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= 0001.0722.p (420 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310193|ref|YP_003774285.1| transcription termination facto... 855 0.0 gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 79 5e-16 gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase... 62 1e-10 >gi|300310193|ref|YP_003774285.1| transcription termination factor Rho protein [Herbaspirillum seropedicae SmR1] Length = 420 Score = 855 bits (2210), Expect = 0.0, Method: Compositional matrix adjust. Identities = 420/420 (100%), Positives = 420/420 (100%) Query: 1 MHLSELKAMHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPD 60 MHLSELKAMHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPD Sbjct: 1 MHLSELKAMHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPD 60 Query: 61 GFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVN 120 GFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVN Sbjct: 61 GFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVN 120 Query: 121 GEPPEASKHRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASP 180 GEPPEASKHRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASP Sbjct: 121 GEPPEASKHRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASP 180 Query: 181 KSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHV 240 KSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHV Sbjct: 181 KSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHV 240 Query: 241 QVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRF 300 QVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRF Sbjct: 241 QVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRF 300 Query: 301 FGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINL 360 FGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINL Sbjct: 301 FGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINL 360 Query: 361 SKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN 420 SKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN Sbjct: 361 SKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN 420 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 79.3 bits (194), Expect = 5e-16, Method: Compositional matrix adjust. Identities = 81/252 (32%), Positives = 116/252 (46%), Gaps = 23/252 (9%) Query: 133 FENLTPLHPNKLLQLE---RDMRGEENI-----TG-RIIDLIAPVGRGQRGLLVASPKSG 183 +NL PLH + L + G I TG R I+ + VGRGQR L A G Sbjct: 142 LDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSMLTVGRGQRMGLFAGSGVG 201 Query: 184 KSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGE-------VVASTFDEPA 236 KSV+L +A + + V++V LI ER EV E + G VVA+ D P Sbjct: 202 KSVLLGMMARYTSAD----VIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPP 257 Query: 237 TRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGK-VLTGGVDANALQ 295 +Q A A+ + KDV++++DS+TR A A + A G+ T G + Sbjct: 258 LMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFA 317 Query: 296 R-PKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRV 354 + P A E GGS+T T L E G D I + + + + L R+LAE Sbjct: 318 KLPALVERAGNGDEGGGSITAFYTVLTE-GDDQQDPIADAARAILDGHIVLNRQLAEAGH 376 Query: 355 YPAINLSKSGTR 366 YPAI++ +S +R Sbjct: 377 YPAIDIEQSISR 388 >gi|300310125|ref|YP_003774217.1| type III secretion ATP synthase [Herbaspirillum seropedicae SmR1] Length = 460 Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust. Identities = 62/218 (28%), Positives = 101/218 (46%), Gaps = 20/218 (9%) Query: 160 RIIDLIAPVGRGQRGLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTE- 218 R ID + +G GQR + A P GK+ ++ IA ++ LI ER E+ E Sbjct: 172 RAIDGLLTMGMGQRIGVFAGPGCGKTTLMAAIARGCQAE----AIVFGLIGERGRELNEF 227 Query: 219 ---------MQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITR 269 ++++V VV +T D + + A A+ + V++L+DS+TR Sbjct: 228 LDHELDAELIRKTV---VVCATSDRTSMERSRAAFTATAIAEGFRDRGMKVLLLVDSLTR 284 Query: 270 LARAYNTVIPASGKVLT-GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMD 328 ARA + A+G+ GG + R A + GS+T + T L++ G Sbjct: 285 FARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGGTPQ-GSITAMYTVLVD-GESSS 342 Query: 329 DVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTR 366 D I +E K + + L R+LAE+ YPAI++ S +R Sbjct: 343 DPIGDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISR 380 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.318 0.135 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,269,090 Number of extensions: 53151 Number of successful extensions: 161 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 3 Length of query: 420 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 332 Effective length of database: 1,203,190 Effective search space: 399459080 Effective search space used: 399459080 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 (21.7 bits) S2: 132 (55.5 bits)