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= 042716
(137 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 61/117 (52%), Gaps = 1/117 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
IIL EAD ++ DA +R +E Y G+ + C+ V+++ P+ S C+ +
Sbjct: 137 IILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASN 196
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILT 116
++ L FI+EQE ++ + E+I D S +LR+ I +++ + +G+ I +
Sbjct: 197 AIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITS 253
>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 = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 62/118 (52%), Gaps = 1/118 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
I L EAD L+ DA +R +E + + C+ SK+ +PI+S C + + P ++
Sbjct: 114 IFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDED 173
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTG 117
I + L +IAE EG++L + + I ++ ++R+AI +A+ ++ + V +
Sbjct: 174 IAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKITDENVFMVA 231
>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 = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 41/138 (29%), Positives = 69/138 (50%), Gaps = 4/138 (2%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
+I+ EA+ L+ DA +R +E+Y ++ C +S + PIKS C +I+ PS E
Sbjct: 138 VIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSE 197
Query: 60 IVEVLEFIAEQEGIQL-PHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQ--VILT 116
I +L + E IQL + ++IA S NLR ++ E+ N ++ +I
Sbjct: 198 ISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKP 257
Query: 117 GWEDDITNIATKIIEEQS 134
W I + KI++E+S
Sbjct: 258 DWIIVIHKLTRKIVKERS 275
>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 = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
I L EAD L+ DA +R +E Y + C+ VS++ +PI+S C V + P K+
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEA 165
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
+ + L I E+EG+++ E + S + R+AI + + +
Sbjct: 166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/102 (30%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
I L EAD L+ DA +R +E Y + C+ VS++ +PI+S C V + P K+
Sbjct: 106 IFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFRFKPVPKEA 165
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
+ + L I E+EG+++ E + S + R+AI + + +
Sbjct: 166 MKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 57/102 (55%), Gaps = 1/102 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKL-QPIKSLCTVIQLLPPSKQE 59
+IL EAD ++ A +R +E Y + F C+ +K+ +P++S C +++ S ++
Sbjct: 111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDED 170
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEAS 101
+++ L I + E ++ + E I ++ ++RQAI + +++
Sbjct: 171 VLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQST 212
>pdb|3F43|A Chain A, Crystal Structure Of A Putative Anti-sigma Factor
Antagonist (tm1081) From Thermotoga Maritima At 1.59 A
Resolution
Length = 125
Score = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 12 DALLYMRWLLERY--KGLNKVFFCCSDVSKLQPIKSLCTVIQLL 53
+A L+ +W+ + + KG NK+F SDV + SL ++ +L
Sbjct: 35 NAHLFKKWVFDEFLNKGYNKIFLVLSDVESIDSF-SLGVIVNIL 77
>pdb|2KA5|A Chain A, Nmr Structure Of The Protein Tm1081
Length = 125
Score = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 12 DALLYMRWLLERY--KGLNKVFFCCSDVSKLQPIKSLCTVIQLL 53
+A L+ +W+ + + KG NK+F SDV + SL ++ +L
Sbjct: 35 NAHLFKKWVFDEFLNKGYNKIFLVLSDVESIDSF-SLGVIVNIL 77
>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 = 30.8 bits (68), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/103 (22%), Positives = 48/103 (46%), Gaps = 1/103 (0%)
Query: 1 IILCEADKLSTDALLYMRWLLERYKGLNKVFFCCSDVSKLQP-IKSLCTVIQLLPPSKQE 59
IIL EAD ++ A +R ++ERY + + KL P + S CT + P ++
Sbjct: 114 IILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEA 173
Query: 60 IVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASR 102
I + + E ++L + + + S ++R+ + ++ +
Sbjct: 174 IERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCK 216
>pdb|2Z4R|A Chain A, Crystal Structure Of Domain Iii From The Thermotoga
Maritima Replication Initiation Protein Dnaa
pdb|2Z4R|B Chain B, Crystal Structure Of Domain Iii From The Thermotoga
Maritima Replication Initiation Protein Dnaa
pdb|2Z4R|C Chain C, Crystal Structure Of Domain Iii From The Thermotoga
Maritima Replication Initiation Protein Dnaa
pdb|2Z4S|A Chain A, Crystal Structure Of Domain Iii From The Thermotoga
Maritima Replication Initiation Protein Dnaa
Length = 440
Score = 26.2 bits (56), Expect = 5.6, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 49 VIQLLPPSKQEIVEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQ 93
V +L PP ++ + + E E +LP ++ +A+N +NLR+
Sbjct: 257 VAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRR 301
>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2P5O|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5G|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
Length = 903
Score = 25.4 bits (54), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 61 VEVLEFIAEQEGIQLPHQLAEKIADNSKNNLRQAIRSFEASRQMNYPFVEGQVILTGW 118
+E+ + EQ G ++P ++ +KI +N ++ + + Q P VILTGW
Sbjct: 164 IEIAAKLQEQGGDEVPSEIIDKIIYXPFDNEKELLXEYLNFWQQKTP-----VILTGW 216
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
0.319 0.135 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,555,792
Number of Sequences: 62578
Number of extensions: 116723
Number of successful extensions: 302
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 290
Number of HSP's gapped (non-prelim): 33
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)