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= 0001.2932.p (319 letters) Database: BlastDatabases/707/707 3697 sequences; 1,221,021 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor Rpo... 476 e-136 gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma fa... 192 3e-50 gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor ... 116 2e-27 gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for... 54 1e-08 >gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS [Janthinobacterium sp. Marseille] Length = 345 Score = 476 bits (1226), Expect = e-136, Method: Compositional matrix adjust. Identities = 233/307 (75%), Positives = 257/307 (83%), Gaps = 2/307 (0%) Query: 15 DGEAAGEPQEAAPAE--GVDELKKVLAAELSTDTTQHYLNKIGAKPLLTAAEELHFATQA 72 DG+A + AP E G+DELKKVLA ELSTD TQHYLN+IG +PLLT EE+HFAT A Sbjct: 39 DGDAVELAERVAPVEVAGIDELKKVLATELSTDATQHYLNQIGTRPLLTVPEEVHFATLA 98 Query: 73 KAGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFS 132 K G F ARQKMIEHNLRLVVSIAKHYINRGV LLDLIEEGNLGLMRAIDKFEPERGFRFS Sbjct: 99 KQGNFAARQKMIEHNLRLVVSIAKHYINRGVILLDLIEEGNLGLMRAIDKFEPERGFRFS 158 Query: 133 TYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHL 192 TYATWWIRQSIERAIMNQARTVRLPVH+VRELNQ LRAK+HLEAQ DG+DA+AEDIAHL Sbjct: 159 TYATWWIRQSIERAIMNQARTVRLPVHVVRELNQTLRAKFHLEAQHHDGKDATAEDIAHL 218 Query: 193 VDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIRE 252 VDR VE+VQD+LALSEHA SLD PLD DPQ+SLMDLL PD AE EM VL+ + Sbjct: 219 VDRSVEDVQDILALSEHATSLDAPLDGDPQSSLMDLLQGDHANDPDALAEHNEMTVLVHD 278 Query: 253 WLKSLSEKQRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEALVKLKRLLASRG 312 WL+ L +KQR+V+ RRFGLDNDDP+TLE LA EM +TRERVRQ+QQEALVKLKR L G Sbjct: 279 WLEKLPDKQRLVITRRFGLDNDDPATLEALAAEMHVTRERVRQIQQEALVKLKRSLMRTG 338 Query: 313 VGRDALF 319 VG+D+L Sbjct: 339 VGKDSLL 345 >gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma factor [Janthinobacterium sp. Marseille] Length = 826 Score = 192 bits (487), Expect = 3e-50, Method: Compositional matrix adjust. Identities = 96/235 (40%), Positives = 153/235 (65%), Gaps = 5/235 (2%) Query: 74 AGEFVARQ---KMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFR 130 AGE AR+ +M E NLRLV+SIAK Y NRG+ LDLI+EGN+GLM+A+DKFE RGF+ Sbjct: 579 AGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFK 638 Query: 131 FSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIA 190 FSTYATWWIRQ+I R+I +QART+R+PVHM+ +N++ R + Q G + +A Sbjct: 639 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLA 696 Query: 191 HLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLI 250 ++ P ++++ ++ +++ S++TP+ +D + L D + P A M ++ Sbjct: 697 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRGVV 756 Query: 251 REWLKSLSEKQRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEALVKLK 305 ++ L SL+ ++ V+ RFG++ TLE++ + +TRER+RQ++ +AL KL+ Sbjct: 757 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 811 >gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille] Length = 298 Score = 116 bits (291), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 90/271 (33%), Positives = 151/271 (55%), Gaps = 15/271 (5%) Query: 50 YLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 108 Y++ + P+LT EE+ A + + + A QK++ +LRLVVSIA+ Y+ G+ DL Sbjct: 31 YISAVNRLPMLTHEEEMSLARRLRDENDLGAAQKLVLSHLRLVVSIARGYLGYGLPHADL 90 Query: 109 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHMV-RELNQI 167 I+EGN+GLM+A+ +F+P++G R +Y+ WI+ + I+ R V++ R+L Sbjct: 91 IQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKNWRLVKVATTKAQRKLFFN 150 Query: 168 LRA-KYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDV-LALSEHAASLDTPLDN-DPQAS 224 LR+ K L++ D D ++A ++ EEV ++ LS +L+ P D+ D + + Sbjct: 151 LRSHKTGLDSMTPDQVD----ELAKTLNVKREEVIEMETRLSGRDIALEAPTDDEDDKFA 206 Query: 225 LMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDPSTL 279 + L S ++E P ESQ+ L E L + K +R+V AR D+ +TL Sbjct: 207 PIAYLSSDMQE-PTKVLESQQFDRLQTEGLSNALGKLDARSRRIVEARWLANDDGSGATL 265 Query: 280 EQLAGEMGITRERVRQVQQEALVKLKRLLAS 310 +LA E G++ ER+RQ++ AL K+K LA+ Sbjct: 266 HELADEFGVSAERIRQIEAVALKKMKGSLAA 296 >gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium sp. Marseille] Length = 243 Score = 54.3 bits (129), Expect = 1e-08, Method: Compositional matrix adjust. Identities = 47/202 (23%), Positives = 98/202 (48%), Gaps = 13/202 (6%) Query: 107 DLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVR-LPVHMVRELN 165 DLI+ G +GL+ A+ ++E G +F TYA Q I A++++ R+ +P M + + Sbjct: 40 DLIQAGMIGLLDAVSRYEETHGAQFETYAV----QRIRGAMLDELRSSDWMPRSMRQNMR 95 Query: 166 QILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDVLA--LSEHAASLDTPLDNDPQA 223 +I A L QQR GR + ++A + + + QD+L+ + D++ Sbjct: 96 KIEVAMNTL--QQRLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHDSEDNE 153 Query: 224 SLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPSTLEQLA 283 +D + P + + E +++L E++++++ GL + L+++ Sbjct: 154 HFLDRYCTDESPDPLQNLMNTGFRAAVIEAIQALPEREKILM----GLYYEQEMNLKEIG 209 Query: 284 GEMGITRERVRQVQQEALVKLK 305 MG+T RV Q+ +A+ +++ Sbjct: 210 AVMGVTESRVSQLHSQAIARMR 231 Database: BlastDatabases/707/707 Posted date: Apr 13, 2011 12:58 PM Number of letters in database: 1,221,021 Number of sequences in database: 3697 Lambda K H 0.316 0.132 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 3697 Number of Hits to DB: 625,684 Number of extensions: 24580 Number of successful extensions: 95 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 91 Number of HSP's successfully gapped: 4 Length of query: 319 Length of database: 1,221,021 Length adjustment: 83 Effective length of query: 236 Effective length of database: 914,170 Effective search space: 215744120 Effective search space used: 215744120 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: 129 (54.3 bits)