Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate CCNA_00123 CCNA_00123 3-hydroxyacyl CoA dehydrogenase
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Caulo:CCNA_00123 Length = 260 Score = 77.4 bits (189), Expect = 3e-19 Identities = 78/263 (29%), Positives = 111/263 (42%), Gaps = 31/263 (11%) Query: 13 IVTGASSGIGKAIVDELLSLKVKVANFDLTDNG----EKHENLLFQKVDVTSREQVEASV 68 +VTG +SG+G+A L + VKVA FD+ + K +F KV+VTS V+A Sbjct: 10 VVTGGASGLGEATARALAAQGVKVALFDMNEERGLQVAKEIGGVFCKVNVTSDADVDAGF 69 Query: 69 AAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQ---YELDDATFEKITMINQKGLY--L 123 G +VN AG G+ + LD F++I IN G + + Sbjct: 70 EKARAAHGQERILVNCAGTGNAAKTASRDKATGETKHFPLD--AFDRIIQINLVGTFRCI 127 Query: 124 VSQAVGRL----LVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKY 179 A G L L ++G I+N AS A +G GQ+AY+ +K V T A++L Sbjct: 128 AKSAKGMLDLEPLEDGERGAIVNTASVAAEDGQMGQAAYSASKGGVVGMTLPIARDLMGE 187 Query: 180 GVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVAD 239 G+RV I PGI E ++AG A++ P R G E A Sbjct: 188 GIRVNTILPGIFNTP-------------LMNNAPEAVKAGLAASVPFP-KRLGHPEEYAQ 233 Query: 240 LVAYYISDRSSYITGITTNVAGG 262 L I+ Y G + GG Sbjct: 234 LALTMIT--CGYFNGEDVRLDGG 254 Lambda K H 0.313 0.131 0.361 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: 147 Number of extensions: 7 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: 266 Length of database: 260 Length adjustment: 25 Effective length of query: 241 Effective length of database: 235 Effective search space: 56635 Effective search space used: 56635 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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