Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate PfGW456L13_3499 Short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3499 Length = 255 Score = 103 bits (258), Expect = 3e-27 Identities = 82/266 (30%), Positives = 123/266 (46%), Gaps = 30/266 (11%) Query: 6 NIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKH--ENLLFQKVDVTS--- 60 ++ GK V+GAS GIG+AI L V G +H + ++ T+ Sbjct: 8 DLDGKIAFVSGASRGIGEAIAKLLAQQGAHVIVSSRKLEGCQHVADAIIAAGGKATAIAC 67 Query: 61 ----REQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMI 116 EQ+ A + E FG +D +VNNA N P+ + D + F+K + Sbjct: 68 HIGEMEQISQVFAGIKEQFGRLDILVNNAATN-PQFC-------NVLDTDLSAFQKTVDV 119 Query: 117 NQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKEL 176 N +G + +S G+L+ G IIN+AS G+ Q Y+ TKAAV + T+ +AKE Sbjct: 120 NIRGYFFMSVEAGKLMRENGGGSIINVASINGVSPGIFQGIYSVTKAAVINMTKVFAKEC 179 Query: 177 GKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSE 236 ++G+R + PG+ + L EA+ T + + PL R SE Sbjct: 180 AQFGIRCNALLPGLTDTKFASALVKNEAILNTALQQI-------------PLKRVADPSE 226 Query: 237 VADLVAYYISDRSSYITGITTNVAGG 262 +A V Y SD SSY TG++ NV GG Sbjct: 227 MAGAVLYLASDASSYTTGVSLNVDGG 252 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: 155 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