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= 045194
(157 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G91|B Chain B, Ccaat-Binding Complex From Aspergillus Nidulans
pdb|4G92|B Chain B, Ccaat-Binding Complex From Aspergillus Nidulans With Dna
Length = 92
Score = 132 bits (333), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 59/92 (64%), Positives = 76/92 (82%)
Query: 2 VEEQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRK 61
++EQD+ LPIANV +IMK LP AKI+KEAK+ MQEC +EFISF+T EAS+KC +E RK
Sbjct: 1 MKEQDRWLPIANVARIMKLALPENAKIAKEAKECMQECVSEFISFITSEASEKCQQEKRK 60
Query: 62 TVNGDDICWALSTLGFDNYTEAIVRYLHKYRE 93
TVNG+DI +A+++LGF+NY EA+ YL KYRE
Sbjct: 61 TVNGEDILFAMTSLGFENYAEALKIYLSKYRE 92
>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 93
Score = 125 bits (315), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 54/90 (60%), Positives = 72/90 (80%)
Query: 4 EQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTV 63
EQD LPIANV +IMK +P KI+K+AK+ +QEC +EFISF+T EAS++CH+E RKT+
Sbjct: 4 EQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTI 63
Query: 64 NGDDICWALSTLGFDNYTEAIVRYLHKYRE 93
NG+DI +A+STLGFD+Y E + YL K+RE
Sbjct: 64 NGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93
>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 125 bits (315), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 54/90 (60%), Positives = 72/90 (80%)
Query: 4 EQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTV 63
EQD LPIANV +IMK +P KI+K+AK+ +QEC +EFISF+T EAS++CH+E RKT+
Sbjct: 5 EQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTI 64
Query: 64 NGDDICWALSTLGFDNYTEAIVRYLHKYRE 93
NG+DI +A+STLGFD+Y E + YL K+RE
Sbjct: 65 NGEDILFAMSTLGFDSYVEPLKLYLQKFRE 94
>pdb|2BYK|B Chain B, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYK|D Chain D, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|B Chain B, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|D Chain D, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
Length = 128
Score = 62.4 bits (150), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 55/93 (59%), Gaps = 1/93 (1%)
Query: 1 MVEEQDKL-LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKEN 59
MVE + L LP A +G+++K+ LP A +SKEA+ + A+ F FVT ++ HK+N
Sbjct: 1 MVERIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQN 60
Query: 60 RKTVNGDDICWALSTLGFDNYTEAIVRYLHKYR 92
KT+ DI L+ L F+++ ++ + L YR
Sbjct: 61 HKTITAKDILQTLTELDFESFVPSLTQDLEVYR 93
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/100 (29%), Positives = 59/100 (59%), Gaps = 1/100 (1%)
Query: 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNG 65
D +P A + K++K+ LP +++ +A++ + C TEFI ++ EA++ C+K +KT++
Sbjct: 13 DLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISP 71
Query: 66 DDICWALSTLGFDNYTEAIVRYLHKYREDERERAKNQSKV 105
+ + AL +LGF +Y + L + + +R K S++
Sbjct: 72 EHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRL 111
>pdb|1BFM|A Chain A, Histone B From Methanothermus Fervidus
pdb|1BFM|B Chain B, Histone B From Methanothermus Fervidus
pdb|1A7W|A Chain A, Crystal Structure Of The Histone Hmfb From
Methanothermus Fervidus
Length = 69
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDI 68
LPIA +G+I+K R +S +A+ T+ + E + EA RKT+ +DI
Sbjct: 3 LPIAPIGRIIKDAGAER--VSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDI 60
Query: 69 CWAL 72
A+
Sbjct: 61 ELAV 64
>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 9 LPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDD 67
LP+A + KIMK L K IS EA + A FI+ +T A R+T+ +D
Sbjct: 17 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 74
Query: 68 ICWALSTLGFDNY 80
I A++ FD +
Sbjct: 75 IAMAIT--KFDQF 85
>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 97
Score = 31.2 bits (69), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 9 LPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDD 67
LP+A + KIMK L K IS EA + A FI+ +T A R+T+ +D
Sbjct: 20 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 77
Query: 68 ICWALSTLGFDNY 80
I A++ FD +
Sbjct: 78 IAMAIT--KFDQF 88
>pdb|1B6W|A Chain A, Crystal Structure Of The Selenomethionine Variant Of
Histone Hmfb From Methanothermus Fervidus
Length = 69
