Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate CA265_RS15850 CA265_RS15850 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Pedo557:CA265_RS15850 Length = 363 Score = 197 bits (500), Expect = 4e-55 Identities = 132/340 (38%), Positives = 188/340 (55%), Gaps = 24/340 (7%) Query: 1 MAYRICLIEGDGIGHEVIP----AARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETV 56 M I +I GDGIG EV A ++ E G F EA G E G +P+ET+ Sbjct: 1 MKKNILVIPGDGIGPEVTTWGKAALEKIAEIFGHEFAFEEALMGHAAIEVTGEPLPDETL 60 Query: 57 EKILSCHATLFGAA------TSPTRKVPGFFGAIRYLRRRLDLYANVRPA--------KS 102 EK A LFGA P+ KV G ++ +R+ L L+AN+RP S Sbjct: 61 EKARQSDAILFGAIGHAKYDNDPSLKVRPEQGLLK-IRKELGLFANLRPILLFDELLQAS 119 Query: 103 RPVPGSRPGVDLVIVRENTEGLYVEQERRYLDVAIAD--AVISKKASERIGRAALRIAEG 160 P G D++ RE T +Y ++ R D A + + ERI A + A+ Sbjct: 120 SIKPEILRGTDILFFRELTGDVYFGEKTRSEDRNTASDLMIYHRYEVERIAHKAYQAAQQ 179 Query: 161 RPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVI 220 R K L KANVL ++ L+ +TV+E+AK +P V + + +DN AMQL+ P++FDV+ Sbjct: 180 R-NKRLCSVDKANVLESSR-LWRETVQEIAKQYPDVETEHMFIDNAAMQLIKNPKKFDVV 237 Query: 221 VTTNLLGDILSDLAAGLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILS 280 +T NL GDIL+D A+ + G +G+ S ++G++T FEP+HGSA DIAGK +ANP A+ILS Sbjct: 238 LTANLFGDILTDEASQIAGSMGMLASASVGESTGFFEPIHGSAHDIAGKDLANPLASILS 297 Query: 281 AAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDAT 319 AA+ML+ G KE AK + +D VL+ G RT D+ +T Sbjct: 298 AALMLEIGFGLKEEAKLLVDTIDQVLKEGFRTHDIADQST 337 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: 272 Number of extensions: 12 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: 363 Length adjustment: 29 Effective length of query: 305 Effective length of database: 334 Effective search space: 101870 Effective search space used: 101870 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 Sep 17 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