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= 036742
(629 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 354
Score = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 77/303 (25%), Positives = 131/303 (43%), Gaps = 31/303 (10%)
Query: 347 FWADKHQPSSLNGFICHRHEAQLLKELVVD-GNCPHILIKGQSGSGKRALAMALLHEIYG 405
W DK++P SLN + LK L + PH+L+ G +G+GK+ MALL I+G
Sbjct: 3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFG 62
Query: 406 DACWNEKWPTQVLVP---------VASSAHHVELN-VNLQANAKYALMGLVKEI------ 449
+ K + V V SS +H+E+ ++ N + + L+KE+
Sbjct: 63 PGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQV 122
Query: 450 -----RDNLAITPEVSNAMIVIYEVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDII 504
+D LA + ++I E + + Q ++ M+ Y+ + +LI+ C+ II
Sbjct: 123 DFQDSKDGLAHRYKC----VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPII 178
Query: 505 ESVKTHCKVIKVDPPVTHEIMEVLIQIARKEDFDL-SMTFAAKIATKAKQNLRKAIMALE 563
+K+ C +I+ P EI +L + E L + +IA + NLR +++ LE
Sbjct: 179 APIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLE 238
Query: 564 ACKALNYPFADDQPIPL---GWXXXXXXXXXXXXXDPSPKRLVMVRGKIQKLLAEFVHPK 620
+ ALN A P+ W + S L+ R + LLA +
Sbjct: 239 S-MALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPAN 297
Query: 621 LIL 623
+IL
Sbjct: 298 IIL 300
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 84.3 bits (207), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 65/244 (26%), Positives = 112/244 (45%), Gaps = 26/244 (10%)
Query: 335 IQKAVVIEKLRPFWADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRA 394
I++ V+EK P W +K++P L+ + H + LK V G+ PH+L G G GK
Sbjct: 5 IREVKVLEK--P-WVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTT 61
Query: 395 LAMALLHEIYGDACWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLA 454
A+AL E++G E W L ELN + + + +++E A
Sbjct: 62 AALALARELFG-----ENWRHNFL----------ELNASDERG-----INVIREKVKEFA 101
Query: 455 ITPEVSNA---MIVIYEVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHC 511
T + A +I + E D + Q ++ M+ ++ + + IL C IIE +++ C
Sbjct: 102 RTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRC 161
Query: 512 KVIKVDPPVTHEIMEVLIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALEACKALNYP 571
+ + P +I + L IA E +L+ I A+ ++R+AI L+A AL+
Sbjct: 162 AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKK 221
Query: 572 FADD 575
D+
Sbjct: 222 ITDE 225
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 78.6 bits (192), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 57/225 (25%), Positives = 100/225 (44%), Gaps = 23/225 (10%)
Query: 348 WADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRALAMALLHEIYGDA 407
W +K++P +L+ + Q LK V N PH+L G G+GK A A+AL +++G
Sbjct: 7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFG-- 64
Query: 408 CWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSNA---MI 464
E W + +E+N + + + +V+ A T + A +I
Sbjct: 65 ---ENW----------RDNFIEMNASDERG-----IDVVRHKIKEFARTAPIGGAPFKII 106
Query: 465 VIYEVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEI 524
+ E D Q ++ M+ Y+ SC+ IL C IIE +++ C V + P +
Sbjct: 107 FLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAM 166
Query: 525 MEVLIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALEACKALN 569
+ L++I KE ++ + + + RKAI AL+ A+
Sbjct: 167 KKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIG 211
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 57/225 (25%), Positives = 100/225 (44%), Gaps = 23/225 (10%)
Query: 348 WADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRALAMALLHEIYGDA 407
W +K++P +L+ + Q LK V N PH+L G G+GK A A+AL +++G
Sbjct: 7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFG-- 64
Query: 408 CWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSNA---MI 464
E W + +E+N + + + +V+ A T + A +I
Sbjct: 65 ---ENW----------RDNFIEMNASDERG-----IDVVRHKIKEFARTAPIGGAPFKII 106
Query: 465 VIYEVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEI 524
+ E D Q ++ M+ Y+ SC+ IL C IIE +++ C V + P +
Sbjct: 107 FLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEAM 166
Query: 525 MEVLIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALEACKALN 569
+ L++I KE ++ + + + RKAI AL+ A+
Sbjct: 167 KKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGAAAIG 211
>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 323
Score = 69.3 bits (168), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 49/220 (22%), Positives = 97/220 (44%), Gaps = 16/220 (7%)
