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= 008606
(560 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GOP|C Chain C, Structure And Conformational Change Of A Replication
Protein A Heterotrimer Bound To Ssdna
pdb|4GOP|Z Chain Z, Structure And Conformational Change Of A Replication
Protein A Heterotrimer Bound To Ssdna
pdb|4GNX|C Chain C, Structure Of
pdb|4GNX|Z Chain Z, Structure Of
Length = 444
Score = 294 bits (752), Expect = 1e-79, Method: Compositional matrix adjust.
Identities = 166/450 (36%), Positives = 246/450 (54%), Gaps = 22/450 (4%)
Query: 115 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 174
I PI L+PYQ RW IKARVT+K D+R ++N RG+GK+FS +LLD D GEI+ T FN V
Sbjct: 3 IYPIEGLSPYQNRWTIKARVTSKSDIRHWSNQRGEGKLFSVNLLD-DSGEIKATGFNDAV 61
Query: 175 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFS 234
DRFY +++ VYLISK + A+K F++L+NE+EI E ++ ++ CT+ D +P+ ++
Sbjct: 62 DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDATD-VPEVKYE 120
Query: 235 FRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGME-TQRRILNLKDTSGRSVELTLW 293
F I+E+ES E I+ K Q+R L L D RSV+LTLW
Sbjct: 121 FVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLW 180
Query: 294 GDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELRE 353
G K + V PVL+ K KV DF G+S+ S+ + INPD E+H LR
Sbjct: 181 G----KTAETFPTNAGVDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHVLRG 236
Query: 354 WFDSGGKNA--------ATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRA 405
W+D+ G +A + GA +T+ Q+K+E LG SEKPD+ VRA
Sbjct: 237 WYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYFNVRA 296
Query: 406 FITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQD 464
+ +IK ++ YTAC CNKKV N W+C++C++ +YRY+L + D
Sbjct: 297 TVVYIKQENLYYTAC----ASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVAD 352
Query: 465 QTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEEL 524
TG W++ F E +++G A EL+ L+ E + + F + Y+F + K +
Sbjct: 353 ATGQMWLSGFNEDATQLIGMSAGELHKLREESESE--FSAALHRAANRMYMFNCRAKMDT 410
Query: 525 YGDEQRVKITVIRADQVNYSSESRYLLDLI 554
+ D RV+ T+ RA V+++ L+D I
Sbjct: 411 FNDTARVRYTISRAAPVDFAKAGMELVDAI 440
>pdb|1FGU|A Chain A, Ssdna-Binding Domain Of The Large Subunit Of Replication
Protein A
pdb|1FGU|B Chain B, Ssdna-Binding Domain Of The Large Subunit Of Replication
Protein A
Length = 252
Score = 191 bits (484), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 102/257 (39%), Positives = 153/257 (59%), Gaps = 11/257 (4%)
Query: 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 172
++++PIA+L PYQ +W I ARVT K +R ++N+RG+GK+FS +L+D + GEIR T FN
Sbjct: 2 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 60
Query: 173 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 232
VD+F+ +IEV +VY SKG+LK A K F +KN++E+ ++V C E+D +P Q
Sbjct: 61 QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 119
Query: 233 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 291
F F I ++E+ + I +R N E +R + L DTSG+ V T
Sbjct: 120 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 179
Query: 292 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 351
LWG+ +K Q PVL++K +V+DF G+S+ + S+ + NPD EA++L
Sbjct: 180 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 231
Query: 352 REWFDSGGKNAATVSIS 368
R WFD+ G+ VSIS
Sbjct: 232 RGWFDAEGQALDGVSIS 248
>pdb|1JMC|A Chain A, Single Stranded Dna-Binding Domain Of Human Replication
Protein A Bound To Single Stranded Dna, Rpa70 Subunit,
Residues 183-420
Length = 246
Score = 187 bits (475), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 98/249 (39%), Positives = 149/249 (59%), Gaps = 11/249 (4%)
Query: 113 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 172
++++PIA+L PYQ +W I ARVT K +R ++N+RG+GK+FS +L+D + GEIR T FN
Sbjct: 6 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 64
Query: 173 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 232
VD+F+ +IEV +VY SKG+LK A K F +KN++E+ ++V C E+D +P Q
Sbjct: 65 QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 123
Query: 233 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 291
F F I ++E+ + I +R N E +R + L DTSG+ V T
Sbjct: 124 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 183
Query: 292 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 351
LWG+ +K Q PVL++K +V+DF G+S+ + S+ + NPD EA++L
Sbjct: 184 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 235
Query: 352 REWFDSGGK 360
R WFD+ G+
Sbjct: 236 RGWFDAEGQ 244
>pdb|1L1O|C Chain C, Structure Of The Human Replication Protein A (Rpa)
Trimerization Core
pdb|1L1O|F Chain F, Structure Of The Human Replication Protein A (Rpa)
Trimerization Core
Length = 181
Score = 111 bits (277), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 65/184 (35%), Positives = 102/184 (55%), Gaps = 7/184 (3%)
Query: 375 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT 434
G N KT+ ++K+E LG+ +KPD+ + A + +++ ++ Y ACP + CNKKV
