RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033394
(120 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 = 55.5 bits (134), Expect = 2e-10
Identities = 9/56 (16%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 9 YNLRSISSSATSVIKVLLGENP---GCELGDSAPSKSGLVTVLEVLKIQMNFWPSL 61
++L +I ++ + + LLG E P+ + + ++ V+++ +W +
Sbjct: 361 HDLTAICDASEACVAALLGNRVDPLSEEGWKQKPNLNAIRSLEAVIRVHSKYWGCM 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 = 40.0 bits (94), Expect = 5e-05
Identities = 8/61 (13%), Positives = 21/61 (34%), Gaps = 3/61 (4%)
Query: 9 YNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVLEVLKIQMNFWPSLASRFTEL 68
Y+ + +VI+ L G + + G T+L+ + + ++
Sbjct: 312 YSPHYLPFCGLAVIEELTGVRSLPDPYHEFLAGMGGNTLLDA---ERAAIEEIVPLLADI 368
Query: 69 Q 69
+
Sbjct: 369 R 369
>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 = 32.3 bits (73), Expect = 0.030
Identities = 5/13 (38%), Positives = 8/13 (61%)
Query: 65 FTELQSLWEIYAA 77
F EL+ L++ Y
Sbjct: 170 FEELRDLYQTYHV 182
Score = 28.1 bits (62), Expect = 0.91
Identities = 16/87 (18%), Positives = 26/87 (29%), Gaps = 22/87 (25%)
Query: 3 YIFVCSY------NLRSISSSATSVIKVLLGENPGCELGDSAPS-KSGLVTVLEVLKIQM 55
Y+ LRS AT + L+ DS S + + VL
Sbjct: 249 YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVA-IAETDSWESFFVSVRKAITVL---- 303
Query: 56 NFW---------PSLASRFTELQSLWE 73
F+ P+ + + L+ E
Sbjct: 304 -FFIGVRCYEAYPNTSLPPSILEDSLE 329
>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 = 30.1 bits (68), Expect = 0.15
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 9 YNLRSISSSATSVIKVLLG 27
Y + I + +V+K + G
Sbjct: 323 YGVPEIGLNVANVLKGVAG 341
>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 = 29.1 bits (64), Expect = 0.20
Identities = 6/21 (28%), Positives = 12/21 (57%), Gaps = 7/21 (33%)
Query: 80 KKKQIKKIRRA------D-AP 93
+K+ +KK++ + D AP
Sbjct: 18 EKQALKKLQASLKLYADDSAP 38
Score = 27.2 bits (59), Expect = 1.1
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 12/31 (38%)
Query: 10 NLRSISSSATSVIKVLLGENPGCELGDSAPS 40
L+ + +S +K+ DSAP+
Sbjct: 21 ALKKLQAS----LKLY---AD-----DSAPA 39
>3men_A Acetylpolyamine aminohydrolase; histone deacetylase; 2.20A
{Burkholderia pseudomallei 1710B}
Length = 362
Score = 29.3 bits (66), Expect = 0.26
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 9 YNLRSISSSATSVIKVLLG 27
Y++ S+ ++A S
Sbjct: 341 YHIESLEANARSFFGGFGA 359
>4a69_A Histone deacetylase 3,; transcription, hydrolase; HET: I0P; 2.06A
{Homo sapiens}
Length = 376
Score = 28.9 bits (65), Expect = 0.39
Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 18/81 (22%)
Query: 9 YNLRSISSSATSVIKVLLGENPGCELGDSAPSKSGLVTVLEVLKIQMNFWPSLASRFTEL 68
Y +R+++ T +L+ E EL S ++ A FT
Sbjct: 298 YTVRNVARCWTYETSLLVEEAISEELPYS------------------EYFEYFAPDFTLH 339
Query: 69 QSLWEIYAAENKKKQIKKIRR 89
+ +N ++ + +IR+
Sbjct: 340 PDVSTRIENQNSRQYLDQIRQ 360
>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 = 28.0 bits (63), Expect = 0.61
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 9 YNLRSISSSATSVIKVLLGENPGCEL 34
YNL + + T + V+LG+ E+
Sbjct: 306 YNLANTARCWTYLTGVILGKTLSSEI 331
>3max_A HD2, histone deacetylase 2; class 2, HDAC, foot pocket, hydrolase;
HET: LLX NHE; 2.05A {Homo sapiens}
Length = 367
Score = 28.0 bits (63), Expect = 0.65
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 9 YNLRSISSSATSVIKVLLGENPGCEL 34
Y +R+++ T V L EL
