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= 0193.0028.p (188 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KDZ9.1 B3KDZ9_9BACI RNA polymerase sigma factor 292 8e-78 B1D5J7.1 B1D5J7_9BACL RNA polymerase sigma factor 280 3e-74 A6CNQ6.1 A6CNQ6_9BACI RNA polymerase sigma factor 207 2e-52 Q8CXN7.1 Q8CXN7_OCEIH RNA polymerase sigma factor 207 3e-52 Q2B5B2.1 Q2B5B2_9BACI RNA polymerase sigma factor 207 4e-52 >B3KDZ9.1 B3KDZ9_9BACI RNA polymerase sigma factor Length = 188 Score = 292 bits (748), Expect = 8e-78, Method: Compositional matrix adjust. Identities = 136/188 (72%), Positives = 165/188 (87%) Query: 1 VENLEGRLTKLALKGDQRAFAELVELYKDKIYHLAYRMLNNRHEAEDIVQETFLRVYRNL 60 ++NL+ RL KLA KGDQRAFAE+VELYKDKI+HLAYRML+NRHEAED+VQETFLRVY+NL Sbjct: 1 MDNLDVRLAKLARKGDQRAFAEIVELYKDKIFHLAYRMLSNRHEAEDVVQETFLRVYKNL 60 Query: 61 DRYDDKQKFSTWIYRIGTNLCIDRLRKRRPTYSLDAEMNDQEGIDGYSMIPSDNVXXXXX 120 DRYD+ QKFSTWIYRIGTNL IDRLRKR+P++SLDA++N+ EG+DGYS+IPSDN Sbjct: 61 DRYDENQKFSTWIYRIGTNLSIDRLRKRKPSFSLDADLNESEGMDGYSLIPSDNRTPESE 120 Query: 121 XXXXXXQSLIYEAIDSLPVKYRSVMILRYLQDLSLQEISDVMDMPVTTIKTRVHRGREFL 180 Q +I++AID LP KY+++MILRY+QDLSLQEIS+++D+PVTTIKTRVHRGREFL Sbjct: 121 MLLSETQRIIHQAIDGLPAKYKTIMILRYIQDLSLQEISEILDLPVTTIKTRVHRGREFL 180 Query: 181 RKKLGPKM 188 RKKL K+ Sbjct: 181 RKKLEYKL 188 >B1D5J7.1 B1D5J7_9BACL RNA polymerase sigma factor Length = 188 Score = 280 bits (717), Expect = 3e-74, Method: Compositional matrix adjust. Identities = 131/185 (70%), Positives = 157/185 (84%) Query: 4 LEGRLTKLALKGDQRAFAELVELYKDKIYHLAYRMLNNRHEAEDIVQETFLRVYRNLDRY 63 LE RL +LALKGDQRAFAELV LY+DK++H+AYRML NR EAED+VQETFLRVY+NL+RY Sbjct: 4 LEARLARLALKGDQRAFAELVGLYQDKLFHMAYRMLYNRQEAEDVVQETFLRVYKNLERY 63 Query: 64 DDKQKFSTWIYRIGTNLCIDRLRKRRPTYSLDAEMNDQEGIDGYSMIPSDNVXXXXXXXX 123 D+ KFSTWIYRI TNLCIDRLRKR+P+YSLDAE D EG+DGYSMIPSD+ Sbjct: 64 DESLKFSTWIYRIATNLCIDRLRKRKPSYSLDAESTDHEGLDGYSMIPSDDRTPESELLL 123 Query: 124 XXXQSLIYEAIDSLPVKYRSVMILRYLQDLSLQEISDVMDMPVTTIKTRVHRGREFLRKK 183 Q +I+E+I+SLP KY+++M+LRY+Q++SLQEI DV+DMPVTTIKTRVHRGREFLRKK Sbjct: 124 SETQRIIHESIESLPPKYKTIMMLRYIQEMSLQEIGDVLDMPVTTIKTRVHRGREFLRKK 183 Query: 184 LGPKM 188 L K+ Sbjct: 184 LEHKL 188 >A6CNQ6.1 A6CNQ6_9BACI RNA polymerase sigma factor Length = 187 Score = 207 bits (528), Expect = 2e-52, Method: Compositional matrix adjust. Identities = 94/175 (53%), Positives = 130/175 (74%) Query: 10 KLALKGDQRAFAELVELYKDKIYHLAYRMLNNRHEAEDIVQETFLRVYRNLDRYDDKQKF 69 K LKGDQ AFAE++ELYKDK++ + +RML NRHEAED+ QE F+R Y N+ ++ K+KF Sbjct: 10 KQVLKGDQDAFAEVIELYKDKVFQICFRMLGNRHEAEDVAQEAFIRAYVNIHTFNQKRKF 69 Query: 70 