Sbjct: 1 GGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVI 56
Query: 435 -QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLK 493
Q ++C++C+ E YR +L I D WVT FQES E ILG A L LK
Sbjct: 57 DQQNGLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK 116
Query: 494 YELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDL 553
+++ F E+ ++ F ++FR+++K E Y DE R+K TV+ V+Y R L+
Sbjct: 117 --DKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMS 174
Query: 554 ISKS 557
I +S
Sbjct: 175 IRRS 178
>pdb|1YNX|A Chain A, Solution Structure Of Dna Binding Domain A (Dbd-A) Of
S.Cerevisiae Replication Protein A (Rpa)
Length = 114
Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 47/112 (41%), Positives = 75/112 (66%), Gaps = 1/112 (0%)
Query: 115 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 174
I I L+PYQ W IKARV+ KG+++ ++N RGDGK+F+ + LD+ GEIR T FN
Sbjct: 4 IFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDT-SGEIRATAFNDFA 62
Query: 175 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDD 226
+F EI++ G+VY +SK L+PA+ F +L + +E+ L+ + ++ C +E +
Sbjct: 63 TKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 114
>pdb|3NQI|A Chain A, Crystal Structure Of A Putative Lipoprotein (Bf3042) From
Bacteroides Fragilis Nctc 9343 At 1.87 A Resolution
pdb|3NQI|B Chain B, Crystal Structure Of A Putative Lipoprotein (Bf3042) From
Bacteroides Fragilis Nctc 9343 At 1.87 A Resolution
pdb|3NQI|C Chain C, Crystal Structure Of A Putative Lipoprotein (Bf3042) From
Bacteroides Fragilis Nctc 9343 At 1.87 A Resolution
pdb|3NQI|D Chain D, Crystal Structure Of A Putative Lipoprotein (Bf3042) From
Bacteroides Fragilis Nctc 9343 At 1.87 A Resolution
Length = 246
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 166 RVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE 223
R + F A YEI ++ R Y + G KPA+ +NE+ LE TST++ E
Sbjct: 187 RTSSFKA-----YEISQILREYTLKSGQTKPAKITIVAQQNEYNNKLEDTSTIEKVYE 239
>pdb|3NTL|A Chain A, Crystal Structure Of Glucose-1-Phosphatase (Agpe) From
Enterobacter Cloacae
pdb|3NTL|B Chain B, Crystal Structure Of Glucose-1-Phosphatase (Agpe) From
Enterobacter Cloacae
Length = 398
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 439 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCP 485
RW NQE+ + +Y Y Q+++ + L+ + Q E+ GCP
Sbjct: 322 RWHDKNANQELMKIEYVYQSSEQLRNASVLSLQSPAQRVTLELKGCP 368
>pdb|3U58|A Chain A, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ab
pdb|3U58|B Chain B, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ab
pdb|3U58|C Chain C, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ab
pdb|3U58|D Chain D, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ab
Length = 213
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 6/97 (6%)
Query: 107 LKNEAPARIIPIAALNPYQGRWAIK--ARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGE 164
L ++ + + I+ L + R++ K RV K + N + D K F D++ E
Sbjct: 3 LSDQLSKQTLLISQLQVGKNRFSFKFEGRVVYKSS--TFQNQQ-DSKYFFITAQDANNQE 59
Query: 165 IRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNF 201
I ++ F VD+ Y+ ++VG+ Y G +K + N
Sbjct: 60 INLS-FWQKVDQSYQTLKVGQYYYFIGGEVKQFKNNL 95
>pdb|1NT4|A Chain A, Crystal Structure Of Escherichia Coli Periplasmic
Glucose-1- Phosphatase H18a Mutant Complexed With
Glucose-1-Phosphate
pdb|1NT4|B Chain B, Crystal Structure Of Escherichia Coli Periplasmic
Glucose-1- Phosphatase H18a Mutant Complexed With
Glucose-1-Phosphate
Length = 391
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 439 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCP 485
RW + N+++ + +Y Y Q+++ LT Q E+ GCP
Sbjct: 324 RWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCP 370
>pdb|3U50|C Chain C, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ob-C
Length = 172
Score = 28.5 bits (62), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 25/114 (21%), Positives = 56/114 (49%), Gaps = 9/114 (7%)
Query: 437 GNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGC--PAKELYMLKY 494
G+ + C+ C Q I+ +L+A +QD TG V F + +++ P+ +
Sbjct: 57 GDSFFCESCQQFINP-QVHLMLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAGQ 115
Query: 495 ELQDDVRFG--EIIRSRV----FNQYLFRLKIKEELYGDEQRVKITVIRADQVN 542
+++ + G EIIR F +++F ++ + + + +EQ + V++ ++ N
Sbjct: 116 YVKNCIENGQEEIIRQLFSKLDFARFIFEIQFENKEFNNEQEIAYKVLKIEKEN 169
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,281,261
Number of Sequences: 62578
Number of extensions: 678853
Number of successful extensions: 1277
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1250
Number of HSP's gapped (non-prelim): 10
length of query: 560
length of database: 14,973,337
effective HSP length: 104
effective length of query: 456
effective length of database: 8,465,225
effective search space: 3860142600
effective search space used: 3860142600
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: 54 (25.4 bits)