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= 038325
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 93
Score = 134 bits (338), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 59/91 (64%), Positives = 75/91 (82%)
Query: 55 REQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKT 114
REQD Y+PIANV RIM+ +P KI+ DAKE VQECVSE+ISFIT EA+ERCH+E+RKT
Sbjct: 3 REQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKT 62
Query: 115 ITAEDVVWAMGKLGFDNYVEPLSIFLNRFRD 145
I ED+++AM LGFD+YVEPL ++L +FR+
Sbjct: 63 INGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93
>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 134 bits (338), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 59/91 (64%), Positives = 75/91 (82%)
Query: 55 REQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKT 114
REQD Y+PIANV RIM+ +P KI+ DAKE VQECVSE+ISFIT EA+ERCH+E+RKT
Sbjct: 4 REQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKT 63
Query: 115 ITAEDVVWAMGKLGFDNYVEPLSIFLNRFRD 145
I ED+++AM LGFD+YVEPL ++L +FR+
Sbjct: 64 INGEDILFAMSTLGFDSYVEPLKLYLQKFRE 94
>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 = 126 bits (316), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 52/92 (56%), Positives = 77/92 (83%)
Query: 54 VREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRK 113
++EQD+++PIANV RIM+ LP +AKI+ +AKE +QECVSE+ISFIT EA+E+C +E+RK
Sbjct: 1 MKEQDRWLPIANVARIMKLALPENAKIAKEAKECMQECVSEFISFITSEASEKCQQEKRK 60
Query: 114 TITAEDVVWAMGKLGFDNYVEPLSIFLNRFRD 145
T+ ED+++AM LGF+NY E L I+L+++R+
Sbjct: 61 TVNGEDILFAMTSLGFENYAEALKIYLSKYRE 92
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 63/106 (59%), Gaps = 2/106 (1%)
Query: 58 DQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITA 117
D +P A + ++++ LP + ++++DA+E V C +E+I I+ EANE C++ ++KTI+
Sbjct: 13 DLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISP 71
Query: 118 EDVVWAMGKLGFDNYVEPLSIFLNRFRD-SEHERTAAQHKEPIPMP 162
E V+ A+ LGF +Y+ + L + + R A+ E + +P
Sbjct: 72 EHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIP 117
>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 = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 52/93 (55%)
Query: 52 CVVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQ 111
V R +D +P A + R+++ LP A +S +A+ + S + F+T + H++
Sbjct: 1 MVERIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQN 60
Query: 112 RKTITAEDVVWAMGKLGFDNYVEPLSIFLNRFR 144
KTITA+D++ + +L F+++V L+ L +R
Sbjct: 61 HKTITAKDILQTLTELDFESFVPSLTQDLEVYR 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 = 33.1 bits (74), Expect = 0.13, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDV 120
+PIA + RI++ ++SDDA+ T+ + + E I EA + RKTI AED+
Sbjct: 3 LPIAPIGRIIKD--AGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDI 60
Query: 121 VWAMGKL 127
A+ +
Sbjct: 61 ELAVRRF 67
>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 = 33.1 bits (74), Expect = 0.14, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDV 120
+PIA V R++R+ ++S+ A + + E + EY I +A E RKT+ ED+
Sbjct: 7 LPIAPVDRLIRK--AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 64
Query: 121 VWAM 124
A+
Sbjct: 65 KLAI 68
>pdb|1B6W|A Chain A, Crystal Structure Of The Selenomethionine Variant Of
Histone Hmfb From Methanothermus Fervidus
Length = 69
Score = 32.7 bits (73), Expect = 0.18, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDV 120
+PIA + RI++ ++SDDA+ T+ + + E I EA + RKTI AED+
Sbjct: 3 LPIAPIGRIIKD--AGAERVSDDARITLAKILEEXGRDIASEAIKLARHAGRKTIKAEDI 60
Query: 121 VWAMGKL 127
A+ +
Sbjct: 61 ELAVRRF 67
>pdb|1HTA|A Chain A, Crystal Structure Of The Histone Hmfa From Methanothermus
Fervidus
Length = 69
Score = 32.3 bits (72), Expect = 0.21, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDV 120
+PIA + RI++ ++SDDA+ + + + E I EA + RKTI AED+
Sbjct: 4 LPIAPIGRIIKN--AGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 61
>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 = 32.3 bits (72), Expect = 0.23, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 61 MPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDV 120
+PIA + RI++ ++SDDA+ + + + E I EA + RKTI AED+
Sbjct: 3 LPIAPIGRIIKN--AGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 60
>pdb|3B0C|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form I
pdb|3B0D|T Chain T, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form Ii
pdb|3B0D|B Chain B, Crystal Structure Of The Chicken Cenp-T Histone FoldCENP-W
Complex, Crystal Form Ii
Length = 111
Score = 30.8 bits (68), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 69 IMRRILPPHAK--ISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGK 126
++++I + K ++ DA + V++C Y I+ + RKT+ DV M +
Sbjct: 12 LIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR 71
Query: 127 LGFDNYVEPLSIFLNRFRDSEHER 150
G PL + + R E+ +
Sbjct: 72 QGLVTDKMPLHVLVERHLPLEYRK 95
>pdb|3AZL|B Chain B, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
pdb|3AZL|F Chain F, Crystal Structure Of Human Nucleosome Core Particle
Containing H4k77q Mutation
Length = 106
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 53 VVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQR 112
V+R+ Q + + R+ RR +IS E + + ++ + +A QR
Sbjct: 25 VLRDNIQGITKPAIRRLARR--GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAQR 82
Query: 113 KTITAEDVVWAMGKLGFDNY 132
KT+TA DVV+A+ + G Y
Sbjct: 83 KTVTAMDVVYALKRQGRTLY 102
>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 = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 98
>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 = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 98
>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 = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 98
