RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy3765
(592 letters)
>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho,
ATPase domain {Escherichia coli [TaxId: 562]}
Length = 289
Score = 278 bits (712), Expect = 2e-90
Identities = 189/262 (72%), Positives = 234/262 (89%)
Query: 88 NRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIIL 147
N+ LF+NLTPLH L +ER S E++T R++DL +PIG+GQRGL+VA PK+GK+++L
Sbjct: 1 NKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLL 60
Query: 148 QHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPAYRHVQVAEMVLE 207
Q+IA +I NH + +++V+LIDERPEEVTEMQR V+GEV+ASTFDEPA RHVQVAEMV+E
Sbjct: 61 QNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIE 120
Query: 208 KAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGGVDSNALQRPKRFFGAARNIE 267
KAKRLVE KKDVIILLDSITRLARAYNTV+PASGKVLTGGVD+NAL RPKRFFGAARN+E
Sbjct: 121 KAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVE 180
Query: 268 EGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRRE 327
EGGSLTIIATALI+TGS+MD+VIYEEFKGTGNME+HL R++AEKRV+PAI+ N+SGTR+E
Sbjct: 181 EGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKE 240
Query: 328 ELLIQDDKLQKIWVLRKLLYSL 349
ELL ++LQK+W+LRK+++ +
Sbjct: 241 ELLTTQEELQKMWILRKIIHPM 262
Score = 81.2 bits (200), Expect = 1e-17
Identities = 73/130 (56%), Positives = 90/130 (69%), Gaps = 27/130 (20%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEP- 547
VA PK+GK+++LQ+IA +I NH + +++V+LIDERPEEVTEMQR V+GEV+ASTFDEP
Sbjct: 49 VAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPA 108
Query: 548 --------------------ALSVMC------KLARAYNTVIPASGKVLTGGVDSNALQR 581
V+ +LARAYNTV+PASGKVLTGGVD+NAL R
Sbjct: 109 SRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHR 168
Query: 582 PKRFFGAARK 591
PKRFFGAAR
Sbjct: 169 PKRFFGAARN 178
>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1
ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}
Length = 276
Score = 180 bits (459), Expect = 3e-53
Identities = 47/248 (18%), Positives = 99/248 (39%), Gaps = 17/248 (6%)
Query: 93 DNLTPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIA 151
+H + +E ++E + +TG +++DL+AP KG + L GK++++ +
Sbjct: 30 KQFAAIHAEAPEFVEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELI 89
Query: 152 HAITTNHSEAIMIVMLIDERPEEVTEMQRSV-------------RGEVIASTFDEPAYRH 198
+ + H + + ER E ++ + + ++ +EP
Sbjct: 90 NNVAKAHGGYSVFA-GVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGAR 148
Query: 199 VQVAEMVLEKAKRLVEMK-KDVIILLDSITRLARAYNTVIPASGKVLTGGVDSNALQRPK 257
+VA L A+ + + +DV++ +D+I R +A + V G++ + L
Sbjct: 149 ARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDM 208
Query: 258 RFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAI 317
+ GS+T + + D F + L R +AE +YPA+
Sbjct: 209 GTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHL-DATTVLSRAIAELGIYPAV 267
Query: 318 NLNKSGTR 325
+ S +R
Sbjct: 268 DPLDSTSR 275
Score = 59.4 bits (144), Expect = 2e-10
Identities = 12/143 (8%), Positives = 36/143 (25%), Gaps = 42/143 (29%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSV------------- 535
GK++++ + + + H + + ER E ++ +
Sbjct: 74 FGGAGVGKTVLIMELINNVAKAHGGYSVFA-GVGERTREGNDLYHEMIESGVINLKDATS 132
Query: 536 RGEVIASTFDEPA----------------------------LSVMCKLARAYNTVIPASG 567
+ ++ +EP + + + +A + V G
