BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14580
(149 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1UW0|A Chain A, Solution Structure Of The Zinc-Finger Domain From Dna
Ligase Iiia
Length = 117
Score = 82.4 bits (202), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 39/94 (41%), Positives = 59/94 (62%), Gaps = 2/94 (2%)
Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFG--SGKMKQWHHIDCILEVFKK 69
++ F VD AK G +GCKKCK+KI G RI K+ NPF G MK+W+HI C+ E ++
Sbjct: 3 EQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLER 62
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEVLSRFPE 103
R TT KIE + ++ GW++L ++E++ +
Sbjct: 63 ARATTKKIEDLTELEGWEELEDNEKEQITQHIAD 96
>pdb|3ODA|A Chain A, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|B Chain B, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|C Chain C, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|D Chain D, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|E Chain E, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|F Chain F, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|G Chain G, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3ODA|H Chain H, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|4DQY|A Chain A, Structure Of Human Parp-1 Bound To A Dna Double Strand
Break
pdb|4DQY|D Chain D, Structure Of Human Parp-1 Bound To A Dna Double Strand
Break
Length = 116
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V
Sbjct: 24 SSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 83
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
R +++ G+ +L +DQ++V
Sbjct: 84 IRHPDVEVD------GFSELRWDDQQKV 105
>pdb|4AV1|A Chain A, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|B Chain B, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|C Chain C, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
pdb|4AV1|D Chain D, Crystal Structure Of The Human Parp-1 Dna Binding Domain
In Complex With Dna
Length = 223
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V
Sbjct: 25 HSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 84
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
R +++ G+ +L +DQ++V
Sbjct: 85 IRHPDVEVD------GFSELRWDDQQKV 106
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 14 NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
+F + AK+ RS CK C +KI+ G VR++K +P G + +W+H C + K +
Sbjct: 133 DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 189
Query: 72 QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFP 102
+ + E + G+ L ED+E + + P
Sbjct: 190 ELGFRPEYSASQLKGFSLLATEDKEALKKQLP 221
>pdb|2DMJ|A Chain A, Solution Structure Of The First Zf-Parp Domain Of Human
Poly(Adp-Ribose)polymerase-1
Length = 106
Score = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 6/88 (6%)
Query: 10 EDDKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKK 69
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V
Sbjct: 11 SSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHS 70
Query: 70 QRQTTAKIEVVDDMGGWDDLTPEDQEEV 97
R +++ G+ +L +DQ++V
Sbjct: 71 IRHPDVEVD------GFSELRWDDQQKV 92
>pdb|2L30|A Chain A, Human Parp-1 Zinc Finger 1
Length = 108
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 6/86 (6%)
Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
DK + V+ AK+GR+ CKKC + I ++R+A M +P GK+ W+H C +V R
Sbjct: 6 DKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFDGKVPHWYHFSCFWKVGHSIR 65
Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
+++ G+ +L +DQ++V
Sbjct: 66 HPDVEVD------GFSELRWDDQQKV 85
>pdb|1V9X|A Chain A, Solution Structure Of The First Zn-Finger Domain Of
Poly(Adp-Ribose) Polymerase-1
Length = 114
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 17 VDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQRQTTAK 76
+ AK+ RS CK CK I+ R+ K+ + G M W+H CIL + T +
Sbjct: 13 AEYAKSSRSSCKTCKSVINKENFRLGKLVQSTHFDGIMPMWNHASCIL-------KKTKQ 65
Query: 77 IEVVDDMGGWDDLTPEDQEEV 97
I+ VDD+ G + L EDQ+++
Sbjct: 66 IKSVDDVEGIESLRWEDQQKI 86
>pdb|3OD8|A Chain A, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|B Chain B, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|C Chain C, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|D Chain D, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|E Chain E, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|F Chain F, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|G Chain G, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
pdb|3OD8|H Chain H, Human Parp-1 Zinc Finger 1 (Zn1) Bound To Dna
Length = 116
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 6/86 (6%)
Query: 12 DKNFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGSGKMKQWHHIDCILEVFKKQR 71
DK + V+ AK+GR+ CKKC + I ++R A +P GK+ W+H C +V R
Sbjct: 26 DKLYRVEYAKSGRASCKKCSESIPKDSLRXAIXVQSPXFDGKVPHWYHFSCFWKVGHSIR 85
Query: 72 QTTAKIEVVDDMGGWDDLTPEDQEEV 97
+++ G+ +L +DQ++V
Sbjct: 86 HPDVEVD------GFSELRWDDQQKV 105
>pdb|3ODC|A Chain A, Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna
pdb|3ODC|B Chain B, Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna
pdb|3ODE|A Chain A, Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna
pdb|3ODE|B Chain B, Human Parp-1 Zinc Finger 2 (Zn2) Bound To Dna
Length = 111
Score = 43.1 bits (100), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 14 NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
+F + AK+ RS CK C +KI+ G VR++K +P G + +W+H C + K +
Sbjct: 9 DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 65
Query: 72 QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFP 102
+ + E + G+ L ED+E + + P
Sbjct: 66 ELGFRPEYSASQLKGFSLLATEDKEALKKQLP 97
>pdb|2L31|A Chain A, Human Parp-1 Zinc Finger 2
Length = 112
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%)
Query: 14 NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
+F + AK+ RS CK C +KI+ G VR++K +P G + +W+H C + K +
Sbjct: 10 DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 66
Query: 72 QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
+ + E + G+ L ED+E + + P E + D
Sbjct: 67 ELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD 109
>pdb|2CS2|A Chain A, Solution Structure Of The Second Zn-Finger Domain Of
Poly(Adp-Ribose) Polymerase-1
Length = 134
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 50/103 (48%), Gaps = 6/103 (5%)
Query: 14 NFWVDRAKTGRSGCKKCKQKIDTGTVRIAKMGYNPFGS--GKMKQWHHIDCILEVFKKQR 71
+F + AK+ RS CK C +KI+ G VR++K +P G + +W+H C + K +
Sbjct: 17 DFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFV---KNRE 73
Query: 72 QTTAKIEV-VDDMGGWDDLTPEDQEEVLSRFPESLRESNKDRD 113
+ + E + G+ L ED+E + + P E + D
Sbjct: 74 ELGFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEGKRKGD 116
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.136 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,471,744
Number of Sequences: 62578
Number of extensions: 167406
Number of successful extensions: 387
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 359
Number of HSP's gapped (non-prelim): 27
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)