Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate SMc01500 SMc01500 sorbitol dehydrogenase
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Smeli:SMc01500 Length = 257 Score = 109 bits (272), Expect = 7e-29 Identities = 82/268 (30%), Positives = 132/268 (49%), Gaps = 30/268 (11%) Query: 7 IAGKTVIVTGASSGIGKAIVDELL--SLKVKVANFDLTDNGEKHENL----LFQKVDVTS 60 + GK+ ++TG++ GIG+A + + V +A+ D+ + + ++DVT Sbjct: 4 LEGKSALITGSARGIGRAFAEAYVREGATVAIADIDIERARQAAAEIGPAAYAVQMDVTR 63 Query: 61 REQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQKG 120 ++ ++A++AA VEH G +D +VNNA + +V E+ ++EK+ IN G Sbjct: 64 QDSIDAAIAATVEHAGGLDILVNNAALFDLAPIV---------EITRESYEKLFAINVAG 114 Query: 121 LYLVSQAVGRLLVAKKKG-VIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKY 179 QA R ++A+ +G IINMAS+AG G + Y TKAAV S T+S +L K+ Sbjct: 115 TLFTLQAAARQMIAQGRGGKIINMASQAGRRGEALVAIYCATKAAVISLTQSAGLDLIKH 174 Query: 180 GVRVVGIAPGIMEA---TGLRTL--AYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKL 234 + V IAPG+++ G+ L YE + + V E P GR G Sbjct: 175 RINVNAIAPGVVDGEHWDGVDALFARYENRPRGEKKRLVGE---------AVPFGRMGTA 225 Query: 235 SEVADLVAYYISDRSSYITGITTNVAGG 262 ++ + + S S YI T NV GG Sbjct: 226 EDLTGMAIFLASAESDYIVSQTYNVDGG 253 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: 175 Number of extensions: 13 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: 257 Length adjustment: 25 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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