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= 041086
(102 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C9K|B Chain B, Model Of Histone Octamer Tubular Crystals
pdb|3C9K|F Chain F, Model Of Histone Octamer Tubular Crystals
Length = 125
Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 48/101 (47%), Positives = 63/101 (62%), Gaps = 20/101 (19%)
Query: 19 DKEMKCAKKSIKTYKIYIFKVL----------NKSILILESRARHNIFEE-------FAR 61
DK+ K A+K ++Y IY++KVL +K++ I+ S ++IFE A
Sbjct: 26 DKKRKRARK--ESYSIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDIFERIAGEASRLAH 82
Query: 62 YKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
Y K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 83 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|3A6N|D Chain D, The Nucleosome Containing A Testis-Specific Histone
Variant, Human H3t
pdb|3A6N|H Chain H, The Nucleosome Containing A Testis-Specific Histone
Variant, Human H3t
pdb|3AFA|D Chain D, The Human Nucleosome Structure
pdb|3AFA|H Chain H, The Human Nucleosome Structure
pdb|3AV1|D Chain D, The Human Nucleosome Structure Containing The Histone
Variant H3.2
pdb|3AV1|H Chain H, The Human Nucleosome Structure Containing The Histone
Variant H3.2
pdb|3AV2|D Chain D, The Human Nucleosome Structure Containing The Histone
Variant H3.3
pdb|3AV2|H Chain H, The Human Nucleosome Structure Containing The Histone
Variant H3.3
pdb|3AYW|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k56q Mutation
pdb|3AYW|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k56q Mutation
pdb|3AZE|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k64q Mutation
pdb|3AZE|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k64q Mutation
pdb|3AZF|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k79q Mutation
pdb|3AZF|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k79q Mutation
pdb|3AZG|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k115q Mutation
pdb|3AZG|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k115q Mutation
pdb|3AZH|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k122q Mutation
pdb|3AZH|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H3k122q Mutation
pdb|3AZI|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k31q Mutation
pdb|3AZI|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k31q Mutation
pdb|3AZJ|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k44q Mutation
pdb|3AZJ|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k44q Mutation
pdb|3AZK|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k59q Mutation
pdb|3AZK|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k59q Mutation
pdb|3AZL|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
pdb|3AZL|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
pdb|3AZM|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k79q Mutation
pdb|3AZM|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k79q Mutation
pdb|3AZN|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k91q Mutation
pdb|3AZN|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k91q Mutation
Length = 129
Score = 72.0 bits (175), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 48/101 (47%), Positives = 62/101 (61%), Gaps = 19/101 (18%)
Query: 20 KEMKCAKKSIK-TYKIYIFKVL----------NKSILILESRARHNIFEE-------FAR 61
K+ K K+S K +Y IY++KVL +K++ I+ S ++IFE A
Sbjct: 28 KDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIAGEASRLAH 86
Query: 62 YKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
Y K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 87 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 127
>pdb|1ZLA|D Chain D, X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus Lana
Peptide Bound To The Nucleosomal Core
pdb|1ZLA|H Chain H, X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus Lana
Peptide Bound To The Nucleosomal Core
Length = 125
Score = 72.0 bits (175), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 47/101 (46%), Positives = 62/101 (61%), Gaps = 19/101 (18%)
Query: 20 KEMKCAKKSIK-TYKIYIFKVL----------NKSILILESRARHNIFEE-------FAR 61
K+ K +KS K +Y IY++KVL +K++ I+ S +++FE A
Sbjct: 24 KDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAH 82
Query: 62 YKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
Y K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 83 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|2PYO|D Chain D, Drosophila Nucleosome Core
pdb|2PYO|H Chain H, Drosophila Nucleosome Core
Length = 122
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 44/90 (48%), Positives = 56/90 (62%), Gaps = 18/90 (20%)
Query: 30 KTYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWE 72
++Y IYI+KVL +K++ I+ S ++IFE A Y K+ ITS E
Sbjct: 32 ESYAIYIYKVLKQVHPDTGISSKAMSIMNSFV-NDIFERIAAEASRLAHYNKRSTITSRE 90
