RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7214
(201 letters)
>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV,
proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV
DMU; 1.95A {Bos taurus}
Length = 129
Score = 92.8 bits (230), Expect = 1e-24
Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
DPY K TSGT++DPNLV S R+VGC+CEED ++W W+ +RC CG
Sbjct: 60 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 119
Query: 60 FKLK 63
+KL
Sbjct: 120 YKLV 123
>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME
TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F*
1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F*
2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F*
3ag1_F* 3ag2_F* ...
Length = 98
Score = 91.5 bits (227), Expect = 1e-24
Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCA-CGHW 59
DPY K TSGT++DPNLV S R+VGC+CEED ++W W+ +RC CG
Sbjct: 29 DPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTH 88
Query: 60 FKLK 63
+KL
Sbjct: 89 YKLV 92
>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein,
metallo-protein, oxidoreductase; NMR {Saccharomyces
cerevisiae}
Length = 80
Score = 81.0 bits (200), Expect = 1e-20
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 7 PFKRTSGTRDDPNLVRSAFKSRLVGCV-CEEDQYHIVWMWVEADMPRRCA-CGHWFKLKL 64
GT DP ++ S R VGC + I+W+ + RC CG +KL
Sbjct: 11 LDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNP 70
Query: 65 I 65
+
Sbjct: 71 V 71
>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 = 39.1 bits (90), Expect = 7e-04
Identities = 21/187 (11%), Positives = 54/187 (28%), Gaps = 47/187 (25%)
Query: 2 PYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQ-----YHIVWMWVEADMPRRCAC 56
+ F +D ++ +S + + + W +
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS--------- 73
Query: 57 GHWFKLKLICRGGVHVAIGSNWSKWILSSVGYLGQSDNLTKKDSNEQ------SVKPIQQ 110
K + + + V + N+ K+++S + + ++ + EQ + +
Sbjct: 74 ----KQEEMVQKFVEEVLRINY-KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
Query: 111 MTRTKSTKFSTQLKASTLCGQLDMALESLLPTPG-----------SLLSKLVLGRDPKVH 159
++ + +L+ AL L P + ++ V KV
Sbjct: 129 YNVSRLQPY-LKLRQ---------ALLELRPAKNVLIDGVLGSGKTWVALDVC-LSYKVQ 177
Query: 160 HFNRFRI 166
F+I
Sbjct: 178 CKMDFKI 184
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase
subunit beta; winged-helix motif, transcription
activation, DNA-binding; 4.33A {Escherichia coli} PDB:
1tlh_B
Length = 99
Score = 28.5 bits (64), Expect = 0.61
Identities = 16/64 (25%), Positives = 20/64 (31%), Gaps = 17/64 (26%)
Query: 126 STLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVF 185
+L L L R+ KV R+RFG N L+ G F
Sbjct: 7 ESLRAATHDVLAGLTA------------REAKV-----LRMRFGIDMNTDYTLEEVGKQF 49
Query: 186 QATR 189
TR
Sbjct: 50 DVTR 53
>3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 257
Score = 28.6 bits (64), Expect = 1.3
Identities = 14/71 (19%), Positives = 22/71 (30%)
Query: 84 SSVGYLGQSDNLTKKDSNEQSVKPIQQMTRTKSTKFSTQLKASTLCGQLDMALESLLPTP 143
+ + G L K +K + R + G+ L++L P P
Sbjct: 15 LASPFKGNVKTLVAKPCLCPCLKIQRTKLRVSVVNKAASAYNVKSSGENVFRLDNLGPQP 74
Query: 144 GSLLSKLVLGR 154
GS GR
Sbjct: 75 GSRKRPKRKGR 85
>3erp_A Putative oxidoreductase; funded by the national institute of
allergy and infectious D of NIH contract number
HHSN272200700058C; 1.55A {Salmonella enterica subsp}
Length = 353
Score = 28.0 bits (63), Expect = 2.1
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 25 FKSRLVGCVCEEDQYHIVWMWVEADMPRRCA 55
+ C+ + +Y + WVE +
Sbjct: 203 LEDLGTPCLIHQPKYSLFERWVEDGLLALLQ 233
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA
complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1
Length = 438
Score = 27.2 bits (60), Expect = 4.1
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 17/59 (28%)
Query: 131 QLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATR 189
+L+ AL L R+ V ++R G R L+ G F TR
Sbjct: 368 ELEKALSKLSE------------REAMV-----LKLRKGLIDGREHTLEEVGAYFGVTR 409
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1
a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F*
2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H
Length = 423
Score = 26.8 bits (59), Expect = 5.0
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 17/59 (28%)
Query: 131 QLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATR 189
+L+ AL L R+ V ++R G R L+ G F TR
Sbjct: 353 ELEKALSKLSE------------REAMV-----LKLRKGLIDGREHTLEEVGAFFGVTR 394
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix,
transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2
Length = 87
Score = 25.4 bits (56), Expect = 5.8
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 17/64 (26%)
Query: 126 STLCGQLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVF 185
+ +L+ L++L P R+ V R+R+G + + L+ G F
Sbjct: 6 MLMREELEKVLKTLSP------------REAMV-----LRMRYGLLDGKPKTLEEVGQYF 48
Query: 186 QATR 189
TR
Sbjct: 49 NVTR 52
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma
70, sigma 70 domain 4, transcription, regulation,
helix-turn-helix; 2.60A {Escherichia coli} SCOP:
a.4.13.2
Length = 68
Score = 24.9 bits (55), Expect = 6.5
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 165 RIRFGSGGNRTERLQGKGNVFQATR 189
R+RFG N L+ G F TR
Sbjct: 15 RMRFGIDMNTDYTLEEVGKQFDVTR 39
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus
aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*
Length = 73
Score = 25.0 bits (55), Expect = 6.5
Identities = 14/59 (23%), Positives = 20/59 (33%), Gaps = 17/59 (28%)
Query: 131 QLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATR 189
+L+ AL L R+ V ++R G R L+ G F TR
Sbjct: 3 ELEKALSKLSE------------REAMV-----LKMRKGLIDGREHTLEEVGAYFGVTR 44
>3evf_A RNA-directed RNA polymerase NS5; NS5 methyltransferase, RNA CAP
binding, binding, capsid protein; HET: GTA SAH; 1.45A
{Yellow fever virus} PDB: 3evb_A* 3evc_A* 3evd_A*
3eve_A* 3eva_A*
Length = 277
Score = 26.1 bits (57), Expect = 7.6
Identities = 10/53 (18%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 120 STQLKASTLCGQ-LDMALESLLPTPGSLLSKLVLGRDPKVHHF-NRFRIRFGS 170
S+ + + LD + L + K++ P V + RFG
Sbjct: 153 SSSVTEGERTVRVLDTVEKWLACGVDNFCVKVLAPYMPDVLEKLELLQRRFGG 205
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 0.136 0.428
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,992,513
Number of extensions: 158670
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 238
Number of HSP's successfully gapped: 16
Length of query: 201
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,216,824
Effective search space: 472284288
Effective search space used: 472284288
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: 55 (25.1 bits)