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= 010991
(496 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ERN|A Chain A, Crystal Structure Of The C-terminal Domain Of Human
Xpb/ercc-3 Excision Repair Protein At 1.80 A
Length = 289
Score = 287 bits (734), Expect = 1e-77, Method: Compositional matrix adjust.
Identities = 167/312 (53%), Positives = 202/312 (64%), Gaps = 49/312 (15%)
Query: 205 LDLVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKKQALYVMNPNKFRACEFLIRFHE 264
++L G+IA VQCAEVWCPM+ EF+ EY+ + +KK+ LY MNPNKFRAC+FLI+FHE
Sbjct: 1 MELQNNGYIAKVQCAEVWCPMSPEFYREYVAIK-TKKRILLYTMNPNKFRACQFLIKFHE 59
Query: 265 QQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVERTKILQAFKCSRDLNTIFLSK-- 322
+ R DKIIVFADN+FAL EYA++L KP IYG TS ER +ILQ FK + +NTIF+SK
Sbjct: 60 R-RNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVG 118
Query: 323 --------------ISSHAGSRRQEAQRLGRILRAKGKLEDRMAGGKEEYNAFFYSLVST 368
ISSH GSRRQEAQRLGR+LRAK + EEYNAFFYSLVS
Sbjct: 119 DTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGM------VAEEYNAFFYSLVSQ 172
Query: 369 DTQEMFYSTKRQQFLIDQGYSFKVITSLPPPDSGADLSYHRLDEQLALLGKVLSAGDDAV 428
DTQEM YSTKRQ+FL+DQGYSFKVIT L + DL++ +EQ LL KVL+A D
Sbjct: 173 DTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEE-EDLAFSTKEEQQQLLQKVLAATD--- 228
Query: 429 GLEQLDEDADDIA------LHKARRIAGSMSAMSGAQGMVYMEYSTXXXXXXXXXXXXPK 482
LD + + +A +A R G+MS+MSGA VYMEY + K
Sbjct: 229 ----LDAEEEVVAGEFGSRSSQASRRFGTMSSMSGADDTVYMEYHSSRS----------K 274
Query: 483 DPSKR-HYLFKR 493
PSK H LFKR
Sbjct: 275 APSKHVHPLFKR 286
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 106/405 (26%), Positives = 172/405 (42%), Gaps = 83/405 (20%)
Query: 27 RPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAACRIKKSCLCLATNAVSVDQWAF 86
R YQEK+L + + R G IVLP G+GK+ V ++A + L + +QW
Sbjct: 95 RDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKE 151
Query: 87 QFKLWSTIQDDQICRFTSDSKERFRGNAGVVVTTYNMVAFGGXXXXXXXXXXXXXXXXXW 146
+ ++ ++ + F+ KE + V+TY+ +
Sbjct: 152 RLGIFG---EEYVGEFSGRIKEL----KPLTVSTYDSAYVNAEKLGNR-----------F 193
Query: 147 GLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLD 206
LL+ DEVH +PA + ++ ++ + +LGLTAT RED R L ++G K++E + D
Sbjct: 194 MLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFEL-FPD 252
Query: 207 LVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKK----QALYVMNPNKF--------- 253
+ G +A ++ P+ ++ EY K+E K+ + + + F
Sbjct: 253 SLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRRAEDFNKIVMASGY 312
Query: 254 --RACEFL--------IRFH------------EQQRGDKIIVFADNLFALTEYAMKLRKP 291
RA E L I F+ E+ R DKII+F + + + P
Sbjct: 313 DERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFLIP 372
Query: 292 MIYGATSHVERTKILQAFKCSR--------------DLNTIFLSKISSHAGSRRQEAQRL 337
I TS ER +IL+ F+ R D+ + I S +GS R+ QRL
Sbjct: 373 AITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRL 432
Query: 338 GRILR-AKGKLEDRMAGGKEEYNAFFYSLVSTDTQEMFYSTKRQQ 381
GRILR +KGK E A Y L+S T E+ + +R+
Sbjct: 433 GRILRPSKGKKE-----------AVLYELISRGTGEVNTARRRKN 466
>pdb|2FZ4|A Chain A, Crystal Structure Of The N-Terminal Half Of Archaeoglobus
Fulgidus Xpb
Length = 237
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 80/182 (43%), Gaps = 21/182 (11%)
Query: 6 DFRNDNVNPDLNMELKPHAQPRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVSAAC 65
+F ++ +P R YQEK+L + + R G IVLP G+GK+ V ++A
Sbjct: 74 EFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAIN 130
Query: 66 RIKKSCLCLATNAVSVDQWAFQFKLWSTIQDDQICRFTSDSKERFRGNAGVVVTTYNMVA 125
+ L + +QW + ++ ++ + F+ KE + V+TY+