Query: 73 IQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
IQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 91 IQTAVRLLLPGELAKHAVSEGTKAVTKYTS 120
>pdb|1P34|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P34|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3A|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3A|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3B|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3B|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3F|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3F|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3G|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3G|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3I|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3I|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3K|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3K|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3L|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3L|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3M|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3M|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3O|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3O|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3P|D Chain D, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3P|H Chain H, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
Length = 125
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 47/101 (46%), Positives = 62/101 (61%), Gaps = 19/101 (18%)
Query: 20 KEMKCAKKSIK-TYKIYIFKVL----------NKSILILESRARHNIFEE-------FAR 61
K+ K +KS K +Y IY++KVL +K++ I+ S +++FE A
Sbjct: 24 KDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAH 82
Query: 62 YKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
Y K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 83 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|2CV5|D Chain D, Crystal Structure Of Human Nucleosome Core Particle
pdb|2CV5|H Chain H, Crystal Structure Of Human Nucleosome Core Particle
Length = 126
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 47/101 (46%), Positives = 62/101 (61%), Gaps = 19/101 (18%)
Query: 20 KEMKCAKKSIK-TYKIYIFKVL----------NKSILILESRARHNIFEE-------FAR 61
K+ K K+S K +Y +Y++KVL +K++ I+ S ++IFE A
Sbjct: 25 KDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIAGEASRLAH 83
Query: 62 YKKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
Y K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 84 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
>pdb|3C1B|D Chain D, The Effect Of H3 K79 Dimethylation And H4 K20
Trimethylation On Nucleosome And Chromatin Structure
pdb|3C1B|H Chain H, The Effect Of H3 K79 Dimethylation And H4 K20
Trimethylation On Nucleosome And Chromatin Structure
pdb|3C1C|D Chain D, The Effect Of H3 K79 Dimethylation And H4 K20
Trimethylation On Nucleosome And Chromatin Structure
pdb|3C1C|H Chain H, The Effect Of H3 K79 Dimethylation And H4 K20
Trimethylation On Nucleosome And Chromatin Structure
Length = 125
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 36 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 95 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|2F8N|H Chain H, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a
Nucleosomes
Length = 123
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 34 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 92
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 93 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 121
>pdb|1S32|D Chain D, Molecular Recognition Of The Nucleosomal 'supergroove'
pdb|1S32|H Chain H, Molecular Recognition Of The Nucleosomal 'supergroove'
pdb|3LJA|D Chain D, Using Soft X-Rays For A Detailed Picture Of Divalent Metal
Binding In The Nucleosome
pdb|3LJA|H Chain H, Using Soft X-Rays For A Detailed Picture Of Divalent Metal
Binding In The Nucleosome
pdb|3KXB|D Chain D, Structural Characterization Of H3k56q Nucleosomes And
Nucleosomal Arrays
pdb|3KXB|H Chain H, Structural Characterization Of H3k56q Nucleosomes And
Nucleosomal Arrays
pdb|3MVD|D Chain D, Crystal Structure Of The Chromatin Factor Rcc1 In Complex
With The Nucleosome Core Particle
pdb|3MVD|H Chain H, Crystal Structure Of The Chromatin Factor Rcc1 In Complex
With The Nucleosome Core Particle
pdb|3O62|D Chain D, Nucleosome Core Particle Modified With A Cisplatin
1,3-Cis-{pt(Nh3) 2}2+-D(Gptpg) Intrastrand Cross-Link
pdb|3O62|H Chain H, Nucleosome Core Particle Modified With A Cisplatin
1,3-Cis-{pt(Nh3) 2}2+-D(Gptpg) Intrastrand Cross-Link
pdb|3TU4|D Chain D, Crystal Structure Of The Sir3 Bah Domain In Complex With A
Nucleosome Core Particle.
pdb|3TU4|H Chain H, Crystal Structure Of The Sir3 Bah Domain In Complex With A
Nucleosome Core Particle.
