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/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor Rpo... 476 e-136 gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA... 192 2e-50 gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas a... 117 9e-28 >gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans] Length = 344 Score = 476 bits (1226), Expect = e-136, Method: Compositional matrix adjust. Identities = 233/299 (77%), Positives = 259/299 (86%), Gaps = 1/299 (0%) Query: 21 EPQEAAPAEGVDELKKVLAAELSTDTTQHYLNKIGAKPLLTAAEELHFATQAKAGEFVAR 80 EP EA G+DELKKVL++ELSTD TQHYLN+IGA+PLLT EE+HFAT AK G F AR Sbjct: 47 EP-EALEVAGIDELKKVLSSELSTDATQHYLNQIGARPLLTVPEEVHFATLAKQGNFAAR 105 Query: 81 QKMIEHNLRLVVSIAKHYINRGVALLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIR 140 QKMIEHNLRLVVSIAKHYINRGV LLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIR Sbjct: 106 QKMIEHNLRLVVSIAKHYINRGVVLLDLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIR 165 Query: 141 QSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEV 200 QSIERAIMNQARTVRLPVH+VRELNQ LRAK+HLEAQ DG+DA+AEDIAHLV+R VE+V Sbjct: 166 QSIERAIMNQARTVRLPVHVVRELNQTLRAKFHLEAQHHDGKDATAEDIAHLVERSVEDV 225 Query: 201 QDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK 260 QD+LALSEHA+SLD PLD DPQ+SLMDLL PD AE QEM VL+R+WL LS+K Sbjct: 226 QDILALSEHASSLDAPLDGDPQSSLMDLLQGDHANDPDVLAEHQEMIVLVRDWLDKLSDK 285 Query: 261 QRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEALVKLKRLLASRGVGRDALF 319 QR+V+ RRFGLDNDDP+TLE+LA EM +TRERVRQ+QQEALVKLKR LA GV +D+L Sbjct: 286 QRLVITRRFGLDNDDPATLEELATEMHVTRERVRQIQQEALVKLKRSLARTGVSKDSLL 344 >gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA polymerase [Herminiimonas arsenicoxydans] Length = 858 Score = 192 bits (488), Expect = 2e-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: 611 AGEMKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFK 670 Query: 131 FSTYATWWIRQSIERAIMNQARTVRLPVHMVRELNQILRAKYHLEAQQRDGRDASAEDIA 190 FSTYATWWIRQ+I R+I +QART+R+PVHM+ +N++ R + Q G + +A Sbjct: 671 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQI--LQETGAEPDPATLA 728 Query: 191 HLVDRPVEEVQDVLALSEHAASLDTPLDNDPQASLMDLLPSAVEEHPDTRAESQEMAVLI 250 ++ P ++++ ++ +++ S++TP+ +D + L D + P A M ++ Sbjct: 729 IKMEMPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDNNTLAPADAALHASMRGVV 788 Query: 251 REWLKSLSEKQRVVVARRFGLDNDDPSTLEQLAGEMGITRERVRQVQQEALVKLK 305 ++ L SL+ ++ V+ RFG++ TLE++ + +TRER+RQ++ +AL KL+ Sbjct: 789 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 843 >gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans] Length = 298 Score = 117 bits (292), Expect = 9e-28, Method: Compositional matrix adjust. Identities = 92/271 (33%), Positives = 148/271 (54%), Gaps = 15/271 (5%) Query: 50 YLNKIGAKPLLTAAEELHFATQAKA-GEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 108 Y++ + P+LT EE+ A + + + A QK++ +LRLVVSIA+ Y+ G+ DL Sbjct: 31 YISAVNRLPMLTHEEEISLAKRLRDDNDLGAAQKLVLSHLRLVVSIARGYLGYGLPHADL 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+A D E +A ++ EEV ++ LS +L+ P D+ D + + Sbjct: 151 LRSHKTGLDAMTPD----QVEALAKTLNVKREEVIEMETRLSGRDIALEAPTDDEDDKFA 206 Query: 225 LMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLSEK-----QRVVVARRFGLDNDDPSTL 279 + L S +E P ESQ L E L S K +R+V AR D+ +TL Sbjct: 207 PIAYLSSDSQE-PTRVLESQRYDRLQTEGLSSALGKLDPRSRRIVEARWLANDDGSGATL 265 Query: 280 EQLAGEMGITRERVRQVQQEALVKLKRLLAS 310 +LA E G++ ER+RQ++ AL K+K LA+ Sbjct: 266 HELANEFGVSAERIRQIETVALKKMKGSLAA 296 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 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: 3295 Number of Hits to DB: 515,477 Number of extensions: 20384 Number of successful extensions: 94 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 92 Number of HSP's successfully gapped: 3 Length of query: 319 Length of database: 1,000,347 Length adjustment: 82 Effective length of query: 237 Effective length of database: 730,157 Effective search space: 173047209 Effective search space used: 173047209 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)