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= 0007.0042.p (418 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... 857 0.0 gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp... 120 3e-28 gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 86 5e-18 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 857 bits (2215), Expect = 0.0, Method: Compositional matrix adjust. Identities = 417/418 (99%), Positives = 418/418 (100%) Query: 1 MSYQHIQVPAEGRKITANADDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYG 60 MSYQHIQVPAEGRKITANADDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYG Sbjct: 1 MSYQHIQVPAEGRKITANADDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYG 60 Query: 61 GARKIHWMEIYAGEKATRLYGPDVWLPEETLAVLKEYLVAIKGPLSTPVGGGIRSLNVAM 120 GARKIHWMEIYAGEKATRLYGPDVWLPEETLAVLK+YLVAIKGPLSTPVGGGIRSLNVAM Sbjct: 61 GARKIHWMEIYAGEKATRLYGPDVWLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAM 120 Query: 121 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDL 180 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDL Sbjct: 121 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDL 180 Query: 181 LTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTE 240 LTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTE Sbjct: 181 LTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTE 240 Query: 241 GAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSV 300 GAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSV Sbjct: 241 GAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSV 300 Query: 301 IATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSIL 360 IATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSIL Sbjct: 301 IATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSIL 360 Query: 361 SAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 SAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM Sbjct: 361 SAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 120 bits (300), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 110/378 (29%), Positives = 165/378 (43%), Gaps = 55/378 (14%) Query: 31 IPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIH--WMEI-YAGEKATRLYGPDVWLP 87 I I GDG+G +V P L+ V AA +K H W Y E + PD W Sbjct: 7 IAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAEHGKMM--PDDWF- 63 Query: 88 EETLAVLKEYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKGVPSPL--RE 145 E+ Y A+ P + P + + R+ DLYV LRPVR GVP PL R+ Sbjct: 64 EQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLANRK 123 Query: 146 PEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGIKPVSR 205 P D + REN+E Y+ I ++ + RE +++ F SR Sbjct: 124 PGDIDFYVVRENTEGEYSSIG--------GRMYEGTERETVIQESVF-----------SR 164 Query: 206 EGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGPW 265 +GT+R+++ A A K +T K N + T + + A+ A Sbjct: 165 KGTDRILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGA------------- 211 Query: 266 MRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIA 325 K P R D +T F ++ P + V+ NL GD +SD A G IGIA Sbjct: 212 ---KYPDVRRDKYHIDILTAHF----VLNPDRFDVVVASNLFGDILSDLGPACAGTIGIA 264 Query: 326 PGANMSDSV---AVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMG-----WIEAADL 377 P AN++ + ++FE HG+AP GK+ NP + I S MML +G + +A D Sbjct: 265 PSANINPTRELPSLFEPVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDA 324 Query: 378 IISAMQKSVSSKRVTYDF 395 +++A++ + + T D Sbjct: 325 MLAAIETVLVNGPTTPDL 342 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 85.9 bits (211), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 109/401 (27%), Positives = 175/401 (43%), Gaps = 61/401 (15%) Query: 31 IPYIVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIHWMEIY-AGEKATRLYGPDVWLPEE 89 I + GDG+G ++ ++V+NA EK ME G +G LP+ Sbjct: 3 IAILPGDGIGPEIVNEAVRVLNALDEK--------FEMETAPVGGAGYEAHGHP--LPDG 52 Query: 90 TLAVLKEYLVAIKGPLSTPVGGGI-RSLN-----VAMRQQLDLYVCLRP-VRYFKGVPSP 142 TL + KE + G + + R+L + +R+ L L+ RP + Y + + Sbjct: 53 TLKLAKEADAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGAS 112 Query: 143 LREPE---KTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALG 199 +PE D++I RE + DIY G G E RE G +R+ E Sbjct: 113 SLKPELVANLDILIVRELNGDIYFG--QPRGMREAPDGPFKGARE-GFDTMRYSEPE--- 166 Query: 200 IKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAEL 259 R+ A Q A K + V K N+++ F+ W + E G E Sbjct: 167 --------IRRIAHVAFQAAAKRGK-RLCSVDKANVLE----TFQFWKDIVT--EVGKEY 211 Query: 260 IDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQV 319 D + + D Q++ P + VI T N+ GD +SDA A Sbjct: 212 PD---------------VELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLT 256 Query: 320 GGIGIAPGANM-SDSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLR-HMGWIEAADL 377 G IG+ P A++ +++ ++E +HG+AP AG+ NP ++ILSA MMLR + E AD Sbjct: 257 GSIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADR 316 Query: 378 IISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 I +A++K ++ T D EG T+V+ GE +++ + Sbjct: 317 IENAVKKVLAQGLRTADIYE--EGCTKVNTQQMGEAVVKAL 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 0.318 0.136 0.399 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: 1,192,752 Number of extensions: 46116 Number of successful extensions: 125 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 121 Number of HSP's successfully gapped: 4 Length of query: 418 Length of database: 1,619,870 Length adjustment: 88 Effective length of query: 330 Effective length of database: 1,203,190 Effective search space: 397052700 Effective search space used: 397052700 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: 132 (55.5 bits)