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= psy6818
(162 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 97.8 bits (242), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 59/163 (36%), Positives = 82/163 (50%), Gaps = 27/163 (16%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP--KALLDIHNVTSLRHQDQEMIK-------------- 44
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 62 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVKKTAEAGGVTGKGQD 121
Query: 45 ------SKILGNI--EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYH 96
K LG+ EYAKSNRSTC+GC KI KG++R+SK D ++ +G I WYH
Sbjct: 122 GIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEK-PQLGMIDRWYH 180
Query: 97 LSCFNAVRLDLEFSA--SGKQIPGFGSLEKKDQKIVEATLPSL 137
CF R +L F S Q+ GF L +D++ ++ LP +
Sbjct: 181 PGCFVKNREELGFRPEYSASQLKGFSLLATEDKEALKKQLPGV 223
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/90 (35%), Positives = 45/90 (50%), Gaps = 7/90 (7%)
Query: 45 SKILGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGG-IPEWYHLSCFNAV 103
S L +EYAKS R++C+ C I K +R++ M Q M G +P WYH SCF V
Sbjct: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMV----QSPMFDGKVPHWYHFSCFWKV 81
Query: 104 RLDLEFSASGKQIPGFGSLEKKDQKIVEAT 133
+ ++ GF L DQ+ V+ T
Sbjct: 82 GHSIRHPDV--EVDGFSELRWDDQQKVKKT 109
>pdb|2L31|A Chain A, Human Parp-1 Zinc Finger 2
Length = 112
Score = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/109 (43%), Positives = 66/109 (60%), Gaps = 10/109 (9%)
Query: 46 KILGNI--EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAV 103
K LG+ EYAKSNRSTC+GC KI KG++R+SK D ++ +G I WYH CF
Sbjct: 6 KTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEK-PQLGMIDRWYHPGCFVKN 64
Query: 104 RLDL----EFSASGKQIPGFGSLEKKDQKIVEATLPSL-SDGVSKTDAI 147
R +L E+SAS Q+ GF L +D++ ++ LP + S+G K D +
Sbjct: 65 REELGFRPEYSAS--QLKGFSLLATEDKEALKKQLPGVKSEGKRKGDEV 111
>pdb|2CS2|A Chain A, Solution Structure Of The Second Zn-Finger Domain Of
Poly(Adp-Ribose) Polymerase-1
Length = 134
Score = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/109 (43%), Positives = 66/109 (60%), Gaps = 10/109 (9%)
Query: 46 KILGNI--EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAV 103
K LG+ EYAKSNRSTC+GC KI KG++R+SK D ++ +G I WYH CF
Sbjct: 13 KTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEK-PQLGMIDRWYHPGCFVKN 71
Query: 104 RLDL----EFSASGKQIPGFGSLEKKDQKIVEATLPSL-SDGVSKTDAI 147
R +L E+SAS Q+ GF L +D++ ++ LP + S+G K D +
Sbjct: 72 REELGFRPEYSAS--QLKGFSLLATEDKEALKKQLPGVKSEGKRKGDEV 118
>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 = 73.6 bits (179), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 46/107 (42%), Positives = 66/107 (61%), Gaps = 10/107 (9%)
Query: 42 MIKSKILGNI--EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSC 99
M K LG+ EYAKSNRSTC+GC KI KG++R+SK D ++ + +G I WYH C
Sbjct: 1 MKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQ-LGMIDRWYHPGC 59
Query: 100 FNAVRLDL----EFSASGKQIPGFGSLEKKDQKIVEATLPSL-SDGV 141
F R +L E+SAS Q+ GF L +D++ ++ LP + S+G+
Sbjct: 60 FVKNREELGFRPEYSAS--QLKGFSLLATEDKEALKKQLPGVKSEGL 104
>pdb|2DMJ|A Chain A, Solution Structure Of The First Zf-Parp Domain Of Human
Poly(Adp-Ribose)polymerase-1
Length = 106
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 47/96 (48%), Gaps = 7/96 (7%)
Query: 48 LGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGG-IPEWYHLSCFNAVRLD 106
L +EYAKS R++C+ C I K +R++ M Q M G +P WYH SCF V
Sbjct: 15 LYRVEYAKSGRASCKKCSESIPKDSLRMAIMV----QSPMFDGKVPHWYHFSCFWKVGHS 70
Query: 107 LEFSASGKQIPGFGSLEKKDQKIVEATLPSLSDGVS 142
+ ++ GF L DQ+ V+ T + G S
Sbjct: 71 IRHPDV--EVDGFSELRWDDQQKVKKTAEAGGSGPS 104
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP--KALLDIHNVTSLRHQDQEMIK 44
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 48 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVK 93
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 44/87 (50%), Gaps = 7/87 (8%)
Query: 48 LGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGG-IPEWYHLSCFNAVRLD 106
L +EYAKS R++C+ C I K +R++ M Q M G +P WYH SCF V
Sbjct: 28 LYRVEYAKSGRASCKKCSESIPKDSLRMAIMV----QSPMFDGKVPHWYHFSCFWKVGHS 83
Query: 107 LEFSASGKQIPGFGSLEKKDQKIVEAT 133
+ ++ GF L DQ+ V+ T
Sbjct: 84 IRHPDV--EVDGFSELRWDDQQKVKKT 108
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP--KALLDIHNVTSLRHQDQEMIK 44
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 61 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVK 106
