RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12569
(94 letters)
>2e6m_A Werner syndrome ATP-dependent helicase homolog; APO form,
hydrolase; 2.00A {Mus musculus} PDB: 2e6l_A 2fby_A
2fbv_A 2fbx_A 2fbt_A 2fc0_A*
Length = 208
Score = 74.1 bits (182), Expect = 4e-18
Identities = 25/67 (37%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 3 IATGASTQGSPQSLSTLVLKCFGKTLNK--QDQFSNWENRPLRPSQISYAALDAFCLLQV 60
+A SL+ LV GK L K + SNW N PL Q YAA DA+ L +
Sbjct: 128 VANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLII 187
Query: 61 YQVLHDQ 67
YQ L +
Sbjct: 188 YQKLGNL 194
>1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase,
tRNA processing, hydrolase,translation; 1.60A
{Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5
Length = 375
Score = 71.3 bits (175), Expect = 2e-16
Identities = 19/70 (27%), Positives = 31/70 (44%)
Query: 3 IATGASTQGSPQSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQ 62
I + +++V + G TL+K + ++W RPL Q YAA D + LL +
Sbjct: 105 ILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITA 164
Query: 63 VLHDQCARQG 72
L + G
Sbjct: 165 KLMVETEASG 174
>3saf_A Exosome component 10; exoribonuclease, RNA exosome, hydrolase;
2.50A {Homo sapiens} PDB: 3sag_A 3sah_A 2cpr_A
Length = 428
Score = 70.3 bits (172), Expect = 5e-16
Identities = 19/59 (32%), Positives = 27/59 (45%)
Query: 14 QSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72
SL L+ NKQ Q ++W RPL +SYA D LL +Y + + +G
Sbjct: 223 HSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMWERG 281
>2hbj_A Exosome complex exonuclease RRP6; RNA metabolism, RNA surveillance,
RNA processing, hydrolase, gene regulation; 2.10A
{Saccharomyces cerevisiae} SCOP: a.60.8.4 c.55.3.5 PDB:
2hbk_A 2hbl_A* 2hbm_A*
Length = 410
Score = 70.2 bits (172), Expect = 6e-16
Identities = 15/59 (25%), Positives = 25/59 (42%)
Query: 14 QSLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72
SL+ L+ +K+ Q ++W RPL + A D LL +Y L ++
Sbjct: 200 HSLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESN 258
>3cym_A Uncharacterized protein BAD_0989; structural genomics, unknown
function; 2.10A {Bifidobacterium adolescentis atcc
1570ORGANISM_TAXID}
Length = 440
Score = 68.8 bits (168), Expect = 2e-15
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 15 SLSTLVLKCFGKTLNKQDQFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQCARQG 72
L+ + G TL K+ ++W RPL +YAALD L+++ + + RQG
Sbjct: 134 GLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQG 191
>1vk0_A Hypothetical protein; homohexamer, AT5G06450, struc genomics,
protein structure initiative, center for eukaryot
structural genomics, CESG; 2.10A {Arabidopsis thaliana}
SCOP: c.55.3.5 PDB: 2q3s_A
Length = 206
Score = 55.8 bits (134), Expect = 3e-11
Identities = 11/54 (20%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 15 SLSTLVLKCFGKTLNKQD-QFSNWENRPLRPSQISYAALDAFCLLQVYQVLHDQ 67
L + L + D + WE + Q+ AA++ + ++ V+ L D+
Sbjct: 154 GTRELAHRVLWSDLGQLDSIEAKWE-KAGPEEQLEAAAIEGWLIVNVWDQLSDE 206
>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 = 28.9 bits (64), Expect = 0.23
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 17/78 (21%)
Query: 11 GSPQSLSTLVL---KCFGKTLNKQDQ----FSNWENRPLRPSQISYAALDA-F---CLLQ 59
G PQSL L L K K + DQ FS R L+ S + + + F L+
Sbjct: 381 GPPQSLYGLNLTLRK--AKAPSGLDQSRIPFS---ERKLKFS-NRFLPVASPFHSHLLVP 434
Query: 60 VYQVLHDQCARQGIELGP 77
+++ + +
Sbjct: 435 ASDLINKDLVKNNVSFNA 452
>3pv8_A DNA polymerase I; DNA polymerase I, protein-DNA complex,
thymine-adenine, CLOS conformation; HET: DNA 2DT D3T;
1.52A {Geobacillus kaustophilus} PDB: 3px0_A* 3px4_A*
3px6_A* 3thv_A* 3ti0_A* 3tan_A* 3tap_A* 3taq_A* 3tar_A*
3hp6_A* 2hhw_A* 3ez5_A* 2hvh_A* 2hvi_A* 3eyz_A* 1nk4_A*
1l3t_A* 1l3u_A* 1l3v_A* 1l5u_A* ...
