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= 0001.3257.p (356 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 725 0.0 gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp... 166 4e-42 gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba... 86 6e-18 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 725 bits (1871), Expect = 0.0, Method: Compositional matrix adjust. Identities = 353/356 (99%), Positives = 356/356 (100%) Query: 1 MKIAILPGDGIGPEIVDEAVRVLNALDEKFEMETAPVGGAGYEAHGHPLPDGTLKLAKEA 60 MKIAILPGDGIGPEIV+EAVRVLNALDEKFEMETAPVGGAGYEAHGHPLPDGTLKLAKEA Sbjct: 1 MKIAILPGDGIGPEIVNEAVRVLNALDEKFEMETAPVGGAGYEAHGHPLPDGTLKLAKEA 60 Query: 61 DAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPELVA 120 DAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPELVA Sbjct: 61 DAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASSLKPELVA 120 Query: 121 NLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAK 180 NLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAK Sbjct: 121 NLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAK 180 Query: 181 RGKRLCSVDKANVLETFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDVIVT 240 RGKRLCSVDKANVLETFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDVIVT Sbjct: 181 RGKRLCSVDKANVLETFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDVIVT 240 Query: 241 GNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGIANPLATILSA 300 GNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAG+GIANPLATILSA Sbjct: 241 GNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATILSA 300 Query: 301 AMMLRFSLNRAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKALA 356 AMMLRFSLN+AEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKALA Sbjct: 301 AMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKALA 356 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 166 bits (419), Expect = 4e-42, Method: Compositional matrix adjust. Identities = 131/381 (34%), Positives = 188/381 (49%), Gaps = 54/381 (14%) Query: 2 KIAILPGDGIGPEIVDEAVRVLNALDEKF--EMETAPVGGAG---YEAHGHPLPDGTLKL 56 +IA++ GDGIG E++ E +R + A +KF ++E A Y HG +PD + Sbjct: 6 RIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAEHGKMMPDDWFEQ 65 Query: 57 AKEADAILFGAVGDWKYDKLERALRPEQ-----AILGLRKHLQLFANFRPAICYPEL-TG 110 K +AI FGAVG W A P+ ++L R+ L+ N RP P + Sbjct: 66 LKGFEAIYFGAVG-WP------ATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCP 118 Query: 111 ASSLKPELVANLDILIVRE--------LNGDIYFGQPRGMREAPDGPFKGAREGFDTMRY 162 ++ KP ++D +VRE + G +Y G R E +R+G D Sbjct: 119 LANRKP---GDIDFYVVRENTEGEYSSIGGRMYEGTER---ETVIQESVFSRKGTD---- 168 Query: 163 SEPEIRRIAHVAFQAAAKRGKR-LCSVDKAN-VLETFQFWKDIVTEVGKEYPDVELSHMY 220 RI AF A R K+ L S K+N + T +W + V +G +YPDV + Sbjct: 169 ------RILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYH 222 Query: 221 VDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNK--GLYEPS 278 +D V P FDV+V N+FGDILSD G+IG+ PSA+++ + L+EP Sbjct: 223 IDILTAHFVLNPDRFDVVVASNLFGDILSDLGPACAGTIGIAPSANINPTRELPSLFEPV 282 Query: 279 HGSAPDIAGKGIANPLATILSAAMMLRF---SLNRAEQA-DRIENAVKKVLAQGLRTADI 334 HGSAPDI GK IANP+A I S AMML F + QA D + A++ VL G T D+ Sbjct: 283 HGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDL 342 Query: 335 YEEGCTKVNTQQMGEAVVKAL 355 K NT ++G+A+ A+ Sbjct: 343 ----GGKSNTAEVGQAIAAAI 359 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 85.5 bits (210), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 109/401 (27%), Positives = 175/401 (43%), Gaps = 61/401 (15%) Query: 3 IAILPGDGIGPEIVDEAVRVLNALDEK--------FEMETAPVGGAGYEAHGHP--LPDG 52 I + GDG+G ++ ++V+NA EK ME G +G LP+ Sbjct: 31 IPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIHWMEIY-AGEKATRLYGPDVWLPEE 89 Query: 53 TLKLAKEADAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGAS 112 TL + K+ + G + + R+L + +R+ L L+ RP + Y + + Sbjct: 90 TLAVLKKYLVAIKGPLSTPVGGGI-RSLN-----VAMRQQLDLYVCLRP-VRYFKGVPSP 142 Query: 113 SLKPELVANLDILIVRELNGDIYFG--QPRGMREAPDGPFKGARE-GFDTMRYSEPE--- 166 +PE D++I RE + DIY G G E RE G +R+ E Sbjct: 143 LREPE---KTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALG 199 Query: 167 --------IRRIAHVAFQAAAKRGK-RLCSVDKANVLE----TFQFWKDIVT--EVGKEY 211 R+ A Q A K + V K N+++ F+ W + E G E Sbjct: 200 IKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAEL 259 Query: 212 PD---------------VELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLT 256 D + + D Q++ P + VI T N+ GD +SDA A Sbjct: 260 IDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQV 319 Query: 257 GSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGIANPLATILSAAMMLRFSLNRAEQADR 316 G IG+ P A++ +++ ++E +HG+AP AGK NP ++ILSA MMLR + E AD Sbjct: 320 GGIGIAPGANM-SDSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLR-HMGWIEAADL 377 Query: 317 IENAVKKVLAQGLRTADIYE--EGCTKVNTQQMGEAVVKAL 355 I +A++K ++ T D EG T+V+ GE +++ + Sbjct: 378 IISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 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 0.136 0.393 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: 1,159,580 Number of extensions: 51033 Number of successful extensions: 159 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 155 Number of HSP's successfully gapped: 3 Length of query: 356 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 270 Effective length of database: 1,212,660 Effective search space: 327418200 Effective search space used: 327418200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 131 (55.1 bits)