RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13858
(70 letters)
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 56.8 bits (136), Expect = 2e-11
Identities = 29/65 (44%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 1 MLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIREAEGE 60
+LSATVPNT EFA+W+G TK+ +YV+ST KRPVPL+ ++ +L + E
Sbjct: 183 LLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAK-----KELIPVINQNSE 237
Query: 61 FLTRG 65
FL
Sbjct: 238 FLEAN 242
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 51.0 bits (121), Expect = 1e-09
Identities = 18/44 (40%), Positives = 27/44 (61%)
Query: 1 MLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGP 44
LSAT+PN +EFA+W+ ++V T RP PL+H+L+
Sbjct: 326 FLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAH 369
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 50.2 bits (119), Expect = 3e-09
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 1 MLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIREAEGE 60
LSAT+PN +EFA+W+ ++V T RP PL+H+L+ + ++L+ + +
Sbjct: 228 FLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPTPLQHYLFPAH---GDGIYLVVDEKST 284
Query: 61 FLTRG 65
F
Sbjct: 285 FREEN 289
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 48.2 bits (115), Expect = 1e-08
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 2 LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIRE 56
LSAT+ N + A W+G V+T RPVPL + +K + ++
Sbjct: 181 LSATISNYKQIAKWLG------AEPVATNWRPVPLIEGVIYPERKKKEYNVIFKD 229
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 47.2 bits (112), Expect = 3e-08
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 2 LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIR 55
LSAT+ N E A+W+ ++ + RPV L+ ++ + + R
Sbjct: 175 LSATIGNPEELAEWLN------AELIVSDWRPVKLRRGVFYQGFVTWEDGSIDR 222
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 47.1 bits (112), Expect = 4e-08
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 2 LSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVGPVLEKN 49
LSAT PN E A+W+ + RPVPL + LE
Sbjct: 178 LSATAPNVTEIAEWLD------ADYYVSDWRPVPLVEGVLCEGTLELF 219
>4em6_D Glucose-6-phosphate isomerase; GPI, phosphoglucose isomerase
phosphohexose isomerase, PHI, ssgcid; 1.90A {Brucella
melitensis BV}
Length = 553
Score = 24.1 bits (53), Expect = 5.1
Identities = 5/10 (50%), Positives = 5/10 (50%)
Query: 8 NTLEFADWVG 17
F DWVG
Sbjct: 261 RVFGFWDWVG 270
>3hjb_A Glucose-6-phosphate isomerase; PGI, IDP01329, gluconeogenesi
glycolysis, structural genomics, center for STRU
genomics of infectious diseases; HET: PG4; 1.50A {Vibrio
cholerae} PDB: 3nbu_A
Length = 574
Score = 23.8 bits (52), Expect = 6.6
Identities = 7/10 (70%), Positives = 7/10 (70%)
Query: 8 NTLEFADWVG 17
N EF DWVG
Sbjct: 284 NMFEFWDWVG 293
>2wu8_A Glucose-6-phosphate isomerase; gluconeogenesis,
5-phosphoarabinonate (PAB), PGI, cytoplasm, glycolysis;
2.25A {Mycobacterium tuberculosis}
Length = 549
Score = 23.7 bits (52), Expect = 6.8
Identities = 6/10 (60%), Positives = 6/10 (60%)
Query: 8 NTLEFADWVG 17
N F DWVG
Sbjct: 255 NMFGFWDWVG 264
>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide,
hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP:
a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*
Length = 324
Score = 23.7 bits (52), Expect = 6.8
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 12 FADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
+++G + K +VY+ + R PL+H L GP
Sbjct: 11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGP 46
>3ujh_A Glucose-6-phosphate isomerase; ssgcid, structural genomics, seattle
structural genomics CEN infectious disease; HET: G6Q;
2.10A {Toxoplasma gondii}
Length = 567
Score = 23.4 bits (51), Expect = 7.1
Identities = 5/10 (50%), Positives = 5/10 (50%)
Query: 8 NTLEFADWVG 17
F DWVG
Sbjct: 270 RVFGFWDWVG 279
>1t10_A GPI, glucose-6-phosphate isomerase, PGI, phosphohexose;
phosphoglucose isomerase, substrate,
D-fructose-6-phosphate; HET: F6P; 2.35A {Leishmania
mexicana mexicana} SCOP: c.80.1.2
Length = 605
Score = 23.4 bits (51), Expect = 7.3
Identities = 6/10 (60%), Positives = 6/10 (60%)
Query: 8 NTLEFADWVG 17
N F DWVG
Sbjct: 314 NMFAFWDWVG 323
>2cxn_A Glucose-6-phosphate isomerase; 1.40A {Mus musculus} PDB: 2cvp_A
2cxo_A* 2cxp_A* 2cxq_A* 2cxr_A* 2cxs_A* 2cxt_A* 2cxu_A
1u0e_A 1u0f_A* 1u0g_A* 1jiq_A 1iri_A 1nuh_A* 1jlh_A
1iat_A 1hm5_A 1g98_A 1hox_A* 1xtb_A* ...
Length = 557
Score = 23.4 bits (51), Expect = 7.7
Identities = 7/10 (70%), Positives = 7/10 (70%)
Query: 8 NTLEFADWVG 17
N EF DWVG
Sbjct: 262 NMFEFWDWVG 271
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 23.3 bits (51), Expect = 7.8
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 12 FADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
F ++G V++ + KR L H L+ GP
Sbjct: 28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGP 63
>3ljk_A Glucose-6-phosphate isomerase; structural genomics, IDP02733,
cytoplasm, gluconeogenesis, glycolysis; HET: MSE MES;
1.48A {Francisella tularensis} PDB: 3m5p_A* 3q7i_A*
3q88_A*
Length = 543
Score = 23.4 bits (51), Expect = 8.0
Identities = 4/10 (40%), Positives = 6/10 (60%)
Query: 8 NTLEFADWVG 17
+ + DWVG
Sbjct: 253 HCYKMWDWVG 262
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase,
winged-helix domain, ATP hydrolysis, walker A, walker
B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga
maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A*
1in8_A* 1in7_A* 1j7k_A*
Length = 334
Score = 23.3 bits (51), Expect = 8.2
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 12 FADWVGNTK---KTKVYVVSTLKRPVPLKHFLYVGP 44
+++G K + + + R L H L GP
Sbjct: 24 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGP 59
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
0.321 0.138 0.425
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,035,123
Number of extensions: 44619
Number of successful extensions: 81
Number of sequences better than 10.0: 1
Number of HSP's gapped: 78
Number of HSP's successfully gapped: 16
Length of query: 70
Length of database: 6,701,793
Length adjustment: 40
Effective length of query: 30
Effective length of database: 5,584,953
Effective search space: 167548590
Effective search space used: 167548590
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 (23.4 bits)