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= 028727
(205 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 54.3 bits (129), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 109 FPMGRIKRIFKTQSSDIG-ITGEAVFLVNKATDKFLEQFCEDAY-ECCAKDRKKSLAYKH 166
P+ R++ I K+ S D G IT E +FL+ K T+ F+ AY E + ++L Y+H
Sbjct: 20 LPLSRVRTIMKS-SMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEH 78
Query: 167 LAAVVSEQSKYDFLSDYVPEKIKAE 191
L+ VV++ +FL VP+KI+
Sbjct: 79 LSQVVNKNKNLEFLLQIVPQKIRVH 103
>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 = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 2/91 (2%)
Query: 95 IERDDDDEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECC 154
+E D+ D K+ P+ RIK++ K I+ EA L K D F+ + A+
Sbjct: 30 LESDNHD--YKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHA 87
Query: 155 AKDRKKSLAYKHLAAVVSEQSKYDFLSDYVP 185
+++++L +AA +S+ +DFL D VP
Sbjct: 88 EDNKRRTLQRSDIAAALSKSDMFDFLIDIVP 118
>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
Length = 97
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%)
Query: 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAY 164
+V P+ RIK+I K I+ EA L KA F+ + A+ +++++L
Sbjct: 16 RVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQR 75
Query: 165 KHLAAVVSEQSKYDFLSDYVP 185
+A +++ ++DFL D VP
Sbjct: 76 NDIAMAITKFDQFDFLIDIVP 96
>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
Functionally A Sequence Specific Histone
Length = 94
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%)
Query: 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAY 164
+V P+ RIK+I K I+ EA L KA F+ + A+ +++++L
Sbjct: 13 RVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQR 72
Query: 165 KHLAAVVSEQSKYDFLSDYVP 185
+A +++ ++DFL D VP
Sbjct: 73 NDIAMAITKFDQFDFLIDIVP 93
>pdb|1JFI|A Chain A, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 98
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 109 FPMGRIKRIFKTQSSDIGITGEAV-FLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHL 167
FP RIK+I +T +IG AV ++++A + FLE + A + K++ HL
Sbjct: 12 FPPARIKKIMQT-DEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 70
>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 98 DDDDEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKD 157
+DDD P I ++ K ++ + +A LV +F+ +A E C K
Sbjct: 10 NDDD-----LTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKS 64
Query: 158 RKKSLAYKHL 167
KK+++ +H+
Sbjct: 65 EKKTISPEHV 74
>pdb|1NEK|A Chain A, Complex Ii (Succinate Dehydrogenase) From E. Coli With
Ubiquinone Bound
pdb|1NEN|A Chain A, Complex Ii (Succinate Dehydrogenase) From E. Coli With
Dinitrophenol-17 Inhibitor Co-Crystallized At The
Ubiquinone Binding Site
pdb|2ACZ|A Chain A, Complex Ii (Succinate Dehydrogenase) From E. Coli With
Atpenin A5 Inhibitor Co-Crystallized At The Ubiquinone
Binding Site
pdb|2WDQ|A Chain A, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Carboxin Bound
pdb|2WDQ|E Chain E, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Carboxin Bound
pdb|2WDQ|I Chain I, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Carboxin Bound
pdb|2WDV|A Chain A, E. Coli Succinate:quinone Oxidoreductase (Sqr) With An
Empty Quinone-Binding Pocket
pdb|2WDV|E Chain E, E. Coli Succinate:quinone Oxidoreductase (Sqr) With An
Empty Quinone-Binding Pocket
pdb|2WDV|I Chain I, E. Coli Succinate:quinone Oxidoreductase (Sqr) With An
Empty Quinone-Binding Pocket
pdb|2WDR|A Chain A, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Pentachlorophenol Bound
pdb|2WDR|E Chain E, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Pentachlorophenol Bound
pdb|2WDR|I Chain I, E. Coli Succinate:quinone Oxidoreductase (Sqr) With
Pentachlorophenol Bound
pdb|2WP9|A Chain A, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhb His207thr Mutant
pdb|2WP9|E Chain E, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhb His207thr Mutant
pdb|2WP9|I Chain I, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhb His207thr Mutant
pdb|2WS3|A Chain A, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd Tyr83phe Mutant
pdb|2WS3|E Chain E, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd Tyr83phe Mutant
pdb|2WS3|I Chain I, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd Tyr83phe Mutant
pdb|2WU2|A Chain A, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhc His84met Mutant
pdb|2WU2|E Chain E, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhc His84met Mutant
pdb|2WU2|I Chain I, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhc His84met Mutant
pdb|2WU5|A Chain A, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd His71met Mutant
pdb|2WU5|E Chain E, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd His71met Mutant
pdb|2WU5|I Chain I, Crystal Structure Of The E. Coli Succinate:quinone
Oxidoreductase (Sqr) Sdhd His71met Mutant
Length = 588
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 126 GITGEAVFLVNKATDKFLEQFCEDAYECCAKD 157
G GE +L+NK ++F+E++ +A + +D
Sbjct: 256 GCRGEGGYLLNKHGERFMERYAPNAKDLAGRD 287
>pdb|1F66|C Chain C, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
pdb|1F66|G Chain G, 2.6 A Crystal Structure Of A Nucleosome Core Particle
Containing The Variant Histone H2a.Z
Length = 128
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 107 CNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRK-KSLAYK 165
FP+GRI R K++++ G G + + A ++L + +KD K K + +
Sbjct: 26 LQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPR 85
Query: 166 HL 167
HL
Sbjct: 86 HL 87
>pdb|3VR8|A Chain A, Mitochondrial Rhodoquinol-Fumarate Reductase From The
Parasitic Nematode Ascaris Suum
pdb|3VR8|E Chain E, Mitochondrial Rhodoquinol-Fumarate Reductase From The
Parasitic Nematode Ascaris Suum
pdb|3VRB|A Chain A, Mitochondrial Rhodoquinol-Fumarate Reductase From The
Parasitic Nematode Ascaris Suum With The Specific
Inhibitor Flutolanil And Substrate Fumarate
pdb|3VRB|E Chain E, Mitochondrial Rhodoquinol-Fumarate Reductase From The
Parasitic Nematode Ascaris Suum With The Specific
Inhibitor Flutolanil And Substrate Fumarate
Length = 645
Score = 26.9 bits (58), Expect = 6.9, Method: Composition-based stats.
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 126 GITGEAVFLVNKATDKFLEQFCEDAYECCAKD 157
G GE FLVN ++F+E++ A + ++D
Sbjct: 290 GSRGEGGFLVNSEGERFMERYAPKAKDLASRD 321
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
0.309 0.126 0.338
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,148,802
Number of Sequences: 62578
Number of extensions: 132177
Number of successful extensions: 220
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 212
Number of HSP's gapped (non-prelim): 9
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 49 (23.5 bits)