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= 006973
(623 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 = 253 bits (647), Expect = 2e-67, Method: Compositional matrix adjust.
Identities = 154/451 (34%), Positives = 251/451 (55%), Gaps = 23/451 (5%)
Query: 174 VHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAA 233
++P+ L+PYQ WTIK RVTSK ++R + N RGEG +F+V L D+ G +I+AT FN+A
Sbjct: 3 IYPIEGLSPYQNRWTIKARVTSKSDIRHWSNQRGEGKLFSVNLLDDSG-EIKATGFNDAV 61
Query: 234 RKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMXXXXXXXXXXXXXXTAFIPQTKFN 293
+FY Q VY IS+ + +A KQF +QN+YE+ T +P+ K+
Sbjct: 62 DRFYPLLQENHVYLISKARVNIAKKQFSNLQNEYEITFENSTEIEECTDATD-VPEVKYE 120
Query: 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSL 353
FV I+EL V + D+IG++ + I K++ V KR++T+ D+ R+V ++L
Sbjct: 121 FVRINEL-ESVEANQQCDVIGILDSYGELSEIVSKASQRPVQKRELTLVDQGNRSVKLTL 179
Query: 354 WNELA----TNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSPDLPEAKK 409
W + A TN G D+ P++A K +KVGDF G SLS ST+L++PD+ E+
Sbjct: 180 WGKTAETFPTNAG------VDEKPVLAFKGVKVGDFGGRSLSMFSSSTMLINPDITESHV 233
Query: 410 LKSWYESEGKGTSM---ASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLG-DEKPVFF 465
L+ WY+++G + G G G++ GA + ++R ++ + + +LG EKP +F
Sbjct: 234 LRGWYDNDGAHAQFQPYTNGGVGGGAMGGGGAGANMAERRTIVQV-KDENLGMSEKPDYF 292
Query: 466 SIKAYISLIKPDQAMWYRACKT--CNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVC 523
+++A + IK + ++Y AC + CNKKV + + CE C ++ RYI+ V
Sbjct: 293 NVRATVVYIKQEN-LYYTACASEGCNKKVNLDHENNWRCEKCDRSYATPEYRYILSTNVA 351
Query: 524 DGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQ 583
D +G+ W+S FNE+A ++IG SA EL++L+ + ++ + L ++
Sbjct: 352 DATGQMWLSGFNEDATQLIGMSAGELHKLREE--SESEFSAALHRAANRMYMFNCRAKMD 409
Query: 584 EYNNEKRQRVTVRAVAPVDFAAESKFLLEEI 614
+N+ R R T+ APVDFA L++ I
Sbjct: 410 TFNDTARVRYTISRAAPVDFAKAGMELVDAI 440
>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 = 204 bits (518), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 106/251 (42%), Positives = 152/251 (60%), Gaps = 9/251 (3%)
Query: 170 MTRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMF 229
M +V P+ SL PYQ WTI RVT+K +RT+ N+RGEG +F++EL DE G +I+AT F
Sbjct: 4 MQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG-EIRATAF 62
Query: 230 NEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMXXXXXXXXXXXXXXTAFIPQ 289
NE KF+ ++ KVYY S+GTL++ANKQF V+NDYEM +P
Sbjct: 63 NEQVDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDD-HHLPT 121
Query: 290 TKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTV 349
+F+F ID+L + LVDIIG+ ++ I +SNN V KR+I + D + + V
Sbjct: 122 VQFDFTGIDDLENKSKDS-LVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVV 180
Query: 350 TVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSPDLPEAKK 409
T +LW E A + + P++AIK +V DF G SLS L ST++ +PD+PEA K
Sbjct: 181 TATLWGEDADKF------DGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYK 234
Query: 410 LKSWYESEGKG 420
L+ W+++EG+
Sbjct: 235 LRGWFDAEGQA 245
>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 = 204 bits (518), Expect = 2e-52, Method: Compositional matrix adjust.
