Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate WP_017598162.1 D471_RS0108155 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >NCBI__GCF_000341125.1:WP_017598162.1 Length = 354 Score = 209 bits (533), Expect = 6e-59 Identities = 134/318 (42%), Positives = 186/318 (58%), Gaps = 23/318 (7%) Query: 5 ICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETVEKIL 60 + +I GDGIG EV+ +VLEA L +E E E G + + R G ++P+ +++ Sbjct: 8 LAVIPGDGIGPEVVGEGLKVLEAVAPQHDLAIEATEYELGAKLWHRTGETLPDSVEDELR 67 Query: 61 SCHATLFGAATSPTRKVPGFF---GAIRYLRRRLDLYANVRPAK-----SRPVPGSRP-G 111 A L GA P+ VP G + LR D Y N+RP + P+ G P Sbjct: 68 EHEAILLGAVGDPS--VPSGVLERGLLLRLRFDFDHYVNLRPVRLFPGVDSPLAGVSPED 125 Query: 112 VDLVIVRENTEGLY-----VEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPRKTL 166 +D+++VRE TEG Y V ++ ++A D+V ++ ER+ R A A RPRK L Sbjct: 126 IDMLVVREGTEGPYAGAGGVLRKGTPHEIATQDSVNTRFGVERVVRYAFAKAAVRPRKKL 185 Query: 167 HIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLL 226 + HK NVL L+ V+EV ++P V+V VD AM V +P RFDV+VT NL Sbjct: 186 TLVHKDNVLTFAGDLWQRVVREVGAEYPQVSVDYCHVDAAAMFFVNQPARFDVVVTDNLF 245 Query: 227 GDILSDLAAGLVGGLGLAPSGNIG-DTT--AVFEPVHGSAPDIAGKGIANPTAAILSAAM 283 GDI++D+ A + GG+GLA SGN+ D T ++FEPVHGSAPDIAG+G A+PTA +LS A Sbjct: 246 GDIITDIGAAVTGGIGLAASGNVNPDNTFPSMFEPVHGSAPDIAGQGKADPTATVLSVAT 305 Query: 284 MLDYLGEKEAAKRVEKAV 301 MLD+LG EAA+R+E AV Sbjct: 306 MLDHLGVPEAARRIEGAV 323 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: 327 Number of extensions: 16 Number of successful extensions: 4 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: 354 Length adjustment: 29 Effective length of query: 305 Effective length of database: 325 Effective search space: 99125 Effective search space used: 99125 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 Apr 09 2024. The underlying query database was built on Sep 17 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