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= 048281
(660 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
Length = 1220
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 17/89 (19%)
Query: 185 MEEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGIWMSRFTVTGVLSA 244
+EE + ELP + VL + MV EV R+ ++ G M+RFT++ A
Sbjct: 1029 IEELSEFVRELPGKPKVLLSGMVE------------EVVRKPTRSGGMMARFTLSDETGA 1076
Query: 245 LIMMGFFKNGRVVHGIVVKMGYDSGVPVM 273
L ++ F GR G+ K+ D +P++
Sbjct: 1077 LEVVVF---GRAYEGVSPKLKED--IPLL 1100
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 17/89 (19%)
Query: 185 MEEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGIWMSRFTVTGVLSA 244
+EE + ELP + VL + MV EV R+ ++ G M+RFT++ A
Sbjct: 1029 IEELSEFVRELPGKPKVLLSGMVE------------EVVRKPTRSGGMMARFTLSDETGA 1076
Query: 245 LIMMGFFKNGRVVHGIVVKMGYDSGVPVM 273
L ++ F GR G+ K+ D +P++
Sbjct: 1077 LEVVVF---GRAYEGVSPKLKED--IPLL 1100
>pdb|3MVD|K Chain K, Crystal Structure Of The Chromatin Factor Rcc1 In Complex
With The Nucleosome Core Particle
pdb|3MVD|L Chain L, Crystal Structure Of The Chromatin Factor Rcc1 In Complex
With The Nucleosome Core Particle
Length = 423
Score = 32.3 bits (72), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 15/133 (11%)
Query: 194 ELPLRDVVLWNAMVNGYAQIGEF---HKALEVFRRMSKEGIWMSRFTVTGVLSALIMMGF 250
ELP R VL N +V G +G+ LE R GI + G + L++
Sbjct: 34 ELPKRRTVLGNVLVCGNGDVGQLGLGEDILERKRLSPVAGIPDAVDISAGGMHNLVLT-- 91
Query: 251 FKNGRVV------HGIVVKMGYDSGVPVMNALIDMYGKGKCV--GEALEIFEMMEEKDIF 302
K+G + G + + + G LID+ GK C+ G++ ++E+ +F
Sbjct: 92 -KSGDIYSFGCNDEGALGRDTSEDGSESKPDLIDLPGKALCISAGDSHSAC-LLEDGRVF 149
Query: 303 SWNSIMTVHEQCG 315
+W S H G
Sbjct: 150 AWGSFRDSHGNMG 162
>pdb|2JLJ|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of Yersinia
Pestis Yscu N263a P264a Mutant
Length = 144
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 186 EEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGI 231
EE + + + +PL + W+A+V+ Y + EV R + ++ I
Sbjct: 91 EEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQNI 136
>pdb|2JLH|A Chain A, Crystal Structure Of The Cytoplasmic Domain Of Yersinia
Pestis Yscu N263a Mutant
Length = 144
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 186 EEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGI 231
EE + + + +PL + W+A+V+ Y + EV R + ++ I
Sbjct: 91 EEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQNI 136
>pdb|2W0R|A Chain A, Crystal Structure Of The Mutated N263d Yscu C-Terminal
Domain
Length = 144
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 186 EEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGI 231
EE + + + +PL + W+A+V+ Y + EV R + ++ I
Sbjct: 91 EEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQNI 136
>pdb|2V5G|A Chain A, Crystal Structure Of The Mutated N263a Yscu C-Terminal
Domain
Length = 144
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 186 EEALKVFEELPLRDVVLWNAMVNGYAQIGEFHKALEVFRRMSKEGI 231
EE + + + +PL + W+A+V+ Y + EV R + ++ I
Sbjct: 91 EEGVPILQRIPLARALYWDALVDHYIPAEQIEATAEVLRWLERQNI 136
>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
Tpr Motif
Length = 125
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 499 EAYELALAM-PNEANPVVWRTLLAASRLHGNTDLAEIAAQRVFQLEPGHCGNYVLMSNIY 557
E Y+ AL + PN A W L A G+ D A Q+ +L+P + + + N Y
Sbjct: 30 EYYQKALELDPNNAE--AWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAY 87
Query: 558 VAGGKYEEVLD 568
G Y+E ++
Sbjct: 88 YKQGDYDEAIE 98
>pdb|2WQH|A Chain A, Crystal Structure Of Ctpr3y3
Length = 125
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 499 EAYELALAM-PNEANPVVWRTLLAASRLHGNTDLAEIAAQRVFQLEPGHCGNYVLMSNIY 557
E Y+ AL + PN A W L A G+ D A Q+ +L P + + + N Y
Sbjct: 30 EYYQKALELYPNNAE--AWYNLGNAYYKQGDYDEAIEYYQKALELYPNNAEAWYNLGNAY 87
Query: 558 VAGGKYEEVLD 568
G Y+E ++
Sbjct: 88 YKQGDYDEAIE 98
>pdb|3OC3|A Chain A, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
pdb|3OC3|B Chain B, Crystal Structure Of The Mot1 N-Terminal Domain In Complex
With Tbp
Length = 800
Score = 28.9 bits (63), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 55 HSYMLRTGIIDSPLSITS-LINMYSKCCQMKYALFVFNNLSCEPNVFTYNAMISGFYSND 113
HS+ + G +++ L S I++Y+K Q++ FVF++ E N+ N + N+
Sbjct: 657 HSFFHKIGSLENRLDFFSKTIHIYTKTSQIQKIGFVFDDALREKNITVINGFMRSLEFNE 716
Query: 114 -FAFKGLD 120
F K L+
Sbjct: 717 KFVRKALE 724
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
0.324 0.138 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,753,494
Number of Sequences: 62578
Number of extensions: 816538
Number of successful extensions: 2485
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2470
Number of HSP's gapped (non-prelim): 26
length of query: 660
length of database: 14,973,337
effective HSP length: 105
effective length of query: 555
effective length of database: 8,402,647
effective search space: 4663469085
effective search space used: 4663469085
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)