Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= metacyc::MONOMER-13092 (266 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 113 bits (283), Expect = 3e-30 Identities = 86/264 (32%), Positives = 128/264 (48%), Gaps = 34/264 (12%) Query: 9 GKTVIVTGASSGIGKAIVDELLSLKVKVANFDLT--DNGEKH----ENLLFQKVDVTSRE 62 GKT IVTGA+ GIGKAI + + +A DL +N EK E + + S Sbjct: 6 GKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNA 65 Query: 63 QVEASVAAVVEH----FGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQ 118 A VVE FG +D +VNNAGI L++ + + ++ + +N Sbjct: 66 ANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMM---------RMSEQQWDMVINVNL 116 Query: 119 KGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGK 178 K + A +++ +K G IINMAS G+ G+ GQ+ YA +KA + + +S A+ELG Sbjct: 117 KSAFNFIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGS 176 Query: 179 YGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVA 238 G+R IAPG + L+ +E+RA +A PL R G +VA Sbjct: 177 RGIRANAIAPGFILTDMTAALS-------------DEVRAEWAK--KIPLRRGGTPEDVA 221 Query: 239 DLVAYYISDRSSYITGITTNVAGG 262 ++ + SD SSY++G V GG Sbjct: 222 NIATFLASDMSSYVSGQVIQVDGG 245 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: 12 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: 248 Length adjustment: 24 Effective length of query: 242 Effective length of database: 224 Effective search space: 54208 Effective search space used: 54208 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