Align isocitrate-homoisocitrate dehydrogenase (EC 1.1.1.286) (characterized)
to candidate WP_011613717.1 TERY_RS21265 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5JFV8 (347 letters) >NCBI__GCF_000014265.1:WP_011613717.1 Length = 360 Score = 172 bits (435), Expect = 2e-47 Identities = 125/312 (40%), Positives = 174/312 (55%), Gaps = 44/312 (14%) Query: 3 RVAVIPGDGIGPEVIDGAVRVLKAVTGR--VRFEYYE---GGVDVFQECGSPIREEDLEE 57 R+ ++PGDGIGPE++ AV VLK V + + FE+ E GGV + G P+ +E LE Sbjct: 5 RITLLPGDGIGPEIMAVAVDVLKVVGKQFNLEFEFQEAPIGGVAI-DATGEPLPKETLEM 63 Query: 58 IRRSDAVLFGATTTPFDLPGYR-----------SLILTLRKELGLYANLR---IIPDLRT 103 R S+AVL A + GY+ + +L LR LGL+ANLR I P L Sbjct: 64 CRNSNAVLLAA------IGGYKWDNLPRHQRPETGLLGLRAGLGLFANLRPAKIFPQLID 117 Query: 104 ----------GREIVIVRENSEGLYFGIGAVV------NGRAVDVRLITREGAERIARFA 147 G +I++VRE + G+YFG V R V+ + +RIA+ Sbjct: 118 ASTLKREIVEGVDIMVVRELTGGVYFGTPKGVFETETKEKRGVNTMAYSESEIDRIAKVG 177 Query: 148 VEQAKARGSFITFVHKANVLTGDKFFRRIVREVAGE-EGVEVRDAIIDSFTIKLVRNPWE 206 E A+ RG + V KANVL +F+R + VA E + VE+ +D+ ++LVR P + Sbjct: 178 FETAQKRGGKLCSVDKANVLEVSQFWRDRINLVAQEYQDVELSHLYVDNAAMQLVRFPKQ 237 Query: 207 HGVILSENLFGDILSDLATVHAGSIGIVPSGNYG-DGIALFEPVHGSAPDIAGKGIANPI 265 I++ NLFGDILSD A + GSIG++PS + G G +FEPVHGSAPDIAG+ ANP+ Sbjct: 238 FDTIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPL 297 Query: 266 GAILSGAMLLDY 277 +LS AM+L Y Sbjct: 298 AQVLSVAMMLRY 309 Lambda K H 0.321 0.143 0.411 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: 300 Number of extensions: 19 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: 347 Length of database: 360 Length adjustment: 29 Effective length of query: 318 Effective length of database: 331 Effective search space: 105258 Effective search space used: 105258 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. 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