Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate H281DRAFT_01534 H281DRAFT_01534 tartrate dehydrogenase/decarboxylase / D-malate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Burk376:H281DRAFT_01534 Length = 364 Score = 204 bits (520), Expect = 2e-57 Identities = 135/346 (39%), Positives = 190/346 (54%), Gaps = 21/346 (6%) Query: 3 YRICLIEGDGIGHEVIPAARRVLEATG-----LPLEFVEAEAGWETFERRGTSVPEETVE 57 YRI I GDGIG EV+PA +VLEA EF + G + + + G +P + ++ Sbjct: 4 YRIATIPGDGIGKEVVPAGAQVLEALARTTKSFAFEFENFDWGGDYYRKHGVMMPADGLD 63 Query: 58 KILSCHATLFGAATSPTRKVPGFFGAIRY-LRRRLDLYANVRPAK-----SRPVPGSRP- 110 I A LFG+A P +R + + D YANVRP + P+ +P Sbjct: 64 AIRGKDAILFGSAGDPDIADHITLWGLRLKICQGFDQYANVRPTRILPGIDAPLKRCKPE 123 Query: 111 GVDLVIVRENTEGLYVEQERRY-----LDVAIADAVISKKASERIGRAALRIAEGRPRKT 165 ++ VIVREN+EG Y R ++ A +++++ ERI R A R+A+ RPRK Sbjct: 124 DLNWVIVRENSEGEYSGVGGRVHQGHPIEAATDVSIMTRAGVERIMRFAFRLAQSRPRKL 183 Query: 166 LHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNL 225 L + K+N ++ + +V+K+FP V +VD +++ RP D IV TNL Sbjct: 184 LTVITKSNAQRHAMVMWDEIALQVSKEFPDVTWDKELVDASTARMINRPASLDTIVATNL 243 Query: 226 LGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILSAA 282 DILSDLAA L G LG+AP+GNI ++FEP+HGSA DI GKG+ANP S Sbjct: 244 HADILSDLAAALAGSLGIAPTGNIDPERRFPSMFEPIHGSAFDIMGKGLANPVGTFWSVV 303 Query: 283 MMLDYLGEKEAAKRVEKAVDLV-LERGPRTPDLGGDATTEAFTEAV 327 M+L++LGE +AA RV +AV+ V ++ T DLGG ATT T AV Sbjct: 304 MLLEHLGELDAANRVMQAVEAVTADKSLHTGDLGGTATTAQVTAAV 349 Lambda K H 0.319 0.137 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 308 Number of extensions: 20 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 334 Length of database: 364 Length adjustment: 29 Effective length of query: 305 Effective length of database: 335 Effective search space: 102175 Effective search space used: 102175 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory