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= 0044.0003.p (197 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 77 2e-14 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 70 1e-12 BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 69 5e-12 Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 69 6e-12 MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 69 6e-12 >PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 165 Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 49/171 (28%), Positives = 80/171 (46%), Gaps = 26/171 (15%) Query: 21 FEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWLYTIAYN 80 +EE+MR YQ+ + C LG+ +A+D QEV LK L + F WLY+I YN Sbjct: 5 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 64 Query: 81 QCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEAVQQALSK------------- 127 +CI ER R + + L+EA ++ K Sbjct: 65 ECI-------------TQYRKERRKRRLMDALSLDPLEEASEEKSPKVEERGGLDRWLVH 111 Query: 128 LSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYA 178 ++ +R +L+LR V E+ +QEI+ I+H S + +Y+R+ + R ++ A Sbjct: 112 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDRLREKFSDA 162 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 70.5 bits (171), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 47/178 (26%), Positives = 81/178 (45%), Gaps = 10/178 (5%) Query: 6 LRRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYN 65 +++ I V +G+ + F +I+ Y+ I CY MLG+ EAED QE F++A+ + ++ Sbjct: 5 IKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFD 64 Query: 66 PDIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDE------ 119 + F WLY IA N ID I Q + L E Sbjct: 65 INRKFSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSL 124 Query: 120 ----AVQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRR 173 +QQ + KL + R +++L+ ++E+S EI IL+ ++ + R + R+ Sbjct: 125 ELSNTIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRK 182 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust. Identities = 45/177 (25%), Positives = 81/177 (45%), Gaps = 10/177 (5%) Query: 7 RRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNP 66 +R++ +V G+ + F E++ Y+ + Y M+G+ EA+D QE FL+A+ + Y+ Sbjct: 6 KRLVREVRAGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDI 65 Query: 67 DIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXD----------ERDNRHVDQQIEGKY 116 F WL+ IA N ID + D VD Q+ Sbjct: 66 QRKFSTWLFRIATNVAIDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQME 125 Query: 117 LDEAVQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRR 173 + +QQ + L + R ++L+ +E++S +EIS IL S ++ + R + R+ Sbjct: 126 TRDWIQQEIQALPPKYRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALRK 182 >Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 44/175 (25%), Positives = 77/175 (44%), Gaps = 4/175 (2%) Query: 15 EGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWL 74 + + ++E++R + + Y + G+ +AED QE F++ FR++ Y P F WL Sbjct: 78 KATMPSWDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQPGT-FEGWL 136 Query: 75 YTIAYNQCIDVIXXXXXXXXXXXXXXDER---DNRHVDQQIEGKYLDEAVQQALSKLSIE 131 + I N +D++ +R D + +Q L +Q AL+ L E Sbjct: 137 HRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALASLPPE 196 Query: 132 ERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAKGEGSCEI 186 R ++L +E +SY+EI L +R + R + R Y A G C + Sbjct: 197 FRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAAHPEHGECAV 251 >MT1259 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 44/175 (25%), Positives = 77/175 (44%), Gaps = 4/175 (2%) Query: 15 EGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIPFGAWL 74 + + ++E++R + + Y + G+ +AED QE F++ FR++ Y P F WL Sbjct: 78 KATMPSWDELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQPGT-FEGWL 136 Query: 75 YTIAYNQCIDVIXXXXXXXXXXXXXXDER---DNRHVDQQIEGKYLDEAVQQALSKLSIE 131 + I N +D++ +R D + +Q L +Q AL+ L E Sbjct: 137 HRITTNLFLDMVRRRARIRMEALPEDYDRVPADEPNPEQIYHDARLGPDLQAALASLPPE 196 Query: 132 ERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAKGEGSCEI 186 R ++L +E +SY+EI L +R + R + R Y A G C + Sbjct: 197 FRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYLAAHPEHGECAV 251 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.320 0.136 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 12,794,350 Number of extensions: 424549 Number of successful extensions: 918 Number of sequences better than 1.0e-05: 21 Number of HSP's gapped: 909 Number of HSP's successfully gapped: 21 Length of query: 197 Length of database: 38,378,431 Length adjustment: 101 Effective length of query: 96 Effective length of database: 26,729,697 Effective search space: 2566050912 Effective search space used: 2566050912 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: 113 (48.1 bits)