Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Ga0059261_2655 Ga0059261_2655 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::Phaeo:GFF1301 (257 letters) >FitnessBrowser__Korea:Ga0059261_2655 Length = 259 Score = 176 bits (446), Expect = 4e-49 Identities = 102/260 (39%), Positives = 139/260 (53%), Gaps = 4/260 (1%) Query: 1 MKRLSGKRALITGAARGIGAAFAEAYANEGARVVIADI--DTARAEATAAQIGAAAIAVE 58 M+R GK A+I+G +GIG A AE +A+EGA +VI I D + AE A G +A Sbjct: 1 MRRFEGKCAVISGGNKGIGLAIAERFASEGANIVIGAIEADLSPAEQALAGYGTGVVAQR 60 Query: 59 LDVTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFM 118 DVT + RAL E FGG+DI + NA V T A + ++T + +N G Sbjct: 61 CDVTKADDV-RALFEAAEAFGGVDIAVQNAGVITIAKVEDLTEGEWDLNLAVNTKGAFLC 119 Query: 119 MQAAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINV 178 Q A +++ +G G++IN AS R G Y A+K V+ +TQS + + GI V Sbjct: 120 CQEAIRRLRARGKPGRLINTASGQARDGFIFTPHYAASKFGVVGMTQSLAKEVATQGITV 179 Query: 179 NAIAPGVVDGEHWDGVDAFFAKYEGK-APGQKKAEVAQSVPYGRMGTAADLTGMAVFLAS 237 NAI PG++ + WD D + + G APG E Q +P R GT AD+ + FLAS Sbjct: 180 NAICPGIIHTDMWDYNDREWGRLMGDYAPGALMEEWVQGIPMKRAGTGADVAALVAFLAS 239 Query: 238 EDADYVVAQTYNVDGGQWMS 257 DA Y+ QT NVDGG MS Sbjct: 240 ADASYITGQTINVDGGLIMS 259 Lambda K H 0.317 0.130 0.365 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: 155 Number of extensions: 6 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: 257 Length of database: 259 Length adjustment: 24 Effective length of query: 233 Effective length of database: 235 Effective search space: 54755 Effective search space used: 54755 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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