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= 024740
         (263 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
           Functionally A Sequence Specific Histone
          Length = 94

 Score =  138 bits (348), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 64/86 (74%), Positives = 75/86 (87%)

Query: 97  VNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRR 156
           V DF+   LPLARIKKIMK DEDV+MISAEAPV+FA+A ++FI ELTLR+W HTE+NKRR
Sbjct: 9   VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 68

Query: 157 TLQKNDIAAAITRTDIFDFLVDIVPR 182
           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 =  138 bits (348), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 64/86 (74%), Positives = 75/86 (87%)

Query: 97  VNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRR 156
           V DF+   LPLARIKKIMK DEDV+MISAEAPV+FA+A ++FI ELTLR+W HTE+NKRR
Sbjct: 12  VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 71

Query: 157 TLQKNDIAAAITRTDIFDFLVDIVPR 182
           TLQ+NDIA AIT+ D FDFL+DIVPR
Sbjct: 72  TLQRNDIAMAITKFDQFDFLIDIVPR 97


>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 =  137 bits (346), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 60/99 (60%), Positives = 84/99 (84%), Gaps = 1/99 (1%)

Query: 85  SFWANQYQEIEKVN-DFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELT 143
           ++W +    +E  N D+K H LPLARIKK+MKAD +V+MISAEAP++FA+ C++FI ELT
Sbjct: 21  TYWQHVINHLESDNHDYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELT 80

Query: 144 LRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIVPR 182
           +R+W H E+NKRRTLQ++DIAAA++++D+FDFL+DIVPR
Sbjct: 81  MRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLIDIVPR 119


>pdb|1JFI|A Chain A, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
          Length = 98

 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKN 161
           N   P ARIKKIM+ DE++  ++A  PVI +RA E+F+  L  ++   T+    +T+  +
Sbjct: 9   NARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTS 68

Query: 162 DIAAAI 167
            +   I
Sbjct: 69  HLKQCI 74


>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRR---TLQKN 161
           LPL+R++ IMK+  D  +I+ E   +  +  E+F+  L      +TEE  +R    L+  
Sbjct: 20  LPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLA--GAAYTEEFGQRPGEALKYE 77

Query: 162 DIAAAITRTDIFDFLVDIVPRE 183
            ++  + +    +FL+ IVP++
Sbjct: 78  HLSQVVNKNKNLEFLLQIVPQK 99


>pdb|1F1E|A Chain A, Crystal Structure Of The Histone From Methanopyrus
           Kandleri
          Length = 154

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 94  IEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN 153
           +E V D+       A +++I+K    +   S++A  ++ +       EL  ++  + +E+
Sbjct: 72  VEGVEDYDGELFGRATVRRILKR-AGIERASSDAVDLYNKLICRATEELGEKAAEYADED 130

Query: 154 KRRTLQKNDIAAAIT 168
            R+T+Q  D+  AIT
Sbjct: 131 GRKTVQGEDVEKAIT 145


>pdb|2F8N|K Chain K, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a
           Nucleosomes
          Length = 149

 Score = 28.1 bits (61), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 164
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+  +    + 
Sbjct: 45  FPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQ 104

Query: 165 AAITRTDIFDFLVDIV 180
            AI   +  + L+  V
Sbjct: 105 LAIRNDEELNKLLGRV 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 = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 164
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+  +    + 
Sbjct: 29  FPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQ 88

Query: 165 AAITRTDIFDFLVDIV 180
            AI   +  + L+  V
Sbjct: 89  LAIRNDEELNKLLGRV 104


>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 = 27.3 bits (59), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 164
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+  +    + 
Sbjct: 25  FPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQ 84

Query: 165 AAITRTDIFDFLVDIV 180
            AI   +  + L+  V
Sbjct: 85  LAIRNDEELNKLLGKV 100


>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 = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKR 155
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+
Sbjct: 25  FPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 75


