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= psy8284
(170 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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 2 DITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLD---DPCPNFETL 58
+++ C+ +L L G A G++ + LEGGY L ++ + + + ALL DP P
Sbjct: 303 NLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQ 362
Query: 59 GTPSERILFIYALLSFSSITETILNCIYEHRPYWNCYKFQDISTEG 104
P+ A+ S + E H YW C + + ST G
Sbjct: 363 QRPNAN-----AVRSMEKVMEI-------HSKYWRCLQ-RTTSTAG 395
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/106 (27%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 2 DITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLD---DPCPNFETL 58
+++ C+ +L L G A G++ + LEGGY L ++ + + + ALL DP P
Sbjct: 303 NLSARCFGYLTKQLMGLAGGRIVLALEGGYDLTAICDASEACVSALLGNELDPLPEKVLQ 362
Query: 59 GTPSERILFIYALLSFSSITETILNCIYEHRPYWNCYKFQDISTEG 104
P+ A+ S + E H YW C + + ST G
Sbjct: 363 QRPNAN-----AVRSMEKVMEI-------HSKYWRCLQ-RTTSTAG 395
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 2 DITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLD---DPCPNFETL 58
+++ C+ +L L G A G++ + LEGG+ L ++ + + + ALL DP P
Sbjct: 303 NLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQ 362
Query: 59 GTPSERILFIYALLSFSSITETILNCIYEHRPYWNCYKFQDISTEG 104
P+ A+ S + E H YW C + + ST G
Sbjct: 363 QRPNAN-----AVRSMEKVMEI-------HSKYWRCLQ-RTTSTAG 395
>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 = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 47/106 (44%), Gaps = 16/106 (15%)
Query: 2 DITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLD---DPCPNFETL 58
+++ C+ +L L G A G++ + LEGG+ L ++ + + + ALL DP P
Sbjct: 303 NLSARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQ 362
Query: 59 GTPSERILFIYALLSFSSITETILNCIYEHRPYWNCYKFQDISTEG 104
P+ A+ S + E H YW C + + ST G
Sbjct: 363 QRPNAN-----AVRSMEKVMEI-------HSKYWRCLQ-RTTSTAG 395
>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 = 33.1 bits (74), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 3 ITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPNFETLGTPS 62
++ C+ ++ L A G V + LEGG+ L ++ + + + ALL + G
Sbjct: 335 VSAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVDPLSEEGWKQ 394
Query: 63 ERILFIYALLSFSSITETILNCIYEHRPYWNCYK 96
+ L A+ S ++ I H YW C +
Sbjct: 395 KPNL--NAIRSLEAV-------IRVHSKYWGCMQ 419
>pdb|3MC6|C Chain C, Crystal Structure Of Scdpl1
Length = 497
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 21/81 (25%)
Query: 3 ITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAE--GAALTLRALLDDPCPNFETLGT 60
I C+A ++N + E GY ++S E GAA+ + + + P+ + +G
Sbjct: 327 IVVGCWATMVN------------MGENGY-IESCQEIVGAAMKFKKYIQENIPDLDIMGN 373
Query: 61 PSERILFIYALLSFSSITETI 81
P Y+++SFSS T I
Sbjct: 374 PR------YSVISFSSKTLNI 388
>pdb|3MC6|A Chain A, Crystal Structure Of Scdpl1
Length = 497
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 21/81 (25%)
Query: 3 ITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAE--GAALTLRALLDDPCPNFETLGT 60
I C+A ++N + E GY ++S E GAA+ + + + P+ + +G
Sbjct: 327 IVVGCWATMVN------------MGENGY-IESCQEIVGAAMKFKKYIQENIPDLDIMGN 373
Query: 61 PSERILFIYALLSFSSITETI 81
P Y+++SFSS T I
Sbjct: 374 PR------YSVISFSSKTLNI 388
>pdb|3EVY|A Chain A, Crystal Structure Of A Fragment Of A Putative Type I
Restriction Enzyme R Protein From Bacteroides Fragilis
pdb|3EVY|B Chain B, Crystal Structure Of A Fragment Of A Putative Type I
Restriction Enzyme R Protein From Bacteroides Fragilis
Length = 239
Score = 27.7 bits (60), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 101 STEGVQSTPLHIPRAEFKYEGNPKQE 126
+ EG+ ST LH +E++Y G PK E
Sbjct: 207 TEEGIDSTLLHEYISEYEYLGKPKNE 232
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
0.322 0.138 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,892,620
Number of Sequences: 62578
Number of extensions: 184332
Number of successful extensions: 395
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 9
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)