>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 = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 42 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 99
>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 = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 98
>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 = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 98
>pdb|2YFW|B Chain B, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4
pdb|2YFW|D Chain D, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4
pdb|2YFW|F Chain F, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4
pdb|2YFW|H Chain H, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4
Length = 103
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 28/54 (51%)
Query: 79 KISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLGFDNY 132
+IS E V+ + ++ + +A +RKT+T+ DVV+A+ + G Y
Sbjct: 46 RISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLY 99
>pdb|1Y1X|A Chain A, Structural Analysis Of A Homolog Of Programmed Cell Death
6 Protein From Leishmania Major Friedlin
pdb|1Y1X|B Chain B, Structural Analysis Of A Homolog Of Programmed Cell Death
6 Protein From Leishmania Major Friedlin
Length = 191
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/21 (66%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 125 GKLGFDNYVEPLSIFLNRFRD 145
G LGFD+YVE LSIF+ R R+
Sbjct: 144 GSLGFDDYVE-LSIFVCRVRN 163
>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 = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 9 VYKVLKQV-HPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 66
>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 = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 38 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 95
>pdb|2F8N|H Chain H, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a
Nucleosomes
Length = 123
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 39 VYKVLKQVHPDTG-ISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 96
>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 = 28.5 bits (62), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 45 VYKVLKQVHPDTG-ISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 102
>pdb|2HIO|B Chain B, Histone Octamer (Chicken), Chromosomal Protein
Length = 125
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 41 VYKVLKQVHPDTG-ISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 98
>pdb|1P3I|B Chain B, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
pdb|1P3I|F Chain F, Crystallographic Studies Of Nucleosome Core Particles
Containing Histone 'sin' Mutants
Length = 102
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 53 VVREQDQYMPIANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQR 112
V+R+ Q + + R+ RR H IS E + + ++ + +A +R
Sbjct: 21 VLRDNIQGITKPAIRRLARRGGVKH--ISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR 78
Query: 113 KTITAEDVVWAMGKLGFDNY 132
KT+TA DVV+A+ + G Y
Sbjct: 79 KTVTAMDVVYALKRQGRTLY 98
>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 = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 6 VYKVLKQV-HPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 63
>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 = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 42 VYKVLKQV-HPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 99
>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 = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 15 VYKVLKQV-HPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAV 72
>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 = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 45 VYKVLKQVHPDTG-ISSKAXGIXNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 102
>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 = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 66 VIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAM 124
V ++++++ P IS A + V++ I GEA+ H +R TIT+ ++ A+
Sbjct: 42 VYKVLKQVHPDTG-ISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV 99
>pdb|2YFV|B Chain B, The Heterotrimeric Complex Of Kluyveromyces Lactis Scm3,
Cse4 And H4
Length = 74
Score = 27.7 bits (60), Expect = 5.6, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 79 KISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWAMGKLG 128
+IS E V+ + ++ + +A +RKT+T+ DVV+A+ + G
Sbjct: 22 RISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG 71
>pdb|3O8O|A Chain A, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|C Chain C, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|E Chain E, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
pdb|3O8O|G Chain G, Structure Of Phosphofructokinase From Saccharomyces
Cerevisiae
Length = 787
Score = 27.7 bits (60), Expect = 6.2, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 64 ANVIRIMRRILPPHAKISDDAKETVQECVSEYISFITGEANERCHREQRKTITAEDVVWA 123
A+ I I R +P H K D+ KE Q S+ T E +Q +TA DV A
Sbjct: 215 ADYIFIPERAVP-HGKWQDELKEVCQRHRSKGRRNNTIIVAEGALDDQLNPVTANDVKDA 273
Query: 124 MGKLGFDNYVEPL 136
+ +LG D V L
Sbjct: 274 LIELGLDTKVTIL 286
>pdb|3C5W|A Chain A, Complex Between Pp2a-Specific Methylesterase Pme-1 And
Pp2a Core Enzyme
Length = 232
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 68 RIMRRILPPHAKISDDAKETVQECVSEYISFITGE 102
R+ + +LP ++++DAK V+ + EY+ + G+
Sbjct: 42 RLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQ 76
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
0.320 0.137 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,340,618
Number of Sequences: 62578
Number of extensions: 174885
Number of successful extensions: 375
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 344
Number of HSP's gapped (non-prelim): 34
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)