RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8284
(170 letters)
>2pqp_A HD7A, histone deacetylase 7A; HDAC, structural genomics, structural
genomics consortium, SGC; HET: TSN; 1.80A {Homo sapiens}
PDB: 2pqo_A* 2nvr_A 3c0y_A 3c0z_A 3c10_A* 2vqm_A*
2vqj_A* 2vqw_G 2vqq_A* 2vqo_A* 2vqv_A*
Length = 421
Score = 83.7 bits (207), Expect = 1e-19
Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 9/96 (9%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPNFETLGT 60
++ C+ ++ L A G V + LEGG+ L ++ + + + ALL + G
Sbjct: 331 YHVSAKCFGYMTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVDPLSEEGW 390
Query: 61 PSERILFIYALLSFSSITETILNCIYEHRPYWNCYK 96
+ + ++ I H YW C +
Sbjct: 391 KQK---------PNLNAIRSLEAVIRVHSKYWGCMQ 417
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 61.2 bits (149), Expect = 7e-12
Identities = 14/100 (14%), Positives = 29/100 (29%), Gaps = 12/100 (12%)
Query: 1 MDITPACYAHLLNSLTGFA----QGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPNFE 56
M +T + + A G++ + EGGY L + L
Sbjct: 278 MMVTADGFRQMARRTIDCAADICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVR----- 332
Query: 57 TLGTPSERILFIYALLSFSSITETILNCIYEHRPYWNCYK 96
+ + A + +++ + I E P +
Sbjct: 333 ---SLPDPYHEFLAGMGGNTLLDAERAAIEEIVPLLADIR 369
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 50.1 bits (120), Expect = 6e-08
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLD 49
+ +T + L + + ++ EGGY ++SL A
Sbjct: 312 VAVTTDGFGRLGHLIGALR-LPTVIVQEGGYHIESLEANARSFFGGFGA 359
>3q9b_A Acetylpolyamine amidohydrolase; HDAC, polyamines, arginase fold,
deacetylase, hydrolase-HYDR inhibitor complex; HET: B3N;
2.25A {Mycoplana ramosa} PDB: 3q9f_A* 3q9c_A* 3q9e_A*
Length = 341
Score = 47.0 bits (112), Expect = 5e-07
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALL 48
+T Y + ++ + + V++EGGY + + A L+ +
Sbjct: 294 FKLTSPDYITMGRTIAA-SGVPLLVVMEGGYGVPEIGLNVANVLKGVA 340
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 45.0 bits (106), Expect = 3e-06
Identities = 30/176 (17%), Positives = 52/176 (29%), Gaps = 43/176 (24%)
Query: 2 DITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALT-LRALLDDPCPNFETLGT 60
D P A L+ G+ V+ ++E G L L + FE
Sbjct: 51 DDEPTTPAELVGKFLGY----VSSLVEPS------KVGQFDQVLNLCLTE----FEN--- 93
Query: 61 PSERILF---IYALL-SFSSITETILNCIYEH-RPYWNCYKFQDISTEGVQSTPL--HIP 113
L I+AL +T L E + Y + ++ L +
Sbjct: 94 ---CYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG 150
Query: 114 RAEFK-Y-----EGNPK------QEIYATRDCYPIQSQEFVRLCDERLDSLIAKAS 157
+ +GN +++Y T Y + + ++ E L LI
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFEELRDLYQT---YHVLVGDLIKFSAETLSELIRTTL 203
Score = 32.7 bits (74), Expect = 0.052
Identities = 19/83 (22%), Positives = 25/83 (30%), Gaps = 23/83 (27%)
Query: 1 MDITPACYAHLLNSLTGFAQGKV-AVILEGGYCLKSLAEGAALTLRAL------------ 47
+ TP L TG +QG V AV + +S + L
Sbjct: 256 LGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYP 315
Query: 48 --------LDDPCPNFETLGTPS 62
L+D N E G PS
Sbjct: 316 NTSLPPSILEDSLENNE--GVPS 336
Score = 30.8 bits (69), Expect = 0.27
Identities = 26/204 (12%), Positives = 50/204 (24%), Gaps = 75/204 (36%)
Query: 9 AHLLNSLTGFA-------QGKVAVILEGGYCLKSLAEG-AALTLRALLDDPCPNFETLGT 60
H ++ GF+ I GG K + E +A+ ++D
Sbjct: 1651 NHFKDTY-GFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGK--------L 1701
Query: 61 PSERILFIYALLSFSSITETILNCIYEHRPYWNCYK---------------FQDISTEGV 105
+E+I F I E + + F+D+ ++G+
