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= 006263
(653 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 (753), Expect = 1e-79, Method: Compositional matrix adjust.
Identities = 166/450 (36%), Positives = 246/450 (54%), Gaps = 22/450 (4%)
Query: 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 267
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: 268 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQFS 327
DRFY +++ VYLISK + A+K F++L+NE+EI E ++ ++ CT+ D +P+ ++
Sbjct: 62 DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDATD-VPEVKYE 120
Query: 328 FRHISEIESAEXXXXXXXXXXXXXXXPSVPILRKNGME-TQRRILNLKDTSGRSVELTLW 386
F I+E+ES E I+ K Q+R L L D RSV+LTLW
Sbjct: 121 FVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLW 180
Query: 387 GDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHELRE 446
G K + V PVL+ K KV DF G+S+ S+ + INPD E+H LR
Sbjct: 181 G----KTAETFPTNAGVDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHVLRG 236
Query: 447 WFDSGGKNA--------ATVSISREIAAGGAKNEIHKTVSQIKNEGLGRSEKPDWVTVRA 498
W+D+ G +A + GA +T+ Q+K+E LG SEKPD+ VRA
Sbjct: 237 WYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYFNVRA 296
Query: 499 FITFIKSDSFCYTACPLMIGDRQCNKKVT-QSGNRWQCDRCNQEIDECDYRYLLQAQIQD 557
+ +IK ++ YTAC CNKKV N W+C++C++ +YRY+L + D
Sbjct: 297 TVVYIKQENLYYTAC----ASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVAD 352
Query: 558 QTGLTWVTAFQESGEEILGCPAKELYMLKYELQDDVRFGEIIRSRVFNQYLFRLKIKEEL 617
TG W++ F E +++G A EL+ L+ E + + F + Y+F + K +
Sbjct: 353 ATGQMWLSGFNEDATQLIGMSAGELHKLREESESE--FSAALHRAANRMYMFNCRAKMDT 410
Query: 618 YGDEQRVKITVIRADQVNYSSESRYLLDLI 647
+ 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 (485), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 102/257 (39%), Positives = 153/257 (59%), Gaps = 11/257 (4%)
Query: 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
++++PIA+L PYQ +W I ARVT K +R ++N+RG+GK+FS +L+D + GEIR T FN
Sbjct: 2 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 60
Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
VD+F+ +IEV +VY SKG+LK A K F +KN++E+ ++V C E+D +P Q
Sbjct: 61 QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 119
Query: 326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
F F I ++E+ + I +R N E +R + L DTSG+ V T
Sbjct: 120 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 179
Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
LWG+ +K Q PVL++K +V+DF G+S+ + S+ + NPD EA++L
Sbjct: 180 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 231
Query: 445 REWFDSGGKNAATVSIS 461
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 (476), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 98/249 (39%), Positives = 149/249 (59%), Gaps = 11/249 (4%)
Query: 206 ARIIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNA 265
++++PIA+L PYQ +W I ARVT K +R ++N+RG+GK+FS +L+D + GEIR T FN
Sbjct: 6 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 64
Query: 266 VVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDDSIPKQQ 325
VD+F+ +IEV +VY SKG+LK A K F +KN++E+ ++V C E+D +P Q
Sbjct: 65 QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 123
Query: 326 FSFRHISEIESAEXXXXXXXXXXXXXXXPSVPI-LRKNGMETQRRILNLKDTSGRSVELT 384
F F I ++E+ + I +R N E +R + L DTSG+ V T
Sbjct: 124 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 183
Query: 385 LWGDFCNKEGQKLQEMVDVGFFPVLSVKSGKVNDFSGKSIGTIPSTQLFINPDFAEAHEL 444
LWG+ +K Q PVL++K +V+DF G+S+ + S+ + NPD EA++L
Sbjct: 184 LWGEDADKFDGSRQ--------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKL 235
Query: 445 REWFDSGGK 453
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: 468 GAKNEIHKTVSQIKNEGLGRSEKPDWVTVRAFITFIKSDSFCYTACPLMIGDRQCNKKVT 527
G N KT+ ++K+E LG+ +KPD+ + A + +++ ++ Y ACP + CNKKV
Sbjct: 1 GGSNTNWKTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVI 56
Query: 528 -QSGNRWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCPAKELYMLK 586
Q ++C++C+ E YR +L I D WVT FQES E ILG A L LK
Sbjct: 57 DQQNGLYRCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK 116
Query: 587 YELQDDVRFGEIIRSRVFNQYLFRLKIKEELYGDEQRVKITVIRADQVNYSSESRYLLDL 646
+++ F E+ ++ F ++FR+++K E Y DE R+K TV+ V+Y R L+
Sbjct: 117 --DKNEQAFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMS 174
Query: 647 ISKS 650
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: 208 IIPIAALNPYQGRWAIKARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGEIRVTCFNAVV 267
I I L+PYQ W IKARV+ KG+++ ++N RGDGK+F+ + LD+ GEIR T FN
Sbjct: 4 IFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDT-SGEIRATAFNDFA 62
Query: 268 DRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTEEDD 319
+F EI++ G+VY +SK L+PA+ F +L + +E+ L+ + ++ C +E +
Sbjct: 63 TKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDESN 114
>pdb|2B29|A Chain A, N-Terminal Domain Of The Rpa70 Subunit Of Human
Replication Protein A.
