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= 0402.0019.p (222 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value all2342 [KT] COG1842 Phage shock protein A (IM30), suppresses si... 110 2e-24 BS_yvqH [KT] COG1842 Phage shock protein A (IM30), suppresses si... 99 6e-21 sll0617 [KT] COG1842 Phage shock protein A (IM30), suppresses si... 91 1e-18 BS_ydjF [KT] COG1842 Phage shock protein A (IM30), suppresses si... 84 2e-16 all2343 [KT] COG1842 Phage shock protein A (IM30), suppresses si... 71 1e-12 >all2342 [KT] COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription Length = 217 Score = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 14/215 (6%), Positives = 38/215 (17%), Gaps = 2/215 (0%) Query: 1 MSIFKRLRDLTMSNVNAIIDKAEDPVKMTDQYIRDMTEDLEDAEKAVAAQIAIEKKFKQL 60 M+ +R + + + V + K + + +L ++ A + Sbjct: 1 MAAPQRRKSMKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEK 60 Query: 61 YEEQEALVSKRNQQAHTAAQAGNADXXXXXXXXXXXXXXXXVEYKASFDQNKASADNLRG 120 + Q + + Sbjct: 61 VTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPV 120 Query: 121 KLEEMRKQLTQMKNKRETLVARYNAAKAQTEINKAMSGFSSDSASAGLKRMEDKMLAAEA 180 + + I+ S L + + A E Sbjct: 121 PYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEK 180 Query: 181 QAEASNEMSSGNKSLDDEFEKLGKDQAVEDELAAL 215 ++ E + D + Sbjct: 181 AHPDVELYTASI--DQGLNEHGYIIPGLGDAGDKI 213 >BS_yvqH [KT] COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription Length = 217 Score = 99.0 bits (245), Expect = 6e-21, Method: Compositional matrix adjust. Identities = 13/197 (6%), Positives = 33/197 (16%) Query: 3 IFKRLRDLTMSNVNAIIDKAEDPVKMTDQYIRDMTEDLEDAEKAVAAQIAIEKKFKQLYE 62 + R M +Q I +E + Sbjct: 2 AAPQRRKSMKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEKV 61 Query: 63 EQEALVSKRNQQAHTAAQAGNADXXXXXXXXXXXXXXXXVEYKASFDQNKASADNLRGKL 122 E + + S + + L Sbjct: 62 TIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPVP 121 Query: 123 EEMRKQLTQMKNKRETLVARYNAAKAQTEINKAMSGFSSDSASAGLKRMEDKMLAAEAQA 182 + + + + + S + + +AA +A Sbjct: 122 YFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEKA 181 Query: 183 EASNEMSSGNKSLDDEF 199 E+ + + Sbjct: 182 HPDVELYTASIDQGLNE 198 >sll0617 [KT] COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription Length = 267 Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 68/215 (31%), Positives = 112/215 (52%), Gaps = 2/215 (0%) Query: 1 MSIFKRLRDLTMSNVNAIIDKAEDPVKMTDQYIRDMTEDLEDAEKAVAAQIAIEKKFKQL 60 M +F RL + +N+N ++ KAEDP K+ +Q + DM EDL +AVA IA EK+ +Q Sbjct: 1 MGLFDRLGRVVRANLNDLVSKAEDPEKVLEQAVIDMQEDLVQLRQAVARTIAEEKRTEQR 60 Query: 61 YEEQEALVSKRNQQAHTAAQAGNADXXXXXXXXXXXXXXXXVEYKASFDQNKASADNLRG 120 + K +A A G + Y+ Q + ++NLR Sbjct: 61 LNQDTQEAKKWEDRAKLALTNGEENLAREALARKKSLTDTAAAYQTQLAQQRTMSENLRR 120 Query: 121 KLEEMRKQLTQMKNKRETLVARYNAAKAQTEINKAMSGFSSDSASAGLKRMEDKMLAAEA 180 L + ++++ K K+ L AR AAKA E+ + + G + SA++ +RME+K+L EA Sbjct: 121 NLAALEAKISEAKTKKNMLQARAKAAKANAELQQTLGGLGTSSATSAFERMENKVLDMEA 180 Query: 181 QAEASNEMSSGNKSLDDEFEKLGKDQAVEDELAAL 215 ++A+ E++ ++++F +L VEDELAAL Sbjct: 181 TSQAAGELAG--FGIENQFAQLEASSGVEDELAAL 213 >BS_ydjF [KT] COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription Length = 217 Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 0/220 (0%), Positives = 0/220 (0%), Gaps = 6/220 (2%) Query: 1 MSIFKRLRDLTMSNVNAIIDKAEDPVKMTDQYIRDMTEDLEDAEKAVAAQIAIEKKFKQL 60 M+ +R + + + V + K + + +L ++ A + Sbjct: 1 MAAPQRRKSMKIVEVKHPLVKHKLGLMREQDISTKRFRELASEVGSLLTYEATADLETEK 60 Query: 61 YEEQEALVSKRNQQAHTAAQAGNADXXXXXXXXXXXXXXXXVEYKASFDQNKASADNLRG 120 + Q + + Sbjct: 61 VTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLENVPSARISVVGMYRNEETLEPV 120 Query: 121 KLEEMRKQLTQMKNKRETLVARYNAAKAQTEINK-AMSGFSSDSASAGLKRMEDKMLAAE 179 + + I+ +G SS + E + Sbjct: 121 PYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAGCSSIKVLVLVAAPEGIAALEK 180 Query: 180 AQAEASNEMSSGNK----SLDDEFEKLGKDQAVEDELAAL 215 A + +S ++ Sbjct: 181 AHPDVELYTASIDQGLNEHGYIIPGLGDAGD- 219 >all2343 [KT] COG1842 Phage shock protein A (IM30), suppresses sigma54-dependent transcription Length = 217 Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 0/218 (0%), Positives = 0/218 (0%), Gaps = 2/218 (0%) Query: 1 MSIFKRLRDLTMSNVNAIIDKAEDPVKMTDQYIRDMTEDLEDAEKAVAAQIAIEKKFKQL 60 ++ + + +K I + + A + + + Sbjct: 40 LASEVGSLLTYEATADLETEKVTIEGWNGPVEIDQIKGKKITVVPILRAGLGMMDGVLEN 99 Query: 61 YEEQEALVSKRNQQAHTAAQAGNADXXXXXXXXXXXXXXXXVEYKASFDQNKASADNLRG 120 V + T + G Sbjct: 100 VPSARISVVGMYRNEETLEPVPYFQKLVSNIDERMALIVDPMLATGGSVIATIDLLKKAG 159 Query: 121 KLEEMRKQLTQMKNKRETLVARYNAAKAQTEINKAMSGFSSDSASAGLKRMEDKMLAAEA 180 Sbjct: 160 219 Query: 181 QAEASNEMSSGNKSLDDEFEKLGKDQAVEDELAALMKQ 218 Sbjct: 220 -- 255 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 0.307 0.120 0.301 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: 11,908,092 Number of extensions: 342003 Number of successful extensions: 2065 Number of sequences better than 1.0e-05: 11 Number of HSP's gapped: 2052 Number of HSP's successfully gapped: 11 Length of query: 222 Length of database: 38,378,431 Length adjustment: 102 Effective length of query: 120 Effective length of database: 26,614,363 Effective search space: 3193723560 Effective search space used: 3193723560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 114 (48.5 bits)