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= 026901
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 144 bits (363), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 65/98 (66%), Positives = 86/98 (87%), Gaps = 1/98 (1%)
Query: 43 FWSYQRQEIEQAN-DFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTI 101
+W + +E N D+K HQLPLARIKK+MKAD +V+MISAEAPILFAK C++FI ELT+
Sbjct: 22 YWQHVINHLESDNHDYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTM 81
Query: 102 RSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIVPR 139
R+W+HAE+NKRRTLQ++DIAAA++++D+FDFL+DIVPR
Sbjct: 82 RAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLIDIVPR 119
>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 135 bits (341), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 62/86 (72%), Positives = 75/86 (87%)
Query: 54 ANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRR 113
DF+ +LPLARIKKIMK DEDV+MISAEAP+LFAKA ++FI ELT+R+W+H E+NKRR
Sbjct: 9 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 68
Query: 114 TLQKNDIAAAITRTDIFDFLVDIVPR 139
TLQ+NDIA AIT+ D FDFL+DIVPR
Sbjct: 69 TLQRNDIAMAITKFDQFDFLIDIVPR 94
>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 97
Score = 135 bits (341), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 62/86 (72%), Positives = 75/86 (87%)
Query: 54 ANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRR 113
DF+ +LPLARIKKIMK DEDV+MISAEAP+LFAKA ++FI ELT+R+W+H E+NKRR
Sbjct: 12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 71
Query: 114 TLQKNDIAAAITRTDIFDFLVDIVPR 139
TLQ+NDIA AIT+ D FDFL+DIVPR
Sbjct: 72 TLQRNDIAMAITKFDQFDFLIDIVPR 97
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 62 LPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRR---TLQKN 118
LPL+R++ IMK+ D +I+ E L K ELF+ L ++ EE +R L+
Sbjct: 20 LPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAY--TEEFGQRPGEALKYE 77
Query: 119 DIAAAITRTDIFDFLVDIVPRD 140
++ + + +FL+ IVP+
Sbjct: 78 HLSQVVNKNKNLEFLLQIVPQK 99
>pdb|1JFI|A Chain A, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 98
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 38/66 (57%)
Query: 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKN 118
N + P ARIKKIM+ DE++ ++A P++ ++A ELF+ L ++ + +T+ +
Sbjct: 9 NARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTS 68
Query: 119 DIAAAI 124
+ I
Sbjct: 69 HLKQCI 74
>pdb|1F1E|A Chain A, Crystal Structure Of The Histone From Methanopyrus
Kandleri
Length = 154
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 51 IEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEEN 110
+E D+ A +++I+K + S++A L+ K EL ++ +A+E+
Sbjct: 72 VEGVEDYDGELFGRATVRRILKR-AGIERASSDAVDLYNKLICRATEELGEKAAEYADED 130
Query: 111 KRRTLQKNDIAAAIT 125
R+T+Q D+ AIT
Sbjct: 131 GRKTVQGEDVEKAIT 145
>pdb|1GMV|A Chain A, Structure Of Uree
pdb|1GMV|B Chain B, Structure Of Uree
Length = 143
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 69 KIMKADEDVRMISAEAPILFAKAC 92
+++ ADE+V ++ + P + AKAC
Sbjct: 66 QVIAADEEVSVVRCDDPFMLAKAC 89
>pdb|1GMU|A Chain A, Structure Of Uree
pdb|1GMU|B Chain B, Structure Of Uree
pdb|1GMU|C Chain C, Structure Of Uree
pdb|1GMU|D Chain D, Structure Of Uree
Length = 143
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 69 KIMKADEDVRMISAEAPILFAKAC 92
+++ ADE+V ++ + P + AKAC
Sbjct: 66 QVIAADEEVSVVRCDDPFMLAKAC 89
>pdb|2F8N|K Chain K, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a
Nucleosomes
Length = 149
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 33/77 (42%)
Query: 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDI 120
Q P+ R+ ++++ + A AP+ A E E+ + A +NK+ + +
Sbjct: 44 QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHL 103
Query: 121 AAAITRTDIFDFLVDIV 137
AI + + L+ V
Sbjct: 104 QLAIRNDEELNKLLGRV 120
>pdb|3A6N|C Chain C, The Nucleosome Containing A Testis-Specific Histone
Variant, Human H3t
pdb|3A6N|G Chain G, The Nucleosome Containing A Testis-Specific Histone
Variant, Human H3t
pdb|3AFA|C Chain C, The Human Nucleosome Structure
pdb|3AFA|G Chain G, The Human Nucleosome Structure
pdb|3AV1|C Chain C, The Human Nucleosome Structure Containing The Histone
Variant H3.2
pdb|3AV1|G Chain G, The Human Nucleosome Structure Containing The Histone
Variant H3.2
pdb|3AV2|C Chain C, The Human Nucleosome Structure Containing The Histone
Variant H3.3
pdb|3AV2|G Chain G, The Human Nucleosome Structure Containing The Histone
Variant H3.3
pdb|3AN2|C Chain C, The Structure Of The Centromeric Nucleosome Containing
Cenp-A
pdb|3AN2|G Chain G, The Structure Of The Centromeric Nucleosome Containing
Cenp-A
pdb|3AYW|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k56q Mutation
pdb|3AYW|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k56q Mutation
pdb|3AZE|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k64q Mutation
pdb|3AZE|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k64q Mutation
pdb|3AZF|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k79q Mutation
pdb|3AZF|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k79q Mutation
pdb|3AZG|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k115q Mutation
pdb|3AZG|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k115q Mutation
