RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy18013
(563 letters)
>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse
transcriptase) {Human immunodeficiency virus type 2
[TaxId: 11709]}
Length = 126
Score = 48.8 bits (115), Expect = 1e-07
Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 8/119 (6%)
Query: 183 YTDGSKS--PDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
YTDGS + + + AEL A + L + + I+
Sbjct: 11 YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66
Query: 241 SDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK 299
DS+ + +A+ + +K+ + + + + W P+H GI GN+ VD
Sbjct: 67 VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123
>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId:
562]}
Length = 152
Score = 40.8 bits (94), Expect = 8e-05
Identities = 28/138 (20%), Positives = 39/138 (28%), Gaps = 18/138 (13%)
Query: 183 YTDGSKS--PDVTGCAFSI---GDMVRSTLLNPINSIFSAE-------LIAIFLCLEAIL 230
+T GS P G + G + + E L A+ E IL
Sbjct: 6 FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65
Query: 231 ENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLK--LCNKEVTFMWCPSHCGI 288
S K ++ K W+ L L ++ + W H G
Sbjct: 66 STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125
Query: 289 RGNEIVD----DAAKNPN 302
NE D AA NP
Sbjct: 126 PENERADELARAAAMNPT 143
>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse
transcriptase) {Human immunodeficiency virus type 1
[TaxId: 11676]}
Length = 110
Score = 37.7 bits (87), Expect = 5e-04
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 12/107 (11%)
Query: 183 YTDGS--KSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
Y DG+ + + + + + + EL AI+L L+ + IV
Sbjct: 12 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDS----GLEVNIV 67
Query: 241 SDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK--EVTFMWCPSH 285
+DS+ AL + + P ++ + ++ K +V W P+H
Sbjct: 68 TDSQYALGIIQ----AQPDQSESELVNQIIEQLIKKEKVYLAWVPAH 110
>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus
[TaxId: 274]}
Length = 147
Score = 37.2 bits (85), Expect = 0.002
Identities = 26/133 (19%), Positives = 40/133 (30%), Gaps = 15/133 (11%)
Query: 183 YTDGSKS--PDVTGCAFSIGDMVRSTLLN---PINSIFSAELIAIFLCLEA--------I 229
+TDG+ P G A + LL+ + EL A L+A +
Sbjct: 7 FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66
Query: 230 LENPSDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKE--VTFMWCPSHCG 287
+ ++ + + K W L L V F + H G
Sbjct: 67 YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126
Query: 288 IRGNEIVDDAAKN 300
NE VD A+
Sbjct: 127 HPENERVDREARR 139
>d1tuga1 c.78.1.1 (A:1-150,A:151-310) Aspartate carbamoyltransferase
catalytic subunit {Escherichia coli [TaxId: 562]}
Length = 310
Score = 35.3 bits (80), Expect = 0.017
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 4/33 (12%)
Query: 270 LKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNPN 302
L + + H R +EI D K P+
Sbjct: 254 LHNAKANMKVL----HPLPRVDEIATDVDKTPH 282
>d1s16a1 d.14.1.3 (A:1217-1383) Topoisomerase IV subunit B
{Escherichia coli [TaxId: 562]}
Length = 167
Score = 30.1 bits (67), Expect = 0.41
Identities = 19/165 (11%), Positives = 35/165 (21%), Gaps = 29/165 (17%)
Query: 316 KPFIASI----IQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGH 371
KPFI + +W + W +S I T
Sbjct: 20 KPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGL------------ 67
Query: 372 TRLTHNHLFTKGGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAFSIGDM 431
+ + + ++ K D A +
Sbjct: 68 -----RQGLLDAMREFCEYRNILPRGVKLSAEDIWDRCAYVL-SVKMQD-PQFAGQTKER 120
Query: 432 VRSTLLNPISSIFSAELIAIFLCLEAILENPSDQFLIVSMKLIQS 476
+ S S + ++L +N L+ I S
Sbjct: 121 LSSRQCAAFVSGVVKDAFILWL-----NQNVQAAELLAE-MAISS 159
>d1nrza_ c.38.1.1 (A:) Sorbose permease subunit IIb , EIIb-sor
{Klebsiella pneumoniae [TaxId: 573]}
Length = 163
Score = 28.2 bits (63), Expect = 1.8
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 6/50 (12%)
Query: 276 EVTFMWCPSHCGIRGNEIV---DDAAKNPNVSAPLKLCTPEDLKPFIASI 322
+VT +W I+ DD + L+ P +K + S+
Sbjct: 16 QVTTVWSKV---ANAQRIIICNDDVFNDEVRRTLLRQAAPPGMKVNVVSL 62
>d1blea_ c.38.1.1 (A:) Fructose permease, subunit IIb {Bacillus
subtilis [TaxId: 1423]}
Length = 161
Score = 27.8 bits (62), Expect = 2.1
Identities = 7/47 (14%), Positives = 15/47 (31%), Gaps = 2/47 (4%)
Query: 277 VTFMWCPSHCGIRGNEIVDD-AAKNPNVSAPLKLCTPEDLKPFIASI 322
+ W +V D A++ + P ++K S+
Sbjct: 17 ILTRWIK-VHAADRIIVVSDDIAQDEMRKTLILSVAPSNVKASAVSV 62
>d3bwuc2 b.7.2.1 (C:122-205) FimC {Escherichia coli [TaxId: 562]}
Length = 84
Score = 25.9 bits (57), Expect = 4.1
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 84 SPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPY 133
P A+KL + + S T+ P P Y+ E+ VLE++ V P
Sbjct: 2 PPDQAAEKLRFRR--SANSLTLINPTPYYLTVTELNAGTRVLENALVPPM 49
>d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS)
{Thermus thermophilus [TaxId: 274]}
Length = 425
Score = 26.8 bits (58), Expect = 8.9
Identities = 19/164 (11%), Positives = 39/164 (23%), Gaps = 5/164 (3%)
Query: 268 RYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAKNP-----NVSAPLKLCTPEDLKPFIASI 322
RY ++ E ++ H GI +V+ ++ L K
Sbjct: 65 RYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGT 124
Query: 323 IQSEWQIQWNNVPNTNKLKSIRPNIKQWNTSTQDRRTKEVILTRMRIGHTRLTHNHLFTK 382
I + + + + + ++ + R E + R
Sbjct: 125 ILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLS 184
Query: 383 GGQTGNRGSLGNREPILREPQAYFEGTNCYTDGSKSPDVTGCAF 426
+ G PQ + + K AF
Sbjct: 185 DLEVETCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAF 228
>d1l4ia2 b.7.2.1 (A:121-205) SfaE {Escherichia coli [TaxId: 562]}
Length = 85
Score = 24.7 bits (54), Expect = 9.9
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 84 SPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSEVAPY 133
P KL + ++ G+ T+ P P Y+ ++ N LE++ V P
Sbjct: 3 PPEQAPGKLEFTRENGGL--TLFNPTPYYLTVTDLKAGNKSLENTMVPPQ 50
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.320 0.134 0.405
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,019,107
Number of extensions: 90983
Number of successful extensions: 170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 170
Number of HSP's successfully gapped: 12
Length of query: 563
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 473
Effective length of database: 1,171,896
Effective search space: 554306808
Effective search space used: 554306808
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: 55 (25.1 bits)