Sbjct: 133 KVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLG 192
Query: 568 KVLTGGVDSNALQRPKRFFGAAR 590
++ + L
Sbjct: 193 RIPSAVGYQPTLATDMGTMQERI 215
>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1
ATP synthase {Cow (Bos taurus) [TaxId: 9913]}
Length = 285
Score = 159 bits (404), Expect = 3e-45
Identities = 48/259 (18%), Positives = 96/259 (37%), Gaps = 27/259 (10%)
Query: 93 DNLTPLHPKKLLLLER---NIESKENI-----TG-RIIDLIAPIGKGQRGLLVASPKSGK 143
D P+ K + I + ++ TG + +D + PIG+GQR L++ ++GK
Sbjct: 22 DGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGK 81
Query: 144 SIILQHIAHAITTNHS------EAIMIVMLIDERPEEVTEMQRSVRGE-------VIAST 190
+ I + + I + I ++ V ++ + + V+++T
Sbjct: 82 TSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSAT 141
Query: 191 FDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVL-TGGVD 249
+ A + + K +I+ D +++ A AY + +
Sbjct: 142 ASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYP 201
Query: 250 SNALQRPKRFFGAARNIEE---GGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLER 306
+ R A + + GGSLT + + G + I + ++ LE
Sbjct: 202 GDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGD-VSAYIPTNVISITDGQIFLET 260
Query: 307 RLAEKRVYPAINLNKSGTR 325
L K + PAIN+ S +R
Sbjct: 261 ELFYKGIRPAINVGLSVSR 279
>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1
ATP synthase {Spinach (Spinacia oleracea), chloroplast
[TaxId: 3562]}
Length = 276
Score = 146 bits (369), Expect = 2e-40
Identities = 45/252 (17%), Positives = 91/252 (36%), Gaps = 19/252 (7%)
Query: 92 FDNLTPLHPKKLLLLER---NIESKENI-----TG-RIIDLIAPIGKGQRGLLVASPKSG 142
D + + L+E I S+ ++ TG ID + P+G+GQR L++ ++G
Sbjct: 20 IDGRGEITASESRLIESPAPGIMSRRSVYEPLQTGLIAIDAMIPVGRGQRELIIGDRQTG 79
Query: 143 KSIILQHIAHAITTNHSEAIMIVM-----LIDERPEEVTEMQRSVRGEVIASTFDEPAYR 197
K+ + + + + + + + E V+A T D PA
Sbjct: 80 KTAVATDTILNQQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATL 139
Query: 198 HVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVL-TGGVDSNALQRP 256
A+ + ++ +I+ D +++ A+AY + + +
Sbjct: 140 QYLAPYTGAALAEYFMYRERHTLIIYDDLSKQAQAYRQMSLLLRRPPGREAYPGDVFYLH 199
Query: 257 KRFFGAARNIEE---GGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRV 313
R A + GS+T + + G + I + ++ L L +
Sbjct: 200 SRLLERAAKLSSLLGEGSMTALPIVETQAGD-VSAYIPTNVISITDGQIFLSADLFNAGI 258
Query: 314 YPAINLNKSGTR 325
PAIN+ S +R
Sbjct: 259 RPAINVGISVSR 270
>d1a62a2 b.40.4.5 (A:48-125) Rho termination factor, RNA-binding
domain {Escherichia coli [TaxId: 562]}
Length = 78
Score = 127 bits (320), Expect = 5e-36
Identities = 55/77 (71%), Positives = 64/77 (83%)
Query: 8 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGE 67
IFGDG LE+L DGFGFLRS S+Y+A DDIY+SPSQIRRFNL TGD + G+IR PK GE
Sbjct: 2 IFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGE 61
Query: 68 RYFALLKIKKVNGEKPE 84
RYFALLK+ +VN +KPE
Sbjct: 62 RYFALLKVNEVNFDKPE 78
Score = 113 bits (284), Expect = 5e-31
Identities = 52/76 (68%), Positives = 59/76 (77%)
Query: 417 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGE 476
IFGDG LE+L DGFGFLRS S+Y+A DDIY+SPSQIRRFNL TG G+IR PK GE
Sbjct: 2 IFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGE 61
Query: 477 RYFALLKIKKVNVASP 492
RYFALLK+ +VN P
Sbjct: 62 RYFALLKVNEVNFDKP 77
>d1a62a1 a.140.3.1 (A:1-47) Rho termination factor, N-terminal
domain {Escherichia coli [TaxId: 562]}
Length = 47