Sbjct: 131 ELSTPTLIVVPTLALAEQWKERLGIFG---EEYVGEFSGRIKEL----KPLTVSTYD--- 180
Query: 126 FGGXXXXXXXXXXXXXXXXXWGLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVRED 185
+ LL+ DEVH +PA + ++ ++ + +LGLTAT RED
Sbjct: 181 --------SAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFERED 232
Query: 186 ER 187
R
Sbjct: 233 GR 234
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/134 (31%), Positives = 59/134 (44%), Gaps = 29/134 (21%)
Query: 249 NPNKFRACEFLIRFHEQQRGDKIIVFADNLFALTEYAMKLRKPMIYGATSHVERTKILQA 308
+ NK R ++ E+ R DKII+F + + + P I TS ER +IL+
Sbjct: 98 SKNKIRKLREIL---ERHRKDKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEG 154
Query: 309 FKCSR--------------DLNTIFLSKISSHAGSRRQEAQRLGRILR-AKGKLEDRMAG 353
F+ R D+ + I S +GS R+ QRLGRILR +KGK E
Sbjct: 155 FRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKE----- 209
Query: 354 GKEEYNAFFYSLVS 367
A Y L+S
Sbjct: 210 ------AVLYELIS 217
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 46/104 (44%), Gaps = 12/104 (11%)
Query: 25 QPRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVS-AACRIKK---SCLCLATNAVS 80
QPR YQE ++ + + +IVLP G GK+L+ + A R+ K L LA
Sbjct: 9 QPRIYQEV----IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPL 64
Query: 81 VDQWAFQFKLWSTIQDDQICRFTSDSKERFR----GNAGVVVTT 120
V Q A F+ + ++I T + R A V+V T
Sbjct: 65 VLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVAT 108
>pdb|3H1T|A Chain A, The Fragment Structure Of A Putative Hsdr Subunit Of A
Type I Restriction Enzyme From Vibrio Vulnificus Yj016
Length = 590
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 53/235 (22%), Positives = 90/235 (38%), Gaps = 42/235 (17%)
Query: 13 NPDLNMELKPHAQ-----PRPYQEKSLSKMFGN---GRARSGIIVLPCGAGKSLVGVSAA 64
+ DL+ L P+ PR YQ+ ++++ + G+ RS +I G GK++V +
Sbjct: 161 DEDLDTLLSPYHHVSGYSPRYYQQIAINRAVQSVLQGKKRS-LITXATGTGKTVVAFQIS 219
Query: 65 CRI------------KKSCLCLATNAVSVDQWAFQFKLWSTIQDDQICRFTSDSKERFRG 112
++ K L LA V VD D + FT R +
Sbjct: 220 WKLWSARWNRTGDYRKPRILFLADRNVLVD-------------DPKDKTFTPFGDARHKI 266
Query: 113 NAGVVVTT---YNMVAFGGXXXXXXXXXXXXXXXXXWGLLLMDEVHVVPAH---MFRKVI 166
G VV + Y + + L+++DE H A +R+++
Sbjct: 267 EGGKVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDNSNWREIL 326
Query: 167 SLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLDLVKGGFIANVQCAEV 221
+ ++G TAT +RED R T F G +Y + + GF+A + V
Sbjct: 327 EYFEPAFQIGXTATPLREDNRDTYRYF--GNPIYTYSLRQGIDDGFLAPYRVHRV 379
>pdb|2VUG|A Chain A, The Structure Of An Archaeal Homodimeric Rna Ligase
pdb|2VUG|B Chain B, The Structure Of An Archaeal Homodimeric Rna Ligase
Length = 389
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 18/105 (17%)
Query: 147 GLLLMDEVHVVPAHMFRKVISLTKSHCKLGLTATLVREDERITDLNFLIGPKLYEANWLD 206
G +++DE +V+P K I +S + +E++ N + +Y+ L
Sbjct: 62 GTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDGYNVRV--VMYKGKMLG 119
Query: 207 LVKGGFIANVQCAEVWCPMTKEFFSEYLKKENSKKKQALYVMNPN 251
+ +GGFI CP T E +++ +E K NPN
Sbjct: 120 ITRGGFI---------CPFTTERIPDFVPQEFFKD-------NPN 148
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
0.322 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,527,432
Number of Sequences: 62578
Number of extensions: 520382
Number of successful extensions: 873
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 861
Number of HSP's gapped (non-prelim): 9
length of query: 496
length of database: 14,973,337
effective HSP length: 103
effective length of query: 393
effective length of database: 8,527,803
effective search space: 3351426579
effective search space used: 3351426579
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)