pdb|3REH|D Chain D, 2.5 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 145 Bp Alpha-Satellite Dna
(Ncp145)
pdb|3REH|H Chain H, 2.5 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 145 Bp Alpha-Satellite Dna
(Ncp145)
pdb|3REI|D Chain D, 2.65 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 145 Bp Alpha-Satellite Dna
(Ncp145) Derivatized With Triamminechloroplatinum(Ii)
Chloride
pdb|3REI|H Chain H, 2.65 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 145 Bp Alpha-Satellite Dna
(Ncp145) Derivatized With Triamminechloroplatinum(Ii)
Chloride
pdb|3REJ|D Chain D, 2.55 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b)
pdb|3REJ|H Chain H, 2.55 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b)
pdb|3REK|D Chain D, 2.6 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b) Derivatized With Oxaliplatin
pdb|3REK|H Chain H, 2.6 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b) Derivatized With Oxaliplatin
pdb|3REL|D Chain D, 2.7 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b) Derivatized With Triamminechloroplatinum(Ii)
Chloride
pdb|3REL|H Chain H, 2.7 Angstrom Crystal Structure Of The Nucleosome Core
Particle Assembled With A 146 Bp Alpha-Satellite Dna
(Ncp146b) Derivatized With Triamminechloroplatinum(Ii)
Chloride
Length = 122
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 33 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 91
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 92 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 120
>pdb|1EQZ|B Chain B, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A
Resolution
pdb|1EQZ|F Chain F, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A
Resolution
pdb|1HQ3|B Chain B, Crystal Structure Of The Histone-Core-Octamer In
KclPHOSPHATE
pdb|1HQ3|F Chain F, Crystal Structure Of The Histone-Core-Octamer In
KclPHOSPHATE
pdb|1TZY|B Chain B, Crystal Structure Of The Core-Histone Octamer To 1.90
Angstrom Resolution
pdb|1TZY|F Chain F, Crystal Structure Of The Core-Histone Octamer To 1.90
Angstrom Resolution
pdb|2ARO|B Chain B, Crystal Structure Of The Native Histone Octamer To 2.1
Angstrom Resolution, Crystalised In The Presence Of
S-nitrosoglutathione
pdb|2ARO|F Chain F, Crystal Structure Of The Native Histone Octamer To 2.1
Angstrom Resolution, Crystalised In The Presence Of
S-nitrosoglutathione
Length = 126
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S ++IFE A Y K+ ITS EI
Sbjct: 37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 96 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
>pdb|2HIO|B Chain B, Histone Octamer (Chicken), Chromosomal Protein
Length = 125
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S ++IFE A Y K+ ITS EI
Sbjct: 36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 95 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|1F66|D Chain D, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
pdb|1F66|H Chain H, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
Length = 126
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 37 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 95
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 96 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
>pdb|1KX3|D Chain D, X-Ray Structure Of The Nucleosome Core Particle, Ncp146,
At 2.0 A Resolution
pdb|1KX3|H Chain H, X-Ray Structure Of The Nucleosome Core Particle, Ncp146,
At 2.0 A Resolution
pdb|1KX4|D Chain D, X-Ray Structure Of The Nucleosome Core Particle, Ncp146b,
At 2.6 A Resolution
pdb|1KX4|H Chain H, X-Ray Structure Of The Nucleosome Core Particle, Ncp146b,
At 2.6 A Resolution
pdb|1KX5|D Chain D, X-ray Structure Of The Nucleosome Core Particle, Ncp147,
At 1.9 A Resolution
pdb|1KX5|H Chain H, X-ray Structure Of The Nucleosome Core Particle, Ncp147,
At 1.9 A Resolution
pdb|1M18|D Chain D, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1M18|H Chain H, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1M19|D Chain D, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1M19|H Chain H, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1M1A|D Chain D, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1M1A|H Chain H, Ligand Binding Alters The Structure And Dynamics Of
