SRVNWVVQSSAVDYLHL DPOG_HUMAN 1095 32
SRVNWVVQSSAVDYLHL DPOG_XENLA 1064 32
TRINWVVQSGAVDFLHL DPOG_DROME 1002 35
SRINWAIQSSGVDYLHL DPOG_YEAST 852 33
SRINWAIQSSGVDYLHL DPOG_PICPA 821 33
SRVNWAIQSSAVDYLHL DPOG_SCHPO 848 33
DNAPOLG8 Length of motif = 16 Motif number = 8
DNA-polymerase gamma motif VIII - 1
PCODE ST INT
RAALALQITNLLTRCM DPOG_MOUSE 1126 36
RAALALQITNLLTRCM DPOG_HUMAN 1148 36
RAALALQITNLLTRCM DPOG_XENLA 1117 36
KAALAMHITNLMTRSF DPOG_DROME 1052 33
RAAMALQISNIWTRAM DPOG_YEAST 905 36
RAAYALQISNLWTRAM DPOG_PICPA 874 36
RVAFALQVANLWTRAF DPOG_SCHPO 901 36
DNAPOLG9 Length of motif = 17 Motif number = 9
DNA-polymerase gamma motif IX - 1
PCODE ST INT
FAYKLGLNDLPQSVAFF DPOG_MOUSE 1142 0
FAYKLGLNDLPQSVAFF DPOG_HUMAN 1164 0
FASRLGIQDVPQSVAFF DPOG_XENLA 1133 0
CVSRIGLQDLPMSVAFF DPOG_DROME 1068 0
FCQQMGINELPQNCAFF DPOG_YEAST 921 0
FCQQLGINEVPQSCAFF DPOG_PICPA 890 0
FCQRLGINELPQSVAFF DPOG_SCHPO 917 0
FINAL MOTIF SETS
DNAPOLG1 Length of motif = 13 Motif number = 1
DNA-polymerase gamma motif I - 2
PCODE ST INT
LPPLYGDNLDQHF DPOG_HUMAN 127 127
LPRLFGGNLDQHF DPOG_MOUSE 110 110
LPKMYGNNIEEHF DPOG_XENLA 101 101
LPSLQGNTLDEHF DPOG_PICPA 75 75
LPPLQGKTISEHF DPOG_SCHPO 100 100
LPPLQGRSLDEHF DPOG_YEAST 101 101
LPALRGANIEEHF DPOG_DROME 112 112
DNAPOLG2 Length of motif = 15 Motif number = 2
DNA-polymerase gamma motif II - 2
PCODE ST INT
GHNVSFDRAHIREQY DPOG_HUMAN 268 128
GHNVSFDRAHIREQY DPOG_MOUSE 251 128
GHNVSFDRAHIKEQY DPOG_XENLA 242 128
GHNVSYDRARALEEY DPOG_PICPA 200 112
GHNVSFDRQRIREEY DPOG_SCHPO 223 110
GHNVAYDRARVLEEY DPOG_YEAST 224 110
GHNVSYDRARLKEQY DPOG_DROME 257 132
DNAPOLG3 Length of motif = 10 Motif number = 3
DNA-polymerase gamma motif III - 2
PCODE ST INT
PLFLERCPHP DPOG_HUMAN 412 129
PLFLERCPHP DPOG_MOUSE 394 128
PLFMERCPHP DPOG_XENLA 386 129
PKFKKLIPHP DPOG_PICPA 353 138
PQFLEVCPHP DPOG_SCHPO 368 130
PVFLKKCPHP DPOG_YEAST 360 121
PLYAERFPHP DPOG_DROME 379 107
DNAPOLG4 Length of motif = 27 Motif number = 4
DNA-polymerase gamma motif IV - 2
PCODE ST INT
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_HUMAN 848 426
GTITRRAVEPTWLTASNARPDRVGSEL DPOG_MOUSE 826 422
GTITRRAVEPTWLTASNARADRVGSEL DPOG_XENLA 818 422
GTITRRAVENTWLTASNAKKNRLGSEL DPOG_PICPA 621 258
GTVTRRAVENTWLTASNSKKNRLGSEL DPOG_SCHPO 639 261
GTITRRAVENAWLTASNAKANRIGSEL DPOG_YEAST 651 281
GTLTRRAMEPTWMTASNSRPDRLGSEL DPOG_DROME 766 377
DNAPOLG5 Length of motif = 9 Motif number = 5
DNA-polymerase gamma motif V - 2
PCODE ST INT
NYGRIYGAG DPOG_HUMAN 950 75
NYGRIYGAG DPOG_MOUSE 928 75
NYGRIYGAG DPOG_XENLA 920 75
NYGRIYGAG DPOG_PICPA 722 74
NYGRLYGAG DPOG_SCHPO 740 74
NYGRIYGAG DPOG_YEAST 752 74
NYARIYGAG DPOG_DROME 868 75
DNAPOLG6 Length of motif = 14 Motif number = 6
DNA-polymerase gamma motif VI - 2
PCODE ST INT
WKGGTESEMFNKLE DPOG_HUMAN 1049 90
WTGGTESEMFNKLE DPOG_MOUSE 1027 90
WTGGTESQMFNKLE DPOG_XENLA 1018 89
WYGGSESIIFNRLE DPOG_PICPA 774 43
WSQGTESFVFNKLE DPOG_SCHPO 801 52
WYGGSESILFNKLE DPOG_YEAST 805 44
WQGGTESAMFNRLE DPOG_DROME 953 76
DNAPOLG7 Length of motif = 17 Motif number = 7
DNA-polymerase gamma motif VII - 2
PCODE ST INT
SRVNWVVQSSAVDYLHL DPOG_HUMAN 1095 32
SRVNWVVQSSAVDYLHL DPOG_MOUSE 1073 32
SRVNWVVQSSAVDYLHL DPOG_XENLA 1064 32
SRINWAIQSSGVDYLHL DPOG_PICPA 821 33
SRVNWAIQSSAVDYLHL DPOG_SCHPO 848 33
SRINWAIQSSGVDYLHL DPOG_YEAST 852 33
TRINWVVQSGAVDFLHL DPOG_DROME 1002 35
DNAPOLG8 Length of motif = 16 Motif number = 8
DNA-polymerase gamma motif VIII - 2
PCODE ST INT
RAALALQITNLLTRCM DPOG_HUMAN 1148 36
RAALALQITNLLTRCM DPOG_MOUSE 1126 36
RAALALQITNLLTRCM DPOG_XENLA 1117 36
RAAYALQISNLWTRAM DPOG_PICPA 874 36
RVAFALQVANLWTRAF DPOG_SCHPO 901 36
RAAMALQISNIWTRAM DPOG_YEAST 905 36
KAALAMHITNLMTRSF DPOG_DROME 1052 33
DNAPOLG9 Length of motif = 17 Motif number = 9
DNA-polymerase gamma motif IX - 2
PCODE ST INT
FAYKLGLNDLPQSVAFF DPOG_HUMAN 1164 0
FAYKLGLNDLPQSVAFF DPOG_MOUSE 1142 0
FASRLGIQDVPQSVAFF DPOG_XENLA 1133 0
FCQQLGINEVPQSCAFF DPOG_PICPA 890 0
FCQRLGINELPQSVAFF DPOG_SCHPO 917 0
FCQQMGINELPQNCAFF DPOG_YEAST 921 0
CVSRIGLQDLPMSVAFF DPOG_DROME 1068 0
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