Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__azobra:AZOBR_RS29790 Length = 250 Score = 125 bits (313), Expect = 1e-33 Identities = 85/263 (32%), Positives = 136/263 (51%), Gaps = 24/263 (9%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYNFWPTDISS---- 62 L K+ +TG A G+GLA+ + + +G V ++DI+G + I++ Sbjct: 5 LDGKVALITGAAQGLGLAMAETFVREGGRVAVVDINGDAAKAVAERLGESAIGIAANVTR 64 Query: 63 ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYE-LNEAAFEKMVNINQK 121 ++V T+ +++FGR+D LVNNAG +G +E + E F+++ +N K Sbjct: 65 MADVEMTIAATVEKFGRLDILVNNAGSTHA---------NGPFENVTEEEFDRVFALNVK 115 Query: 122 GVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKH 181 ++L S+AV M Q+SGVI+N+ S +GL G Y ATK A+++ T+S + EL Sbjct: 116 SIYLYSKAVVATMRAQKSGVILNLGSTAGLRPRPGLVWYNATKGAVHNITKSLALELAPD 175 Query: 182 GIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADF 241 IRV +AP E L T + T E + +PLGR G+ T+VA+ Sbjct: 176 NIRVCALAPVATETPLLAT--------FMGGDTPE--KRARMMGIVPLGRLGQPTDVANA 225 Query: 242 VCYLLSERASYMTGVTTNIAGGK 264 YL S+ A+++TGV I GG+ Sbjct: 226 ALYLASDEAAFLTGVVLEIDGGR 248 Lambda K H 0.315 0.132 0.378 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: 170 Number of extensions: 9 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: 267 Length of database: 250 Length adjustment: 24 Effective length of query: 243 Effective length of database: 226 Effective search space: 54918 Effective search space used: 54918 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: 42 (22.0 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