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= 003281
(834 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 = 300 bits (769), Expect = 1e-81, Method: Compositional matrix adjust.
Identities = 160/459 (34%), Positives = 260/459 (56%), Gaps = 33/459 (7%)
Query: 219 IIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVA 278
I PI L+PY +WTIKARVT+K ++RH++NQRG+GK+F +LLD D GEI+ T FN
Sbjct: 3 IYPIEGLSPYQNRWTIKARVTSKSDIRHWSNQRGEGKLFSVNLLD-DSGEIKATGFNDAV 61
Query: 279 DQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQFH 338
D+FY ++ +YL+S+ + A+K F++L N+ EI + ++ ++ C D +P ++
Sbjct: 62 DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEEC-TDATDVPEVKYE 120
Query: 339 FRPINDVEGMENNSVVDLIGVVSYISPTASLMRKNGTE-TQKRTLHLRDMSGRSVELTLW 397
F IN++E +E N D+IG++ + ++ K QKR L L D RSV+LTLW
Sbjct: 121 FVRINELESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTLW 180
Query: 398 G----NFCNDDGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFPEAH 453
G F + G+ + P+LA K +V DF G+ + S++ + I PD E+H
Sbjct: 181 GKTAETFPTNAGVDEK--------PVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESH 232
Query: 454 RLKEWFEKEGKNTQ---------SVSISRDSLSVGRADIRKTVSQIKDEGLGTKEKPDWI 504
L+ W++ +G + Q + R+T+ Q+KDE LG EKPD+
Sbjct: 233 VLRGWYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQVKDENLGMSEKPDYF 292
Query: 505 TVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRWHCDRCDQSVVECDYRYILQF 564
V AT+VYIK +N YTAC CNKKV + + W C++CD+S +YRYIL
Sbjct: 293 NVRATVVYIKQENLYYTAC----ASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILST 348
Query: 565 QIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDEKFGEVVRNATFTKYLFKLKV 624
+ D TG W++ F E A +++GMSA +L+ L+ ++++ +F + A Y+F +
Sbjct: 349 NVADATGQMWLSGFNEDATQLIGMSAGELHKLR--EESESEFSAALHRAANRMYMFNCRA 406
Query: 625 KEETFSDEQRVKSTVVKAERYNYSSETRFILDLMDKLKS 663
K +TF+D RV+ T+ +A +++ ++L+D +++
Sbjct: 407 KMDTFNDTARVRYTISRAAPVDFAKAG---MELVDAIRA 442
>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 = 211 bits (538), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 109/258 (42%), Positives = 157/258 (60%), Gaps = 13/258 (5%)
Query: 217 SRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNA 276
S+++PIA+L PY KWTI ARVT K ++R ++N RG+GK+F +L+D + GEIR T FN
Sbjct: 2 SKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRATAFNE 60
Query: 277 VADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASIPRQQ 336
D+F+ +E K+Y S+G+LK A K F + ND E+ + + V C EDD +P Q
Sbjct: 61 QVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHLPTVQ 119
Query: 337 FHFRPINDVEGMENNSVVDLIGVV-SYISPTASLMRKNGTETQKRTLHLRDMSGRSVELT 395
F F I+D+E +S+VD+IG+ SY T +R N E KR ++L D SG+ V T
Sbjct: 120 FDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 179
Query: 396 LWGNFCND-DGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFPEAHR 454
LWG + DG R P+LA+K RVSDF G+ + +S++ + PD PEA++
Sbjct: 180 LWGEDADKFDGSRQ---------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYK 230
Query: 455 LKEWFEKEGKNTQSVSIS 472
L+ WF+ EG+ VSIS
Sbjct: 231 LRGWFDAEGQALDGVSIS 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 = 207 bits (527), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 106/254 (41%), Positives = 155/254 (61%), Gaps = 13/254 (5%)
Query: 213 SEVPSRIIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVT 272
S + S+++PIA+L PY KWTI ARVT K ++R ++N RG+GK+F +L+D + GEIR T
Sbjct: 2 SHMQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVD-ESGEIRAT 60
Query: 273 CFNAVADQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYEDDASI 332
FN D+F+ +E K+Y S+G+LK A K F + ND E+ + + V C EDD +
Sbjct: 61 AFNEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPC-EDDHHL 119
Query: 333 PRQQFHFRPINDVEGMENNSVVDLIGVV-SYISPTASLMRKNGTETQKRTLHLRDMSGRS 391
P QF F I+D+E +S+VD+IG+ SY T +R N E KR ++L D SG+
Sbjct: 120 PTVQFDFTGIDDLENKSKDSLVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKV 179
Query: 392 VELTLWGNFCND-DGLRLQHMCDSGVFPILAVKAGRVSDFNGKVVGTISTTQLFIEPDFP 450
V TLWG + DG R P+LA+K RVSDF G+ + +S++ + PD P
Sbjct: 180 VTATLWGEDADKFDGSRQ---------PVLAIKGARVSDFGGRSLSVLSSSTIIANPDIP 230
Query: 451 EAHRLKEWFEKEGK 464
EA++L+ WF+ EG+
Sbjct: 231 EAYKLRGWFDAEGQ 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 = 132 bits (332), Expect = 8e-31, Method: Compositional matrix adjust.