Nucleosomal Dna
pdb|1ZBB|D Chain D, Structure Of The 4_601_167 Tetranucleosome
pdb|1ZBB|H Chain H, Structure Of The 4_601_167 Tetranucleosome
pdb|1ZBB|DD Chain d, Structure Of The 4_601_167 Tetranucleosome
pdb|1ZBB|HH Chain h, Structure Of The 4_601_167 Tetranucleosome
pdb|2FJ7|D Chain D, Crystal Structure Of Nucleosome Core Particle Containing A
Poly (Da.Dt) Sequence Element
pdb|2FJ7|H Chain H, Crystal Structure Of Nucleosome Core Particle Containing A
Poly (Da.Dt) Sequence Element
pdb|2NZD|D Chain D, Nucleosome Core Particle Containing 145 Bp Of Dna
pdb|2NZD|H Chain H, Nucleosome Core Particle Containing 145 Bp Of Dna
pdb|3B6F|D Chain D, Nucleosome Core Particle Treated With Cisplatin
pdb|3B6F|H Chain H, Nucleosome Core Particle Treated With Cisplatin
pdb|3B6G|D Chain D, Nucleosome Core Particle Treated With Oxaliplatin
pdb|3B6G|H Chain H, Nucleosome Core Particle Treated With Oxaliplatin
pdb|3KUY|D Chain D, Dna Stretching In The Nucleosome Facilitates Alkylation By
An Intercalating Antitumor Agent
pdb|3KUY|H Chain H, Dna Stretching In The Nucleosome Facilitates Alkylation By
An Intercalating Antitumor Agent
pdb|3LEL|D Chain D, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|H Chain H, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|N Chain N, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3LEL|R Chain R, Structural Insight Into The Sequence-Dependence Of
Nucleosom Positioning
pdb|3MGP|D Chain D, Binding Of Cobalt Ions To The Nucleosome Core Particle
pdb|3MGP|H Chain H, Binding Of Cobalt Ions To The Nucleosome Core Particle
pdb|3MGQ|D Chain D, Binding Of Nickel Ions To The Nucleosome Core Particle
pdb|3MGQ|H Chain H, Binding Of Nickel Ions To The Nucleosome Core Particle
pdb|3MGR|D Chain D, Binding Of Rubidium Ions To The Nucleosome Core Particle
pdb|3MGR|H Chain H, Binding Of Rubidium Ions To The Nucleosome Core Particle
pdb|3MGS|D Chain D, Binding Of Cesium Ions To The Nucleosome Core Particle
pdb|3MGS|H Chain H, Binding Of Cesium Ions To The Nucleosome Core Particle
pdb|3LZ0|D Chain D, Crystal Structure Of Nucleosome Core Particle Composed Of
The Widom 601 Dna Sequence (Orientation 1)
pdb|3LZ0|H Chain H, Crystal Structure Of Nucleosome Core Particle Composed Of
The Widom 601 Dna Sequence (Orientation 1)
pdb|3LZ1|D Chain D, Crystal Structure Of Nucleosome Core Particle Composed Of
The Widom 601 Dna Sequence (Orientation 2)
pdb|3LZ1|H Chain H, Crystal Structure Of Nucleosome Core Particle Composed Of
The Widom 601 Dna Sequence (Orientation 2)
pdb|3MNN|D Chain D, A Ruthenium Antitumour Agent Forms Specific Histone
Protein Adducts In The Nucleosome Core
pdb|3MNN|H Chain H, A Ruthenium Antitumour Agent Forms Specific Histone
Protein Adducts In The Nucleosome Core
pdb|3UT9|D Chain D, Crystal Structure Of Nucleosome Core Particle Assembled
With A Palindromic Widom '601' Derivative (Ncp-601l)
pdb|3UT9|H Chain H, Crystal Structure Of Nucleosome Core Particle Assembled
With A Palindromic Widom '601' Derivative (Ncp-601l)
pdb|3UTA|D Chain D, Crystal Structure Of Nucleosome Core Particle Assembled
With An Alpha- Satellite Sequence Containing Two Ttaaa
Elements (Ncp-Ta2)
pdb|3UTA|H Chain H, Crystal Structure Of Nucleosome Core Particle Assembled
With An Alpha- Satellite Sequence Containing Two Ttaaa
Elements (Ncp-Ta2)
pdb|3UTB|D Chain D, Crystal Structure Of Nucleosome Core Particle Assembled
With The 146b Alpha-Satellite Sequence (Ncp146b)
pdb|3UTB|H Chain H, Crystal Structure Of Nucleosome Core Particle Assembled
With The 146b Alpha-Satellite Sequence (Ncp146b)
Length = 125
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 36 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 95 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
>pdb|2XQL|B Chain B, Fitting Of The H2a-H2b Histones In The Electron Microscopy
Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5).