>pdb|2L30|A Chain A, Human Parp-1 Zinc Finger 1
Length = 108
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 44/87 (50%), Gaps = 7/87 (8%)
Query: 48 LGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGG-IPEWYHLSCFNAVRLD 106
L +EYAKS R++C+ C I K +R++ M Q M G +P WYH SCF V
Sbjct: 8 LYRVEYAKSGRASCKKCSESIPKDSLRMAIMV----QSPMFDGKVPHWYHFSCFWKVGHS 63
Query: 107 LEFSASGKQIPGFGSLEKKDQKIVEAT 133
+ ++ GF L DQ+ V+ T
Sbjct: 64 IRHPDV--EVDGFSELRWDDQQKVKKT 88
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP--KALLDIHNVTSLRHQDQEMIK 44
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 41 SPMFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVK 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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 43/93 (46%), Gaps = 13/93 (13%)
Query: 45 SKILGNIEYAKSNRSTCRGCEAKIAKGEIR----VSKMNYDSDQGKMIGGIPEWYHLSCF 100
S L +EYAKS R++C+ C I K +R V +D G +P WYH SCF
Sbjct: 25 SDKLYRVEYAKSGRASCKKCSESIPKDSLRXAIXVQSPXFD-------GKVPHWYHFSCF 77
Query: 101 NAVRLDLEFSASGKQIPGFGSLEKKDQKIVEAT 133
V + ++ GF L DQ+ V+ T
Sbjct: 78 WKVGHSIRHPDV--EVDGFSELRWDDQQKVKKT 108
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP--KALLDIHNVTSLRHQDQEMIK 44
SP FDGK P W+H CFWK +++ + LR DQ+ +K
Sbjct: 61 SPXFDGKVPHWYHFSCFWKVGHSIRHPDVEVDGFSELRWDDQQKVK 106
>pdb|1UW0|A Chain A, Solution Structure Of The Zinc-Finger Domain From Dna
Ligase Iiia
Length = 117
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 55/112 (49%), Gaps = 14/112 (12%)
Query: 51 IEYAKSNRSTCRGCEAKIAKGEIRVSKM--NYDSDQGKMIGGIPEWYHLSCFNAVRLDLE 108
++YAK + C+ C+ KI KG R+ K+ N S+ G G + EWYH+ C +L+
Sbjct: 8 VDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESG---GDMKEWYHIKCMFE-KLERA 63
Query: 109 FSASGK-----QIPGFGSLEKKDQKIVE---ATLPSLSDGVSKTDAISHFLL 152
+ + K ++ G+ LE +++ + A L S + G K A+ L
Sbjct: 64 RATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKAAGTPKKKAVVQAKL 115
>pdb|1V9X|A Chain A, Solution Structure Of The First Zn-Finger Domain Of
Poly(Adp-Ribose) Polymerase-1
Length = 114
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRP-KALLDIHNVTSLRHQDQEMIK 44
S FDG P W H C KK + K++ D+ + SLR +DQ+ I+
Sbjct: 43 STHFDGIMPMWNHASCILKKTKQIKSVDDVEGIESLRWEDQQKIR 87
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 52 EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSA 111
EYAKS+RS+C+ C++ I K R+ K+ + G +P W H SC ++
Sbjct: 14 EYAKSSRSSCKTCKSVINKENFRLGKLVQSTH---FDGIMPMWNHASCILKKTKQIK--- 67
Query: 112 SGKQIPGFGSLEKKDQKIVEATLPS 136
S + G SL +DQ+ + + S
Sbjct: 68 SVDDVEGIESLRWEDQQKIRKYVES 92
>pdb|1HDF|A Chain A, Evolution Of The Eye Lens Beta-Gamma-Crystallin Domain
Fold
pdb|1HDF|B Chain B, Evolution Of The Eye Lens Beta-Gamma-Crystallin Domain
Fold
Length = 102
Score = 30.8 bits (68), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 59 STCRGCEAKIAKGEIRVSK-MNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQI- 116
S C+G AKGE+ + K +N+ D K+ G + ++ +S N V ++ + K
Sbjct: 1 SVCKGVSGNPAKGEVFLYKHVNFQGDSWKVTGNVYDFRSVSGLNDVVSSVKVGPNTKAFI 60
Query: 117 -------PGFGSLEKKDQKIVEATLPSLSDGVS 142
F LE+ Q + + T +L+D +S
Sbjct: 61 FKDDRFNGNFIRLEESSQ-VTDLTTRNLNDAIS 92
>pdb|1AG4|A Chain A, Nmr Structure Of Spherulin 3a (S3a) From Physarum
Polycephalum, Minimized Average Structure
Length = 103
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 43/93 (46%), Gaps = 10/93 (10%)
Query: 59 STCRGCEAKIAKGEIRVSK-MNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSASGKQI- 116
S C+G AKGE+ + K +N+ D K+ G + ++ +S N V ++ + K
Sbjct: 2 SVCKGVSGNPAKGEVFLYKHVNFQGDSWKVTGNVYDFRSVSGLNDVVSSVKVGPNTKAFI 61
Query: 117 -------PGFGSLEKKDQKIVEATLPSLSDGVS 142
F LE+ Q + + T +L+D +S
Sbjct: 62 FKDDRFNGNFIRLEESSQ-VTDLTTRNLNDAIS 93
>pdb|3IF8|A Chain A, Crystal Structure Of Zwilch, A Member Of The Rzz
Kinetochore
Length = 339
Score = 26.6 bits (57), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 90 GIPEWYH-LSCFNAVRLDLEFSASGKQIPGFGSLEKKDQKI 129
G+ EW L +AV L EF ++ GFG KKD ++
Sbjct: 287 GVTEWLEPLEAKSAVELVQEFLNDLNKLDGFGDSTKKDTEV 327
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 0.135 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,731,264
Number of Sequences: 62578
Number of extensions: 171859
Number of successful extensions: 504
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 24
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
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)