pdb|3AZH|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k122q Mutation
pdb|3AZH|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k122q Mutation
pdb|3AZI|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k31q Mutation
pdb|3AZI|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k31q Mutation
pdb|3AZJ|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k44q Mutation
pdb|3AZJ|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k44q Mutation
pdb|3AZK|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k59q Mutation
pdb|3AZK|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k59q Mutation
pdb|3AZL|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
pdb|3AZL|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
pdb|3AZM|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k79q Mutation
pdb|3AZM|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k79q Mutation
pdb|3AZN|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k91q Mutation
pdb|3AZN|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k91q Mutation
Length = 133
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 33/77 (42%)
Query: 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDI 120
Q P+ R+ ++++ + A AP+ A E E+ + A +NK+ + +
Sbjct: 28 QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHL 87
Query: 121 AAAITRTDIFDFLVDIV 137
AI + + L+ V
Sbjct: 88 QLAIRNDEELNKLLGRV 104
>pdb|1KX3|C Chain C, X-Ray Structure Of The Nucleosome Core Particle, Ncp146,
At 2.0 A Resolution
pdb|1KX3|G Chain G, X-Ray Structure Of The Nucleosome Core Particle, Ncp146,
At 2.0 A Resolution
pdb|1KX4|C Chain C, X-Ray Structure Of The Nucleosome Core Particle, Ncp146b,
At 2.6 A Resolution
pdb|1KX4|G Chain G, X-Ray Structure Of The Nucleosome Core Particle, Ncp146b,
At 2.6 A Resolution
pdb|1KX5|C Chain C, X-ray Structure Of The Nucleosome Core Particle, Ncp147,
At 1.9 A Resolution
pdb|1KX5|G Chain G, X-ray Structure Of The Nucleosome Core Particle, Ncp147,
At 1.9 A Resolution
pdb|3B6F|C Chain C, Nucleosome Core Particle Treated With Cisplatin
pdb|3B6F|G Chain G, Nucleosome Core Particle Treated With Cisplatin
pdb|3B6G|C Chain C, Nucleosome Core Particle Treated With Oxaliplatin
pdb|3B6G|G Chain G, Nucleosome Core Particle Treated With Oxaliplatin
pdb|3LEL|C Chain C, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|G Chain G, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|M Chain M, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|Q Chain Q, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3O62|C Chain C, Nucleosome Core Particle Modified With A Cisplatin
1,3-Cis-{pt(Nh3) 2}2+-D(Gptpg) Intrastrand Cross-Link
pdb|3O62|G Chain G, Nucleosome Core Particle Modified With A Cisplatin
1,3-Cis-{pt(Nh3) 2}2+-D(Gptpg) Intrastrand Cross-Link
Length = 128
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 24/52 (46%)
Query: 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKR 112
Q P+ R+ ++++ + A AP+ A E E+ + A +NK+
Sbjct: 24 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 75
>pdb|2HIO|A Chain A, Histone Octamer (Chicken), Chromosomal Protein
pdb|3C9K|A Chain A, Model Of Histone Octamer Tubular Crystals
pdb|3C9K|E Chain E, Model Of Histone Octamer Tubular Crystals
Length = 128
Score = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 33/77 (42%)
Query: 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDI 120
Q P+ R+ ++++ + A AP+ A E E+ + A +NK+ + +
Sbjct: 24 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHL 83
Query: 121 AAAITRTDIFDFLVDIV 137
AI + + L+ V
Sbjct: 84 QLAIRNDEELNKLLGKV 100
>pdb|1EQZ|A Chain A, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A
Resolution
pdb|1EQZ|E Chain E, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A
Resolution
pdb|1HQ3|A Chain A, Crystal Structure Of The Histone-Core-Octamer In
KclPHOSPHATE
pdb|1HQ3|E Chain E, Crystal Structure Of The Histone-Core-Octamer In
KclPHOSPHATE
pdb|1TZY|A Chain A, Crystal Structure Of The Core-Histone Octamer To 1.90
Angstrom Resolution
pdb|1TZY|E Chain E, Crystal Structure Of The Core-Histone Octamer To 1.90
Angstrom Resolution
pdb|2ARO|A Chain A, Crystal Structure Of The Native Histone Octamer To 2.1
Angstrom Resolution, Crystalised In The Presence Of
S-nitrosoglutathione
pdb|2ARO|E Chain E, Crystal Structure Of The Native Histone Octamer To 2.1
Angstrom Resolution, Crystalised In The Presence Of
S-nitrosoglutathione
Length = 129
Score = 26.9 bits (58), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 33/77 (42%)
Query: 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDI 120
Q P+ R+ ++++ + A AP+ A E E+ + A +NK+ + +
Sbjct: 25 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHL 84
Query: 121 AAAITRTDIFDFLVDIV 137
AI + + L+ V
Sbjct: 85 QLAIRNDEELNKLLGKV 101
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 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,043,739
Number of Sequences: 62578
Number of extensions: 239104
Number of successful extensions: 460
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 434
Number of HSP's gapped (non-prelim): 26
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
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: 50 (23.9 bits)