Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= uniprot:D8IS13 (254 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 132 bits (333), Expect = 5e-36 Identities = 86/250 (34%), Positives = 130/250 (52%), Gaps = 22/250 (8%) Query: 12 TVLITAAAQGIGRASTELFAREGARVIATDISKPHLDEL--AGI----AGVETHLLDVTD 65 T L+T ++GIG+A E AREG +V T +SKP E AGI LDV+D Sbjct: 7 TALVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSD 66 Query: 66 DAAIKAL----VAKIGTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121 AA+ A + + T+DVL N AG G IL D +D ++N F +R Sbjct: 67 AAAVAAFFQEEIREKVTLDVLVNNAGITKDGLILRMKDDDFDRVLDVNLSGAFTCLREAA 126 Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIRCNAICP 181 M ++ G IVNI S + G A + Y A+KA ++G+TKS A + + + NA+ P Sbjct: 127 KLMTRQRKGRIVNITSVVGQM-GNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAP 185 Query: 182 GTIESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLASDESNFT 241 G IE+ T K +EVRAA++ P+ R+G+ +++A +LASD++ + Sbjct: 186 GFIETDM-----------TAKLTDEVRAAYIEAIPLRRLGQPQDIADAVAFLASDKAGYI 234 Query: 242 TGSIHMIDGG 251 TG + ++GG Sbjct: 235 TGQVIAVNGG 244 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: 146 Number of extensions: 9 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: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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