Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate HSERO_RS11255 HSERO_RS11255 3-ketoacyl-ACP reductase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS11255 Length = 252 Score = 160 bits (406), Expect = 2e-44 Identities = 98/256 (38%), Positives = 148/256 (57%), Gaps = 11/256 (4%) Query: 4 RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDVKPADSFG--DSLRATYGDRVLTVS 61 RLQDKVAI+TG SG GE +A+ Y EGA V+ D+ A + ++A G R + Sbjct: 2 RLQDKVAIVTGGGSGFGEGIAKAYAREGAAIVVADIGEAGGLRVVEEIKAA-GGRAVFAK 60 Query: 62 ADVTRRDDIQRIVASTLERFGQIDILFNNAALFDM-RPILEESWDVFDRLFAVNVKGMFF 120 ADV++R D+ +++A+ LE FG++DI+ NNA RP+LE D FDR++AVNVK +F Sbjct: 61 ADVSKRADMDQLLATALEHFGKLDIVVNNAGTTHRNRPMLEVEEDEFDRVYAVNVKSIFL 120 Query: 121 LMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKIN 180 + + G GG IN++S AG R ++ Y +K AV++ ++S A L P KI Sbjct: 121 SAKTFVPYFRQVG-GGAFINIASTAGIRPRPGLTWYNGSKGAVITTSKSMAAELGPDKIR 179 Query: 181 VNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLAS 240 VN + P + T + +E + ENR K+ V +P+GR P+D+ A L+L S Sbjct: 180 VNCVNPVISATGLLSEFMGVPDTPENR-----KKFVA-TIPMGRFSTPEDIANACLYLGS 233 Query: 241 ADADYITAQTLNVDGG 256 +A+++T + VDGG Sbjct: 234 DEAEFVTGVCIEVDGG 249 Lambda K H 0.321 0.135 0.393 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: 175 Number of extensions: 12 Number of successful extensions: 5 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: 260 Length of database: 252 Length adjustment: 24 Effective length of query: 236 Effective length of database: 228 Effective search space: 53808 Effective search space used: 53808 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 (21.9 bits) S2: 47 (22.7 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