RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy12553
(401 letters)
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Methanococcus jannaschii [TaxId: 2190]}
Length = 225
Score = 132 bits (333), Expect = 3e-37
Identities = 74/238 (31%), Positives = 108/238 (45%), Gaps = 20/238 (8%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
++GIDEAGRGPVLGPMV K+ EEL K LG DSK LT+ KR + +
Sbjct: 3 IIGIDEAGRGPVLGPMVVCAFAIEKEREEEL-KKLGVKDSKELTKNKRAYLKKLLENLGY 61
Query: 102 WLGWMVEIISPNVICNSMLRRQ--KYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGP 159
++E N + NS+ + ++V+ + L + + + +T
Sbjct: 62 VEKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKF 121
Query: 160 PESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSAL 219
+S+K K+ +I E + + A+ KAD+ YPVV AASI AK RD +
Sbjct: 122 EDSFKDKIEDIIKERNLNIKIIAEH-----------KADAKYPVVSAASIIAKAERDEII 170
Query: 220 KSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEK 277
+ + GSGYP DP T KFL + P + R W T +IL +
Sbjct: 171 DYY------KKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKS 222
>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Pyrococcus horikoshii [TaxId: 53953]}
Length = 211
Score = 123 bits (310), Expect = 4e-34
Identities = 66/235 (28%), Positives = 106/235 (45%), Gaps = 30/235 (12%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRGPV+GP+V G A + N E L+++G DSK LT +R+ + +
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVIDEKN-IERLRDIGVKDSKQLTPGQREKLFSKLIDILD 61
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
++ + + + + + + + +++YVD+
Sbjct: 62 DYYVLLVTPKEIDERHHSMNELEAEKF----------VVALNSLRIKPQKIYVDSADVDP 111
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKS 221
L + + TV ++ KAD+ Y +V AASI AKV+RD
Sbjct: 112 KRFASLIKAGLKYEATVIAEH-------------KADAKYEIVSAASIIAKVTRDR---- 154
Query: 222 WTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276
E ++ + +GSGYP DP TK++L E FP +VR +W TA KI +
Sbjct: 155 --EIEKLKQKYGEFGSGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETARKIEER 207
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Thermococcus kodakaraensis [TaxId: 311400]}
Length = 213
Score = 123 bits (310), Expect = 5e-34
Identities = 68/235 (28%), Positives = 102/235 (43%), Gaps = 30/235 (12%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV +++ +L + L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKL-EELKVRDSKKLTPKRREKLFNEILGVLD 61
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
+ + ++ ++ +LNE + + + + V +Y D E
Sbjct: 62 DYVILE-------LPPDVIGSREGTLNEFEVENFA---KALNSLKVKPDVIYADAADVDE 111
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKS 221
+ V +K KAD +PVV AASI AKV+RD A++
Sbjct: 112 ERFARELGERLNFEAEVVAKH-------------KADDIFPVVSAASILAKVTRDRAVEK 158
Query: 222 WTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276
+ E GSGYP DP T+ FL FP +VR W T KI ++
Sbjct: 159 L------KEEYGEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKIAEK 207
>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Archaeoglobus fulgidus [TaxId: 2234]}
Length = 200
Score = 108 bits (269), Expect = 2e-28
Identities = 60/232 (25%), Positives = 95/232 (40%), Gaps = 36/232 (15%)
Query: 44 GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWL 103
GIDEAG+G V+GP+V C ++ L+ LG DSK L++ +R+++ +
Sbjct: 4 GIDEAGKGCVIGPLVVAGVACSDEDR---LRKLGVKDSKKLSQGRREEL---AEEIRKIC 57
Query: 104 GWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESY 163
V +SP + M + + + + I ++ YVD+
Sbjct: 58 RTEVLKVSPENLDERMAAKTINEILKECYAEIILRLKP--------EIAYVDSPDVIPER 109
