RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032833
(132 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 = 88.7 bits (220), Expect = 6e-22
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENP---GCELGDSAPSKSGLV 57
MT L L+GG +++ LEGG++L +I ++ + + LLG E P+ + +
Sbjct: 341 MTQQLMNLAGGAVVLALEGGHDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIR 400
Query: 58 TVLEVLKIQMNFWPSL 73
++ V+++ +W +
Sbjct: 401 SLEAVIRVHSKYWGCM 416
>1zz1_A Histone deacetylase-like amidohydrolase; HET: SHH; 1.57A
{Alcaligenaceae bacterium} PDB: 1zz0_A* 1zz3_A* 2gh6_A*
2vcg_A*
Length = 369
Score = 68.5 bits (168), Expect = 7e-15
Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 7/85 (8%)
Query: 1 MTHML----NALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGL 56
M + G+++ + EGGY+ + +VI+ L G + + G
Sbjct: 288 MARRTIDCAADICDGRIVFVQEGGYSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGG 347
Query: 57 VTVLEVLKIQMNFWPSLASRFTELQ 81
T+L+ + + +++
Sbjct: 348 NTLLDA---ERAAIEEIVPLLADIR 369
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 57.1 bits (138), Expect = 7e-11
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLG 39
+ H++ AL +++ EGGY++ S+ ++A S
Sbjct: 322 LGHLIGAL-RLPTVIVQEGGYHIESLEANARSFFGGFGA 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 = 56.3 bits (136), Expect = 2e-10
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLG 39
M + A G LLV++EGGY + I + +V+K + G
Sbjct: 304 MGRTIAAS-GVPLLVVMEGGYGVPEIGLNVANVLKGVAG 341
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 49.3 bits (118), Expect = 4e-08
Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 19/101 (18%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVL 60
+ + LLV+ GGY +R+++ T +L+ E EL S
Sbjct: 279 CVEYVKSF-NIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYS----------- 326
Query: 61 EVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRR 101
++ A FT + +N ++ + +IR+
Sbjct: 327 -------EYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQ 360
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 48.8 bits (117), Expect = 5e-08
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCEL 46
++ LL++ GGY +R+++ T V L EL
Sbjct: 278 CVEVVKTF-NLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNEL 322
>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 = 47.0 bits (112), Expect = 3e-07
Identities = 9/52 (17%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCELGDSAPS 52
+++ + G+ + + GGY+ +++ + T + L G +L + A
Sbjct: 278 AFNIVREV-FGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNNKAKE 328
>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 = 46.9 bits (112), Expect = 3e-07
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 1 MTHMLNALSGGKLLVILEGGYNLRSISSSATSVIKVLLGENPGCEL 46
+ L++ GGYNL + + T + V+LG+ E+
Sbjct: 287 CLKYILQW-QLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEI 331
>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 = 31.9 bits (72), Expect = 0.044
Identities = 5/13 (38%), Positives = 8/13 (61%)
Query: 77 FTELQSLWEIYAA 89
F EL+ L++ Y
Sbjct: 170 FEELRDLYQTYHV 182
Score = 25.8 bits (56), Expect = 5.4
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 19/79 (24%)
Query: 20 GYN---LRSISSSATSVIKVLLGENPGCELGDSAPS-KSGLVTVLEVLKIQMNFW----- 70
G+ LRS AT + L+ DS S + + VL F+
Sbjct: 257 GFTPGELRSYLKGATGHSQGLVTAVA-IAETDSWESFFVSVRKAITVL-----FFIGVRC 310
Query: 71 ----PSLASRFTELQSLWE 85
P+ + + L+ E
Sbjct: 311 YEAYPNTSLPPSILEDSLE 329
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 0.19
Identities = 6/21 (28%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 92 KKKQIKKIRRA------D-AP 105
+K+ +KK++ + D AP
Sbjct: 18 EKQALKKLQASLKLYADDSAP 38
Score = 27.6 bits (60), Expect = 1.0
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 12/31 (38%)
Query: 22 NLRSISSSATSVIKVLLGENPGCELGDSAPS 52
L+ + +S +K+ DSAP+
Sbjct: 21 ALKKLQAS----LKLY---AD-----DSAPA 39
>3bvr_A NOTI restriction endonuclease; protein-DNA complex; HET: DNA; 2.50A
{Nocardia otitidiscaviarum} PDB: 3bvq_A* 3c25_A*
Length = 383
Score = 28.2 bits (61), Expect = 0.78
Identities = 8/71 (11%), Positives = 21/71 (29%), Gaps = 1/71 (1%)
Query: 60 LEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKWGRKRLLYQI 119
++ + ++ ++ + L + + + + KR YQ+
Sbjct: 183 IQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQM 242
Query: 120 I-KGHLRVRSR 129
K L R
Sbjct: 243 AYKFALSGHQR 253
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 26.2 bits (58), Expect = 4.1
Identities = 5/75 (6%), Positives = 22/75 (29%), Gaps = 4/75 (5%)
Query: 53 KSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKWGR 112
++G++ LE + + + L + + + + + +
Sbjct: 743 RAGVLAQLEEERASE---QTKSDYLKRANELVQWINDKQASLESRDFGDS-IESVQSFMN 798
Query: 113 KRLLYQIIKGHLRVR 127
Y+ + + +
Sbjct: 799 AHKEYKKTEKPPKGQ 813
>3ha2_A NADPH-quinone reductase; structural genomics, PSI-2, protein
structure initiative, no structural genomics,
consortium, NESG; HET: MSE; 1.80A {Pediococcus
pentosaceus atcc 25745}
Length = 177
Score = 25.5 bits (56), Expect = 5.2
Identities = 5/29 (17%), Positives = 13/29 (44%), Gaps = 5/29 (17%)
Query: 85 EIYAAENKKKQIKKIRRADA-----PIWW 108
+ A N +++ + + D P++W
Sbjct: 35 PLVADFNVEQEQSLLLQNDRIILEFPLYW 63
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 25.9 bits (56), Expect = 5.4
Identities = 8/68 (11%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 39 GENPGCELGDSAPSKSGLVTVL------------EVLKIQM-NFWPSLASRFTELQSLWE 85
G + G S + + L+ +L E + + W +++ ++++L++
Sbjct: 3 GSHHHHHHGSSLTTAAPLLALLRENQDSVKTYALESINNVVDQLWSEISNELPDIEALYD 62
Query: 86 IYAAENKK 93
+++
Sbjct: 63 DDTFSDRE 70
>1kk8_A Myosin heavy chain, striated muscle; actin-detached, mechanics of
motor, contractIle PROT; HET: ADP; 2.30A {Argopecten
irradians} SCOP: b.34.3.1 c.37.1.9 PDB: 1kk7_A* 1qvi_A*
1s5g_A* 1sr6_A 1b7t_A* 1kqm_A* 1kwo_A* 1l2o_A* 1dfl_A*
2w4t_C 2w4v_C 2w4w_C 1dfk_A 2ec6_A 2otg_A* 2os8_A*
2ovk_A 2ekv_A 2ekw_A 2oy6_A* ...
Length = 837
Score = 25.7 bits (57), Expect = 5.8
Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 11/79 (13%)
Query: 53 KSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKW-- 110
K+G++ LE ++ + L+ + Q+ Y K+++ R + I
Sbjct: 763 KAGVLGNLEEMRDER-----LSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRK 817
Query: 111 --GRKRLLYQIIKGHLRVR 127
+ +Q K + +V+
Sbjct: 818 WLVLRN--WQWWKLYSKVK 834
>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane,
nucleotide-binding, RNA replication, transmembrane,
viral protein; 1.80A {Japanese encephalitis virus} PDB:
2v8o_A 2qeq_A
Length = 459
Score = 25.6 bits (56), Expect = 6.3
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 89 AENKKKQIKKIRRADAPIW--WKW 110
E KK ++ +R AD P+W +K
Sbjct: 362 GEEKKNFLELLRTADLPVWLAYKV 385
>1hdh_A Arylsulfatase; hydrolase, formylglycine hydrate; 1.3A {Pseudomonas
aeruginosa} SCOP: c.76.1.2
Length = 536
Score = 25.6 bits (56), Expect = 6.4
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 76 RFTELQSLWEIYAAEN 91
+ EL W+ Y +E
Sbjct: 509 KLAELIEHWKRYVSET 524
>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure,
backbone dynamics, folding, ribonucleoprotein,
RNA-binding, rRNA-binding; NMR {Thermus thermophilus}
Length = 96
Score = 24.5 bits (53), Expect = 7.0
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 109 KWGRKRLLYQIIK 121
+ G +RL Y I K
Sbjct: 84 ELGLRRLAYPIAK 96
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 168
Score = 24.9 bits (54), Expect = 8.3
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 110 WGRKRLLYQIIKGH 123
G L Y I + +
Sbjct: 104 RGVIPLAYSIKRKN 117
>3sl1_A Arginase; metallohydrolase, hydrolase-hydrolase inhibit complex;
HET: FB6; 1.90A {Plasmodium falciparum} PDB: 3mmr_A*
3sl0_A*
Length = 413
Score = 25.2 bits (55), Expect = 9.4
Identities = 11/80 (13%), Positives = 22/80 (27%), Gaps = 2/80 (2%)
Query: 42 PGCELGDSAPSKSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRR 101
G +L K GL V++VL + ++ + + E
Sbjct: 40 GGVQLACDDLRKLGLHNVIDVLGWKYEDIGNI--DNGDNEMKQEKKTNNYINNNDNNNDN 97
Query: 102 ADAPIWWKWGRKRLLYQIIK 121
+ + +IK
Sbjct: 98 NNDNNNDNNNNCYIPNGVIK 117
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
0.319 0.134 0.406
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,936,785
Number of extensions: 101330
Number of successful extensions: 209
Number of sequences better than 10.0: 1
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 34
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
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 (21.8 bits)
S2: 52 (23.8 bits)