Length = 592
Score = 27.9 bits (63), Expect = 0.46
Identities = 7/43 (16%), Positives = 16/43 (37%), Gaps = 9/43 (20%)
Query: 49 YAALDAFCLLQVYQVLHDQCARQG-------IELGPLLTEVLS 84
+ A + ++ + D+ R +E PL +L+
Sbjct: 162 HLVRKAAAIWELERPFLDELRRNEQDRLLVELEQ-PLS-SILA 202
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP-
binding, DNA-binding; 2.50A {Geobacillus
stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB:
1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C*
2pjr_B*
Length = 724
Score = 26.0 bits (58), Expect = 2.4
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 35 SNWENRPLRPSQISYAALDAF--CLLQVYQVLHDQCARQG 72
S +N L P Q + A + + VYQ + R
Sbjct: 149 SAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNH 188
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase,
disease mutation, DNA replication, DNA-binding,
DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo
sapiens}
Length = 1172
Score = 24.9 bits (53), Expect = 4.9
Identities = 10/47 (21%), Positives = 17/47 (36%), Gaps = 5/47 (10%)
Query: 23 CFGKTLNKQ--DQFSNW---ENRPLRPSQISYAALDAFCLLQVYQVL 64
G L K+ + F + R + Y A D + +V+Q
Sbjct: 297 VGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQ 343
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex
(helicase/DNA), DNA unwinding, hydrolase/DNA complex;
HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19
c.37.1.19
Length = 673
Score = 24.4 bits (54), Expect = 6.3
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 35 SNWENRPLRPSQISYAALDAF--CLLQVYQVLHDQCAR 70
SNW+N PSQ + +A+ Y +
Sbjct: 140 SNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAHLKA 177
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA),
exonuclease, transferase, transferase/DNA complex; HET:
US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1
PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A*
2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*
Length = 605
Score = 24.4 bits (54), Expect = 7.0
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 49 YAALDAFCLLQVYQVLHDQCARQG--------IELGPLLTEVLS 84
YAA DA LQ++ + + IE+ PL+ VLS
Sbjct: 174 YAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEM-PLV-PVLS 215
>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA
complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus}
PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A*
3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3t3f_A* 4df4_A*
4df8_A* 4dfj_A* 3rrh_A* 4dfm_A* 4dfp_A* 1ktq_A* 5ktq_A*
...
Length = 540
Score = 24.1 bits (53), Expect = 8.0
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 10/44 (22%)
Query: 49 YAALDAFCLLQVYQVLHDQCARQG--------IELGPLLTEVLS 84
A A +++ L + + +E PL VL+
Sbjct: 109 EAGERAALSERLFANLWGRLEGEERLLWLYREVER-PLS-AVLA 150
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
0.318 0.129 0.376
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,210,557
Number of extensions: 53222
Number of successful extensions: 65
Number of sequences better than 10.0: 1
Number of HSP's gapped: 64
Number of HSP's successfully gapped: 13
Length of query: 94
Length of database: 6,701,793
Length adjustment: 61
Effective length of query: 33
Effective length of database: 4,998,612
Effective search space: 164954196
Effective search space used: 164954196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.3 bits)