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= 0002.0617.p (363 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba... 600 e-173 gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp... 99 7e-22 gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 85 1e-17 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 600 bits (1547), Expect = e-173, Method: Compositional matrix adjust. Identities = 279/338 (82%), Positives = 315/338 (93%) Query: 26 GADVWLPEETVAAVKEFVVSIKGPLTTPVGGGIRSLNVSLRQQLDLYVCLRPVRYFKAVP 85 G DVWLPEET+A +K+++V+IKGPL+TPVGGGIRSLNV++RQQLDLYVCLRPVRYFK VP Sbjct: 81 GPDVWLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKGVP 140 Query: 86 SPLREPEKTNMVIFRENSEDIYAGIEWQAGTDGAKKLIDFLVKEMGVKKLRFPETSSLGI 145 SPLREPEKT+MVIFRENSEDIYAGIEW AGT KLID L +EMGVKKLRFPE+S+LGI Sbjct: 141 SPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGI 200 Query: 146 KPVSQEGTERLVRKAIQYAIDHDKPSVTIVHKGNIMKFTEGSFRDWAYALAQKEFGGVVI 205 KPVS+EGTERLVR+AIQYAIDHDKPSVT+VHKGNIMKFTEG+FRDW YALA +EFG +I Sbjct: 201 KPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELI 260 Query: 206 DDGPWVRIKNPKTGRDIIVKDVIADAFMQQILLRPAEYSVIATLNLNGDYISDALAAQVG 265 DDGPW+R+KNPKTGR II+KD I DAF QQ+L+RPAEYSVIATLNLNGDYISDA+AAQVG Sbjct: 261 DDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVG 320 Query: 266 GIGIAPGANMSDSVAMFEATHGTSPRYAGKDYVNPGSLILSAEMMLRHIGWTEAAALIIE 325 GIGIAPGANMSDSVA+FEATHGT+P+YAGKDYVNPGS ILSAEMMLRH+GW EAA LII Sbjct: 321 GIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMGWIEAADLIIS 380 Query: 326 AMQKTISSKKVTYDFARLMEGATQVSCSGFGDAVIENL 363 AMQK++SSK+VTYDFARL+EGATQVSCSGFG+ +IEN+ Sbjct: 381 AMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 98.6 bits (244), Expect = 7e-22, Method: Compositional matrix adjust. Identities = 86/324 (26%), Positives = 141/324 (43%), Gaps = 53/324 (16%) Query: 31 LPEETVAAVKEFVVSIKG----PLTTPVGGGIRSLNVSLRQQLDLYVCLRPVRYFKAVPS 86 +P++ +K F G P T P + + R+ DLYV LRPVR VP Sbjct: 58 MPDDWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPC 117 Query: 87 PL--REPEKTNMVIFRENSEDIYAGIEWQAGTDGAKKLIDFLVKEMGVKKLRFPETSSLG 144 PL R+P + + REN+E Y+ I ++ + +E +++ F Sbjct: 118 PLANRKPGDIDFYVVRENTEGEYSSI--------GGRMYEGTERETVIQESVF------- 162 Query: 145 IKPVSQEGTERLVRKAIQYAIDHDKPSVTIVHKGNIMKFTEGSFRDWAYALAQKEFGGVV 204 S++GT+R+++ A A K +T K N + T + + A+ K Sbjct: 163 ----SRKGTDRILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGAKY----- 213 Query: 205 IDDGPWVRIKNPKTGRDIIVKDVIADAFMQQILLRPAEYSVIATLNLNGDYISDALAAQV 264 P RD D++ F +L P + V+ NL GD +SD A Sbjct: 214 -----------PDVRRDKYHIDILTAHF----VLNPDRFDVVVASNLFGDILSDLGPACA 258 Query: 265 GGIGIAPGANMSDSV---AMFEATHGTSPRYAGKDYVNPGSLILSAEMMLRHIG-----W 316 G IGIAP AN++ + ++FE HG++P GK+ NP ++I S MML +G + Sbjct: 259 GTIGIAPSANINPTRELPSLFEPVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKY 318 Query: 317 TEAAALIIEAMQKTISSKKVTYDF 340 +A ++ A++ + + T D Sbjct: 319 RQAHDAMLAAIETVLVNGPTTPDL 342 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 84.7 bits (208), Expect = 1e-17, Method: Compositional matrix adjust. Identities = 85/309 (27%), Positives = 139/309 (44%), Gaps = 48/309 (15%) Query: 63 VSLRQQLDLYVCLRP-VRYFKAVPSPLREPE---KTNMVIFRENSEDIYAGIE--WQAGT 116 + LR+ L L+ RP + Y + + +PE +++I RE + DIY G + Sbjct: 87 LGLRKHLQLFANFRPAICYPELTGASSLKPELVANLDILIVRELNGDIYFGQPRGMREAP 146 Query: 117 DGAKKLIDFLVKEMGVKKLRFPETSSLGIKPVSQEGTERLVRKAIQYAIDHDKPSVTIVH 176 DG F G +R+ E R+ A Q A K + V Sbjct: 147 DGP-----FKGAREGFDTMRYSEPE-----------IRRIAHVAFQAAAKRGK-RLCSVD 189 Query: 177 KGNIMKFTEGSFRDWAYALAQKEFGGVVIDDGPWVRIKNPKTGRDIIVKDVIADAFMQQI 236 K N+++ +F+ W +V + G K D+ + + D Q+ Sbjct: 190 KANVLE----TFQFWK---------DIVTEVG--------KEYPDVELSHMYVDNAAMQL 228 Query: 237 LLRPAEYSVIATLNLNGDYISDALAAQVGGIGIAPGANM-SDSVAMFEATHGTSPRYAGK 295 + P + VI T N+ GD +SDA A G IG+ P A++ +++ ++E +HG++P AG+ Sbjct: 229 VKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGR 288 Query: 296 DYVNPGSLILSAEMMLR-HIGWTEAAALIIEAMQKTISSKKVTYDFARLMEGATQVSCSG 354 NP + ILSA MMLR + E A I A++K ++ T D EG T+V+ Sbjct: 289 GIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYE--EGCTKVNTQQ 346 Query: 355 FGDAVIENL 363 G+AV++ L Sbjct: 347 MGEAVVKAL 355 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 0.317 0.135 0.396 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: 1,172,537 Number of extensions: 49911 Number of successful extensions: 139 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 136 Number of HSP's successfully gapped: 3 Length of query: 363 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 277 Effective length of database: 1,212,660 Effective search space: 335906820 Effective search space used: 335906820 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)