STWIYRIGTNLCIDRLRKRRPTYSLDAEMNDQEGIDGYSMIPSDNVXXXXXXXXXXXQSL 129 STW+YRI TNLCIDR+RK++P Y LDAE+ EG+ YS + ++ Q+ Sbjct: 70 STWLYRIATNLCIDRIRKKKPDYYLDAEVKGTEGLTMYSHVAAEGQLPEEEVEEMELQAE 129 Query: 130 IYEAIDSLPVKYRSVMILRYLQDLSLQEISDVMDMPVTTIKTRVHRGREFLRKKL 184 I I LP KYRSV++L+Y+++LSLQEIS+++D+P+ T+KTR+HRGRE LRK+L Sbjct: 130 IQRQILKLPDKYRSVIVLKYIEELSLQEISEILDLPLGTVKTRIHRGREALRKQL 184 >Q8CXN7.1 Q8CXN7_OCEIH RNA polymerase sigma factor Length = 187 Score = 207 bits (527), Expect = 3e-52, Method: Compositional matrix adjust. Identities = 95/171 (55%), Positives = 125/171 (73%) Query: 14 KGDQRAFAELVELYKDKIYHLAYRMLNNRHEAEDIVQETFLRVYRNLDRYDDKQKFSTWI 73 KGDQ AFAE+V Y++KI+ YRML N+HEAEDI QE F+R Y N+D +D+K+KFSTW+ Sbjct: 14 KGDQSAFAEVVSFYQNKIFQHCYRMLGNKHEAEDIAQEAFIRAYINIDSFDEKRKFSTWL 73 Query: 74 YRIGTNLCIDRLRKRRPTYSLDAEMNDQEGIDGYSMIPSDNVXXXXXXXXXXXQSLIYEA 133 YRI TNL IDR+RKR+P Y LDAE+ EG+D YS + S Q I+ Sbjct: 74 YRIATNLTIDRIRKRKPDYYLDAEVKGTEGLDMYSQLASTERLPGEEVESRELQRYIHHE 133 Query: 134 IDSLPVKYRSVMILRYLQDLSLQEISDVMDMPVTTIKTRVHRGREFLRKKL 184 I LP KYRS+++LRYL++ SLQEIS+++D+P+ T+KTR+HRGRE LRK+L Sbjct: 134 ISQLPAKYRSIIMLRYLEEFSLQEISEILDIPLGTVKTRIHRGREALRKRL 184 >Q2B5B2.1 Q2B5B2_9BACI RNA polymerase sigma factor Length = 187 Score = 207 bits (527), Expect = 4e-52, Method: Compositional matrix adjust. Identities = 96/175 (54%), Positives = 125/175 (71%) Query: 10 KLALKGDQRAFAELVELYKDKIYHLAYRMLNNRHEAEDIVQETFLRVYRNLDRYDDKQKF 69 K LKGDQ AF E+VE+YKDK++ L +RML NRHEAEDI QE FLR Y N+ ++ KF Sbjct: 10 KQVLKGDQNAFGEIVEIYKDKVFQLCFRMLGNRHEAEDIAQEAFLRAYVNIQSFNIDLKF 69 Query: 70 STWIYRIGTNLCIDRLRKRRPTYSLDAEMNDQEGIDGYSMIPSDNVXXXXXXXXXXXQSL 129 STW+YRI TNLCIDR+RK++P Y LDAE+ +G+ YS I +D Q Sbjct: 70 STWLYRIATNLCIDRIRKKKPDYFLDAEVAGTDGLTMYSQIAADTRLPEEDVESLELQET 129 Query: 130 IYEAIDSLPVKYRSVMILRYLQDLSLQEISDVMDMPVTTIKTRVHRGREFLRKKL 184 I I LP KYRSV++L+Y+++LSL EIS++MD+P+ T+KTR+HRGRE LRK+L Sbjct: 130 IQNEISKLPEKYRSVIVLKYIEELSLNEISEIMDLPLGTVKTRIHRGREALRKQL 184 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.322 0.138 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 974,898,201 Number of extensions: 35228293 Number of successful extensions: 109911 Number of sequences better than 1.0e-05: 4849 Number of HSP's gapped: 106862 Number of HSP's successfully gapped: 4855 Length of query: 188 Length of database: 3,060,696,203 Length adjustment: 128 Effective length of query: 60 Effective length of database: 1,854,806,283 Effective search space: 111288376980 Effective search space used: 111288376980 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 (21.9 bits) S2: 127 (53.5 bits)