pdb|2B3G|A Chain A, P53n (Fragment 33-60) Bound To Rpa70n
Length = 123
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/110 (34%), Positives = 71/110 (64%), Gaps = 9/110 (8%)
Query: 11 SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
+++ GD N KP++QV++I+ I G++ RYR L+SD ++T + MLATQLN V+ Q+
Sbjct: 15 AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQL 74
Query: 68 KKGSVVQLIDYICSTVQN-RKIIVVLNMETIILDCEP----IGNPKIFSE 112
V Q+ +I +T+++ R++++++ +E ++ E IGNP ++E
Sbjct: 75 SSNCVCQIHRFIVNTLKDGRRVVILMELE-VLKSAEAVGVKIGNPVPYNE 123
>pdb|1EWI|A Chain A, Human Replication Protein A: Global Fold Of The N-Terminal
Rpa-70 Domain Reveals A Basic Cleft And Flexible C-
Terminal Linker
Length = 114
Score = 58.9 bits (141), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 62/91 (68%), Gaps = 4/91 (4%)
Query: 11 SLINGGDVNSKPLVQVMDIKLI--GSTQERYRFLISDSVSTQHA-MLATQLNDRVKTGQV 67
+++ GD N KP++QV++I+ I G++ RYR L+SD ++T + MLATQLN V+ Q+
Sbjct: 12 AIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQL 71
Query: 68 KKGSVVQLIDYICSTVQN-RKIIVVLNMETI 97
V Q+ +I +T+++ R++++++ +E +
Sbjct: 72 SSNCVCQIHRFIVNTLKDGRRVVILMELEVL 102
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 259 RVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKNFNHLKNEWEIFLEATSTVDLCTE 316
R + F A YEI ++ R Y + G KPA+ +NE+ LE TST++ E
Sbjct: 187 RTSSFKA-----YEISQILREYTLKSGQTKPAKITIVAQQNEYNNKLEDTSTIEKVYE 239
>pdb|3AC0|A Chain A, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|B Chain B, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|C Chain C, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
pdb|3AC0|D Chain D, Crystal Structure Of Beta-Glucosidase From Kluyveromyces
Marxianus In Complex With Glucose
Length = 845
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/63 (23%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 27 MDIKLIGSTQERYRFLISDSVSTQHAMLATQLNDRVKTGQVKKGSVVQLIDYICSTVQNR 86
+DI+ G T+ R R L+S S++++ + ++DRV+ V+++I ++ ++
Sbjct: 240 LDIEFPGPTRWRTRALVSHSLNSREQITTEDVDDRVR-------QVLKMIKFVVDNLEKT 292
Query: 87 KII 89
I+
Sbjct: 293 GIV 295
>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 = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCP 578
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 = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 6/96 (6%)
Query: 200 LKNEAPARIIPIAALNPYQGRWAIK--ARVTAKGDLRRYNNARGDGKVFSFDLLDSDGGE 257
L ++ + + I+ L + R++ K RV K + N + D K F D++ E
Sbjct: 3 LSDQLSKQTLLISQLQVGKNRFSFKFEGRVVYKSS--TFQNQQ-DSKYFFITAQDANNQE 59
Query: 258 IRVTCFNAVVDRFYEIIEVGRVYLISKGSLKPAQKN 293
I ++ F VD+ Y+ ++VG+ Y G +K + N
Sbjct: 60 INLS-FWQKVDQSYQTLKVGQYYYFIGGEVKQFKNN 94
>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 = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 532 RWQCDRCNQEIDECDYRYLLQAQIQDQTGLTWVTAFQESGEEILGCP 578
RW + N+++ + +Y Y Q+++ LT Q E+ GCP
Sbjct: 324 RWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCP 370
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 0.134 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,586,685
Number of Sequences: 62578
Number of extensions: 765407
Number of successful extensions: 1487
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1454
Number of HSP's gapped (non-prelim): 13
length of query: 653
length of database: 14,973,337
effective HSP length: 105
effective length of query: 548
effective length of database: 8,402,647
effective search space: 4604650556
effective search space used: 4604650556
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: 55 (25.8 bits)