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= 0005.0040.p (662 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312273|ref|YP_003776365.1| 2-oxoglutarate dehydrogenase ox... 660 0.0 gi|300311960|ref|YP_003776052.1| G3E family GTPase [Herbaspirill... 403 e-113 gi|300311859|ref|YP_003775951.1| CobW/P47K family protein [Herba... 96 1e-20 gi|300310263|ref|YP_003774355.1| cobalamin synthesis P47K protei... 92 1e-19 gi|300314043|ref|YP_003778135.1| cobalamin synthesis protein/P47... 75 2e-14 >gi|300312273|ref|YP_003776365.1| 2-oxoglutarate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 954 Score = 660 bits (1703), Expect = 0.0, Method: Compositional matrix adjust. Identities = 309/328 (94%), Positives = 322/328 (98%) Query: 335 AGRGTFVHRHAVLHDQNRERWDAGTYIPLQNVAENQAPYTVIDSVLSEEAVLGFEYGYST 394 AGRGTF HRHAVLHDQNRERWDAGT+IPLQNVAENQ+ +TVIDSVLSEEAVL FEYGYST Sbjct: 627 AGRGTFTHRHAVLHDQNRERWDAGTFIPLQNVAENQSTFTVIDSVLSEEAVLAFEYGYST 686 Query: 395 AEPNTLTIWEAQFGDFANGAQVVMDQFISSGEVKWGRASGLVQMLPHGYEGQGPEHSSAR 454 AEPNTLTIWEAQFGDFANGAQVVMDQFISSGEVKWGRASGLVQMLPHGYEGQGPEHSSAR Sbjct: 687 AEPNTLTIWEAQFGDFANGAQVVMDQFISSGEVKWGRASGLVQMLPHGYEGQGPEHSSAR 746 Query: 455 LERYLQLCADNNMQVVQPTTAAQIFHLLRRQMIRLFRKPLIILTPKSLLRNKDAGSPLSD 514 +ERYLQLCADNNMQVVQPTTAAQIFHLLRRQMIRLFRKPLII+TPKSLLRNKDAGSPLSD Sbjct: 747 IERYLQLCADNNMQVVQPTTAAQIFHLLRRQMIRLFRKPLIIMTPKSLLRNKDAGSPLSD 806 Query: 515 LAKGSFQTVIPELDDKLDAKKVKRIIACSGKVYYDLVNARKERGQTDTAIIRVEQLYPFP 574 LAKGSFQTVIPE+D+ +DAKKVKRI+ACSGKVYYDLVNARKERGQTDTAIIRVEQLYPFP Sbjct: 807 LAKGSFQTVIPEVDETIDAKKVKRIVACSGKVYYDLVNARKERGQTDTAIIRVEQLYPFP 866 Query: 575 HKAFAAALKQFPNFQELVWTQDEPQNQGAWLQIQHNIFENLTDGQKLAYAGRPASASPAV 634 HKAFAAALKQFPNF ELVW QDEPQNQGAWLQIQHNIFENL++GQKLAYAGRPASASPAV Sbjct: 867 HKAFAAALKQFPNFNELVWAQDEPQNQGAWLQIQHNIFENLSEGQKLAYAGRPASASPAV 926 Query: 635 GYYDKHYAQQKALIDTAFSKLKGFVLTK 662 GYYDKHYAQQKALI+TAF+KLKGFVLTK Sbjct: 927 GYYDKHYAQQKALIETAFAKLKGFVLTK 954 >gi|300311960|ref|YP_003776052.1| G3E family GTPase [Herbaspirillum seropedicae SmR1] Length = 377 Score = 403 bits (1036), Expect = e-113, Method: Compositional matrix adjust. Identities = 225/314 (71%), Positives = 249/314 (79%), Gaps = 3/314 (0%) Query: 6 PIPVTIVTGFLGAGKTTLLRSLVQHRQTRRLALLINEFGEVTIDGDLIRASSSDAGGQVR 65 PIPVT+VTGFLGAGKTTLLR L+Q RQ+RRLALLINEFGEV IDGDL+RA DA GQV+ Sbjct: 16 