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= 0005.0273.p (355 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp... 286 2e-78 gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 137 9e-34 gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba... 96 4e-21 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 286 bits (731), Expect = 2e-78, Method: Compositional matrix adjust. Identities = 146/318 (45%), Positives = 202/318 (63%), Gaps = 8/318 (2%) Query: 33 SXFDWGG-DYYRKTGAMMPADGLDALRNKDAILFGSAGDP-HIPDHITLWGLRLKICQGF 90 + FDW +YY + G MMP D + L+ +AI FG+ G P +PDH++LWG LK + F Sbjct: 41 THFDWAHCNYYAEHGKMMPDDWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDF 100 Query: 91 DQYANVRPTRILPGIDAPLKRCAQEDLNWVIVRENSEGEYAGVGGRVHQGHPIEAATDVS 150 D Y N+RP R++PG+ PL D+++ +VREN+EGEY+ +GGR+++G E S Sbjct: 101 DLYVNLRPVRLMPGVPCPLANRKPGDIDFYVVRENTEGEYSSIGGRMYEGTERETVIQES 160 Query: 151 MMTRAGVERIMRFAFKLAQSRPRKLLTVITKSNAQRHAMVMWDEIAVQISKEFPDVKWDK 210 + +R G +RI++FAF LAQSRP+K LT TKSN M WDE + ++PDV+ DK Sbjct: 161 VFSRKGTDRILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDK 220 Query: 211 ELVDAATARMVNRPATLDTIVATNLHADILSDLAAALAGSLGIAPTGNIDPERRYPSMFE 270 +D TA V P D +VA+NL DILSDL A AG++GIAP+ NI+P R PS+FE Sbjct: 221 YHIDILTAHFVLNPDRFDVVVASNLFGDILSDLGPACAGTIGIAPSANINPTRELPSLFE 280 Query: 271 PIHGSAFDIMGKGLANPVGTFWSVVMMLEHLGE-----HEAANQVMDAVEAVTADPALHT 325 P+HGSA DI GK +ANPV WS MML+ LG+ +A + ++ A+E V + T Sbjct: 281 PVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVN-GPTT 339 Query: 326 GDLGGKATTAQVTDAVCA 343 DLGGK+ TA+V A+ A Sbjct: 340 PDLGGKSNTAEVGQAIAA 357 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 137 bits (346), Expect = 9e-34, Method: Compositional matrix adjust. Identities = 110/325 (33%), Positives = 158/325 (48%), Gaps = 30/325 (9%) Query: 38 GGDYYRKTGAMMPADGLDALRNKDAILFGSAGDPHI--------PDHITLWGLRLKICQG 89 GG Y G +P L + DAILFG+ GD P+ L GLR + Sbjct: 38 GGAGYEAHGHPLPDGTLKLAKEADAILFGAVGDWKYDKLERALRPEQAIL-GLR----KH 92 Query: 90 FDQYANVRPTRILPGID--APLKRCAQEDLNWVIVRENSEGEYAGV--GGRVHQGHPIEA 145 +AN RP P + + LK +L+ +IVRE + Y G G R P + Sbjct: 93 LQLFANFRPAICYPELTGASSLKPELVANLDILIVRELNGDIYFGQPRGMREAPDGPFKG 152 Query: 146 AT---DVSMMTRAGVERIMRFAFKLAQSRPRKLLTVITKSNAQRHAMVMWDEIAVQISKE 202 A D + + RI AF+ A R ++L +V K+N W +I ++ KE Sbjct: 153 AREGFDTMRYSEPEIRRIAHVAFQAAAKRGKRLCSV-DKANVL-ETFQFWKDIVTEVGKE 210 Query: 203 FPDVKWDKELVDAATARMVNRPATLDTIVATNLHADILSDLAAALAGSLGIAPTGNIDPE 262 +PDV+ VD A ++V P D IV N+ DILSD AA L GS+G+ P+ ++D Sbjct: 211 YPDVELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDAN 270 Query: 263 RRYPSMFEPIHGSAFDIMGKGLANPVGTFWSVVMMLEH-LGEHEAANQVMDAVEAVTADP 321 + ++EP HGSA DI G+G+ANP+ T S MML L + E A+++ +AV+ V A Sbjct: 271 NK--GLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQ- 327 Query: 322 ALHTGDL----GGKATTAQVTDAVC 342 L T D+ K T Q+ +AV Sbjct: 328 GLRTADIYEEGCTKVNTQQMGEAVV 352 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 95.9 bits (237), Expect = 4e-21, Method: Compositional matrix adjust. Identities = 76/273 (27%), Positives = 121/273 (44%), Gaps = 44/273 (16%) Query: 82 LRLKICQGFDQYANVRPTRILPGIDAPLKRCAQEDLNWVIVRENSEGEYAGVG------- 134 L + + Q D Y +RP R G+ +PL+ + D+ VI RENSE YAG+ Sbjct: 116 LNVAMRQQLDLYVCLRPVRYFKGVPSPLREPEKTDM--VIFRENSEDIYAGIEWAAGTPE 173 Query: 135 ------------GRVHQGHPIEAATDVSMMTRAGVERIMRFAFKLAQSRPRKLLTVITKS 182 G P +A + ++R G ER++R A + A + +T++ K Sbjct: 174 VNKLIDLLTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKG 233 Query: 183 NAQRHAMVMWDEIAVQIS-KEF-----PDVKWDK--------------ELVDAATARMVN 222 N + + + ++ +EF D W + + DA +++ Sbjct: 234 NIMKFTEGAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLM 293 Query: 223 RPATLDTIVATNLHADILSDLAAALAGSLGIAPTGNIDPERRYPSMFEPIHGSAFDIMGK 282 RPA I NL+ D +SD AA G +GIAP N+ ++FE HG+A GK Sbjct: 294 RPAEYSVIATLNLNGDYISDAVAAQVGGIGIAPGANMSDSV---AVFEATHGTAPKYAGK 350 Query: 283 GLANPVGTFWSVVMMLEHLGEHEAANQVMDAVE 315 NP + S MML H+G EAA+ ++ A++ Sbjct: 351 DYVNPGSSILSAEMMLRHMGWIEAADLIISAMQ 383 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 0.320 0.133 0.402 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: 1,064,259 Number of extensions: 43465 Number of successful extensions: 125 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 116 Number of HSP's successfully gapped: 3 Length of query: 355 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 269 Effective length of database: 1,212,660 Effective search space: 326205540 Effective search space used: 326205540 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: 131 (55.1 bits)