BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0502.0030.p (209 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_828600.1| putative RNA polymerase ECF-subfamily sigma fac... 115 5e-25 ref|NP_774452.1| blr7812 [Bradyrhizobium japonicum] >gi|27356096... 109 5e-23 ref|NP_625104.1| putative RNA polymerase sigma factor. [Streptom... 104 1e-21 ref|NP_627820.1| putative RNA polymerase sigma factor [Streptomy... 97 3e-19 ref|NP_961100.1| hypothetical protein MAP2166 [Mycobacterium avi... 93 4e-18 >ref|NP_828600.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces avermitilis MA-4680] dbj|BAC75135.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces avermitilis MA-4680] Length = 322 Score = 115 bits (289), Expect = 5e-25, Method: Compositional matrix adjust. Identities = 73/197 (37%), Positives = 100/197 (50%), Gaps = 5/197 (2%) Query: 13 DPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXXX 72 DPE E LLADSVGLA+LVVL +L PAE++AFVLHD+FA+PF++IAPIV RS Sbjct: 125 DPEQEVLLADSVGLALLVVLETLEPAERLAFVLHDMFAVPFDDIAPIVDRSSAATRQLAS 184 Query: 73 XXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXXXSGAA 132 V G A DL RQ++++DAFLAA+R G+F +G Sbjct: 185 RARRRVQGSAPAPDPDLGRQKQVLDAFLAASRGGDFEALLSVLDPDVVLRADAGALAGGV 244 Query: 133 QEIHXXXXXXXXXXXXXXXXXXP-----ILIDGDVGIVVAPRGELQFVIKVAITDGKIAG 187 +L++G VG+V G+ V+ V + DG+I Sbjct: 245 AVSKLVRGAAAVAEQALMFRQLAQFSRLVLVNGAVGVVTVLDGQPMGVMGVTVADGRIVD 304 Query: 188 FHIISDKERIREMDLAA 204 I+SD +R+ +DL A Sbjct: 305 ICILSDPDRLARLDLPA 321 >ref|NP_774452.1| blr7812 [Bradyrhizobium japonicum] dbj|BAC53077.1| blr7812 [Bradyrhizobium japonicum USDA 110] Length = 289 Score = 109 bits (272), Expect = 5e-23, Method: Compositional matrix adjust. Identities = 71/192 (36%), Positives = 99/192 (51%), Gaps = 3/192 (1%) Query: 15 ECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXXXXX 74 E EA +ADSVG A+L+VL +L PAE++AFVLHD+FA+PFEEIAPIVGRS + Sbjct: 98 EREAEMADSVGAALLIVLETLQPAERLAFVLHDMFAVPFEEIAPIVGRSVDASRQLASRA 157 Query: 75 XXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXXXS-GAAQ 133 V G DL+RQR++VDAFLAA+R GNF G Sbjct: 158 RRRVQGAPVP-ETDLSRQRKIVDAFLAASREGNFEGLLAVLDPDVVFRADQAAVRLGTLP 216 Query: 134 EIHXXXXXXXXXXXXXXXXXXPILIDGDVGIVVAPRGELQFVIKVAITDGKIAGFHIISD 193 EI L+DG++G+ V G+L+ ++V + +IA ++D Sbjct: 217 EIRGADAVAKLYKGRAQAARTA-LVDGEIGVAVILGGQLRIALRVTFSGDRIAAIEAVAD 275 Query: 194 KERIREMDLAAL 205 E I +++ L Sbjct: 276 AEAIASLEVEVL 287 >ref|NP_625104.1| putative RNA polymerase sigma factor. [Streptomyces coelicolor A3(2)] emb|CAB66203.1| putative RNA polymerase sigma factor. [Streptomyces coelicolor A3(2)] Length = 324 Score = 104 bits (260), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 73/201 (36%), Positives = 97/201 (48%), Gaps = 5/201 (2%) Query: 12 SDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXX 71 +DPE EAL DSVG+A+LVVL L PAE++AFVLHD+FA+PF++IA +V RS Sbjct: 124 ADPEAEALHTDSVGIALLVVLERLEPAERLAFVLHDMFAVPFDDIAGVVERSPAATRQLA 183 Query: 72 XXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXX-XXXSG 130 V A DL RQR +V+AFLAA+RAG+F G Sbjct: 184 