Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate RR42_RS17660 RR42_RS17660 3-oxoacyl-ACP synthase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Cup4G11:RR42_RS17660 Length = 246 Score = 133 bits (334), Expect = 4e-36 Identities = 89/266 (33%), Positives = 138/266 (51%), Gaps = 30/266 (11%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIH------GGDKHQSSG-NYNFWP 57 + L+ ++ +TG A+GIG A A+GA V + D+ + +SG + + Sbjct: 1 MKLQGRVAIITGAAAGIGFATAQRFAAEGALVVLCDVQEERVRAAAETLAASGATVSAYK 60 Query: 58 TDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVN 117 D++ EV V + R GR+D LVNNAG+ L ++ EA F+ +++ Sbjct: 61 VDVTRRDEVDAMVAATLARHGRVDILVNNAGITKDARLT---------KMTEAQFDAVID 111 Query: 118 INQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177 +N KGVF +QAVA M +Q GVI+N SS GL G+ GQ+ YAA+K + T++W++E Sbjct: 112 VNLKGVFNCAQAVADIMTEQGKGVILNASSVVGLYGNFGQTNYAASKFGVIGLTKTWARE 171 Query: 178 LGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTE 237 LG G+RV V PG + L+T E++ +G K+S L R + E Sbjct: 172 LGPKGVRVNAVCPGFVATEILQT-------------VPEKVLDG-MKSSCWLRRLAQPAE 217 Query: 238 VADFVCYLLSERASYMTGVTTNIAGG 263 +A +L S+ ASY+ GV +GG Sbjct: 218 IASIYTFLASDDASYVNGVAIEASGG 243 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: 135 Number of extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 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