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= 0001.1208.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... 819 0.0 gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp... 118 9e-28 gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase... 84 2e-17 >gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 418 Score = 819 bits (2116), Expect = 0.0, Method: Compositional matrix adjust. Identities = 394/418 (94%), Positives = 408/418 (97%) Query: 1 MSYQHIQVPAEGHKITANADDTLNVPNNPIIPFIMGDGVGVDVTPVMLKVVDAAVAKAYG 60 MSYQHIQVPAEG KITANADDTLNVPNNPIIP+I+GDGVGVDVTPVMLKVV+AAV KAYG Sbjct: 1 MSYQHIQVPAEGRKITANADDTLNVPNNPIIPYIVGDGVGVDVTPVMLKVVNAAVEKAYG 60 Query: 61 GARKIHWMEIYAGEKATKLYGQDVWLPDETLEVLKQYLVSIKGPLSTPVGGGIRSLNVTM 120 GARKIHWMEIYAGEKAT+LYG DVWLP+ETL VLK+YLV+IKGPLSTPVGGGIRSLNV M Sbjct: 61 GARKIHWMEIYAGEKATRLYGPDVWLPEETLAVLKKYLVAIKGPLSTPVGGGIRSLNVAM 120 Query: 121 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWQAGTPEVKKLIEL 180 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEW AGTPEV KLI+L Sbjct: 121 RQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVIFRENSEDIYAGIEWAAGTPEVNKLIDL 180 Query: 181 LTREMGVKKLRFPETSALGIKPVSREGTERLVRKAIQYAIDHDKPSVTLVHKGNIMKYTE 240 LTREMGVKKLRFPE+SALGIKPVSREGTERLVR+AIQYAIDHDKPSVTLVHKGNIMK+TE Sbjct: 181 LTREMGVKKLRFPESSALGIKPVSREGTERLVRQAIQYAIDHDKPSVTLVHKGNIMKFTE 240 Query: 241 GAFRDWGYALAGREFGAELIDDGPWMRLKNPKTGRQIIIKDAITDAFFQQVLMRPAEYSV 300 GAFRDWGYALA REFGAELIDDGPWMRLKNPKTGR IIIKDAITDAFFQQVLMRPAEYSV Sbjct: 241 GAFRDWGYALAAREFGAELIDDGPWMRLKNPKTGRAIIIKDAITDAFFQQVLMRPAEYSV 300 Query: 301 IATMNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSIIL 360 IAT+NLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGS IL Sbjct: 301 IATLNLNGDYISDAVAAQVGGIGIAPGANMSDSVAVFEATHGTAPKYAGKDYVNPGSSIL 360 Query: 361 SAEMMLRHMGWIEAADLIITAMQKSVSAKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 SAEMMLRHMGWIEAADLII+AMQKSVS+KRVTYDFARLLEGATQVSCSGFGEVMIENM Sbjct: 361 SAEMMLRHMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 >gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbaspirillum seropedicae SmR1] Length = 359 Score = 118 bits (295), Expect = 9e-28, Method: Compositional matrix adjust. Identities = 108/370 (29%), Positives = 164/370 (44%), Gaps = 63/370 (17%) Query: 31 IPFIMGDGVGVDVTPVMLKVVDAAVAKAYG---GARKIHWMEIYAGEKATKLYGQDVWLP 87 I I GDG+G +V P L+ V AA +K +G W + K+ +P Sbjct: 7 IAVIAGDGIGQEVMPEGLRAVQAA-SKKFGIDIEFTHFDWAHCNYYAEHGKM------MP 59 Query: 88 DETLEVLKQ----YLVSIKGPLSTPVGGGIRSLNVTMRQQLDLYVCLRPVRYFKGVPSPL 143 D+ E LK Y ++ P + P + + R+ DLYV LRPVR GVP PL Sbjct: 60 DDWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPL 119 Query: 144 --REPEKTDMVIFRENSEDIYAGIEWQAGTPEVKKLIELLTREMGVKKLRFPETSALGIK 201 