RPS-BLAST 2.2.22 [Sep-27-2009] Database: scop70_1_75 13,730 sequences; 2,407,596 total letters Searching..................................................done Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (340 letters) >d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 126 Score = 132 bits (332), Expect = 6e-32 Identities = 56/126 (44%), Positives = 81/126 (64%), Gaps = 4/126 (3%) Query: 57 GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116 G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G VTA Sbjct: 1 GCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTA 60 Query: 117 GDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLIT 172 DI D+E++ P HVIC+L +A + M + V +G GYVPA H + PIG + Sbjct: 61 ADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLL 120 Query: 173 IDALYS 178 +DA YS Sbjct: 121 VDACYS 126 >d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 123 Score = 130 bits (328), Expect = 2e-31 Identities = 50/124 (40%), Positives = 75/124 (60%), Gaps = 3/124 (2%) Query: 57 GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK--RVTIFKRGPGVV 114 G A+T+V I+ VLHE S+I GV ED+ +IILN+K + ++ S + + + GP V Sbjct: 1 GTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEV 60 Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174 A D V D+E++NPD I L+ + ME+ V +G GYVPA+ H + D I I +D Sbjct: 61 KARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVD 119 Query: 175 ALYS 178 A++S Sbjct: 120 AVFS 123 >d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 72 Score = 108 bits (272), Expect = 7e-25 Identities = 41/72 (56%), Positives = 55/72 (76%) Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N G+KSL EIK VL + Sbjct: 1 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 60 Query: 313 MGLFLGMNLPDW 324 GL LGM L +W Sbjct: 61 RGLSLGMRLENW 72 >d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Length = 105 Score = 90.7 bits (225), Expect = 2e-19 Identities = 29/111 (26%), Positives = 54/111 (48%), Gaps = 9/111 (8%) Query: 123 NDIEVLNPDHVICNLDVDAVVRMEL-TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181 + E L P V ++ L + +G G+ R + + P++ Sbjct: 3 SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRA--------ILLSSMPPVE 54 Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 +++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F+ Sbjct: 55 RIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 105 Score = 60.6 bits (147), Expect = 2e-10 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 9/88 (10%) Query: 3 QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62 Q + E +KP ++ + Q + EPL RGF HTLGNALR +L+SS+ A Sbjct: 1 QGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIA 57 Query: 63 VQIDGVLHEISSIKGVHEDLTDIILNIK 90 ++ E DL +++ ++ Sbjct: 58 YNVEAARVEQR------TDLDKLVIEME 79 >d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Length = 67 Score = 90.8 bits (226), Expect = 2e-19 Identities = 30/65 (46%), Positives = 41/65 (63%) Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+K L Sbjct: 2 EKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE 61 Query: 313 MGLFL 317 +GL L Sbjct: 62 LGLGL 66 >d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 69 Score = 87.4 bits (217), Expect = 1e-18 Identities = 21/65 (32%), Positives = 29/65 (44%) Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 L +EEL LS R + L+ E I + L+ D+ + G +SL EIK L Sbjct: 3 EEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEK 62 Query: 313 MGLFL 317 G L Sbjct: 63 KGFTL 67 >d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Length = 106 Score = 74.2 bits (182), Expect = 2e-14 Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 8/106 (7%) Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHR-------TENDPIGLITIDALYSPIKKVSYTVES 189 LD + ++G Y T +P+ I + + P+++V++ VE Sbjct: 2 LDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI-LLSSIPPVRRVAFQVED 60 Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235 R GQ D DKL++ I TDGS+T +++ A IL++ L F N + Sbjct: 61 TRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 106 Score = 55.7 bits (134), Expect = 5e-09 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 8/70 (11%) Query: 23 EEENRTLM--IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80 + R + EPL RGF TLGN LRR+L+SS+ A Q++ + G Sbjct: 14 RTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVE------DTRLGQRT 67 Query: 81 DLTDIILNIK 90 DL + L I Sbjct: 68 DLDKLTLRIW 77 >d1by5a_ f.4.3.3 (A:) Ferric hydroxamate uptake receptor FhuA {Escherichia coli [TaxId: 562]} Length = 697 Score = 31.4 bits (69), Expect = 0.11 Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 2/72 (2%) Query: 81 DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140 + + + G+++ G S+ + RG +N +++ + +D Sbjct: 48 SVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPY 107 Query: 141 AVVRMELTVSKG 152 + R E + +G Sbjct: 108 MLERAE--IMRG 117 >d3bjha_ a.39.2.1 (A:) Pheromone-binding protein asp1 {Common honeybee (Apis mellifera) [TaxId: 7460]} Length = 117 Score = 27.2 bits (60), Expect = 2.1 Identities = 5/18 (27%), Positives = 10/18 (55%) Query: 323 DWPPESIEELAKKYEDKC 340 DW P + +L + + +C Sbjct: 1 DWVPPEVFDLVAEDKARC 18 >d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 135 Score = 27.1 bits (60), Expect = 2.4 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 4/59 (6%) Query: 179 PIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 P K + EG DY D M +++ GSI + V LQ ++ + Sbjct: 69 PQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILL 127 >d1n8fa_ c.1.10.4 (A:) 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase, AroG) {Escherichia coli, phenylalanine-regulated isozyme [TaxId: 562]} Length = 343 Score = 26.7 bits (59), Expect = 2.5 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 3/71 (4%) Query: 271 NCLRGENIVYMGDLIQ--RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328 N G I D I L + +G ++V G + G P++ + Sbjct: 180 NGTDG-TIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 238 Query: 329 IEELAKKYEDK 339 + E+ + Sbjct: 239 VAEVKEGLNKA 249 >d5ruba1 c.1.14.1 (A:138-457) Ribulose 1,5-bisphosphate carboxylase-oxygenase {Rhodospirillum rubrum [TaxId: 1085]} Length = 320 Score = 26.3 bits (58), Expect = 3.8 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 1/61 (1%) Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300 +K D + PF P L + + ++R GE ++ ++ +++ + Sbjct: 53 IKNDEPQGNQPFAP-LRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVL 111 Query: 301 K 301 + Sbjct: 112 E 112 >d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 114 Score = 26.3 bits (58), Expect = 4.0 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 7/50 (14%) Query: 11 KPNNIEYIVLGQEEENRTLMIAEPLPRGFA-------HTLGNALRRVLMS 53 P+ E +LG+ E + P HTLGN +R L++ Sbjct: 3 APDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLN 52 >d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333 Score = 25.3 bits (54), Expect = 8.2 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 11/61 (18%) Query: 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT--AVQIDGVLHEISSIK 76 ++GQE+ L++ P G VL+ RG + + +L EI +++ Sbjct: 9 IVGQEDMKLALLLTAVDPGI-----GG----VLVFGDRGTGKSTAVRALAALLPEIEAVE 59 Query: 77 G 77 G Sbjct: 60 G 60 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 0.317 0.136 0.386 Gapped Lambda K H 0.267 0.0637 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 13730 Number of Hits to DB: 1,247,912 Number of extensions: 58395 Number of successful extensions: 189 Number of sequences better than 10.0: 1 Number of HSP's gapped: 183 Number of HSP's successfully gapped: 21 Length of query: 340 Length of database: 2,407,596 Length adjustment: 86 Effective length of query: 254 Effective length of database: 1,226,816 Effective search space: 311611264 Effective search space used: 311611264 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: 53 (24.4 bits)