Sbjct: 1702 KTEKI--------FKEINEHSTSYTFRS-EKGLLSATQFTQPALTLMEKAAFEDLKSKGL 1752
Query: 106 QSTPL----H--------------IP----------RAEFKYEGNPKQEI----YATRDC 133
H + R P+ E+ Y
Sbjct: 1753 IPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI 1812
Query: 134 YPIQSQEFVRLCDERLDSLIAKAS 157
P + E L ++ +
Sbjct: 1813 NP--GRVAASFSQEALQYVVERVG 1834
Score = 30.4 bits (68), Expect = 0.30
Identities = 18/85 (21%), Positives = 28/85 (32%), Gaps = 23/85 (27%)
Query: 36 LAEGAALTLRALLDDPCP-NFETLGTPSERILFIYA------LLSFS-SITETILNCIYE 87
L + L + L+ + N + + P +Y L S SI+E I++CI
Sbjct: 432 LVPASDLINKDLVKNNVSFNAKDIQIP------VYDTFDGSDLRVLSGSISERIVDCIIR 485
Query: 88 HRPYWNCYKFQDISTEGVQSTPLHI 112
W Q HI
Sbjct: 486 LPVKW---------ETTTQFKATHI 501
>1c3p_A Protein (HDLP (histone deacetylase-like protein) ); alpha/beta
fold, lyase; 1.80A {Aquifex aeolicus} SCOP: c.42.1.2
PDB: 1c3r_A* 1c3s_A*
Length = 375
Score = 42.3 bits (100), Expect = 2e-05
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPN 54
+++ + N + G+ + GGY +LA L L P
Sbjct: 268 FNLSNVAFLKAFNIVREVF-GEGVYLGGGGYHPYALARAWTLIWCELSGREVPE 320
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 40.8 bits (96), Expect = 7e-05
Identities = 7/54 (12%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPN 54
+++ + + + F + V+ GGY ++++A L+++
Sbjct: 269 FNLSIRGHGECVEYVKSFN-IPLLVLGGGGYTVRNVARCWTYETSLLVEEAISE 321
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 40.8 bits (96), Expect = 8e-05
Identities = 11/54 (20%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPN 54
++T +A + + F + ++ GGY ++++A LD PN
Sbjct: 268 FNLTVKGHAKCVEVVKTFN-LPLLMLGGGGYTIRNVARCWTYETAVALDCEIPN 320
>3ew8_A HD8, histone deacetylase 8; hydrolase, HDAC, metalloenzyme,
arginase fold, HDAC8, histon deacetylase, hydroxamate
inhibitor, unliganded; HET: B3N; 1.80A {Homo sapiens}
PDB: 3f06_A* 3ezp_A* 3ezt_A* 3f0r_A* 3f07_A* 2v5w_A*
2v5x_A* 3ewf_A* 3mz4_A* 3mz6_A* 3mz7_A* 3rqd_A* 3mz3_A*
1t64_A* 1t67_A* 1t69_A* 1vkg_A* 1w22_A* 3sff_A* 3sfh_A*
Length = 388
Score = 39.2 bits (92), Expect = 3e-04
Identities = 9/54 (16%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 1 MDITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLRALLDDPCPN 54
++TP L + + ++ GGY L + A +L +
Sbjct: 277 FNMTPVGIGKCLKYILQWQ-LATLILGGGGYNLANTARCWTYLTGVILGKTLSS 329
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.8 bits (66), Expect = 0.48
Identities = 29/136 (21%), Positives = 46/136 (33%), Gaps = 44/136 (32%)
Query: 34 KSLAE--GAALTLRALLDDPCPNFETLGTPSERILFIYALLSFSSITETILNCIYEHRPY 91
K + + AA T LD TP E +LL L+C
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTL----TPDEVK----SLLL------KYLDC------- 313
Query: 92 WNCYKFQDISTEGVQSTPLHIPR-AEFKYEGNPKQEIYATRDCYPIQSQEFVRLCDERLD 150
+ QD+ E + + P + AE RD + + ++L
Sbjct: 314 ----RPQDLPREVLTTNPRRLSIIAESI------------RD-GLATWDNWKHVNCDKLT 356
Query: 151 SLIAKASPVLVVLSPA 166
++I ++S L VL PA
Sbjct: 357 TII-ESS--LNVLEPA 369
>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A
{Streptococcus mutans}
Length = 295
Score = 28.4 bits (63), Expect = 1.3
Identities = 10/98 (10%), Positives = 29/98 (29%), Gaps = 11/98 (11%)
Query: 3 ITPACYAHLLNSLTGFAQGKVAVILEGGYCLKSLAEGAALTLR-------ALLDDPCPNF 55
+ + + V +++E + S+ + R +++D
Sbjct: 195 GNRGKVEGIGERI----ESMVDLVIEADDYVASIQPDKTIETRYEQGVMVSMVDKDGKLI 250
Query: 56 ETLGTPSERILFIYALLSFSSITETILNCIYEHRPYWN 93
G S + ++ + I+ + + WN
Sbjct: 251 PQQGADSRSVEPCPVVIRKGLDIDKIMMHLSDQFNSWN 288
>3o4o_C Interleukin-1 receptor type 2; cytokine-receptor complex,