R+P D + REN+E Y+ I ++ E RE +++ F Sbjct: 120 ANRKPGDIDFYVVRENTEGEYSSIG--------GRMYEGTERETVIQESVF--------- 162 Query: 202 PVSREGTERLVRKAIQYAIDHDKPSVTLVHKGNIMKYTEGAFRDWGYALAGREFGAELID 261 SR+GT+R+++ A A K +T K N + T + E ++ Sbjct: 163 --SRKGTDRILKFAFDLAQSRPKKHLTSATKSNGIAIT-------------MPYWDERVE 207 Query: 262 DGPWMRLKNPKTGRQIIIKDAITDAFFQQVLMRPAEYSVIATMNLNGDYISDAVAAQVGG 321 M K P R D +T F ++ P + V+ NL GD +SD A G Sbjct: 208 A---MGAKYPDVRRDKYHIDILTAHF----VLNPDRFDVVVASNLFGDILSDLGPACAGT 260 Query: 322 IGIAPGANMSDS---VAVFEATHGTAPKYAGKDYVNPGSIILSAEMMLRHMG-----WIE 373 IGIAP AN++ + ++FE HG+AP GK+ NP ++I S MML +G + + Sbjct: 261 IGIAPSANINPTRELPSLFEPVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQ 320 Query: 374 AADLIITAMQ 383 A D ++ A++ Sbjct: 321 AHDAMLAAIE 330 >gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase oxidoreductase [Herbaspirillum seropedicae SmR1] Length = 356 Score = 84.3 bits (207), Expect = 2e-17, Method: Compositional matrix adjust. Identities = 105/400 (26%), Positives = 172/400 (43%), Gaps = 59/400 (14%) Query: 31 IPFIMGDGVGVDVTPVMLKVVDAAVAKAYGGARKIHWMEIYAGEKATKLYGQDVWLPDET 90 I + GDG+G ++ ++V++A K G + +G LPD T Sbjct: 3 IAILPGDGIGPEIVNEAVRVLNAL-------DEKFEMETAPVGGAGYEAHGHP--LPDGT 53 Query: 91 LEVLKQYLVSIKGPLSTPVGGGI-RSLN-----VTMRQQLDLYVCLRP-VRYFKGVPSPL 143 L++ K+ + G + + R+L + +R+ L L+ RP + Y + + Sbjct: 54 LKLAKEADAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYPELTGASS 113 Query: 144 REPE---KTDMVIFRENSEDIYAGIEWQAGTPEVKKLIELLTREMGVKKLRFPETSALGI 200 +PE D++I RE + DIY G G E RE G +R+ E Sbjct: 114 LKPELVANLDILIVRELNGDIYFG--QPRGMREAPDGPFKGARE-GFDTMRYSEPE---- 166 Query: 201 KPVSREGTERLVRKAIQYAIDHDKPSVTLVHKGNIMKYTEGAFRDWGYALAGREFGAELI 260 R+ A Q A K + V K N+++ F+ W + E G E Sbjct: 167 -------IRRIAHVAFQAAAKRGK-RLCSVDKANVLE----TFQFWKDIVT--EVGKEYP 212 Query: 261 DDGPWMRLKNPKTGRQIIIKDAITDAFFQQVLMRPAEYSVIATMNLNGDYISDAVAAQVG 320 D + + D Q++ P + VI T N+ GD +SDA A G Sbjct: 213 D---------------VELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTG 257 Query: 321 GIGIAPGANM-SDSVAVFEATHGTAPKYAGKDYVNPGSIILSAEMMLR-HMGWIEAADLI 378 IG+ P A++ +++ ++E +HG+AP AG+ NP + ILSA MMLR + E AD I Sbjct: 258 SIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADRI 317 Query: 379 ITAMQKSVSAKRVTYDFARLLEGATQVSCSGFGEVMIENM 418 A++K ++ T D EG T+V+ GE +++ + Sbjct: 318 ENAVKKVLAQGLRTADIYE--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 0.319 0.136 0.401 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: 1,279,001 Number of extensions: 52752 Number of successful extensions: 144 Number of sequences better than 1.0e-08: 3 Number of HSP's gapped: 140 Number of HSP's successfully gapped: 3 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 132 (55.5 bits)