Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_015944143.1 DHAF_RS13285 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-13092 (266 letters) >NCBI__GCF_000021925.1:WP_015944143.1 Length = 252 Score = 108 bits (269), Expect = 1e-28 Identities = 81/269 (30%), Positives = 127/269 (47%), Gaps = 32/269 (11%) Query: 5 LNIAGKTVIVTGASSGIGKAIVDELL----SLKVKVANFDLTDNGEKHENL-------LF 53 + + K IVTGA+SG+GK+I LL KV V++ +L + E + L Sbjct: 1 MRLMNKVAIVTGAASGMGKSIA--LLYAKEGAKVVVSDLNLEGAHKVAEEITSAGGTALA 58 Query: 54 QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKI 113 K +V E ++A V V +GTVD VNNAGI +D +P +++D +E+I Sbjct: 59 IKTNVAVEEDIQALVDTAVSTYGTVDIFVNNAGI------MDNFEPAA--DIEDKNWERI 110 Query: 114 TMINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWA 173 +N + ++ V + + K GVI+N+AS GL G+ + Y +K AV +T++ Sbjct: 111 FAVNTTSVMRATRKVLPIFLEKSSGVIVNVASAGGLNGARAGATYTASKHAVIGFTKNTG 170 Query: 174 KELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGK 233 + G+R IAPG +E T+ G R YA T P R GK Sbjct: 171 FMYAQQGIRCNAIAPGAVETNIGSTITDPHKFGSAR---------AYAGMATNP--RMGK 219 Query: 234 LSEVADLVAYYISDRSSYITGITTNVAGG 262 E+A + + ++ SS++ G GG Sbjct: 220 PEEIAQVALFLAAEESSFVNGAVIVADGG 248 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: 10 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: 252 Length adjustment: 24 Effective length of query: 242 Effective length of database: 228 Effective search space: 55176 Effective search space used: 55176 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 24 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