Identities = 107/254 (42%), Positives = 153/254 (60%), Gaps = 9/254 (3%)
Query: 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA 232
+V P+ SL PYQ WTI RVT+K +RT+ N+RGEG +F++EL DE G +I+AT FNE
Sbjct: 3 KVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESG-EIRATAFNEQ 61
Query: 233 ARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMXXXXXXXXXXXXXXTAFIPQTKF 292
KF+ ++ KVYY S+GTL++ANKQF V+NDYEM +P +F
Sbjct: 62 VDKFFPLIEVNKVYYFSKGTLKIANKQFTAVKNDYEMTFNNETSVMPCEDD-HHLPTVQF 120
Query: 293 NFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVS 352
+F ID+L + LVDIIG+ ++ I +SNN V KR+I + D + + VT +
Sbjct: 121 DFTGIDDLENKSKDS-LVDIIGICKSYEDATKITVRSNNREVAKRNIYLMDTSGKVVTAT 179
Query: 353 LWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSPDLPEAKKLKS 412
LW E A + + P++AIK +V DF G SLS L ST++ +PD+PEA KL+
Sbjct: 180 LWGEDADKF------DGSRQPVLAIKGARVSDFGGRSLSVLSSSTIIANPDIPEAYKLRG 233
Query: 413 WYESEGKGTSMASI 426
W+++EG+ SI
Sbjct: 234 WFDAEGQALDGVSI 247
>pdb|1YNX|A Chain A, Solution Structure Of Dna Binding Domain A (Dbd-A) Of
S.Cerevisiae Replication Protein A (Rpa)
Length = 114
Score = 92.4 bits (228), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 45/99 (45%), Positives = 64/99 (64%), Gaps = 1/99 (1%)
Query: 171 TRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFN 230
TR + + L+PYQ WTIK RV+ KG ++T+ N RG+G +FNV D G +I+AT FN
Sbjct: 1 TRPIFAIEQLSPYQNVWTIKARVSYKGEIKTWHNQRGDGKLFNVNFLDTSG-EIRATAFN 59
Query: 231 EAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEM 269
+ A KF + Q GKVYY+S+ L+ A QF + + YE+
Sbjct: 60 DFATKFNEILQEGKVYYVSKAKLQPAKPQFTNLTHPYEL 98
>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 = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 53/167 (31%), Positives = 82/167 (49%), Gaps = 6/167 (3%)
Query: 452 TSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKT--CNKKVTDALGSGYWCEGCQKND 509
+ N GD KP +FS A + ++ + M Y+AC T CNKKV D Y CE C
Sbjct: 15 SENLGQGD-KPDYFSSVATVVYLRKENCM-YQACPTQDCNKKVIDQQNGLYRCEKCDTEF 72
Query: 510 EECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKLKEV 569
R I+ + D W++ F E AE I+G +A L ELK + ++ +++ +
Sbjct: 73 PNFKYRMILSVNIADFQENQWVTCFQESAEAILGQNAAYLGELKDK--NEQAFEEVFQNA 130
Query: 570 TWVPHLLRVSVAQQEYNNEKRQRVTVRAVAPVDFAAESKFLLEEISK 616
+ + RV V + YN+E R + TV V PVD+ + L+ I +
Sbjct: 131 NFRSFIFRVRVKVETYNDESRIKATVMDVKPVDYREYGRRLVMSIRR 177
>pdb|3U50|C Chain C, Crystal Structure Of The Tetrahymena Telomerase
Processivity Factor Teb1 Ob-C
Length = 172
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 460 EKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVTDALGSGYWCEGCQKNDEECSLRYIMV 519
+K F+ +S+ ++ +YR C K V G ++CE CQ+ + ++
Sbjct: 21 QKKEFYVYGNLVSIQMKNKLYYYR-CTCQGKSVLKYHGDSFFCESCQQFINP-QVHLMLR 78
Query: 520 ARVCDGSGEAWISIFNEEAERII 542
A V D +G + IF++++ ++I
Sbjct: 79 AFVQDSTGTIPVMIFDQQSSQLI 101
>pdb|3E2J|A Chain A, Crystal Structure Of Bovine Coupling Factor B
pdb|3E2J|B Chain B, Crystal Structure Of Bovine Coupling Factor B
pdb|3E2J|C Chain C, Crystal Structure Of Bovine Coupling Factor B
pdb|3E2J|D Chain D, Crystal Structure Of Bovine Coupling Factor B
Length = 176
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 52 RLKAILPSNLSSEVIS-GNIQNKGLIRLLDYA------LNEIPTKSEKYLIVTKCEVVSP 104
+L+ + S L E+IS GN+ +KG+I L + L+++P EK IV + P
Sbjct: 108 QLENLQKSMLEMEIISCGNVTDKGIIALHHFRNLKYLFLSDLPGVKEKEKIVQAFKTSLP 167
Query: 105 ALEMEIKIE 113
+LE+++ ++
Sbjct: 168 SLELKLDLK 176
>pdb|3DZE|A Chain A, Crystal Structure Of Bovine Coupling Factor B Bound With
Cadmium
pdb|3E3Z|A Chain A, Crystal Structure Of Bovine Coupling Factor B Bound With
Phenylarsine Oxide
pdb|3E4G|A Chain A, Crystal Structure Of Bovine Coupling Factor B, G28e Mutant
Length = 176
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 52 RLKAILPSNLSSEVIS-GNIQNKGLIRLLDYA------LNEIPTKSEKYLIVTKCEVVSP 104
+L+ + S L E+IS GN+ +KG+I L + L+++P EK IV + P
Sbjct: 108 QLENLQKSMLEMEIISCGNVTDKGIIALHHFRNLKYLFLSDLPGVKEKEKIVQAFKTSLP 167
Query: 105 ALEMEIKIE 113
+LE+++ ++
Sbjct: 168 SLELKLDLK 176
>pdb|1BF2|A Chain A, Structure Of Pseudomonas Isoamylase
Length = 750
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 443 SDRVSLTHITSNPSLGDEKPVFFSIKAYISLIK------PDQAMWYRACKTCN 489
+ ++ + + PSLGD ++ + + S + P WYR TC+
Sbjct: 661 TSNYAIAYAINGPSLGDSNSIYVAYNGWSSSVTFTLPAPPSGTQWYRVTDTCD 713
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
0.315 0.131 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,119,737
Number of Sequences: 62578
Number of extensions: 692669
Number of successful extensions: 1925
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1902
Number of HSP's gapped (non-prelim): 23
length of query: 623
length of database: 14,973,337
effective HSP length: 105
effective length of query: 518
effective length of database: 8,402,647
effective search space: 4352571146
effective search space used: 4352571146
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)