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= 044287
(188 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 = 140 bits (354), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 66/92 (71%), Positives = 80/92 (86%)
Query: 30 IKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRK 89
+KEQ+R LPIANV RIMK LP NAKI+KEAKE MQECVSEFISFITSEASEKC++E+RK
Sbjct: 1 MKEQDRWLPIANVARIMKLALPENAKIAKEAKECMQECVSEFISFITSEASEKCQQEKRK 60
Query: 90 TVNGDDICWALGTLGFDDYAGPIRRYLHKYRE 121
TVNG+DI +A+ +LGF++YA ++ YL KYRE
Sbjct: 61 TVNGEDILFAMTSLGFENYAEALKIYLSKYRE 92
>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 131 bits (329), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 58/92 (63%), Positives = 74/92 (80%)
Query: 30 IKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRK 89
+EQ+ LPIANV RIMK +P KI+K+AKE +QECVSEFISFITSEASE+C +E+RK
Sbjct: 3 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK 62
Query: 90 TVNGDDICWALGTLGFDDYAGPIRRYLHKYRE 121
T+NG+DI +A+ TLGFD Y P++ YL K+RE
Sbjct: 63 TINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 94
>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 93
Score = 131 bits (329), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 58/92 (63%), Positives = 74/92 (80%)
Query: 30 IKEQERLLPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRK 89
+EQ+ LPIANV RIMK +P KI+K+AKE +QECVSEFISFITSEASE+C +E+RK
Sbjct: 2 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK 61
Query: 90 TVNGDDICWALGTLGFDDYAGPIRRYLHKYRE 121
T+NG+DI +A+ TLGFD Y P++ YL K+RE
Sbjct: 62 TINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 64.3 bits (155), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 56/90 (62%), Gaps = 1/90 (1%)
Query: 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDI 96
+P A + +++K+ LP N +++ +A+E + C +EFI I+SEA+E C K +KT++ + +
Sbjct: 16 IPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHV 74
Query: 97 CWALGTLGFDDYAGPIRRYLHKYRELEGER 126
AL +LGF Y ++ L + + + +R
Sbjct: 75 IQALESLGFGSYISEVKEVLQECKTVALKR 104
>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 = 3e-09, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 46/84 (54%)
Query: 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDI 96
LP A +GR++K+ LP +A +SKEA+ + S F F+TS ++ K+ KT+ DI
Sbjct: 10 LPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDI 69
Query: 97 CWALGTLGFDDYAGPIRRYLHKYR 120
L L F+ + + + L YR
Sbjct: 70 LQTLTELDFESFVPSLTQDLEVYR 93
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 37 LPIANVGRIMKQILPANA-KISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95
LPIA +GRI+K A A ++S +A+ T+ + + E I SEA + R RKT+ +D
Sbjct: 3 LPIAPIGRIIKD---AGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAED 59
Query: 96 ICWAL 100
I A+
Sbjct: 60 IELAV 64
>pdb|1B6W|A Chain A, Crystal Structure Of The Selenomethionine Variant Of
Histone Hmfb From Methanothermus Fervidus
Length = 69
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDI 96
LPIA +GRI+K ++S +A+ T+ + + E I SEA + R RKT+ +DI
Sbjct: 3 LPIAPIGRIIKD--AGAERVSDDARITLAKILEEXGRDIASEAIKLARHAGRKTIKAEDI 60
Query: 97 CWAL 100
A+
Sbjct: 61 ELAV 64
>pdb|1HTA|A Chain A, Crystal Structure Of The Histone Hmfa From
Methanothermus Fervidus
Length = 69
Score = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 37 LPIANVGRIMKQILPANA-KISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95
LPIA +GRI+K A A ++S +A+ + + + E I SEA + + RKT+ +D
Sbjct: 4 LPIAPIGRIIKN---AGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAED 60
Query: 96 ICWA 99
I A
Sbjct: 61 IELA 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 = 35.0 bits (79), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDI 96
LPIA +GRI+K ++S +A+ + + + E I SEA + + RKT+ +DI
Sbjct: 3 LPIAPIGRIIKN--AGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 60
Query: 97 CWA 99
A
Sbjct: 61 ELA 63
>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 = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 37 LPIANVGRIMKQILPANA-KISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95
LPIA V R++++ A A ++S++A + + E + E+ I +A E R RKTV +D
Sbjct: 7 LPIAPVDRLIRK---AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVED 63
Query: 96 ICWAL 100
I A+
Sbjct: 64 IKLAI 68
>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 97
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 37 LPIANVGRIMKQILPANAK-ISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95
LP+A + +IMK L + K IS EA + FI+ +T A +R+T+ +D
Sbjct: 20 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 77
Query: 96 ICWALGTLGFDDY 108
I A+ FD +
Sbjct: 78 I--AMAITKFDQF 88
>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 37 LPIANVGRIMKQILPANAK-ISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDD 95
LP+A + +IMK L + K IS EA + FI+ +T A +R+T+ +D
Sbjct: 17 LPLARIKKIMK--LDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRND 74
Query: 96 ICWALGTLGFDDY 108
I A+ FD +
Sbjct: 75 I--AMAITKFDQF 85
>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 = 2.6, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 37 LPIANVGRIMKQILPANAKISKEAKETMQECVSEFISFITSEASEKCRKERRKTVNGDDI 96
LP+A + ++MK P IS EA + FI+ +T A +R+T+ DI
Sbjct: 42 LPLARIKKVMKAD-PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDI 100
Query: 97 CWAL 100
AL
Sbjct: 101 AAAL 104
>pdb|1LWR|A Chain A, Solution Structure Of The Ncam Fibronectin Type Iii Module
2
Length = 96
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 12/20 (60%)
Query: 106 DDYAGPIRRYLHKYRELEGE 125
DD PIR YL KYR L E
Sbjct: 27 DDGGSPIRHYLVKYRALASE 46
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
0.312 0.128 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,232,704
Number of Sequences: 62578
Number of extensions: 139847
Number of successful extensions: 172
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 163
Number of HSP's gapped (non-prelim): 18
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)