Identities = 68/171 (39%), Positives = 105/171 (61%), Gaps = 6/171 (3%)
Query: 485 KTVSQIKDEGLGTKEKPDWITVSATIVYIKCDNFCYTACPIMIGDRPCNKKVMNNGDGRW 544
KT+ ++K E LG +KPD+ + AT+VY++ +N Y ACP + CNKKV++ +G +
Sbjct: 8 KTLYEVKSENLGQGDKPDYFSSVATVVYLRKENCMYQACPT----QDCNKKVIDQQNGLY 63
Query: 545 HCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLYSLKYVDQNDE 604
C++CD YR IL I D WVT FQE AE I+G +A L LK D+N++
Sbjct: 64 RCEKCDTEFPNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELK--DKNEQ 121
Query: 605 KFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKAERYNYSSETRFIL 655
F EV +NA F ++F+++VK ET++DE R+K+TV+ + +Y R ++
Sbjct: 122 AFEEVFQNANFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLV 172
>pdb|1YNX|A Chain A, Solution Structure Of Dna Binding Domain A (Dbd-A) Of
S.Cerevisiae Replication Protein A (Rpa)
Length = 114
Score = 104 bits (259), Expect = 2e-22, Method: Composition-based stats.
Identities = 48/110 (43%), Positives = 75/110 (68%), Gaps = 1/110 (0%)
Query: 219 IIPIAALNPYMGKWTIKARVTAKGELRHYNNQRGDGKVFHFDLLDSDGGEIRVTCFNAVA 278
I I L+PY WTIKARV+ KGE++ ++NQRGDGK+F+ + LD+ GEIR T FN A
Sbjct: 4 IFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTS-GEIRATAFNDFA 62
Query: 279 DQFYHQVEAGKIYLVSRGSLKPAQKNFNHLHNDLEIFLDMTSMVQLCYED 328
+F ++ GK+Y VS+ L+PA+ F +L + E+ LD ++++ C+++
Sbjct: 63 TKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYELNLDRDTVIEECFDE 112
>pdb|3U50|C Chain C, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ob-C
Length = 172
Score = 36.2 bits (82), Expect = 0.083, Method: Composition-based stats.
Identities = 34/175 (19%), Positives = 76/175 (43%), Gaps = 19/175 (10%)
Query: 481 ADIRKTVSQIKDEGLGTKEKPDWITVSATIVYIKCDN-FCYTACPIMIGDRPCNKKVMNN 539
+ I + + Q + +G K++ V +V I+ N Y C K V+
Sbjct: 5 SSIEEIIQQAQASEIGQKKE---FYVYGNLVSIQMKNKLYYYRCTCQ------GKSVLKY 55
Query: 540 GDGRWHCDRCDQSVVECDYRYILQFQIQDHTGLTWVTAFQECAEEIMGMSAKDLY---SL 596
+ C+ C Q + +L+ +QD TG V F + + +++ ++ +
Sbjct: 56 HGDSFFCESC-QQFINPQVHLMLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAG 114
Query: 597 KYV-----DQNDEKFGEVVRNATFTKYLFKLKVKEETFSDEQRVKSTVVKAERYN 646
+YV + +E ++ F +++F+++ + + F++EQ + V+K E+ N
Sbjct: 115 QYVKNCIENGQEEIIRQLFSKLDFARFIFEIQFENKEFNNEQEIAYKVLKIEKEN 169
>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The
Tramp Complex
Length = 124
Score = 34.3 bits (77), Expect = 0.31, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 740 ARQSCSSCGAVGHSSMNCPSIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWAR 799
A C++C GH +CP I+ S G + +S A +C KC + GH+
Sbjct: 3 AAPKCNNCSQRGHLKKDCPHIIC----SYCGATDDHYSRHCPKAI--QCSKCDEVGHYRS 56
Query: 800 DCP 802
CP
Sbjct: 57 QCP 59
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 5/50 (10%)
Query: 759 SIMSGPGQSSGGGYANSFSSGAGIATSSECYKCHKTGHWARDCPSLNAAP 808
+++SG Q GG +C C + GHWA+DCP P
Sbjct: 2 TVVSGQKQDRQGGERRRSQ-----LDRDQCAYCKEKGHWAKDCPKKPRGP 46
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 30.4 bits (67), Expect = 3.9, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 787 ECYKCHKTGHWARDCPSLNAAP 808
+C C + GHWA+DCP P
Sbjct: 12 QCAYCKEKGHWAKDCPKKPRGP 33
>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 = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 657 LMDKLKSG--DSTSFALKAENIIPKPEMTYTGTGNIGSRQTAPVVANYVGNNSNAGAASG 714
++ KLK+G DS + + + KP ++Y + R +AP + VG++SN AS
Sbjct: 239 VLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSN--IASL 296
Query: 715 LLANQMGQYGNQYSGSRLPAAG 736
L A Y R P G
Sbjct: 297 LTALDFKPYQLHDQNERTPIGG 318
>pdb|1CHU|A Chain A, Structure Of L-Aspartate Oxidase: Implications For The
Succinate Dehydrogenase FUMARATE REDUCATSE FAMILY
Length = 540
Score = 29.3 bits (64), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 370 MRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRL 408
+ + G + +R LH D +GR VE TL N +R+
Sbjct: 118 LTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRV 156
>pdb|1KNP|A Chain A, E. Coli L-aspartate Oxidase: Mutant R386l In Complex With
Succinate
pdb|1KNR|A Chain A, L-aspartate Oxidase: R386l Mutant
Length = 540
Score = 29.3 bits (64), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 370 MRKNGTETQKRTLHLRDMSGRSVELTLWGNFCNDDGLRL 408
+ + G + +R LH D +GR VE TL N +R+
Sbjct: 118 LTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRV 156
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
0.317 0.132 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,703,579
Number of Sequences: 62578
Number of extensions: 1001650
Number of successful extensions: 2169
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2132
Number of HSP's gapped (non-prelim): 27
length of query: 834
length of database: 14,973,337
effective HSP length: 107
effective length of query: 727
effective length of database: 8,277,491
effective search space: 6017735957
effective search space used: 6017735957
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: 56 (26.2 bits)