Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate GFF1039 PS417_05265 short-chain dehydrogenase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__WCS417:GFF1039 Length = 253 Score = 88.6 bits (218), Expect = 1e-22 Identities = 81/255 (31%), Positives = 132/255 (51%), Gaps = 14/255 (5%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINS-RYGAGRAYGFKVD 61 +VA++ G +G L A+ G V V ++ + T++ G +D Sbjct: 4 KVALITGAASGIGQALAVAYARNGVAV-VGGYYPADPHDPQTTVSLVEEAGGECLMLPLD 62 Query: 62 ATDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSR 121 D ASV+ALA + FGR D V +AG+ + AP+ + +D L V+L G R Sbjct: 63 VGDTASVDALAAQTIQHFGRLDYAVANAGLLRRAPLLEMTDALWDEMLNVDLTGVMRTFR 122 Query: 122 EFSKLMIRDGIKGRIIQINSKSGKV-GSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVH 180 ++ M ++G G ++ I+S +G V G + +S Y+AAK G GL +SLA++LA GI + Sbjct: 123 AATRHM-QEG--GALVAISSIAGGVYGWQEHSHYAAAKAGVPGLCRSLAVELAAKGIRCN 179 Query: 181 SLMLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASD 240 +++ G L+++P QSL K + PE + +PL R +V +++ F SD Sbjct: 180 AVIPG-LIETP--QSL----DAKNSLGPEGLAK-AARAIPLGRVGRADEVASLVQFLTSD 231 Query: 241 KAAYCTGQSINVTGG 255 ++Y TGQSI + GG Sbjct: 232 ASSYLTGQSIVIDGG 246 Lambda K H 0.319 0.136 0.387 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: 168 Number of extensions: 8 Number of successful extensions: 3 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: 259 Length of database: 253 Length adjustment: 24 Effective length of query: 235 Effective length of database: 229 Effective search space: 53815 Effective search space used: 53815 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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