>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 = 27.3 bits (59), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 164
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+  +    + 
Sbjct: 26  FPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQ 85

Query: 165 AAITRTDIFDFLVDIV 180
            AI   +  + L+  V
Sbjct: 86  LAIRNDEELNKLLGKV 101


>pdb|1S32|C Chain C, Molecular Recognition Of The Nucleosomal 'supergroove'
 pdb|1S32|G Chain G, Molecular Recognition Of The Nucleosomal 'supergroove'
 pdb|2NZD|C Chain C, Nucleosome Core Particle Containing 145 Bp Of Dna
 pdb|2NZD|G Chain G, Nucleosome Core Particle Containing 145 Bp Of Dna
 pdb|3KUY|C Chain C, Dna Stretching In The Nucleosome Facilitates Alkylation By
           An Intercalating Antitumor Agent
 pdb|3KUY|G Chain G, Dna Stretching In The Nucleosome Facilitates Alkylation By
           An Intercalating Antitumor Agent
 pdb|3MGP|C Chain C, Binding Of Cobalt Ions To The Nucleosome Core Particle
 pdb|3MGP|G Chain G, Binding Of Cobalt Ions To The Nucleosome Core Particle
 pdb|3MGQ|C Chain C, Binding Of Nickel Ions To The Nucleosome Core Particle
 pdb|3MGQ|G Chain G, Binding Of Nickel Ions To The Nucleosome Core Particle
 pdb|3MGR|C Chain C, Binding Of Rubidium Ions To The Nucleosome Core Particle
 pdb|3MGR|G Chain G, Binding Of Rubidium Ions To The Nucleosome Core Particle
 pdb|3MGS|C Chain C, Binding Of Cesium Ions To The Nucleosome Core Particle
 pdb|3MGS|G Chain G, Binding Of Cesium Ions To The Nucleosome Core Particle
 pdb|3LZ0|C Chain C, Crystal Structure Of Nucleosome Core Particle Composed Of
           The Widom 601 Dna Sequence (Orientation 1)
 pdb|3LZ0|G Chain G, Crystal Structure Of Nucleosome Core Particle Composed Of
           The Widom 601 Dna Sequence (Orientation 1)
 pdb|3LZ1|C Chain C, Crystal Structure Of Nucleosome Core Particle Composed Of
           The Widom 601 Dna Sequence (Orientation 2)
 pdb|3LZ1|G Chain G, Crystal Structure Of Nucleosome Core Particle Composed Of
           The Widom 601 Dna Sequence (Orientation 2)
 pdb|3MNN|C Chain C, A Ruthenium Antitumour Agent Forms Specific Histone
           Protein Adducts In The Nucleosome Core
 pdb|3MNN|G Chain G, A Ruthenium Antitumour Agent Forms Specific Histone
           Protein Adducts In The Nucleosome Core
          Length = 119

 Score = 27.3 bits (59), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKR 155
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+
Sbjct: 25  FPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 75


>pdb|2CV5|C Chain C, Crystal Structure Of Human Nucleosome Core Particle
 pdb|2CV5|G Chain G, Crystal Structure Of Human Nucleosome Core Particle
          Length = 130

 Score = 27.3 bits (59), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 16/76 (21%), Positives = 32/76 (42%)

Query: 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 164
            P+ R+ ++++       + A APV  A   E    E+   + N   +NK+  +    + 
Sbjct: 26  FPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQ 85

Query: 165 AAITRTDIFDFLVDIV 180
            AI   +  + L+  V
Sbjct: 86  LAIRNDEELNKLLGRV 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
   0.316    0.133    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,835,138
Number of Sequences: 62578
Number of extensions: 300358
Number of successful extensions: 703
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 680
Number of HSP's gapped (non-prelim): 24
length of query: 263
length of database: 14,973,337
effective HSP length: 97
effective length of query: 166
effective length of database: 8,903,271
effective search space: 1477942986
effective search space used: 1477942986
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)