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= 0032.0024.p (406 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... 810 0.0 gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase... 78 1e-15 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 = 810 bits (2093), Expect = 0.0, Method: Compositional matrix adjust. Identities = 395/404 (97%), Positives = 402/404 (99%) Query: 1 MAIGLDIDNAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSPDASYMAST 60 MAI LDI+NAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSPDASYMAST Sbjct: 17 MAISLDIENAARLRKQELMFAILKKRAKSGEQIFGDGALEVLPDGFGFLRSPDASYMAST 76 Query: 61 DDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGEAPEASKHRILFENL 120 DDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGE PEASKHRILFENL Sbjct: 77 DDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKVDKVNGEPPEASKHRILFENL 136 Query: 121 TPLHPNKIMQLEREMRGEENITGRIIDLIAPIGRGQRGLLVASPKSGKSVMLQHIAHAIT 180 TPLHPNK++QLER+MRGEENITGRIIDLIAP+GRGQRGLLVASPKSGKSVMLQHIAHAIT Sbjct: 137 TPLHPNKLLQLERDMRGEENITGRIIDLIAPVGRGQRGLLVASPKSGKSVMLQHIAHAIT 196 Query: 181 TNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEM 240 TNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEM Sbjct: 197 TNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFDEPATRHVQVAEMVLEKAKRLVEM 256 Query: 241 KKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNIEEGGSLTII 300 KKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARN+EEGGSLTII Sbjct: 257 KKDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNVEEGGSLTII 316 Query: 301 ATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQ 360 ATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQ Sbjct: 317 ATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLSKSGTRREELLIKPDQ 376 Query: 361 LQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGS 404 LQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRG+ Sbjct: 377 LQKIWVLRKLMYDMDEIEAMEFILDKMKSTKNNAEFFDMMRRGN 420 >gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase [Herbaspirillum seropedicae SmR1] Length = 468 Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 80/252 (31%), Positives = 115/252 (45%), Gaps = 23/252 (9%) Query: 117 FENLTPLHPNKIMQLEREMR---GEENI-----TG-RIIDLIAPIGRGQRGLLVASPKSG 167 +NL PLH + L G I TG R I+ + +GRGQR L A G Sbjct: 142 LDNLGPLHTERSAPLAVRAANPLGRAPIRDILDTGIRAINSMLTVGRGQRMGLFAGSGVG 201 Query: 168 KSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGE-------VVASTFDEPA 220 KSV+L +A + + V++V LI ER EV E + G VVA+ D P Sbjct: 202 KSVLLGMMARYTSAD----VIVVGLIGERGREVKEFIEQILGAEGLARSVVVAAPADTPP 257 Query: 221 TRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGK-VLTGGVDANALQ 279 +Q A A+ + KDV++++DS+TR A A + A G+ T G + Sbjct: 258 LMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVFA 317 Query: 280 R-PKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRV 338 + P A E GGS+T T L E G D I + + + + L R+LAE Sbjct: 318 KLPALVERAGNGDEGGGSITAFYTVLTE-GDDQQDPIADAARAILDGHIVLNRQLAEAGH 376 Query: 339 YPAINLSKSGTR 350 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 = 69/253 (27%), Positives = 113/253 (44%), Gaps = 15/253 (5%) Query: 107 APEASKHRILFENLTPLHPNKIMQLEREMRGEENITG-RIIDLIAPIGRGQRGLLVASPK 165 AP A ++ + ++P+ + R TG R ID + +G GQR + A P Sbjct: 134 APAAQENVATWRAMSPVIRDAPPATSRPRIATPLPTGVRAIDGLLTMGMGQRIGVFAGPG 193 Query: 166 SGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTE-MQRSVRGE------VVASTFDE 218 GK+ ++ IA ++ LI ER E+ E + + E VV +T D Sbjct: 194 CGKTTLMAAIARGCQAE----AIVFGLIGERGRELNEFLDHELDAELIRKTVVVCATSDR 249 Query: 219 PATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLARAYNTVIPASGKVLT-GGVDANA 277 + + A A+ + V++L+DS+TR ARA + A+G+ GG + Sbjct: 250 TSMERSRAAFTATAIAEGFRDRGMKVLLLVDSLTRFARAQREIGLAAGEPPARGGFTPSV 309 Query: 278 LQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKR 337 R A + GS+T + T L++ G D I +E K + + L R+LAE+ Sbjct: 310 YTMLPRLIERAGGTPQ-GSITAMYTVLVD-GESSSDPIGDEAKSLLDGHILLTRKLAEQG 367 Query: 338 VYPAINLSKSGTR 350 YPAI++ S +R Sbjct: 368 HYPAIDVLASISR 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 0.319 0.136 0.375 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: 1,235,230 Number of extensions: 51563 Number of successful extensions: 165 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 162 Number of HSP's successfully gapped: 3 Length of query: 406 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 319 Effective length of database: 1,207,925 Effective search space: 385328075 Effective search space used: 385328075 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)