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= 0188.0085.p (206 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KKI7.1 B3KKI7_9BACI RNA polymerase sigma-H factor 387 e-106 B1DJZ3.1 B1DJZ3_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 372 e-101 C0ZIG1.1 C0ZIG1_BREBN RNA polymerase sigma-H factor 343 4e-93 C1PXD0.1 C1PXD0_ALIAC RNA polymerase, sigma 30 subunit, SigH 342 1e-92 B7DS10.1 B7DS10_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 342 1e-92 >B3KKI7.1 B3KKI7_9BACI RNA polymerase sigma-H factor Length = 214 Score = 387 bits (994), Expect = e-106, Method: Compositional matrix adjust. Identities = 192/206 (93%), Positives = 198/206 (96%) Query: 1 MLSEYDFISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIG 60 MLS YD ISDE+IVE R GDSGALE+LINKYRNFVRAKARSYFLIGADREDIVQEGMIG Sbjct: 9 MLSGYDVISDEDIVEAVREGDSGALEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIG 68 Query: 61 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDR 120 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDR Sbjct: 69 LYKAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDR 128 Query: 121 TLMDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLK 180 TL+DVICGT V DPEELIINQEEF+GLEDKM+EILSDLERKVLMLYLDGRSYQEIA DL+ Sbjct: 129 TLLDVICGTAVSDPEELIINQEEFVGLEDKMSEILSDLERKVLMLYLDGRSYQEIAVDLR 188 Query: 181 RHVKSIDNALQRVKRKLERYLEVRDN 206 RHVKSIDNALQRVKRKLERYLEVRDN Sbjct: 189 RHVKSIDNALQRVKRKLERYLEVRDN 214 >B1DJZ3.1 B1DJZ3_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 216 Score = 372 bits (954), Expect = e-101, Method: Compositional matrix adjust. Identities = 184/202 (91%), Positives = 193/202 (95%) Query: 4 EYDFISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYK 63 EYD SDE+IVE R GDS ALE+LINKY+NFVRAKARSYFLIGADREDIVQEGMIGLYK Sbjct: 12 EYDCSSDEDIVEAVRNGDSLALEYLINKYKNFVRAKARSYFLIGADREDIVQEGMIGLYK 71 Query: 64 AIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLM 123 +IRDFKGDKL+SFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL+ Sbjct: 72 SIRDFKGDKLASFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTLL 131 Query: 124 DVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRHV 183 DVICGT+V DPEELIINQEEF+GLEDKM+EILSDLERKVLMLYLDGRSYQEIA DL RHV Sbjct: 132 DVICGTRVSDPEELIINQEEFVGLEDKMSEILSDLERKVLMLYLDGRSYQEIAVDLDRHV 191 Query: 184 KSIDNALQRVKRKLERYLEVRD 205 KSIDNALQRVKRKLERYLEVRD Sbjct: 192 KSIDNALQRVKRKLERYLEVRD 213 >C0ZIG1.1 C0ZIG1_BREBN RNA polymerase sigma-H factor Length = 222 Score = 343 bits (881), Expect = 4e-93, Method: Compositional matrix adjust. Identities = 167/203 (82%), Positives = 190/203 (93%) Query: 3 SEYDFISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLY 62 ++Y+ ++DEE+V++ R D+ ALE+LINKY+NFVRAKARSYFLIGADREDIVQEGMIGLY Sbjct: 17 AQYELMTDEEVVDLVRDNDAEALEYLINKYKNFVRAKARSYFLIGADREDIVQEGMIGLY 76 Query: 63 KAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 122 K+IRDF+GDKL+SFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL Sbjct: 77 KSIRDFRGDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 136 Query: 123 MDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRH 182 +DVI GT+V DPEEL IN+EEF +E KM+EILSDLER+VLMLYLDGRSYQ+IA +LKRH Sbjct: 137 LDVISGTKVTDPEELFINREEFDDIEGKMSEILSDLERQVLMLYLDGRSYQQIAVELKRH 196 Query: 183 VKSIDNALQRVKRKLERYLEVRD 205 VKSIDNALQRVKRKLERYLE R+ Sbjct: 197 VKSIDNALQRVKRKLERYLEGRE 219 >C1PXD0.1 C1PXD0_ALIAC RNA polymerase, sigma 30 subunit, SigH Length = 223 Score = 342 bits (877), Expect = 1e-92, Method: Compositional matrix adjust. Identities = 167/203 (82%), Positives = 187/203 (92%) Query: 3 SEYDFISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLY 62 + Y+ ++DEE+VE GD+ AL++LI+KY+NFVRAKARSYFLIGADREDIVQEGMIGLY Sbjct: 19 APYENMTDEELVEAVHRGDTDALDYLIHKYKNFVRAKARSYFLIGADREDIVQEGMIGLY 78 Query: 63 KAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 122 K+IRDF+GDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL Sbjct: 79 KSIRDFRGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 138 Query: 123 MDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRH 182 +DVIC +V DPEELIINQEEF +E KM+E+LSDLER+VLMLYLDGRSYQEIA DL RH Sbjct: 139 LDVICTVRVADPEELIINQEEFDDIEGKMSELLSDLERQVLMLYLDGRSYQEIAVDLARH 198 Query: 183 VKSIDNALQRVKRKLERYLEVRD 205 VKSIDNALQRVKRKLE+YL VR+ Sbjct: 199 VKSIDNALQRVKRKLEKYLTVRN 221 >B7DS10.1 B7DS10_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 223 Score = 342 bits (877), Expect = 1e-92, Method: Compositional matrix adjust. Identities = 167/203 (82%), Positives = 187/203 (92%) Query: 3 SEYDFISDEEIVEIFRGGDSGALEHLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLY 62 + Y+ ++DEE+VE GD+ AL++LI+KY+NFVRAKARSYFLIGADREDIVQEGMIGLY Sbjct: 19 APYENMTDEELVEAVHRGDTDALDYLIHKYKNFVRAKARSYFLIGADREDIVQEGMIGLY 78 Query: 63 KAIRDFKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 122 K+IRDF+GDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL Sbjct: 79 KSIRDFRGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSYVSLDKPIYDEDSDRTL 138 Query: 123 MDVICGTQVLDPEELIINQEEFIGLEDKMAEILSDLERKVLMLYLDGRSYQEIAEDLKRH 182 +DVIC +V DPEELIINQEEF +E KM+E+LSDLER+VLMLYLDGRSYQEIA DL RH Sbjct: 139 LDVICTVRVADPEELIINQEEFDDIEGKMSELLSDLERQVLMLYLDGRSYQEIAVDLARH 198 Query: 183 VKSIDNALQRVKRKLERYLEVRD 205 VKSIDNALQRVKRKLE+YL VR+ Sbjct: 199 VKSIDNALQRVKRKLEKYLTVRN 221 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 0.321 0.139 0.383 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: 1,151,312,071 Number of extensions: 46598239 Number of successful extensions: 175428 Number of sequences better than 1.0e-05: 515 Number of HSP's gapped: 175732 Number of HSP's successfully gapped: 515 Length of query: 206 Length of database: 3,060,696,203 Length adjustment: 129 Effective length of query: 77 Effective length of database: 1,845,385,268 Effective search space: 142094665636 Effective search space used: 142094665636 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: 128 (53.9 bits)