Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate N515DRAFT_3783 N515DRAFT_3783 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Dyella79:N515DRAFT_3783 Length = 255 Score = 107 bits (266), Expect = 3e-28 Identities = 82/261 (31%), Positives = 132/261 (50%), Gaps = 33/261 (12%) Query: 13 IVTGASSGIGKAIVDELLSLKVKVANFDLT-DNGEKHENLL-----FQKVDVTSREQVEA 66 I+TG +SG+G A+ L++ +VA FD+ D G++ L F + DVTS + V A Sbjct: 9 IITGGASGLGYAVAQHLVAAGGQVALFDVNEDKGQEAARALGASAHFFRTDVTSEDGVSA 68 Query: 67 SVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQKGLYLVSQ 126 +VAA E G ++ V+N AGI ++ + P + TF M+N G + V++ Sbjct: 69 NVAAAREAMGGLNVVMNCAGILGAGRVLGKEGP-----MPLGTFASTVMVNLVGSFNVAK 123 Query: 127 AVGRLLVAKK------KGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKYG 180 A L+ + + +GVI+N AS A EG GQ+AY+ +K V T A+EL ++G Sbjct: 124 AAAALMQSNEAGEDGERGVIVNTASVAAYEGQIGQAAYSASKGGVVGMTLPMARELSRFG 183 Query: 181 VRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVADL 240 +RV IAPGI + + +++ +++ P R G+ E A L Sbjct: 184 IRVATIAPGIFWTPMVDGMP-------------PQVQESLSASIPFP-SRLGRPEEFASL 229 Query: 241 VAYYISDRSSYITGITTNVAG 261 VA+ +++R YI G T + G Sbjct: 230 VAFILTNR--YINGETIRLDG 248 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: 162 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: 266 Length of database: 255 Length adjustment: 24 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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