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= 017612
(368 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A1J|B Chain B, Crystal Structure Of The Complex Between The C-Terminal
Domains Of Human Xpf And Ercc1
Length = 91
Score = 95.5 bits (236), Expect = 4e-20, Method: Composition-based stats.
Identities = 43/78 (55%), Positives = 60/78 (76%)
Query: 200 PADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIG 259
PADL+ +++ D++SR+T LT+V+SVNKTD TL +TFGSL ++ AS EDLA CPG+G
Sbjct: 14 PADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLG 73
Query: 260 ERKVKRLYDTFHEPFKRV 277
+K +RL+D HEPF +V
Sbjct: 74 PQKARRLFDVLHEPFLKV 91
>pdb|1Z00|A Chain A, Solution Structure Of The C-Terminal Domain Of Ercc1
Complexed With The C-Terminal Domain Of Xpf
Length = 89
Score = 93.6 bits (231), Expect = 2e-19, Method: Composition-based stats.
Identities = 42/77 (54%), Positives = 59/77 (76%)
Query: 201 ADLIQGQMDTDYLSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGE 260
ADL+ +++ D++SR+T LT+V+SVNKTD TL +TFGSL ++ AS EDLA CPG+G
Sbjct: 2 ADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGP 61
Query: 261 RKVKRLYDTFHEPFKRV 277
+K +RL+D HEPF +V
Sbjct: 62 QKARRLFDVLHEPFLKV 78
>pdb|2JPD|A Chain A, Solution Structure Of The Ercc1 Central Domain
Length = 135
Score = 73.2 bits (178), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL Y N
Sbjct: 5 NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 53
Query: 199 KPADLIQGQMDT 210
D I G++ +
Sbjct: 54 LHPDYIHGRLQS 65
>pdb|2JNW|A Chain A, Solution Structure Of A Ercc1-Xpa Heterodimer
Length = 133
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL Y N
Sbjct: 18 NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 66
Query: 199 KPADLIQGQMDT 210
D I G++ +
Sbjct: 67 LHPDYIHGRLQS 78
>pdb|2A1I|A Chain A, Crystal Structure Of The Central Domain Of Human Ercc1
Length = 146
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 11/72 (15%)
Query: 139 NAILVSQRQKGNPLLKYIRNVRWAFADVVCDYLVGQNSCALYLSLEECGRYLETIKVYEN 198
N+I+VS RQ+GNP+LK++RNV W F DV+ DY++GQ++CAL+LSL Y N
Sbjct: 18 NSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLR-----------YHN 66
Query: 199 KPADLIQGQMDT 210
D I G++ +
Sbjct: 67 LHPDYIHGRLQS 78
>pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna
Ligase Bound To Nicked Dna-Adenylate
Length = 671
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
+R +AL +R V + L + FG+L + AS+E+L + P +G +++ F E
Sbjct: 508 FARFLYAL-GIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAE 566
Query: 273 PFKRVVSS-------HPPIP 285
R V S H P P
Sbjct: 567 ESNRNVISELLAEGVHWPAP 586
>pdb|4GLX|A Chain A, Dna Ligase A In Complex With Inhibitor
Length = 586
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHE 272
+R +AL +R V + L + FG+L + AS+E+L + P +G +++ F E
Sbjct: 508 FARFLYAL-GIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAE 566
Query: 273 PFKRVVSS-------HPPIP 285
R V S H P P
Sbjct: 567 ESNRNVISELLAEGVHWPAP 586
>pdb|2BHN|A Chain A, Xpf From Aeropyrum Pernix
pdb|2BHN|B Chain B, Xpf From Aeropyrum Pernix
pdb|2BHN|C Chain C, Xpf From Aeropyrum Pernix
pdb|2BHN|D Chain D, Xpf From Aeropyrum Pernix
Length = 214
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFKR 276
+ L S + + + FGSL AS ++++ GIGE++ + + P+KR
Sbjct: 155 YILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYKR 213
>pdb|3SGI|A Chain A, Crystal Structure Of Dna Ligase A Brct Domain Deleted
Mutant Of Mycobacterium Tuberculosis
Length = 615
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 213 LSRLTHALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIG 259
L R+ AL S+R V T L + FGSL I AS + LA G+G
Sbjct: 525 LWRVLVAL-SIRHVGPTAARALATEFGSLDAIAAASTDQLAAVEGVG 570
>pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna
pdb|2BGW|B Chain B, Xpf From Aeropyrum Pernix, Complex With Dna
Length = 219
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 218 HALTSVRSVNKTDVVTLGSTFGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPFK 275
+ L S + + + FGSL AS ++++ GIGE++ + + P+K
Sbjct: 162 YILQSFPGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 219
>pdb|3C1Y|A Chain A, Structure Of Bacterial Dna Damage Sensor Protein With Co-
Purified And Co-Crystallized Ligand
pdb|3C1Y|B Chain B, Structure Of Bacterial Dna Damage Sensor Protein With Co-
Purified And Co-Crystallized Ligand
pdb|3C1Z|A Chain A, Structure Of The Ligand-Free Form Of A Bacterial Dna
Damage Sensor Protein
pdb|3C1Z|B Chain B, Structure Of The Ligand-Free Form Of A Bacterial Dna
Damage Sensor Protein
pdb|3C21|A Chain A, Structure Of A Bacterial Dna Damage Sensor Protein With
Reaction Product
pdb|3C21|B Chain B, Structure Of A Bacterial Dna Damage Sensor Protein With
Reaction Product
pdb|3C23|A Chain A, Structure Of A Bacterial Dna Damage Sensor Protein With
Non- Reactive Ligand
pdb|3C23|B Chain B, Structure Of A Bacterial Dna Damage Sensor Protein With
Non- Reactive Ligand
Length = 377
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 238 FGSLSHIMDASMEDLARCPGIGERKVK 264
F +L I AS+EDL + GIGE++ +
Sbjct: 335 FKTLDQISKASVEDLKKVEGIGEKRAR 361
>pdb|1X2I|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
Pyrococcus Furiosus, Helix-Hairpin-Helix Domain
pdb|1X2I|B Chain B, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
Pyrococcus Furiosus, Helix-Hairpin-Helix Domain
Length = 75
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 238 FGSLSHIMDASMEDLARCPGIGERKVKRLYDTFHEPF 274
FGS+ + AS+ +L + GIGE+ K + P+
Sbjct: 34 FGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPY 70
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
0.311 0.127 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,347,319
Number of Sequences: 62578
Number of extensions: 281920
Number of successful extensions: 472
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 453
Number of HSP's gapped (non-prelim): 19
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)