pdb|2XQL|D Chain D, Fitting Of The H2a-H2b Histones In The Electron Microscopy
Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5).
pdb|2XQL|F Chain F, Fitting Of The H2a-H2b Histones In The Electron Microscopy
Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5).
pdb|2XQL|H Chain H, Fitting Of The H2a-H2b Histones In The Electron Microscopy
Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5).
pdb|2XQL|J Chain J, Fitting Of The H2a-H2b Histones In The Electron Microscopy
Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5)
Length = 90
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S ++IFE A Y K+ ITS EI
Sbjct: 1 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIAGEASRLAHYNKRSTITSREI 59
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 60 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 88
>pdb|1AOI|D Chain D, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b)
And 146 Bp Long Dna Fragment
pdb|1AOI|H Chain H, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b)
And 146 Bp Long Dna Fragment
Length = 99
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ I+ S +++FE A Y K+ ITS EI
Sbjct: 10 SYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSREI 68
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 69 QTAVRLLLPGELAKHAVSEGTKAVTKYTS 97
>pdb|1ID3|D Chain D, Crystal Structure Of The Yeast Nucleosome Core Particle
Reveals Fundamental Differences In Inter-Nucleosome
Interactions
pdb|1ID3|H Chain H, Crystal Structure Of The Yeast Nucleosome Core Particle
Reveals Fundamental Differences In Inter-Nucleosome
Interactions
Length = 130
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 54/89 (60%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFE-------EFARYKKKPMITSWEI 73
TY YI+KVL KS+ IL S ++IFE + A Y KK I++ EI
Sbjct: 39 TYSSYIYKVLKQTHPDTGISQKSMSILNSFV-NDIFERIATEASKLAAYNKKSTISAREI 97
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGT+AVTK++S
Sbjct: 98 QTAVRLILPGELAKHAVSEGTRAVTKYSS 126
>pdb|1U35|D Chain D, Crystal Structure Of The Nucleosome Core Particle
Containing The Histone Domain Of Macroh2a
pdb|1U35|H Chain H, Crystal Structure Of The Nucleosome Core Particle
Containing The Histone Domain Of Macroh2a
pdb|2F8N|D Chain D, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a
Nucleosomes
Length = 126
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 18/90 (20%)
Query: 30 KTYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWE 72
++Y IY++KVL +K++ I+ S ++IFE A Y K+ ITS E
Sbjct: 36 ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFV-NDIFERIASEASRLAHYNKRSTITSRE 94
Query: 73 IQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
+QT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 95 VQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
>pdb|3KWQ|D Chain D, Structural Characterization Of H3k56q Nucleosomes And
Nucleo Arrays
pdb|3KWQ|H Chain H, Structural Characterization Of H3k56q Nucleosomes And
Nucleo Arrays
Length = 93
Score = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 18/90 (20%)
Query: 30 KTYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWE 72
++Y IY++KVL +K++ I+ S +++FE A Y K+ ITS E
Sbjct: 3 ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFV-NDVFERIAGEASRLAHYNKRSTITSRE 61
Query: 73 IQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
IQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 62 IQTAVRLLLPGELAKHAVSEGTKAVTKYTS 91
>pdb|3AN2|D Chain D, The Structure Of The Centromeric Nucleosome Containing
Cenp-A
pdb|3AN2|H Chain H, The Structure Of The Centromeric Nucleosome Containing
Cenp-A
Length = 129
Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 47/100 (47%), Positives = 60/100 (60%), Gaps = 17/100 (17%)
Query: 20 KEMKCAKKSIK-TYKIYIFKVLNK--SILILESRAR-------HNIFEE-------FARY 62
K+ K K+S K +Y IY++KVL + + S+A ++IFE A Y
Sbjct: 28 KDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAXGIXNSFVNDIFERIAGEASRLAHY 87
Query: 63 KKKPMITSWEIQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
K+ ITS EIQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 88 NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 127
>pdb|2NQB|D Chain D, Drosophila Nucleosome Structure
pdb|2NQB|H Chain H, Drosophila Nucleosome Structure
Length = 123
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 43/90 (47%), Positives = 55/90 (61%), Gaps = 18/90 (20%)
Query: 30 KTYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWE 72
++Y IYI+ VL +K++ I+ S ++IFE A Y K+ ITS E
Sbjct: 33 ESYAIYIYTVLKQVHPDTGISSKAMSIMNSFV-NDIFERIAAEASRLAHYNKRSTITSRE 91
Query: 73 IQTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
IQT RL+LPGEL KH VSEGTKAVTK+TS
Sbjct: 92 IQTAVRLLLPGELAKHAVSEGTKAVTKYTS 121
>pdb|2JSS|A Chain A, Nmr Structure Of Chaperone Chz1 Complexed With Histone
H2a.Z-H2b
Length = 192
Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/88 (47%), Positives = 53/88 (60%), Gaps = 18/88 (20%)
Query: 30 KTYKIYIFKVL----------NKSILILESRARHNIFE-------EFARYKKKPMITSWE 72
+TY YI+KVL KS+ IL S ++IFE + A Y KK I++ E
Sbjct: 3 ETYSSYIYKVLKQTHPDTGISQKSMSILNSFV-NDIFERIATEASKLAAYNKKSTISARE 61
Query: 73 IQTVGRLVLPGELVKHIVSEGTKAVTKF 100
IQT RL+LPGEL KH VSEGT+AVTK+
Sbjct: 62 IQTAVRLILPGELAKHAVSEGTRAVTKY 89
>pdb|1HIO|B Chain B, Histone Octamer (Chicken), Chromosomal Protein, Alpha
Carbons Only
Length = 90
Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/89 (47%), Positives = 53/89 (59%), Gaps = 18/89 (20%)
Query: 31 TYKIYIFKVL----------NKSILILESRARHNIFEE-------FARYKKKPMITSWEI 73
+Y IY++KVL +K++ + S ++IFE A Y K+ ITS EI
Sbjct: 1 SYSIYVYKVLKQVHPDTGISSKAMGSMNSFV-NDIFERIAGLASRLAHYNKRSTITSREI 59
Query: 74 QTVGRLVLPGELVKHIVSEGTKAVTKFTS 102
QT RL+LPGEL KH VSEGTKAVTK TS
Sbjct: 60 QTAVRLLLPGELAKHAVSEGTKAVTKHTS 88
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 25.8 bits (55), Expect = 6.4, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 20 KEMKCAKKSIKTYKIYIFKVLNKSILILESRARHNIFEEFARYKKKPMITSWEIQTVGRL 79
KE+K A+K++KT + K L +++ ++R ++E R+ P + + + V R+
Sbjct: 329 KEVKHARKTLKTLRDQWEKALCRALRETKNRLEREVYE--GRFSLYPFLCLLDEREVVRM 386
Query: 80 VL 81
+L
Sbjct: 387 LL 388
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
0.318 0.132 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,205,116
Number of Sequences: 62578
Number of extensions: 66886
Number of successful extensions: 122
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 94
Number of HSP's gapped (non-prelim): 30
length of query: 102
length of database: 14,973,337
effective HSP length: 67
effective length of query: 35
effective length of database: 10,780,611
effective search space: 377321385
effective search space used: 377321385
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)