Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 8501058 DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Miya:8501058 Length = 358 Score = 195 bits (495), Expect = 2e-54 Identities = 135/349 (38%), Positives = 189/349 (54%), Gaps = 35/349 (10%) Query: 1 MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56 M +ICL+ GDGIG E++ A +VL+ G + + A G + G +P+ETV Sbjct: 1 MDMKICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETV 60 Query: 57 EKILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPG- 107 + A L GA P R G G +R+ L L+AN+RPA P Sbjct: 61 AACKAADAVLLGAVGGPKWDTLPTAIRPEKGLLG----IRKALGLFANLRPATLLPELAG 116 Query: 108 --------SRPGVDLVIVRENTEGLYV------EQERRYLDVAIADAVISKKASERIGRA 153 + G+D+++VRE T G+Y E+ R L + + +++ RI R Sbjct: 117 ACLLRADIAAQGLDVMVVRELTGGVYFGEPVCEEELRDGLRTSYNTMIYNEEEVRRIARV 176 Query: 154 ALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMR 213 A A R RK + KANVL +++ L+ V EVA+++P V + + VDN AMQLV Sbjct: 177 AFEAARKRSRKVCSV-DKANVLAVSR-LWRAVVIEVAREYPDVELTHMYVDNAAMQLVRW 234 Query: 214 PERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDT-TAVFEPVHGSAPDIAGKGIA 272 P +FDVIVT NL GDILSD AA + G +G+ PS ++G + +FEP+HGSAPDIAG+ A Sbjct: 235 PAQFDVIVTENLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKA 294 Query: 273 NPTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATT 320 NP A ILS AMML Y G ++ A +E+AV VL G RT D+ + T Sbjct: 295 NPVATILSVAMMLRYTFGLEKEAVAIEQAVSGVLREGYRTGDIMEEGKT 343 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: 317 Number of extensions: 19 Number of successful extensions: 5 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: 358 Length adjustment: 29 Effective length of query: 305 Effective length of database: 329 Effective search space: 100345 Effective search space used: 100345 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