Sbjct: 297 YTIRNVARCWTYETAVALDCEIPNEL 322
>3bvr_A NOTI restriction endonuclease; protein-DNA complex; HET: DNA; 2.50A
{Nocardia otitidiscaviarum} PDB: 3bvq_A* 3c25_A*
Length = 383
Score = 27.8 bits (60), Expect = 0.83
Identities = 8/71 (11%), Positives = 21/71 (29%), Gaps = 1/71 (1%)
Query: 48 LEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKWGRKRLLYQI 107
++ + ++ ++ + L + + + + KR YQ+
Sbjct: 183 IQTMDFHGSYKHAVGAIDIALVEGIDFHGWLPTPAGRAALSKKMEGPNLSNVFKRTFYQM 242
Query: 108 I-KGHLRVRSR 117
K L R
Sbjct: 243 AYKFALSGHQR 253
>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 = 27.3 bits (61), Expect = 1.2
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 9 YNLRSISSSATSVIKVLLGENPGCELGDSAPS 40
Y+ +++ + T + L G +L + A
Sbjct: 297 YHPYALARAWTLIWCELSGREVPEKLNNKAKE 328
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 26.3 bits (57), Expect = 3.2
Identities = 8/68 (11%), Positives = 27/68 (39%), Gaps = 13/68 (19%)
Query: 27 GENPGCELGDSAPSKSGLVTVL------------EVLKIQM-NFWPSLASRFTELQSLWE 73
G + G S + + L+ +L E + + W +++ ++++L++
Sbjct: 3 GSHHHHHHGSSLTTAAPLLALLRENQDSVKTYALESINNVVDQLWSEISNELPDIEALYD 62
Query: 74 IYAAENKK 81
+++
Sbjct: 63 DDTFSDRE 70
>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 = 3.7
Identities = 5/75 (6%), Positives = 22/75 (29%), Gaps = 4/75 (5%)
Query: 41 KSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKWGR 100
++G++ LE + + + L + + + + + +
Sbjct: 743 RAGVLAQLEEERASE---QTKSDYLKRANELVQWINDKQASLESRDFGDS-IESVQSFMN 798
Query: 101 KRLLYQIIKGHLRVR 115
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 = 3.9
Identities = 5/29 (17%), Positives = 13/29 (44%), Gaps = 5/29 (17%)
Query: 73 EIYAAENKKKQIKKIRRADA-----PIWW 96
+ A N +++ + + D P++W
Sbjct: 35 PLVADFNVEQEQSLLLQNDRIILEFPLYW 63
>3sl1_A Arginase; metallohydrolase, hydrolase-hydrolase inhibit complex;
HET: FB6; 1.90A {Plasmodium falciparum} PDB: 3mmr_A*
3sl0_A*
Length = 413
Score = 26.0 bits (57), Expect = 4.2
Identities = 11/80 (13%), Positives = 22/80 (27%), Gaps = 2/80 (2%)
Query: 30 PGCELGDSAPSKSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRR 89
G +L K GL V++VL + ++ + + E
Sbjct: 40 GGVQLACDDLRKLGLHNVIDVLGWKYEDIGNI--DNGDNEMKQEKKTNNYINNNDNNNDN 97
Query: 90 ADAPIWWKWGRKRLLYQIIK 109
+ + +IK
Sbjct: 98 NNDNNNDNNNNCYIPNGVIK 117
>1hdh_A Arylsulfatase; hydrolase, formylglycine hydrate; 1.3A {Pseudomonas
aeruginosa} SCOP: c.76.1.2
Length = 536
Score = 26.0 bits (57), Expect = 4.5
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 64 RFTELQSLWEIYAAEN 79
+ EL W+ Y +E
Sbjct: 509 KLAELIEHWKRYVSET 524
>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 = 4.6
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 77 AENKKKQIKKIRRADAPIW--WKW 98
E KK ++ +R AD P+W +K
Sbjct: 362 GEEKKNFLELLRTADLPVWLAYKV 385
>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 = 25.4 bits (56), Expect = 5.5
Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 11/79 (13%)
Query: 41 KSGLVTVLEVLKIQMNFWPSLASRFTELQSLWEIYAAENKKKQIKKIRRADAPIWWKW-- 98
K+G++ LE ++ + L+ + Q+ Y K+++ R + I
Sbjct: 763 KAGVLGNLEEMRDER-----LSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRK 817
Query: 99 --GRKRLLYQIIKGHLRVR 115
+ +Q K + +V+
Sbjct: 818 WLVLRN--WQWWKLYSKVK 834
>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 = 6.6
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 97 KWGRKRLLYQIIK 109
+ 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 = 7.4
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 98 WGRKRLLYQIIKGH 111
G L Y I + +
Sbjct: 104 RGVIPLAYSIKRKN 117
>1xjd_A Protein kinase C, theta type; PKC-theta, ATP, AMP,, transferase;
HET: TPO SEP STU; 2.00A {Homo sapiens} SCOP: d.144.1.7
PDB: 2jed_A*
Length = 345
Score = 24.9 bits (55), Expect = 8.6
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 12 RSISSSATSVIKVLLGENPGCELG 35
R + A ++ L P LG
Sbjct: 239 RWLEKEAKDLLVKLFVREPEKRLG 262
>1g5a_A Amylosucrase; glycosyltransferase, glycoside hydrolase,
(beta-alpha)8 barrel; HET: EPE; 1.40A {Neisseria
polysaccharea} SCOP: b.71.1.1 c.1.8.1 PDB: 1jg9_A*
1mw1_A* 1mw2_A* 1mw3_A* 3ueq_A* 1jgi_A* 1mvy_A* 1mw0_A*
1s46_A* 1zs2_A*
Length = 628
Score = 24.8 bits (54), Expect = 9.1
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 68 LQSLWEIYAAENKKKQIKKIRRADAPIWWKWGRKRLLYQI 107
L W+ Y+ N + I R + P W K++
Sbjct: 65 LAQAWQSYSQRNSSLKDIDIARENNPDWILSN-KQVGGVC 103
>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F
1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F
2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F*
2vho_F ...
Length = 135
Score = 24.2 bits (53), Expect = 9.2
Identities = 8/17 (47%), Positives = 10/17 (58%), Gaps = 3/17 (17%)
Query: 98 WGRKRLLYQI---IKGH 111
WGR++L Y I K H
Sbjct: 42 WGRRQLAYPINKLHKAH 58
>1q6o_A Humps, 3-keto-L-gulonate 6-phosphate decarboxylase, D-; beta
barrel, lyase; HET: LG6; 1.20A {Escherichia coli} SCOP:
c.1.2.3 PDB: 1kw1_A* 1q6l_A* 1kv8_A* 1q6q_A* 1q6r_A*
1xbv_A* 1so5_A* 1so4_A* 1xby_A* 1so3_A* 1so6_A* 1xbz_A*
1xbx_A*
Length = 216
Score = 24.6 bits (53), Expect = 9.3
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 74 IYAAENKKKQIKKIRRADAPIW 95
I A + + ++ +R+ A +W
Sbjct: 194 IRDAASPVEAARQFKRSIAELW 215
>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A
{Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A
1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F*
1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F*
1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...
Length = 101
Score = 24.1 bits (53), Expect = 9.3
Identities = 6/12 (50%), Positives = 7/12 (58%)
Query: 98 WGRKRLLYQIIK 109
G +RL Y I K
Sbjct: 43 LGLRRLAYPIAK 54
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG,
structure initiative, PSI, joint center for structural
GENO translation; 1.70A {Thermotoga maritima} SCOP:
d.58.14.1
Length = 140
Score = 24.3 bits (53), Expect = 9.7
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 98 WGRKRLLYQIIK 109
G ++ Y+I K
Sbjct: 61 MGMRKFAYEIKK 72
>3r3t_A 30S ribosomal protein S6; structural genomics, center for
structural genomics of infec diseases, csgid,
beta-barrel, cytosol; 2.30A {Bacillus anthracis}
Length = 99
Score = 24.1 bits (53), Expect = 10.0
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 98 WGRKRLLYQIIK 109
WG++RL Y+I
Sbjct: 46 WGKRRLAYEIND 57
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
0.320 0.134 0.412
Gapped
Lambda K H
0.267 0.0487 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,746,681
Number of extensions: 87625
Number of successful extensions: 195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 34
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
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: 51 (24.0 bits)