Score = 38.0 bits (89), Expect = 9e-05
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 388 DLEVNSVKRLRKQELMFAIFKKKTKIGE 415
++ + ++ R+RKQ+++FAI K+ K GE
Sbjct: 20 NMGLENLARMRKQDIIFAILKQHAKSGE 47
>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter
MsbA, C-terminal domain {Salmonella typhimurium [TaxId:
90371]}
Length = 253
Score = 35.6 bits (82), Expect = 0.012
Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 2/121 (1%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEV 186
I G+ LV SGKS I I + +M + E ++ V
Sbjct: 38 IPAGKTVALVGRSGSGKSTIASLITRFYDIDEGHILMDGHDLREYTLA--SLRNQVALVS 95
Query: 187 IASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTG 246
+ E ++ +E + +D I ++ +T+I +G +L+G
Sbjct: 96 QNVHLFNDTVANNIAYARTEEYSREQIEEAARMAYAMDFINKMDNGLDTIIGENGVLLSG 155
Query: 247 G 247
G
Sbjct: 156 G 156
>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase
domain {Bacteriophage T7 [TaxId: 10760]}
Length = 277
Score = 31.2 bits (69), Expect = 0.36
Identities = 13/85 (15%), Positives = 31/85 (36%), Gaps = 6/85 (7%)
Query: 106 LERNIESKENITG------RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHS 159
+ ++ S+E++ I D G+ ++ + GKS ++ A T
Sbjct: 5 IREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMG 64
Query: 160 EAIMIVMLIDERPEEVTEMQRSVRG 184
+ + + ML + E ++
Sbjct: 65 KKVGLAMLEESVEETAEDLIGLHNR 89
>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA
{Escherichia coli [TaxId: 562]}
Length = 274
Score = 30.8 bits (68), Expect = 0.36
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 123 LIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHS 159
++ + G G LV+ +GKS++ +A I
Sbjct: 22 VLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPD 58
>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein
{Escherichia coli [TaxId: 562]}
Length = 241
Score = 30.3 bits (68), Expect = 0.49
Identities = 22/125 (17%), Positives = 44/125 (35%), Gaps = 11/125 (8%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEV 186
I +G+ +V SGKS + + I + + +LID + +
Sbjct: 26 IKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQ-----VLIDGHD--LALADPNWLRRQ 78
Query: 187 IASTFDEPAYRHVQVAEMVLEKAKRL----VEMKKDVIILLDSITRLARAYNTVIPASGK 242
+ + + + + + + V + D I+ L YNT++ G
Sbjct: 79 VGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGA 138
Query: 243 VLTGG 247
L+GG
Sbjct: 139 GLSGG 143
>d2dfka2 b.55.1.1 (A:240-401) Rho guanine nucleotide exchange factor
9, Collybistin {Rat (Rattus norvegicus) [TaxId: 10116]}
Length = 162
Score = 29.7 bits (66), Expect = 0.56
Identities = 18/125 (14%), Positives = 41/125 (32%), Gaps = 2/125 (1%)
Query: 46 RRFNLHTGDFVEGEIRVPKNGERYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLL 105
++TG+ +N +R F L + V +K + ++ + + +++
Sbjct: 25 SEL-IYTGEMAWIYQPYGRNQQRVFFLFDHQMVLCKKDLIRRDILYYKGRIDMDKYEVID 83
Query: 106 LERNIESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIV 165
+E + N++ + + + L A K L+ E I
Sbjct: 84 IEDGRDDDFNVSMKNAFKLHNKETEEVHLFFAKKLEEKIRWLRAFREER-KMVQEDEKIG 142
Query: 166 MLIDE 170
I E
Sbjct: 143 FEISE 147
>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia
coli [TaxId: 562]}
Length = 79
Score = 28.1 bits (63), Expect = 0.59
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIR 61
G ++ GFGFL ++ P Q+++ +H GD + I
Sbjct: 21 GVVKATEKGFGFLEVDA------QKSYFIPPPQMKKV-MH-GDRIIAVIH 62