beta-trefoil, IG-like fold, immun; HET: NAG; 3.30A {Homo
sapiens}
Length = 339
Score = 27.7 bits (61), Expect = 1.9
Identities = 7/48 (14%), Positives = 11/48 (22%)
Query: 106 QSTPLHIPRAEFKYEGNPKQEIYATRDCYPIQSQEFVRLCDERLDSLI 153
S L P +I +D + L L+
Sbjct: 136 TSGVLVCPDLSEFTRDKTDVKIQWYKDSLLLDKDNEKFLSVRGTTHLL 183
>3uor_A ABC transporter sugar binding protein; ALFA/beta protein,
periplasmic-binding protein, maltose, SUG binding
protein; 2.20A {Xanthomonas axonopodis PV}
Length = 458
Score = 27.0 bits (60), Expect = 4.0
Identities = 6/29 (20%), Positives = 9/29 (31%)
Query: 13 NSLTGFAQGKVAVILEGGYCLKSLAEGAA 41
N F G A L G + ++
Sbjct: 249 NVWYEFFNGYYAFYLSGPWNVREFKLRQP 277
>2heu_A Sugar ABC transporter, sugar-binding protein; periplasmic binding
protein, transport protein; 1.04A {Streptococcus
pneumoniae} PDB: 2hq0_A 2i58_A* 2hfb_A
Length = 401
Score = 26.3 bits (58), Expect = 6.3
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 13 NSLTGFAQGKVAVILEGGYCLKSLAEGA 40
+ + FA+G V + G + + ++ E
Sbjct: 241 DVIGAFARGDVLMTPNGSWAITAINEQK 268
>3cmg_A Putative beta-galactosidase; structural genomics, PSI-2, Pro
structure initiative, NEW YORK SGX research center for
STRU genomics, nysgxrc; 1.90A {Bacteroides fragilis}
Length = 667
Score = 26.2 bits (58), Expect = 6.5
Identities = 5/14 (35%), Positives = 7/14 (50%), Gaps = 1/14 (7%)
Query: 134 YPIQSQEFVRLCDE 147
YP Q+ L D+
Sbjct: 326 YP-QATYMYDLMDK 338
>4dep_C Interleukin-1 receptor accessory protein; B-trefoil,
immunoglobulin, immune system, extracellular; HET: NAG;
3.10A {Homo sapiens} PDB: 3o4o_B*
Length = 349
Score = 26.0 bits (56), Expect = 6.7
Identities = 9/40 (22%), Positives = 14/40 (35%)
Query: 110 LHIPRAEFKYEGNPKQEIYATRDCYPIQSQEFVRLCDERL 149
+ P + + + K I CY IQ+ V L
Sbjct: 140 ITCPNVDGYFPSSVKPTITWYMGCYKIQNFNNVIPEGMNL 179
>3kw0_A Cysteine peptidase; structural genomics, joint center for ST
genomics, JCSG, protein structure initiative, PSI-2,
hydrol; HET: LYS; 2.50A {Bacillus cereus}
Length = 214
Score = 25.9 bits (56), Expect = 7.4
Identities = 9/82 (10%), Positives = 23/82 (28%), Gaps = 5/82 (6%)
Query: 65 ILFIYALLSFSSITETILNCIYEHRPYW-----NCYKFQDISTEGVQSTPLHIPRAEFKY 119
I S + + + ++ H + + + +GV+ PL ++
Sbjct: 45 IFLCSGNYLVSKLIKKVSESMFSHTGIIVKWGEHTLIMESVEDDGVRIVPLEHYIKNYEN 104
Query: 120 EGNPKQEIYATRDCYPIQSQEF 141
N +Q+
Sbjct: 105 SNNRYNGSLFIARHELLQNVND 126
>3fn9_A Putative beta-galactosidase; structural genomics, glycosidas
hydrolase, PSI-2, protein structure initiative; 2.70A
{Bacteroides fragilis}
Length = 692
Score = 26.2 bits (58), Expect = 7.6
Identities = 5/14 (35%), Positives = 5/14 (35%), Gaps = 1/14 (7%)
Query: 134 YPIQSQEFVRLCDE 147
Y QS CD
Sbjct: 340 YQ-QSDYLYSRCDT 352
>3lpf_A Beta-glucuronidase; alpha/beta barrel, sugar-binding domain,
beta-sandwich domai glycosyl hydrolase, glycosida
hydrolase; HET: Z77; 2.26A {Escherichia coli} PDB:
3k46_A* 3k4d_A* 3lpg_A* 3k4a_A
Length = 605
Score = 25.8 bits (57), Expect = 8.5
Identities = 5/14 (35%), Positives = 8/14 (57%), Gaps = 1/14 (7%)
Query: 134 YPIQSQEFVRLCDE 147
YP ++E + DE
Sbjct: 333 YP-YAEEMLDWADE 345
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.138 0.423
Gapped
Lambda K H
0.267 0.0469 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,502,535
Number of extensions: 136365
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 327
Number of HSP's successfully gapped: 24
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.2 bits)