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= 0029.0006.p (359 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... 743 0.0 gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 166 3e-42 gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba... 120 2e-28 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 743 bits (1919), Expect = 0.0, Method: Compositional matrix adjust. Identities = 357/359 (99%), Positives = 359/359 (100%) Query: 1 MSKTHRIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAQHGKMMPD 60 MSKTHRIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYA+HGKMMPD Sbjct: 1 MSKTHRIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAEHGKMMPD 60 Query: 61 DWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLA 120 DWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLA Sbjct: 61 DWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLA 120 Query: 121 NRKPGDIDFYVVRENTEGEYSSIGGRMYEGTERETVIQESVFSRKGTDRILKFAFDLAQS 180 NRKPGDIDFYVVRENTEGEYSSIGGRMYEGTERETVIQESVFSRKGTDRILKFAFDLAQS Sbjct: 121 NRKPGDIDFYVVRENTEGEYSSIGGRMYEGTERETVIQESVFSRKGTDRILKFAFDLAQS 180 Query: 181 RPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYHIDILTAHFVLNPDRFDVV 240 RPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYHIDILTAHFVLNPDRFDVV Sbjct: 181 RPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYHIDILTAHFVLNPDRFDVV 240 Query: 241 VASNLFGDILSDLGPACAGTIGIAPSANINPSRELPSLFEPVHGSAPDIFGKNIANPVAM 300 VASNLFGDILSDLGPACAGTIGIAPSANINP+RELPSLFEPVHGSAPDIFGKNIANPVAM Sbjct: 241 VASNLFGDILSDLGPACAGTIGIAPSANINPTRELPSLFEPVHGSAPDIFGKNIANPVAM 300 Query: 301 IWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDLGGKSNTAEVGQAIAAAI 359 IWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDLGGKSNTAEVGQAIAAAI Sbjct: 301 IWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDLGGKSNTAEVGQAIAAAI 359 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 166 bits (420), Expect = 3e-42, Method: Compositional matrix adjust. Identities = 131/381 (34%), Positives = 189/381 (49%), Gaps = 54/381 (14%) Query: 6 RIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAQHGKMMPDDWFEQ 65 +IA++ GDGIG E++ E +R + A +KF ++E A Y HG +PD + Sbjct: 2 KIAILPGDGIGPEIVNEAVRVLNALDEKF--EMETAPVGGAG---YEAHGHPLPDGTLKL 56 Query: 66 LKGFEAIYFGAVG-WP------ATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCP 118 K +AI FGAVG W A P+ ++L R+ L+ N RP P + Sbjct: 57 AKEADAILFGAVGDWKYDKLERALRPEQ-----AILGLRKHLQLFANFRPAICYPEL-TG 110 Query: 119 LANRKP---GDIDFYVVRENTEGEYSSIGGRMYEGTER---ETVIQESVFSRKGTD---- 168 ++ KP ++D +VRE + G +Y G R E +R+G D Sbjct: 111 ASSLKPELVANLDILIVRE--------LNGDIYFGQPRGMREAPDGPFKGAREGFDTMRY 162 Query: 169 ------RILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYH 222 RI AF A R K+ L S K+N + T +W + V +G +YPDV + Sbjct: 163 SEPEIRRIAHVAFQAAAKRGKR-LCSVDKAN-VLETFQFWKDIVTEVGKEYPDVELSHMY 220 Query: 223 IDILTAHFVLNPDRFDVVVASNLFGDILSDLGPACAGTIGIAPSANINPSRELPSLFEPV 282 +D V P FDV+V N+FGDILSD G+IG+ PSA+++ + + L+EP Sbjct: 221 VDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNK--GLYEPS 278 Query: 283 HGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDL 342 HGSAPDI G+ IANP+A I S AMML F K QA D + A++ VL G T D+ Sbjct: 279 HGSAPDIAGRGIANPLATILSAAMMLRF---SLNKAEQA-DRIENAVKKVLAQGLRTADI 334 Query: 343 ----GGKSNTAEVGQAIAAAI 359 K NT ++G+A+ A+ Sbjct: 335 YEEGCTKVNTQQMGEAVVKAL 355 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 120 bits (300), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 110/378 (29%), Positives = 165/378 (43%), Gaps = 55/378 (14%) Query: 7 IAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAQHGKMM--PDDWF- 63 I I GDG+G +V P L+ V AA +K H W Y + + PD W Sbjct: 31 IPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIH--WMEI-YAGEKATRLYGPDVWLP 87 Query: 64 EQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLANRK 123 E+ Y A+ P + P + + R+ DLYV LRPVR GVP PL R+ Sbjct: 88 EETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKGVPSPL--RE 145 Query: 124 PGDIDFYVVRENTEGEYSSIG--------GRMYEGTERETVIQESVF-----------SR 164 P D + REN+E Y+ I ++ + RE +++ F SR Sbjct: 146 PEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGIKPVSR 205 Query: 165 KGTDRILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGA------------- 211 +GT+R+++ A A K +T K N + T + + A+ A Sbjct: 206 EGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGPW 265 Query: 212 ---KYPDVRRDKYHIDILTAHF----VLNPDRFDVVVASNLFGDILSDLGPACAGTIGIA 264 K P R D +T F ++ P + V+ NL GD +SD A G IGIA Sbjct: 266 MRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIA 325 Query: 265 PSANINPSRELPSLFEPVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDA 324 P AN++ S ++FE HG+AP GK+ NP + I S MML +G + +A D Sbjct: 326 PGANMSDSV---AVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMG-----WIEAADL 377 Query: 325 MLAAIETVLVNGPTTPDL 342 +++A++ + + T D Sbjct: 378 IISAMQKSVSSKRVTYDF 395 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 0.138 0.425 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: 1,225,783 Number of extensions: 54955 Number of successful extensions: 140 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 133 Number of HSP's successfully gapped: 4 Length of query: 359 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 273 Effective length of database: 1,212,660 Effective search space: 331056180 Effective search space used: 331056180 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)