RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62] (340 letters) >3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (A:49-180) Length = 132 Score = 156 bits (397), Expect = 3e-39 Identities = 60/132 (45%), Positives = 87/132 (65%), Gaps = 4/132 (3%) Query: 53 SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112 SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G Sbjct: 1 SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIG 60 Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPI 168 VTA DI D+E++ P HVIC+L D +A + M + V +G GYVPA H + PI Sbjct: 61 PVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 120 Query: 169 GLITIDALYSPI 180 G + +DA YSP+ Sbjct: 121 GRLLVDACYSPV 132 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:48-172) Length = 125 Score = 149 bits (378), Expect = 5e-37 Identities = 52/126 (41%), Positives = 77/126 (61%), Gaps = 3/126 (2%) Query: 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI--FKRGPG 112 + G A+T+V I+ VLHE S+I GV ED+ +IILN+K + ++ S + VT+ GP Sbjct: 1 IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPK 60 Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172 V A D V D+E++NPD I L+ + ME+ V +G GYVPA+ H + D I I Sbjct: 61 EVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIP 119 Query: 173 IDALYS 178 +DA++S Sbjct: 120 VDAVFS 125 >1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:51-178) Length = 128 Score = 148 bits (376), Expect = 7e-37 Identities = 57/128 (44%), Positives = 83/128 (64%), Gaps = 4/128 (3%) Query: 55 LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114 + G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +T+ K G G V Sbjct: 1 MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPV 60 Query: 115 TAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGL 170 TA DI D+E++ P HVIC+L D +A + M + V +G GYVPA H + PIG Sbjct: 61 TAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGR 120 Query: 171 ITIDALYS 178 + +DA YS Sbjct: 121 LLVDACYS 128 >2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (A:1-47,A:173-315) Length = 190 Score = 140 bits (353), Expect = 3e-34 Identities = 47/144 (32%), Positives = 70/144 (48%), Gaps = 2/144 (1%) Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235 L SP+++V++ VE R GQ D DKL++ I TDGS+T +++ A IL++ L F N + Sbjct: 45 LSSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 104 Query: 236 EPKKEVKEDINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293 E+ L +EEL LS R + L+ E I + L+ D+ Sbjct: 105 AAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLK 164 Query: 294 RMANFGRKSLVEIKGVLGTMGLFL 317 + G +SL EIK L G L Sbjct: 165 NIPGIGERSLEEIKEALEKKGFTL 188 Score = 50.7 bits (121), Expect = 3e-07 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%) Query: 7 QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54 +K + + EPL RGF TLGN LRR+L+SS Sbjct: 3 DSKLKAPVFTVR---TQGREYGEFVLEPLERGFGVTLGNPLRRILLSS 47 >1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} (A:) Length = 98 Score = 107 bits (269), Expect = 2e-24 Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 3/100 (3%) Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291 ++ + ++ ++ + F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE + Sbjct: 1 MDLRDVREPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 57 Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331 +L+ N G+KSL EIK VL + GL LGM L +WPP SI + Sbjct: 58 LLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 97 >1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} (B:) Length = 84 Score = 105 bits (264), Expect = 7e-24 Identities = 46/80 (57%), Positives = 61/80 (76%) Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ N G+KSL EIK VL Sbjct: 4 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63 Query: 312 TMGLFLGMNLPDWPPESIEE 331 + GL LGM L +WPP SI + Sbjct: 64 SRGLSLGMRLENWPPASIAD 83 >3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} (B:) Length = 79 Score = 87.8 bits (218), Expect = 2e-18 Identities = 30/74 (40%), Positives = 43/74 (58%) Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306 + L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+ Sbjct: 5 KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEV 64 Query: 307 KGVLGTMGLFLGMN 320 K L +GL L + Sbjct: 65 KAKLEELGLGLRKD 78 >1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} (B:) Length = 73 Score = 86.6 bits (215), Expect = 5e-18 Identities = 30/71 (42%), Positives = 43/71 (60%) Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 + L +EEL+LSVRS NCL+ I + +L +TE DM+++ N GRKSL E+K Sbjct: 1 MEKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAK 60 Query: 310 LGTMGLFLGMN 320 L +GL L + Sbjct: 61 LEELGLGLRKD 71 >3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (A:1-48,A:181-246) Length = 114 Score = 84.4 bits (209), Expect = 2e-17 Identities = 20/65 (30%), Positives = 43/65 (66%) Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239 +++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ + ++ Sbjct: 48 LERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQ 107 Query: 240 EVKED 244 ++ Sbjct: 108 PEVKE 112 Score = 64.7 bits (158), Expect = 2e-11 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 3/51 (5%) Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLM 52 +Q + E +KP ++ Q + EPL RGF HTLGNALRR+L+ Sbjct: 1 MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILL 48 >1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} (A:1-50,A:179-235) Length = 107 Score = 82.8 bits (205), Expect = 6e-17 Identities = 23/59 (38%), Positives = 41/59 (69%) Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234 L SP+++++Y VE+AR Q D DKL + ++T+G+I E+++ A+ IL +QL F++ Sbjct: 48 LSSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 106 Score = 61.3 bits (149), Expect = 2e-10 Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 3/53 (5%) Query: 2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54 +Q + E +KP ++ + Q + EPL RGF HTLGNALR +L+SS Sbjct: 1 MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSS 50 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} (A:1-326) Length = 326 Score = 27.8 bits (61), Expect = 1.9 Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 19/69 (27%) Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL-----FLGMNLPD----------WPPE 327 DL++R + L + L E +L GL + LP + Sbjct: 248 DLMKRRQ---LDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSER 304 Query: 328 SIEELAKKY 336 +E+ A+++ Sbjct: 305 -VEKYAERF 312 >2j9l_A Chloride channel protein 5; domain, membrane, transport, CBS domain, CLC, disease mutation, ION channel, ION transport, transmembrane; HET: ATP; 2.30A {Homo sapiens} (A:1-114) Length = 114 Score = 27.9 bits (62), Expect = 2.0 Identities = 8/129 (6%), Positives = 22/129 (17%), Gaps = 21/129 (16%) Query: 99 DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158 ++ + V+ + + D + + P Sbjct: 2 EAKEEFAHKTLAMDVMKPRRNDP-LLTVLTQDSMTV----EDVETIIS---ETTYSGFPV 53 Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218 R +G + L + D + + T Sbjct: 54 VVSRESQRLVGFVLRRDLII---------SIENARKKQDG----VVSTSIIYFTEHSPPL 100 Query: 219 LASRILQDQ 227 + Sbjct: 101 PPYTPPTLK 109 >1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium tuberculosis} (A:126-246) Length = 121 Score = 27.9 bits (62), Expect = 2.1 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 6/47 (12%) Query: 57 GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD 99 G A++ V +G L S+ G ED+T I + +++ Sbjct: 1 GVALSLVYREGRLTRASTRGDGRTG--EDVTLNARTIADVPERLTPG 45 >2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} (A:1-60,A:117-236) Length = 180 Score = 27.5 bits (61), Expect = 2.7 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%) Query: 57 GAAITAVQIDGVLHE-ISSIKGVH-EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114 G A++ + +GVL + G ED+T + I+ I LK+ G++ RG + Sbjct: 62 GLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEV-RGEVFL 120 Query: 115 TAGDIQTVND 124 + +N+ Sbjct: 121 PQAGFEKINE 130 >3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA replication, magnesium, manganese, metal-binding, NAD, zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB: 3jsn_A* (A:115-227) Length = 113 Score = 27.1 bits (60), Expect = 3.5 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%) Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGDSH 101 G A++ +DG + + +G ED+T+ + I I LKM + Sbjct: 1 GLAVSLKYVDGYFVQGLT-RGDGTTGEDITENLKTIHAIPLKMKEPLN 47 >3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (C:1-38,C:171-297) Length = 165 Score = 26.7 bits (59), Expect = 4.1 Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 2/55 (3%) Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251 + + M +++ GSI + + RILQ++L + + + +E ++ L Sbjct: 93 EPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLV--RDLDEEQPTQLSANELN 145 >3bac_A DNA ligase; adenylation domain, DNA damage, DNA repair, DNA replication, NAD; HET: DNA 3B9; 3.00A {Haemophilus influenzae} (A:56-173) Length = 118 Score = 26.7 bits (59), Expect = 4.2 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 7/72 (9%) Query: 57 GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112 G A++ + ++G L + ++ G ED+T I I+ + L++ D+ RG Sbjct: 1 GLAVSILYVNGELTQAATRGDGTTG--EDITANIRTIRNVPLQLLTDNPPARLEV-RGEV 57 Query: 113 VVTAGDIQTVND 124 + + +N Sbjct: 58 FMPHAGFERLNK 69 >1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold; HET: DNA NMN; 1.80A {Enterococcus faecalis V583} (A:64-76,A:122-254) Length = 146 Score = 25.6 bits (56), Expect = 8.8 Identities = 9/43 (20%), Positives = 24/43 (55%), Gaps = 4/43 (9%) Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKM 96 G AI+ +GV ++ +G V E++T+ + ++ + +++ Sbjct: 15 GLAISLRYENGVFVRGAT-RGDGTVGENITENLRTVRSVPMRL 56 >1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} (A:169-391) Length = 223 Score = 25.7 bits (56), Expect = 8.9 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%) Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339 L +G +P+W PE ++ L + + Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223 >1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus stearothermophilus} (A:117-248) Length = 132 Score = 25.6 bits (56), Expect = 9.1 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%) Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGD 99 G A++ DG + ++ +G ED+T+ + I+ + L++ Sbjct: 1 GLAVSVRYEDGYFVQGAT-RGDGTTGEDITENLKTIRSLPLRLKEP 45 >1r6x_A ATP:sulfate adenylyltransferase; APS kinase-like domain; 1.40A {Saccharomyces cerevisiae} (A:168-395) Length = 228 Score = 25.8 bits (56), Expect = 9.3 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%) Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339 L +G +P+W PE ++ L + + Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.317 0.136 0.386 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 2,535,118 Number of extensions: 114402 Number of successful extensions: 325 Number of sequences better than 10.0: 1 Number of HSP's gapped: 316 Number of HSP's successfully gapped: 37 Length of query: 340 Length of database: 4,956,049 Length adjustment: 89 Effective length of query: 251 Effective length of database: 1,947,404 Effective search space: 488798404 Effective search space used: 488798404 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: 55 (25.2 bits)