Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate 14732 b0596 2,3-dihydroxybenzoate-2,3-dehydrogenase (NCBI)
Query= uniprot:D8IS13 (254 letters) >FitnessBrowser__Keio:14732 Length = 248 Score = 104 bits (260), Expect = 1e-27 Identities = 77/252 (30%), Positives = 123/252 (48%), Gaps = 21/252 (8%) Query: 9 AGKTVLITAAAQGIGRASTELFAREGARVIATDISKPHLDELAGIAGVETHLLDVTDDAA 68 +GK V +T A +GIG A+ F GA+V T + E A T ++DV D A Sbjct: 4 SGKNVWVTGAGKGIGYATALAFVEAGAKV--TGFDQAFTQEQYPFA---TEVMDVADAAQ 58 Query: 69 I----KALVAKIGTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGM 124 + + L+A+ +D L N AG + G + + W +F +N F+ + + Sbjct: 59 VAQVCQRLLAETERLDALVNAAGILRMGATDQLSKEDWQQTFAVNVGGAFNLFQQTMNQF 118 Query: 125 LAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIRCNAICPGTI 184 ++ G+IV +AS A+ + AYGASKAA+ L SV + G+RCN + PG+ Sbjct: 119 RRQRGGAIVTVASDAAHTPRIGMS-AYGASKAALKSLALSVGLELAGSGVRCNVVSPGST 177 Query: 185 ESPSLNQRISTQAKETGKSEEEVRAAFVGRQ-----PMGRIGKAEEVAALALYLASDESN 239 ++ QR + + EE R G Q P+G+I + +E+A L+LASD ++ Sbjct: 178 DTDM--QRTLWVSDDA----EEQRIRGFGEQFKLGIPLGKIARPQEIANTILFLASDLAS 231 Query: 240 FTTGSIHMIDGG 251 T ++DGG Sbjct: 232 HITLQDIVVDGG 243 Lambda K H 0.317 0.130 0.365 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: 133 Number of extensions: 8 Number of successful extensions: 3 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: 254 Length of database: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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