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= 032833
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VQW|G Chain G, Structure Of Inhibitor-Free Hdac4 Catalytic Domain (With
Gain-Of-Function Mutation His332tyr)
Length = 413
Score = 44.7 bits (104), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 56/99 (56%), Gaps = 4/99 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCE-LGDSAPSKSGLV 57
+T L L+GG++++ LEGGY+L +I ++ + + LLG +P E + P+ + +
Sbjct: 312 LTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVR 371
Query: 58 TVLEVLKIQMNFWPSLA-SRFTELQSLWEIYAAENKKKQ 95
++ +V++I +W L + T +SL E EN++ +
Sbjct: 372 SMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAE 410
>pdb|2VQO|A Chain A, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Muation Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQO|B Chain B, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Muation Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQV|A Chain A, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Mutation Bound To A Hydroxamic Acid
Inhibitor
pdb|2VQV|B Chain B, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Mutation Bound To A Hydroxamic Acid
Inhibitor
Length = 413
Score = 44.7 bits (104), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 56/99 (56%), Gaps = 4/99 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCE-LGDSAPSKSGLV 57
+T L L+GG++++ LEGGY+L +I ++ + + LLG +P E + P+ + +
Sbjct: 312 LTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVR 371
Query: 58 TVLEVLKIQMNFWPSLA-SRFTELQSLWEIYAAENKKKQ 95
++ +V++I +W L + T +SL E EN++ +
Sbjct: 372 SMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAE 410
>pdb|2VQQ|A Chain A, Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To-
Alanine Mutant) Bound To A Trifluoromethylketone
Inhbitor
pdb|2VQQ|B Chain B, Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To-
Alanine Mutant) Bound To A Trifluoromethylketone
Inhbitor
Length = 413
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 56/99 (56%), Gaps = 4/99 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCE-LGDSAPSKSGLV 57
+T L L+GG++++ LEGG++L +I ++ + + LLG +P E + P+ + +
Sbjct: 312 LTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVR 371
Query: 58 TVLEVLKIQMNFWPSLA-SRFTELQSLWEIYAAENKKKQ 95
++ +V++I +W L + T +SL E EN++ +
Sbjct: 372 SMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAE 410
>pdb|2VQJ|A Chain A, Structure Of Hdac4 Catalytic Domain Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQM|A Chain A, Structure Of Hdac4 Catalytic Domain Bound To A Hydroxamic
Acid Inhbitor
Length = 413
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 27/99 (27%), Positives = 56/99 (56%), Gaps = 4/99 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCE-LGDSAPSKSGLV 57
+T L L+GG++++ LEGG++L +I ++ + + LLG +P E + P+ + +
Sbjct: 312 LTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVR 371
Query: 58 TVLEVLKIQMNFWPSLA-SRFTELQSLWEIYAAENKKKQ 95
++ +V++I +W L + T +SL E EN++ +
Sbjct: 372 SMEKVMEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAE 410
>pdb|3C0Y|A Chain A, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7
pdb|3C0Y|B Chain B, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7
pdb|3C0Y|C Chain C, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7
pdb|3C0Z|A Chain A, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Saha
pdb|3C0Z|B Chain B, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Saha
pdb|3C0Z|C Chain C, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Saha
pdb|3C10|A Chain A, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Trichostatin A (Tsa)
pdb|3C10|B Chain B, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Trichostatin A (Tsa)
pdb|3C10|C Chain C, Crystal Structure Of Catalytic Domain Of Human Histone
Deacetylase Hdac7 In Complex With Trichostatin A (Tsa)
Length = 423
Score = 40.0 bits (92), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGE--NPGCELG-DSAPSKSGLV 57
MT L L+GG +++ LEGG++L +I ++ + + LLG +P E G P+ + +
Sbjct: 343 MTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIR 402
Query: 58 TVLEVLKIQMNFW 70
++ V+++ +W
Sbjct: 403 SLEAVIRVHSKYW 415
>pdb|2ONG|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONG|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorogeranyl Diphosphate (Fgpp).
pdb|2ONH|A Chain A, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
pdb|2ONH|B Chain B, Crystal Structure Of Of Limonene Synthase With 2-
Fluorolinalyl Diphosphate(flpp)
Length = 543
Score = 29.3 bits (64), Expect = 0.67, Method: Composition-based stats.
