Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate Ga0059261_2906 Ga0059261_2906 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Korea:Ga0059261_2906 Length = 257 Score = 113 bits (283), Expect = 4e-30 Identities = 86/275 (31%), Positives = 139/275 (50%), Gaps = 36/275 (13%) Query: 1 MADWLNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKH-------ENLLF 53 M + +++ G++VI+TGA+ GIG A L L V D + + +L Sbjct: 1 MINPMSLDGRSVIITGAAQGIGLATAHLLYELGAHVTLLDRNEERLSEAASAFDAQRILV 60 Query: 54 QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKI 113 Q +T R V ++AA + FG VD +VNNAGI ++ + L+D ++ + Sbjct: 61 QCGSITDRSFVGRAMAAHIARFGAVDGLVNNAGITRTAMIE-------KMTLED--WQAV 111 Query: 114 TMINQKGLYLVSQAVGRLLVAKKK------GVIINMASEAGLEGSEGQSAYAGTKAAVYS 167 +N G++ + QAVG ++A+ K G I+N++S+AG +G+ GQ Y K+ V Sbjct: 112 IDVNLTGVFNMLQAVGTTMIARAKEGEANPGAIVNISSDAGRKGTIGQINYGAAKSGVLG 171 Query: 168 YTRSWAKELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTP 227 T S A+E G++G+RV +A G++E T + +A E+ R Y S P Sbjct: 172 ITMSAAREWGRHGIRVNSVAYGVVE-TEMTEIARS-----------EKFRDRYLS--NIP 217 Query: 228 LGRSGKLSEVADLVAYYISDRSSYITGITTNVAGG 262 LGR E A +A+ +S S++ITG +V GG Sbjct: 218 LGRFLSPDEAAYSIAFLLSPASAFITGQHLSVNGG 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: 165 Number of extensions: 11 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