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= 027605
(221 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 = 156 bits (394), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 71/91 (78%), Positives = 84/91 (92%)
Query: 22 KEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKT 81
KEQDR+LPIANV+RIMK +LP NAKI+KEAKE +QECVSEFISFIT EAS+KCQ+EKRKT
Sbjct: 2 KEQDRWLPIANVARIMKLALPENAKIAKEAKECMQECVSEFISFITSEASEKCQQEKRKT 61
Query: 82 INGDDLLWAMTTLGFENYVSPLKIYLNKYRE 112
+NG+D+L+AMT+LGFENY LKIYL+KYRE
Sbjct: 62 VNGEDILFAMTSLGFENYAEALKIYLSKYRE 92
>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 145 bits (366), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 64/94 (68%), Positives = 83/94 (88%)
Query: 19 ISDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREK 78
+S +EQD +LPIANV+RIMK ++P KI+K+AKE VQECVSEFISFIT EAS++C +EK
Sbjct: 1 MSFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEK 60
Query: 79 RKTINGDDLLWAMTTLGFENYVSPLKIYLNKYRE 112
RKTING+D+L+AM+TLGF++YV PLK+YL K+RE
Sbjct: 61 RKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 94
>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 93
Score = 145 bits (365), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 64/93 (68%), Positives = 82/93 (88%)
Query: 20 SDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKR 79
S +EQD +LPIANV+RIMK ++P KI+K+AKE VQECVSEFISFIT EAS++C +EKR
Sbjct: 1 SFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKR 60
Query: 80 KTINGDDLLWAMTTLGFENYVSPLKIYLNKYRE 112
KTING+D+L+AM+TLGF++YV PLK+YL K+RE
Sbjct: 61 KTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 67.4 bits (163), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 33/102 (32%), Positives = 67/102 (65%), Gaps = 5/102 (4%)
Query: 10 PIGSPTSGNISDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGE 69
P + +SGN + D +P A +++++K++LP N +++ +A+E V C +EFI I+ E
Sbjct: 2 PHMASSSGN----DDDLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSE 56
Query: 70 ASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLNKYR 111
A++ C + ++KTI+ + ++ A+ +LGF +Y+S +K L + +
Sbjct: 57 ANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQECK 98
>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 = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 50/88 (56%)
Query: 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTIN 83
+D LP A + R++K++LP +A +SKEA+ + S F F+T ++ ++ KTI
Sbjct: 6 EDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTIT 65
Query: 84 GDDLLWAMTTLGFENYVSPLKIYLNKYR 111
D+L +T L FE++V L L YR
Sbjct: 66 AKDILQTLTELDFESFVPSLTQDLEVYR 93
>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 97
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 28 LPIANVSRIMKKSLPANAK-ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDD 86
LP+A + +IMK L + K IS EA + FI+ +T A + KR+T+ +D
Sbjct: 20 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 77
Query: 87 LLWAMT 92
+ A+T
Sbjct: 78 IAMAIT 83
>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 = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 28 LPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDL 87
LP+A + ++MK P IS EA + FI+ +T A + KR+T+ D+
Sbjct: 42 LPLARIKKVMKAD-PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDI 100
Query: 88 LWAMT 92
A++
Sbjct: 101 AAALS 105
>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 28 LPIANVSRIMKKSLPANAK-ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDD 86
LP+A + +IMK L + K IS EA + FI+ +T A + KR+T+ +D
Sbjct: 17 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 74
Query: 87 LLWAMTTLGFENY 99
+ AM F+ +
Sbjct: 75 I--AMAITKFDQF 85
>pdb|2BYK|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYK|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
pdb|2BYM|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
Complex
Length = 140
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 3 GKRNQTSPIGSPTSGNISDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEF 62
G+ P+ P + + FLP++ V IMK S+ I+ E + +C F
Sbjct: 2 GEPRSQPPVERPPTA-------ETFLPLSRVRTIMKSSM-DTGLITNEVLFLMTKCTELF 53
Query: 63 ISFITGEA 70
+ + G A
Sbjct: 54 VRHLAGAA 61
>pdb|3KKZ|A Chain A, Crystal Structure Of The Q5les9_bacfn Protein From
Bacteroides Fragilis. Northeast Structural Genomics
Consortium Target Bfr250.
pdb|3KKZ|B Chain B, Crystal Structure Of The Q5les9_bacfn Protein From
Bacteroides Fragilis. Northeast Structural Genomics
Consortium Target Bfr250
Length = 267
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 149 SSDNKA--DFQ-NFNMGFYSLGAQVAPNSNGEGTRVMGYGENLGVEAFNLSRIYDNGDGN 205
S++NK DF+ N F+S + P S + + + +NL + S I D G G
Sbjct: 2 SNENKTIHDFELNLICDFFSNXERQGPGSPEVTLKALSFIDNLTEK----SLIADIGCGT 57
Query: 206 GGNRSAMAAHVHG 218
GG +A HV G
Sbjct: 58 GGQTXVLAGHVTG 70
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
0.310 0.128 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,315,635
Number of Sequences: 62578
Number of extensions: 242635
Number of successful extensions: 492
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 484
Number of HSP's gapped (non-prelim): 18
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)