PIPVTVVTGFLGAGKTTLLRGLLQRRQSRRLALLINEFGEVAIDGDLLRAEG-DAQGQVQ 74 Query: 66 IQDFPYGLIAYGDDERFIPTMLALAARRAQVDHVLIETSGLALPTAVMESLQTPELAAHF 125 IQDF +GLIAYGDD F+P MLALAARRAQ+DHVLIETSGLALP+AVME LQ E+A HF Sbjct: 75 IQDFAHGLIAYGDDAHFVPAMLALAARRAQIDHVLIETSGLALPSAVMEVLQGAEMARHF 134 Query: 126 ILDATLAVVDTPLLLDDRFEQQGSGADDAVAAMFERQLEYADVVVLNKIDDLNEDQLLDA 185 +LDATLAVVDTPLLL+D F A A +F +QLE ADVVVLNKID + E LL A Sbjct: 135 VLDATLAVVDTPLLLEDAFA-SADAVGAATAQLFRQQLECADVVVLNKIDGMEEAPLLQA 193 Query: 186 EQRVRSRAPNVRFLELAYKAQLDIRLALGLRLHQPTLQAHQHTYTHVRMPGADASVLNDQ 245 EQ VR+ APNVRFLELAY A+LDIRLALGLRLHQ H H YT V MPG A V DQ Sbjct: 194 EQAVRALAPNVRFLELAYGARLDIRLALGLRLHQAGATVHHH-YTPVSMPGERAQVAPDQ 252 Query: 246 GRLNGHAHSGLGAHSHGLATHKHFHEQDPGWLSFTLRSQSPQPADKLKQAIAEAAKSEPI 305 R NGH HSGLGAHSHGL+THKHFHEQDPGW SFTLRS + Q A++L+QA+A AA +EPI Sbjct: 253 RRFNGHVHSGLGAHSHGLSTHKHFHEQDPGWQSFTLRSLAHQDAERLRQAVAAAALAEPI 312 Query: 306 LRTKGFVRTLDGKR 319 LR KGFV T G R Sbjct: 313 LRAKGFVHTDQGAR 326 >gi|300311859|ref|YP_003775951.1| CobW/P47K family protein [Herbaspirillum seropedicae SmR1] Length = 404 Score = 95.5 bits (236), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 66/191 (34%), Positives = 103/191 (53%), Gaps = 16/191 (8%) Query: 7 IPVTIVTGFLGAGKTTLLRSLVQHRQTRRLALLINEFGEVTIDGDLIRASSSD-AGGQVR 65 +PVT+++GFLGAGKTTLL ++ +R+ RR+A+++N+ EV ID L+R +D A + + Sbjct: 13 LPVTVLSGFLGAGKTTLLNHILHNREGRRVAVIVNDMSEVNIDAALVRDGGADLARTEEK 72 Query: 66 IQDFPYGLIAYGDDERFIPTMLALAARRAQVDHVLIETSGLALPTAVMESLQ-TPELAAH 124 + + G I E + + L AR + D ++IE++G++ P V E+ T E A Sbjct: 73 LVEMSNGCICCTLREDLLMEVRKL-ARERRFDQLVIESTGISEPLPVAETFTFTDEDGAS 131 Query: 125 FI----LDATLAVVDTPLLLDDRFEQ-------QGSGADD--AVAAMFERQLEYADVVVL 171 LD + VVD L D Q Q G +D V + Q+E+ DV+VL Sbjct: 132 LSDVARLDTMVTVVDAFNFLKDYSSQDSLDQRGQSMGEEDNRTVVDLLIEQIEFCDVIVL 191 Query: 172 NKIDDLNEDQL 182 NK+D + D L Sbjct: 192 NKLDLVAADDL 202 >gi|300310263|ref|YP_003774355.1| cobalamin synthesis P47K protein [Herbaspirillum seropedicae SmR1] Length = 413 Score = 92.0 bits (227), Expect = 1e-19, Method: Compositional matrix adjust. Identities = 86/328 (26%), Positives = 160/328 (48%), Gaps = 59/328 (17%) Query: 4 AQPIPVTIVTGFLGAGKTTLLRSLVQHRQTRRLALLINEFGEVTIDGDLIRASSSDAGGQ 63 AQ IPVT+++GFLG+GKTTLL ++++R ++A+++N+ EV +DGD +R ++ G Sbjct: 14 AQRIPVTVLSGFLGSGKTTLLNHILRNRAGMKVAVIVNDMSEVNMDGDDVRRNTELYRGN 73 Query: 64 