Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate Ga0059261_1900 Ga0059261_1900 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Korea:Ga0059261_1900 Length = 250 Score = 110 bits (275), Expect = 3e-29 Identities = 87/265 (32%), Positives = 127/265 (47%), Gaps = 36/265 (13%) Query: 10 KTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENL----------LFQKVDVT 59 K IVTG IGK+I L + KV +D L L + DVT Sbjct: 6 KVAIVTGGGRDIGKSISLRLAAEGAKVVINYRSDEAAAKATLDAIEAAGGTALLARADVT 65 Query: 60 SREQVEASVAAVVEHFG-TVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQ 118 ++V A V A + FG VD +VN AG + R + E+D+A F+ + +N Sbjct: 66 KADEVVALVKAATDAFGGKVDILVNCAGGMVARKTLA--------EMDEAFFDTVMDLNL 117 Query: 119 KGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGS-EGQSAYAGTKAAVYSYTRSWAKELG 177 K +LV++AV L + I+N+AS+AG +G G S YA +K A+ + TRSWAKELG Sbjct: 118 KSAFLVTKAV--LPHLESGAAIVNIASQAGRDGGGPGASIYAASKGALMTLTRSWAKELG 175 Query: 178 KYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEV 237 G+RV + PG++ ++ + G+ A TPL R G EV Sbjct: 176 PQGIRVNALNPGLIGT------SFHDIFSKPEGRA--------AVAGNTPLRREGHPDEV 221 Query: 238 ADLVAYYISDRSSYITGITTNVAGG 262 A VA+ S +S++TG ++ GG Sbjct: 222 AAAVAFLASGDASFLTGTNVDINGG 246 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: 171 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: 250 Length adjustment: 24 Effective length of query: 242 Effective length of database: 226 Effective search space: 54692 Effective search space used: 54692 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