Query: 164 KKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKSWT 223
+ E L + KAD YP+V AASI AKV R+ ++
Sbjct: 110 LSRELEEITGLRVV---------------AEHKADEKYPLVAAASIIAKVEREREIERL- 153
Query: 224 FQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILK 275
+ + +GSGY DP T++ L E I P VR W T S + +
Sbjct: 154 -----KEKFGDFGSGYASDPRTREVLKEWIAS-GRIPSCVRMRWKTVSNLRQ 199
>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII)
{Thermotoga maritima [TaxId: 2336]}
Length = 221
Score = 87.4 bits (216), Expect = 1e-20
Identities = 59/261 (22%), Positives = 87/261 (33%), Gaps = 61/261 (23%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRG + GP+V K+ G DSK L+ KR+
Sbjct: 14 VAGVDEAGRGCLAGPVVAAAVVLEKEIE-------GINDSKQLSPAKRE----------R 56
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
L ++E + + S Y++ + A R + V V VD G
Sbjct: 57 LLDEIMEKAAVGIGIASPEEIDLYNIFNATKLAM---NRALENLSVKPSFVLVDGKGIEL 113
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKS 221
S + K D ++GAASI AKV RD
Sbjct: 114 SVPGT-------------------------CL-VKGDQKSKLIGAASIVAKVFRD--RLM 145
Query: 222 WTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEKAVLV 281
F + GY TK+ L I G + R S+ ++L +
Sbjct: 146 SEFHRMYPQFSFHKHKGYA----TKEHL-NEIR-KNGVLPIHRLSFEPVLELLTD----- 194
Query: 282 EGDEIDDEEEEGENKKTRSIR 302
D + + E+G + R R
Sbjct: 195 --DLLREFFEKGLISENRFER 213
>d1kija2 d.122.1.2 (A:9-220) DNA gyrase B {Thermus thermophilus
[TaxId: 274]}
Length = 212
Score = 26.2 bits (57), Expect = 5.7
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 6/44 (13%)
Query: 255 PVFGFPQLVRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
P +RF S L+E A LV G D +EE
Sbjct: 164 PDPEIFGNLRFDPSKIRARLREVAYLVAGLKLVFQDRQHGKEEV 207
>d1ei1a2 d.122.1.2 (A:2-220) DNA gyrase B {Escherichia coli [TaxId:
562]}
Length = 219
Score = 26.5 bits (58), Expect = 5.8
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 259 FPQLVRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
F + F + +K L+E + L G D+ D +E+
Sbjct: 175 FTNVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKEDH 214
>d1s14a_ d.122.1.2 (A:) Topoisomerase IV subunit B {Escherichia coli
[TaxId: 562]}
Length = 168
Score = 25.9 bits (57), Expect = 6.1
Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 15/100 (15%)
Query: 203 VVGAAS--ICAKVSRDSALKSWTFQEGIQIE--NNAWGSGYPGDPVTKKFLSENIDPVFG 258
VV A S + V RD + + F+ G +++ G + F P
Sbjct: 69 VVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFW-----PDET 123
Query: 259 FPQLVRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
F RFS S + +LK KAVL G DEI++ E+
Sbjct: 124 FFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQR 163
>d1kewa_ c.2.1.2 (A:) dTDP-glucose 4,6-dehydratase (RmlB)
{Streptococcus suis, serotype 2 [TaxId: 1307]}
Length = 361
Score = 26.3 bits (57), Expect = 7.5
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 307 PKADENVESPVVEERHAFFKESPYGGSKVF 336
+ + +V P+ E A+ SPY SK
Sbjct: 144 DEVENSVTLPLFTETTAYAPSSPYSASKAS 173
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
0.316 0.134 0.388
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,491,253
Number of extensions: 70844
Number of successful extensions: 156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 147
Number of HSP's successfully gapped: 12
Length of query: 401
Length of database: 2,407,596
Length adjustment: 87
Effective length of query: 314
Effective length of database: 1,213,086
Effective search space: 380909004
Effective search space used: 380909004
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 (21.6 bits)
S2: 54 (24.9 bits)