VRIQDFPYGLIAYGDDERFIPTMLALAARRAQVDHVLIETSGLALPTAVMES-------- 115 + + G I + + AL AR + D++LIE++G++ P V E+ Sbjct: 74 DELVEMSNGCICCTLRADLLEQVSAL-ARSGRFDYLLIESTGISEPIPVAETFAFLDSDG 132 Query: 116 LQTPELAAHFILDATLAVVDTPLLLDDRFEQQGSG------ADDA----VAAMFERQLEY 165 ELA LD + VV+ + FEQQ + AD A ++ + Q+EY Sbjct: 133 FSLSELAR---LDTLVTVVN-----GETFEQQLADHVAIAQADGASTRPLSDLLIEQVEY 184 Query: 166 ADVVVLNKIDDLNEDQLLDAEQRVRSRAPNVRFLELAYKAQLDIRLALGLRLHQ-PTLQA 224 A+V++++++D ++ + ++ P R L +A+ ++D+ L RL P+L Sbjct: 185 ANVILVSRVDLIDASAFASLKAVLQKLNPTARILPMAH-GEVDLDQVLDTRLFDLPSL-- 241 Query: 225 HQHTYTHVRMPGADASVLNDQGRLNGHAHSGLGAHSHGLATHKHFHEQDPGWLSFTLRSQ 284 RMPG + ++G AH A ++G+++ + R++ Sbjct: 242 -------ARMPGWMQT-------MDG-AHPPSEADTYGISSSVY-------------RAR 273 Query: 285 SPQPADKLKQAIAEAAKSEPILRTKGFV 312 P +L + ++ +LR KG++ Sbjct: 274 LPFHPGRLLDWLGRPWRNGRLLRCKGYL 301 >gi|300314043|ref|YP_003778135.1| cobalamin synthesis protein/P47K family protein [Herbaspirillum seropedicae SmR1] Length = 388 Score = 74.7 bits (182), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 62/202 (30%), Positives = 101/202 (50%), Gaps = 23/202 (11%) Query: 6 PIPVTIVTGFLGAGKTTLLRSLVQHRQTRRLALLINEFGEVTIDGDLIRASSSDAGGQVR 65 PIPV+++TGFLG+GKTTLL L+ + + ++INEFGE+ +D L+ S + Sbjct: 11 PIPVSLLTGFLGSGKTTLLNHLITQPEMKDTLVIINEFGEIGLDHLLVAHSQEET----- 65 Query: 66 IQDFPYGLIAY---GDDERFIPTM---LALAARRAQVDHVLIETSGLALPTAVMESLQTP 119 I + G + GD ++ + + A RR + + V+IET+GLA P ++ +L T Sbjct: 66 IVEMSSGCLCCTIRGDLKKTLKDITWRFAEGGRR-KFNRVVIETTGLASPAPILHTLMTD 124 Query: 120 E-LAAHFILDATLAVVDTPLLLDDRFEQQGSGADDAVAAMFERQLEYADVVVLNKIDDLN 178 +A + LD + VD S D A+ +Q AD ++L K D ++ Sbjct: 125 AFIAERYRLDGVIVTVDA--------VNGMSTLDHHEEAV--QQAAVADRLLLTKTDLVD 174 Query: 179 EDQLLDAEQRVRSRAPNVRFLE 200 L + R+R+ P R L+ Sbjct: 175 AATLAALQARLRTLNPGARQLQ 196 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 0.135 0.395 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: 2,111,480 Number of extensions: 90322 Number of successful extensions: 352 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 345 Number of HSP's successfully gapped: 5 Length of query: 662 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 571 Effective length of database: 1,188,985 Effective search space: 678910435 Effective search space used: 678910435 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 (21.8 bits) S2: 134 (56.2 bits)