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= 007505
(601 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 65/246 (26%), Positives = 109/246 (44%), Gaps = 34/246 (13%)
Query: 28 LKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAEL 87
L+ +L LE PTG+GKTI L Y E +K++Y RT + E+ + EL
Sbjct: 15 LRSSLQKSYGVALESPTGSGKTIMALKSALQY---SSERKLKVLYLVRTNSQEEQVIKEL 71
Query: 88 KLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRV---LAAENRDSVDAACRKRTASWVRA 144
R L KI AI + R N+C+ R+ L N +S+ C + R
Sbjct: 72 --------RSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKK----RE 119
Query: 145 LAAENPNIETCEFFENYE--KAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFA 202
+ A N C +F N++ + L + T ++ +G++ CPY + + A
Sbjct: 120 VMAGNE--AACPYF-NFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDA 176
Query: 203 NVVVYSYQYLLDPKVA-------GIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQT 255
++V+ Y Y L+ VA G+ ++ V++ DEAHN+ ++ S + ++
Sbjct: 177 DIVIAPYAYFLNRSVAEKFLSHWGVSRNQI----VIILDEAHNLPDIGRSIGSFRISVES 232
Query: 256 LEGATR 261
L A R
Sbjct: 233 LNRADR 238
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 62/233 (26%), Positives = 102/233 (43%), Gaps = 32/233 (13%)
Query: 40 LEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLG 99
LE PTG+GKTI L Y E +K++Y RT + E+ + EL R L
Sbjct: 9 LESPTGSGKTIMALKSALQY---SSERKLKVLYLVRTNSQEEQVIKEL--------RSLS 57
Query: 100 PAAKILAIGLSSRKNLCVNSRV---LAAENRDSVDAACRKRTASWVRALAAENPNIETCE 156
KI AI + R N+C+ R+ L N +S+ C + R + A N C
Sbjct: 58 STMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKK----REVMAGNE--AACP 111
Query: 157 FFE-NYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDP 215
+F + L + T ++ +G++ CPY + + A++V+ Y Y L+
Sbjct: 112 YFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNR 171
Query: 216 KVA-------GIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATR 261
VA G+ ++ V++ DEAHN+ ++ S + ++L A R
Sbjct: 172 SVAEKFLSHWGVSRNQI----VIILDEAHNLPDIGRSIGSFRISVESLNRADR 220
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 58/116 (50%), Gaps = 9/116 (7%)
Query: 177 LQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEA 236
++ L+ G Q +CPY+ + + A+V+ +Y Y + I ++ +E ++V DEA
Sbjct: 124 VKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDL-REYMIVIDEA 182
Query: 237 HNIDNVC-IEALSVS-------VRRQTLEGATRNLSRINQEIERFKATDAGRLRAE 284
HN+D V +E S+S +++ E + R LS++ ++ D ++ E
Sbjct: 183 HNLDKVNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVLPDEKYIKVE 238
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 77/171 (45%), Gaps = 32/171 (18%)
Query: 137 RTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQD------LRAFGKQQGWC 190
++AS + A E P+ C S L + T++D + F +C
Sbjct: 84 KSASCIYAQGDEEPDEINC----------SKCRLKDKIKTIEDKEPSKLIEEFKDAVDYC 133
Query: 191 PYFLARHMVQFANVVVYSYQYLLDPKVAGII--SKE---MQKESVVVFDEAHNIDNVCIE 245
PY+ R ++ +V+ +Y YL + + +K+ ++ ++V DEAHN+ +E
Sbjct: 134 PYYSLRANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL----LE 189
Query: 246 A---LSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLA 293
A + + R+ LE A + + + +ER DA +++ N L++ ++
Sbjct: 190 ADKWFTRKISRKMLERALKEI----EIVERLNRIDAKKVKDYINLLIDYMS 236
>pdb|2GK1|A Chain A, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|C Chain C, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|E Chain E, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|G Chain G, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GJX|A Chain A, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|D Chain D, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|E Chain E, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|H Chain H, Crystallographic Structure Of Human Beta-Hexosaminidase A
Length = 507
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 393 EFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHD 439
E +IQT+ D +V +Y +G+ + E FD ++ PD ++Q+ D
Sbjct: 330 ESFYIQTLLD---IVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWRED 373
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
0.323 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,870,514
Number of Sequences: 62578
Number of extensions: 672260
Number of successful extensions: 1517
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 1509
Number of HSP's gapped (non-prelim): 22
length of query: 601
length of database: 14,973,337
effective HSP length: 104
effective length of query: 497
effective length of database: 8,465,225
effective search space: 4207216825
effective search space used: 4207216825
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)