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 98 KIRRADAPIWWKWGRKR 114
+I+R +AP+W +W RKR
Sbjct: 197 RIKRPNAPVWIEWYRKR 213
>pdb|3Q9B|A Chain A, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|B Chain B, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|C Chain C, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|D Chain D, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|E Chain E, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|F Chain F, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|G Chain G, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|H Chain H, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|I Chain I, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|J Chain J, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|K Chain K, Crystal Structure Of Apah Complexed With M344
pdb|3Q9B|L Chain L, Crystal Structure Of Apah Complexed With M344
pdb|3Q9F|A Chain A, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|B Chain B, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|C Chain C, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|D Chain D, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|E Chain E, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|F Chain F, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|G Chain G, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|H Chain H, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|I Chain I, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|J Chain J, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|K Chain K, Crystal Structure Of Apah Complexed With Caps
pdb|3Q9F|L Chain L, Crystal Structure Of Apah Complexed With Caps
Length = 341
Score = 28.9 bits (63), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 7 ALSGGKLLVILEGGYNLRSISSSATSVIKVLLG 39
A SG LLV++EGGY + I + +V+K + G
Sbjct: 309 AASGVPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
>pdb|3Q9C|A Chain A, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|B Chain B, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|C Chain C, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|D Chain D, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|E Chain E, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|F Chain F, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|G Chain G, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|H Chain H, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|I Chain I, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|J Chain J, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|K Chain K, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9C|L Chain L, Crystal Structure Of H159a Apah Complexed With
N8-Acetylspermidine
pdb|3Q9E|A Chain A, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|B Chain B, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|C Chain C, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|D Chain D, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|E Chain E, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|F Chain F, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|G Chain G, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|H Chain H, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|I Chain I, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|J Chain J, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|K Chain K, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
pdb|3Q9E|L Chain L, Crystal Structure Of H159a Apah Complexed With
Acetylspermine
Length = 341
Score = 28.9 bits (63), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 7 ALSGGKLLVILEGGYNLRSISSSATSVIKVLLG 39
A SG LLV++EGGY + I + +V+K + G
Sbjct: 309 AASGVPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
>pdb|1P94|A Chain A, Nmr Structure Of Parg Symmetric Dimer
pdb|1P94|B Chain B, Nmr Structure Of Parg Symmetric Dimer
Length = 76
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 25 SISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVLEVLKIQMNFWPSLASRF 77
S+ + TSV K+ GEN E +AP SG ++ ++ +NF +RF
Sbjct: 2 SLEKAHTSVKKMTFGENRDLERVVTAPVSSG-----KIKRVNVNFDEEKHTRF 49
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 25.8 bits (55), Expect = 6.4, Method: Composition-based stats.
Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 53 KSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKWGR 112
++G + +LE++ ++ SRF +++W I ++K I A+ + W W
Sbjct: 987 ENGAIEILELVNNRI-----FQSRFQHKKTVWHIQFTADEKTLISSSDDAEIQV-WNWQL 1040
Query: 113 KRLLYQIIKGH 123
+ ++ ++GH
Sbjct: 1041 DKCIF--LRGH 1049
>pdb|2ZZV|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Calcium And Lactate
pdb|2ZZV|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Calcium And Lactate
pdb|2ZZW|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Zinc And Lactate
pdb|2ZZW|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Zinc And Lactate
pdb|2ZZX|A Chain A, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Lactate
pdb|2ZZX|B Chain B, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Lactate
pdb|2ZZX|C Chain C, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Lactate
pdb|2ZZX|D Chain D, Crystal Structure Of A Periplasmic Substrate Binding
Protein In Complex With Lactate
Length = 361
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 94 KQIKKIRRADAPIWWKWGR 112
+ ++K RR PIW+KW +
Sbjct: 311 EDVRKFRRLAIPIWFKWAK 329
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 0.134 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,610,903
Number of Sequences: 62578
Number of extensions: 122572
Number of successful extensions: 322
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 312
Number of HSP's gapped (non-prelim): 13
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
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: 46 (22.3 bits)