Query: 348 WADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRALAMALLHEIYGDA 407
W +K++P L+ + ++ L+++ DGN PH++I G G GK L HE+ G
Sbjct: 11 WVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLG-- 68
Query: 408 CWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSNAMIVIY 467
+ VL AS +++ N +K P + ++++
Sbjct: 69 ---RSYADGVLELNASDDRGIDVVRN-----------QIKHFAQKKLHLPPGKHKIVILD 114
Query: 468 EVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEIMEV 527
E D Q ++ M+ Y++S + C IIE +++ C +++ ++++
Sbjct: 115 EADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKR 174
Query: 528 LIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALEACKA 567
L+QI + ED + I A+ ++R+AI L++ A
Sbjct: 175 LLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVA 214
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 50/224 (22%), Positives = 96/224 (42%), Gaps = 7/224 (3%)
Query: 348 WADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRALAMALLHEIYGDA 407
W +K++P +L+ H +LK+ + N PH+L G G+GK + +AL E+YG
Sbjct: 27 WVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGP- 85
Query: 408 CWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSNAMIVIY 467
+ +++L AS + + N +A + + K + +L P +I++
Sbjct: 86 ---DLMKSRILELNASDERGISIVREKVKN--FARLTVSKPSKHDLENYPCPPYKIIILD 140
Query: 468 EVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEIMEV 527
E D Q ++ M+ Y+ + L C II+ + + C + ++
Sbjct: 141 EADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDR 200
Query: 528 LIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALE-ACKALNY 570
L I+ +E+ +I + +LR+ I L+ A K Y
Sbjct: 201 LRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQY 244
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 48/232 (20%), Positives = 99/232 (42%), Gaps = 24/232 (10%)
Query: 348 WADKHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQSGSGKRALAMALLHEIYGDA 407
W +K++P +L+ +++ V +G PH+L G G+GK + +AL EIYG
Sbjct: 15 WVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYG-- 72
Query: 408 CWNEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSN---AMI 464
+ + VL AS +++ N +I+D A T ++ + +I
Sbjct: 73 ---KNYSNMVLELNASDDRGIDVVRN--------------QIKD-FASTRQIFSKGFKLI 114
Query: 465 VIYEVDKAAEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEI 524
++ E D Q ++ +++ YT + + + + ++ + C + P I
Sbjct: 115 ILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAI 174
Query: 525 MEVLIQIARKEDFDLSMTFAAKIATKAKQNLRKAIMALEACKA-LNYPFADD 575
+ + E LS + + ++R+ + L++CKA L+ P D+
Sbjct: 175 ERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDE 226
>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|L Chain L, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|M Chain M, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|N Chain N, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|O Chain O, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U60|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U61|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
Length = 324
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 51/227 (22%), Positives = 97/227 (42%), Gaps = 40/227 (17%)
Query: 351 KHQPSSLNGFICHRHEAQLLKELVVDGNCPHILIKGQS-GSGKRALAMALLHEIYGDACW 409
K++PS+++ I + + K + G PHI++ S G+GK +A AL H++ D +
Sbjct: 19 KYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMF 78
Query: 410 NEKWPTQVLVPVASSAHHVELNVNLQANAKYALMGLVKEIRDNLAITPEVSN--AMIVIY 467
N + V+ N A +IVI
Sbjct: 79 --------------------------VNGSDCKIDFVRGPLTNFASAASFDGRQKVIVID 112
Query: 468 EVDKA--AEHIQYLIKWIMDGYTDSCKLILCCEDDVDIIESVKTHCKVIKVDPPVTHEIM 525
E D++ AE ++L + M+ Y+ +C +I+ + II+ +++ C+VI P + +
Sbjct: 113 EFDRSGLAESQRHL-RSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKI 171
Query: 526 EVLIQIARK-------EDFDLS-MTFAAKIATKAKQNLRKAIMALEA 564
E++ Q+ R+ E ++ M A + K + RK I L++
Sbjct: 172 EMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDS 218
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 0.131 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,844,957
Number of Sequences: 62578
Number of extensions: 634540
Number of successful extensions: 1317
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1300
Number of HSP's gapped (non-prelim): 10
length of query: 629
length of database: 14,973,337
effective HSP length: 105
effective length of query: 524
effective length of database: 8,402,647
effective search space: 4402987028
effective search space used: 4402987028
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)