Score = 31.2 bits (69), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDI 68
LPIA +G+I+K R +S +A+ T+ + E + EA RKT+ +DI
Sbjct: 3 LPIAPIGRIIKDAGAER--VSDDARITLAKILEEXGRDIASEAIKLARHAGRKTIKAEDI 60
Query: 69 CWAL 72
A+
Sbjct: 61 ELAV 64
>pdb|1B67|A Chain A, Crystal Structure Of The Histone Hmfa From
Methanothermus Fervidus
pdb|1B67|B Chain B, Crystal Structure Of The Histone Hmfa From
Methanothermus Fervidus
Length = 68
Score = 29.3 bits (64), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDI 68
LPIA +G+I+K R +S +A+ + + E + EA RKT+ +DI
Sbjct: 3 LPIAPIGRIIKNAGAER--VSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 60
Query: 69 CWA 71
A
Sbjct: 61 ELA 63
>pdb|1HTA|A Chain A, Crystal Structure Of The Histone Hmfa From
Methanothermus Fervidus
Length = 69
Score = 29.3 bits (64), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDI 68
LPIA +G+I+K R +S +A+ + + E + EA RKT+ +DI
Sbjct: 4 LPIAPIGRIIKNAGAER--VSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 61
Query: 69 CWA 71
A
Sbjct: 62 ELA 64
>pdb|4G91|C Chain C, Ccaat-Binding Complex From Aspergillus Nidulans
pdb|4G92|C Chain C, Ccaat-Binding Complex From Aspergillus Nidulans With Dna
Length = 119
Score = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 9 LPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDD 67
LP+A + K+MK P K IS EA + FI+ +T A R+T+ D
Sbjct: 42 LPLARIKKVMKA--DPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSD 99
Query: 68 ICWALS 73
I ALS
Sbjct: 100 IAAALS 105
>pdb|1KU5|A Chain A, Crystal Structure Of Recombinant Histone Hpha From
Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3
pdb|1KU5|B Chain B, Crystal Structure Of Recombinant Histone Hpha From
Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3
Length = 70
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDI 68
LPIA V +++++ R +S++A + + E E+ + +A + RKTV +DI
Sbjct: 7 LPIAPVDRLIRKAGAER--VSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 64
Query: 69 CWALST 74
A+ +
Sbjct: 65 KLAIKS 70
>pdb|3HTZ|A Chain A, Crystal Structure Of The Catalytic Fragment Of Alanyl-Trna
Synthetase In Complex With L-Serine: Re-Refined
Length = 464
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 50 EASDKCHKENRKTVNGDDICWALSTLGFD-NYTEAIVRY------LHKYR---EDERERA 99
E K +E RKT++G ++ A T GF + + I R L ++ E++RERA
Sbjct: 365 EVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERA 424
Query: 100 KNQSKVTA 107
+ KV A
Sbjct: 425 RKHFKVEA 432
>pdb|1YFR|A Chain A, Crystal Structure Of Alanyl-Trna Synthetase In Complex
With Atp And Magnesium
pdb|1YFR|B Chain B, Crystal Structure Of Alanyl-Trna Synthetase In Complex
With Atp And Magnesium
pdb|1YFS|A Chain A, The Crystal Structure Of Alanyl-Trna Synthetase In Complex
With L-Alanine
pdb|1YFS|B Chain B, The Crystal Structure Of Alanyl-Trna Synthetase In Complex
With L-Alanine
pdb|1YFT|A Chain A, The Crystal Structure Of The Catalytic Fragment Of Alanyl-
Trna Synthetase In Complex Wtih Glycine
pdb|1YGB|A Chain A, Crystal Structure Of The Catalytic Fragment Of Alanyl-Trna
Synthetase In Complex With L-Serine
Length = 465
Score = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 50 EASDKCHKENRKTVNGDDICWALSTLGFD-NYTEAIVRY------LHKYR---EDERERA 99
E K +E RKT++G ++ A T GF + + I R L ++ E++RERA
Sbjct: 366 EVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERA 425
Query: 100 KNQSKVTA 107
+ KV A
Sbjct: 426 RKHFKVEA 433
>pdb|1RIQ|A Chain A, The Crystal Structure Of The Catalytic Fragment Of The
Alanyl-Trna Synthetase
Length = 465
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 50 EASDKCHKENRKTVNGDDICWALSTLGFD-NYTEAIVRY------LHKYR---EDERERA 99
E K +E RKT++G ++ A T GF + + I R L ++ E++RERA
Sbjct: 366 EVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERA 425
Query: 100 KNQSKVTA 107
+ KV A
Sbjct: 426 RKHFKVEA 433
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
0.307 0.122 0.334
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,960,753
Number of Sequences: 62578
Number of extensions: 134233
Number of successful extensions: 269
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 264
Number of HSP's gapped (non-prelim): 19
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 47 (22.7 bits)