>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export
ATP-binding/permease protein SAV1866 {Staphylococcus
aureus [TaxId: 1280]}
Length = 255
Score = 30.1 bits (68), Expect = 0.67
Identities = 25/125 (20%), Positives = 39/125 (31%), Gaps = 11/125 (8%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEV 186
I KG+ V GKS ++ I + +LID + +
Sbjct: 41 IEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQ-----ILIDGHN--IKDFLTGSLRNQ 93
Query: 187 IASTFDEPAYRHVQVAEMVL----EKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGK 242
I + V E +L V + D I L + Y+T + G
Sbjct: 94 IGLVQQDNILFSDTVKENILLGRPTATDEEVVEAAKMANAHDFIMNLPQGYDTEVGERGV 153
Query: 243 VLTGG 247
L+GG
Sbjct: 154 KLSGG 158
>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC
{Synechococcus sp. strain PCC 7942 (Anacystis nidulans
R2) [TaxId: 1140]}
Length = 242
Score = 29.9 bits (66), Expect = 0.70
Identities = 22/113 (19%), Positives = 38/113 (33%), Gaps = 7/113 (6%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSV---- 182
K L + +GK++++ N AI+ +E ++ S
Sbjct: 23 FFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY--EESRAQLLRNAYSWGMDF 80
Query: 183 -RGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYN 234
E AY E L+ K + K I +DS++ LAR +
Sbjct: 81 EEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVS 133
>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC
domain {Human (Homo sapiens) [TaxId: 9606]}
Length = 251
Score = 29.5 bits (66), Expect = 0.92
Identities = 22/126 (17%), Positives = 46/126 (36%), Gaps = 12/126 (9%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEV 186
+ G+ LV SGKS + + + + +L+D +P + + +
Sbjct: 37 LRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ-----LLLDGKP--LPQYEHRYLHRQ 89
Query: 187 IASTFDEPAYRHVQVAEMV-----LEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASG 241
+A+ EP + E + + + I+ L + Y+T + +G
Sbjct: 90 VAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVDEAG 149
Query: 242 KVLTGG 247
L+GG
Sbjct: 150 SQLSGG 155
>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever
virus [TaxId: 11089]}
Length = 140
Score = 27.3 bits (59), Expect = 2.7
Identities = 9/53 (16%), Positives = 17/53 (32%)
Query: 127 IGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQ 179
+ KG +L P +GK+ A +++ E+ E
Sbjct: 4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAF 56
>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus
stearothermophilus, PcrA [TaxId: 1422]}
Length = 318
Score = 27.7 bits (60), Expect = 4.7
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 7/74 (9%)
Query: 134 LLVASPKSGKSIILQH-IAHAITTNHSEAIMIVML------IDERPEEVTEMQRSVRGEV 186
L++A SGK+ +L H IA+ + H I+ + E E V + +V
Sbjct: 28 LIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDV 87
Query: 187 IASTFDEPAYRHVQ 200
STF R ++
Sbjct: 88 WISTFHSMCVRILR 101
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
0.319 0.136 0.379
Gapped
Lambda K H
0.267 0.0624 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,180,935
Number of extensions: 108101
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 26
Length of query: 592
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 502
Effective length of database: 1,171,896
Effective search space: 588291792
Effective search space used: 588291792
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: 56 (25.6 bits)