Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate 203460 SO4382 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= SwissProt::A9CES4 (256 letters) >FitnessBrowser__MR1:203460 Length = 241 Score = 110 bits (274), Expect = 3e-29 Identities = 86/254 (33%), Positives = 126/254 (49%), Gaps = 19/254 (7%) Query: 3 LNNKVALITGAARGIGLGFAQAFAAEGAKVIIA-DIDIARATTSAA---AIGPAAKAVKL 58 +NN+V L+TG++RGIG A AA G + + + A A SAA A+G +K Sbjct: 1 MNNRV-LVTGSSRGIGKAIALKLAAAGHDIALHYHSNQAAADASAAELRALGVNVSLLKF 59 Query: 59 DVTDLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMM 118 DV D + A ++A E G +V NA I ++E ++ V NL G ++ Sbjct: 60 DVADRVAVRAALEADIEANGAYYGVVLNAGINRDNAFPAMSEAEWDSVIHTNLDGFYNVI 119 Query: 119 KAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINVN 178 M+ +GG+II +AS +G G Y ASKA +I AT++ +L L K I VN Sbjct: 120 HPCVMPMVQARKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVN 179 Query: 179 AIAPGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASAD 238 IAPG+++ + V D K V + VP+ R P++I LA FL S D Sbjct: 180 CIAPGLIETD--MVADI------------PKDMVEQLVPMRRMGKPNEIAALAAFLMSDD 225 Query: 239 SDYILAQTYNVDGG 252 + YI Q +V+GG Sbjct: 226 AAYITRQVISVNGG 239 Lambda K H 0.319 0.133 0.376 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: 114 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: 256 Length of database: 241 Length adjustment: 24 Effective length of query: 232 Effective length of database: 217 Effective search space: 50344 Effective search space used: 50344 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 (21.8 bits) S2: 46 (22.3 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