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= 0584.0019.p (178 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K9R9.1 B3K9R9_9BACI RNA polymerase sigma factor, sigma-70 family 166 5e-40 B3KD50.1 B3KD50_9BACI RNA polymerase sigma factor 160 6e-38 B3K6S0.1 B3K6S0_9BACI RNA polymerase sigma factor 150 4e-35 C2Y3G7.1 C2Y3G7_BACCE RNA polymerase sigma-70 factor 149 9e-35 C2ZPV7.1 C2ZPV7_BACCE RNA polymerase sigma-70 factor 148 2e-34 >B3K9R9.1 B3K9R9_9BACI RNA polymerase sigma factor, sigma-70 family Length = 178 Score = 166 bits (421), Expect = 5e-40, Method: Compositional matrix adjust. Identities = 81/164 (49%), Positives = 114/164 (69%), Gaps = 4/164 (2%) Query: 3 IVTNEAATMTAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGE 62 + N+ +T+ +G ME++G DVWNYA++LT+ + AADDI+Q+ F+RAYK+ N F G Sbjct: 8 VAVNDPSTLLSG----WMESFGQDVWNYAFFLTKRKDAADDISQDVFLRAYKHWNDFEGR 63 Query: 63 AAVRTWLLQITRNRWLSYRSSSFIRRVTLQESAGGKSFSPSAEEVYMQQSLSSEVWKIVL 122 ++VRTWLL ITRN L+Y SSF+ RV+L K PSAE+ +M + S++WK V+ Sbjct: 64 SSVRTWLLTITRNLSLNYLKSSFMTRVSLTGWITSKQTEPSAEKEFMDAAAVSQIWKCVM 123 Query: 123 QLPRKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQK 166 +LP K+REVL+L HY L +E+A LLD+S KSRLHRAR + Sbjct: 124 ELPPKYREVLILEFHYQLPRKEMAQLLDLSEGTIKSRLHRARAR 167 >B3KD50.1 B3KD50_9BACI RNA polymerase sigma factor Length = 183 Score = 160 bits (404), Expect = 6e-38, Method: Compositional matrix adjust. Identities = 77/174 (44%), Positives = 118/174 (67%), Gaps = 9/174 (5%) Query: 8 AATMTAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRT 67 +A + ++ LME+YG+DVWNYA+ +TR+ ADD+AQ+ FI+AY++ +FRGEA+V+T Sbjct: 4 SAELKTSDIRMLMESYGEDVWNYAFAITRNTHTADDVAQDVFIKAYQHFASFRGEASVKT 63 Query: 68 WLLQITRNRWLSYRSSSFIRRVTL---------QESAGGKSFSPSAEEVYMQQSLSSEVW 118 WLL+ITRN LSY +F+RRV L Q+ A SPSAE Y++++ + E+W Sbjct: 64 WLLKITRNTALSYLKRAFLRRVVLMGEQSPGTGQKGAMRTPISPSAEAEYLERAEADELW 123 Query: 119 KIVLQLPRKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKEGWE 172 K VL+LP K R+ L+L H+ LS++E++ + +S KSR++RA+QK W+ Sbjct: 124 KQVLKLPAKFRDPLVLSLHHQLSIDEISAITGLSPGTVKSRIYRAKQKVAAAWK 177 >B3K6S0.1 B3K6S0_9BACI RNA polymerase sigma factor Length = 178 Score = 150 bits (380), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 74/164 (45%), Positives = 108/164 (65%) Query: 6 NEAATMTAGALQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAV 65 + M + L +M YG+DVWNYAY+LT+ + ADDIAQE FI+AY ++TFRG+A + Sbjct: 7 KQMTVMDSQTLDKIMNEYGNDVWNYAYFLTKQHALADDIAQEAFIKAYYGIHTFRGQATL 66 Query: 66 RTWLLQITRNRWLSYRSSSFIRRVTLQESAGGKSFSPSAEEVYMQQSLSSEVWKIVLQLP 125 +TWLL ITR+ Y+ + F R+V L++ S S SAE Y+ + + E+W +++ LP Sbjct: 67 KTWLLTITRHTAFRYKQAFFFRKVILKDKLTASSSSRSAEAEYLDEQYTDEIWAMIMTLP 126 Query: 126 RKHREVLMLYAHYGLSMEELAGLLDISLPAAKSRLHRARQKAKE 169 K REVL+L +Y + M E+A LL I+ KSRLHRAR+K ++ Sbjct: 127 SKLREVLVLDLYYEMPMHEIAKLLHIATGTVKSRLHRARKKVQK 170 >C2Y3G7.1 C2Y3G7_BACCE RNA polymerase sigma-70 factor Length = 179 Score = 149 bits (376), Expect = 9e-35, Method: Compositional matrix adjust. Identities = 66/152 (43%), Positives = 106/152 (69%) Query: 16 LQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRTWLLQITRN 75 L ++++Y DVWNY++ +T+ +DDI Q+ FI+ +K+ ++FR E++++TW+L+ITRN Sbjct: 16 LDYVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKHWHSFRKESSIKTWILKITRN 75 Query: 76 RWLSYRSSSFIRRVTLQESAGGKSFSPSAEEVYMQQSLSSEVWKIVLQLPRKHREVLMLY 135 ++Y SS+ +R++L SPSAE+ + +Q ++VW +VL+LP+KHRE+L+L Sbjct: 76 TAINYLKSSYFKRISLVGFFSDDKQSPSAEQEFFKQEEMNDVWDVVLKLPKKHREILILD 135 Query: 136 AHYGLSMEELAGLLDISLPAAKSRLHRARQKA 167 A Y LS EE+A LD+S+ KSRL RAR K Sbjct: 136 AKYELSYEEMAETLDVSIGTVKSRLSRARSKV 167 >C2ZPV7.1 C2ZPV7_BACCE RNA polymerase sigma-70 factor Length = 179 Score = 148 bits (373), Expect = 2e-34, Method: Compositional matrix adjust. Identities = 65/152 (42%), Positives = 107/152 (70%) Query: 16 LQTLMENYGDDVWNYAYYLTRSRSAADDIAQETFIRAYKYMNTFRGEAAVRTWLLQITRN 75 L+ ++++Y DVWNY++ +T+ +DDI Q+ FI+ +K+ ++FR E++++TW+L+ITRN Sbjct: 16 LEYVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKHWHSFRKESSIKTWILKITRN 75 Query: 76 RWLSYRSSSFIRRVTLQESAGGKSFSPSAEEVYMQQSLSSEVWKIVLQLPRKHREVLMLY 135 ++Y SS+ +R++L SPSAE+ + +Q ++VW +VL+LP+KHRE+L+L Sbjct: 76 TAINYLKSSYFKRISLVGFFSDDKQSPSAEQEFFKQEEMNDVWDVVLKLPKKHREILILD 135 Query: 136 AHYGLSMEELAGLLDISLPAAKSRLHRARQKA 167 A Y LS EE+A L++S+ KSRL RAR K Sbjct: 136 AKYELSYEEMAETLEVSIGTVKSRLSRARSKV 167 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 0.317 0.128 0.369 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: 963,380,196 Number of extensions: 33352250 Number of successful extensions: 104850 Number of sequences better than 1.0e-05: 3111 Number of HSP's gapped: 104210 Number of HSP's successfully gapped: 3111 Length of query: 178 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 51 Effective length of database: 1,864,227,298 Effective search space: 95075592198 Effective search space used: 95075592198 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 (21.7 bits) S2: 126 (53.1 bits)