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= 0004.0019.p (412 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... 839 0.0 gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 79 6e-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 = 839 bits (2168), Expect = 0.0, Method: Compositional matrix adjust. Identities = 412/412 (100%), Positives = 412/412 (100%) Query: 1 MHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSP 60 MHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSP Sbjct: 9 MHVSALLEMAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSP 68 Query: 61 DASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGEPPEASK 120 DASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGEPPEASK Sbjct: 69 DASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGEPPEASK 128 Query: 121 HRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASPKSGKSVML 180 HRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASPKSGKSVML Sbjct: 129 HRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASPKSGKSVML 188 Query: 181 QHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLE 240 QHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLE Sbjct: 189 QHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLE 248 Query: 241 KAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNVE 300 KAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNVE Sbjct: 249 KAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNVE 308 Query: 301 EGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRRE 360 EGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRRE Sbjct: 309 EGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRRE 368 Query: 361 ELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN 412 ELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN Sbjct: 369 ELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN 420 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 79.0 bits (193), Expect = 6e-16, Method: Compositional matrix adjust. Identities = 81/252 (32%), Positives = 116/252 (46%), Gaps = 23/252 (9%) Query: 125 FENLTPLHPNKLLQLE---RDMRGEENI-----TG-RIIDLIAPVGRGQRGLLVASPKSG 175 +NL PLH + L + G I TG R I+ + VGRGQR L A G Sbjct: 142 LDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSMLTVGRGQRMGLFAGSGVG 201 Query: 176 KSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGE-------VVASTFDEPA 228 KSV+L +A + + V++V LI ER EV E + G VVA+ D P Sbjct: 202 KSVLLGMMARYTSAD----VIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPP 257 Query: 229 TRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGK-VLTGGVDANALQ 287 +Q A A+ + KDV++++DS+TR A A + A G+ T G + Sbjct: 258 LMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFA 317 Query: 288 R-PKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRV 346 + P A E GGS+T T L E G D I + + + + L R+LAE Sbjct: 318 KLPALVERAGNGDEGGGSITAFYTVLTE-GDDQQDPIADAARAILDGHIVLNRQLAEAGH 376 Query: 347 YPAINLSKSGTR 358 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 = 69/263 (26%), Positives = 119/263 (45%), Gaps = 24/263 (9%) Query: 152 RIIDLIAPVGRGQRGLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTE- 210 R ID + +G GQR + A P GK+ ++ IA ++ LI ER E+ E Sbjct: 172 RAIDGLLTMGMGQRIGVFAGPGCGKTTLMAAIARGCQAE----AIVFGLIGERGRELNEF 227 Query: 211 ---------MQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITR 261 ++++V VV +T D + + A A+ + V++L+DS+TR Sbjct: 228 LDHELDAELIRKTV---VVCATSDRTSMERSRAAFTATAIAEGFRDRGMKVLLLVDSLTR 284 Query: 262 LARAYNTVIPASGKVLT-GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMD 320 ARA + A+G+ GG + R A + GS+T + T L++ G Sbjct: 285 FARAQREIGLAAGEPPARGGFTPSVYTMLPRLIERAGGTPQ-GSITAMYTVLVD-GESSS 342 Query: 321 DVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMY 380 D I +E K + + L R+LAE+ YPAI++ S +R + + + R+L+ Sbjct: 343 DPIGDEAKSLLDGHILLTRKLAEQGHYPAIDVLASISRVMSNVTSREHRRAASRFRELLA 402 Query: 381 DMDEIEAMEFILDKMKSTKNNAE 403 E+E +L ++ K+ A+ Sbjct: 403 RYQEME----LLIRLGEYKSGAD 421 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 0.374 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: 1,250,558 Number of extensions: 52586 Number of successful extensions: 160 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 157 Number of HSP's successfully gapped: 3 Length of query: 412 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 324 Effective length of database: 1,203,190 Effective search space: 389833560 Effective search space used: 389833560 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)