SRARRRVRDATPAAEPDLGRQRRVVEAFLAASRAGDFEALVSVLHPDVVLRADAGAPARG 243 Query: 131 AAQEIHXXXXXXXXXXXXXXXXXXP----ILIDGDVGIVVAPRGELQFVIKVAITDGKIA 186 A P +L++ VG V G V V + DG I Sbjct: 244 VAASKVVRGARTVATGAFHFRHLAPLARVVLVNDAVGTVAVSDGRPVSVTYVTVADGLIT 303 Query: 187 GFHIISDKERIREMDLAALSA 207 G +I+SD ER+ +D++ L A Sbjct: 304 GLYILSDPERLAGLDVSGLEA 324 >ref|NP_627820.1| putative RNA polymerase sigma factor [Streptomyces coelicolor A3(2)] pir||T36516 probable RNA polymerase sigma factor - Streptomyces coelicolor emb|CAB42013.1| putative RNA polymerase sigma factor [Streptomyces coelicolor A3(2)] Length = 294 Score = 96.7 bits (239), Expect = 3e-19, Method: Compositional matrix adjust. Identities = 66/209 (31%), Positives = 101/209 (48%), Gaps = 15/209 (7%) Query: 6 SSGGDVSDPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKE 65 ++ G +DP E LAD VG+A+L+VL +L PAE++AFVLHD+F +PF++IA ++ ++ Sbjct: 91 AATGTAADPAEEVQLADEVGIALLIVLDTLGPAERLAFVLHDMFDVPFDDIAAMLDKTPA 150 Query: 66 XXXXXXXXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXX--------XXXX 117 V G A ADL R+R VDA+LAATR G+F Sbjct: 151 ATRQLASRARRRVRGV-PAPEADLPRRRRAVDAYLAATRGGDFDALVALLHPDVVLSADA 209 Query: 118 XXXXXXXXXXXSGAAQEIHXXXXXXXXXXXXXXXXXXPILIDGDVGIVVAPRGELQFVIK 177 SG Q +L+DG VG+ +A G L+ V++ Sbjct: 210 AVVPTPEPVTVSGMEQVARGAMASMARARSAAV-----VLVDGMVGMAMAENGRLRVVLR 264 Query: 178 VAI-TDGKIAGFHIISDKERIREMDLAAL 205 DG+I G +I++ R+ E+D+ + Sbjct: 265 FDFAADGRITGIDVIAEPARLNELDITGI 293 >ref|NP_961100.1| hypothetical protein MAP2166 [Mycobacterium avium subsp. paratuberculosis str. k10] gb|AAS04483.1| hypothetical protein MAP2166 [Mycobacterium avium subsp. paratuberculosis str. k10] Length = 296 Score = 92.8 bits (229), Expect = 4e-18, Method: Compositional matrix adjust. Identities = 63/196 (32%), Positives = 93/196 (47%), Gaps = 1/196 (0%) Query: 13 DPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXXX 72 DPE A+LAD+VG+A+ VVL +L PAE++AFVLHDVFA+PF +IA IV + E Sbjct: 99 DPEHRAMLADAVGMALFVVLDTLPPAERLAFVLHDVFAVPFAQIAAIVDGTPESARKLAS 158 Query: 73 XXXXXVHGFDTARHADLARQRELVDAFLAATRAGNFXXXXXXXXXXXXXXXXXXXXSGAA 132 + D DLA QRE+VDAF AA R+G+F + Sbjct: 159 RARRRIERADPVPDGDLAAQREVVDAFFAAGRSGDFDRLVSVLHPDVVLRGDFGPATATV 218 Query: 133 Q-EIHXXXXXXXXXXXXXXXXXXPILIDGDVGIVVAPRGELQFVIKVAITDGKIAGFHII 191 + + ++G G V+ G V+ + G+I ++ Sbjct: 219 RVQGAAAVAKLARSYAGPEREAWAATVNGAAGAVIFVAGRAASVMGFVVRGGRIRAIDVL 278 Query: 192 SDKERIREMDLAALSA 207 +D +RI +++L AL A Sbjct: 279 ADPDRIAKLELGALRA 294 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.321 0.139 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 208,247,277 Number of extensions: 5975359 Number of successful extensions: 10654 Number of sequences better than 1.0e-05: 24 Number of HSP's gapped: 10648 Number of HSP's successfully gapped: 24 Length of query: 209 Length of database: 757,237,578 Length adjustment: 120 Effective length of query: 89 Effective length of database: 431,425,698 Effective search space: 38396887122 Effective search space used: 38396887122 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: 123 (52.0 bits)