Align Short-chain alcohol dehydrogenase protein (characterized, see rationale)
to candidate WP_008483001.1 B3C1_RS03700 3-oxoacyl-ACP reductase FabG
Query= uniprot:D8IS13 (254 letters) >NCBI__GCF_000299915.1:WP_008483001.1 Length = 241 Score = 90.9 bits (224), Expect = 2e-23 Identities = 74/253 (29%), Positives = 116/253 (45%), Gaps = 27/253 (10%) Query: 11 KTVLITAAAQGIGRASTELFAREGARVIA-----TDISKPHLDELAGIAGVETHL-LDVT 64 K +L+T A++GIG A + A EG V+ D + E+ G + L DV+ Sbjct: 2 KRILVTGASRGIGAAIAKTLAAEGIAVVIHYRNRQDAALAVQAEIEAAGGQASLLAFDVS 61 Query: 65 DDAAIKA-----LVAKIGTIDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIR- 118 D AA KA + A V+ N AG G D WD + N ++ ++ Sbjct: 62 DRAAAKAALEADMAANGPYYGVVVN-AGITRDGAFPALTDDDWDSVIHTNLDGFYNVLKP 120 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVAQGIRCNA 178 V+P + +K G IV +AS + + G + Y ASKA ++G TK++A + + I N Sbjct: 121 VVMPMVQGRKGGRIVTLASVSGLI-GNRGQVNYSASKAGIIGATKALALELAKRKITVNC 179 Query: 179 ICPGTIESPSLNQRISTQAKETGKSEEEVRAAFVGRQPMGRIGKAEEVAALALYLASDES 238 + PG IES +E E V P+ R G+A+EVA +L SD++ Sbjct: 180 VAPGLIESDM-------------TAELEHGEHIVDLIPLRRAGQAQEVADAVAFLCSDKA 226 Query: 239 NFTTGSIHMIDGG 251 + T + ++GG Sbjct: 227 GYITRQVLAVNGG 239 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: 122 Number of extensions: 10 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: 254 Length of database: 241 Length adjustment: 24 Effective length of query: 230 Effective length of database: 217 Effective search space: 49910 Effective search space used: 49910 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 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