Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= SwissProt::A9CES4 (256 letters) >FitnessBrowser__Cola:Echvi_3928 Length = 252 Score = 147 bits (370), Expect = 3e-40 Identities = 94/250 (37%), Positives = 133/250 (53%), Gaps = 10/250 (4%) Query: 3 LNNKVALITGAARGIGLGFAQAFAAEGAKVIIADIDIARATTSAAAIGPAAKAVKLDVTD 62 LN KVA++TG GIG A+ EGA+VII + +AA +G + DV + Sbjct: 4 LNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRSAEKVNVAAAELG--VTGITADVLE 61 Query: 63 LAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMMKAVS 122 LA IDA V V +FG +DIL NA IF API TE+ +++ DINLKG +F ++ Sbjct: 62 LAAIDAAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVFTIEKFL 121 Query: 123 NVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINVNAIAP 182 ++ GG IIN++S G ++Y ASKAA+ S T++AA L I VNA+ P Sbjct: 122 PIL---KDGGSIINLSSINAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRVNAVNP 178 Query: 183 GVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASADSDYI 242 G V + + G+ AA+ +P+ R+ P+DI L FLAS + +I Sbjct: 179 GPVYTPIFSKTGMSEDQLNGM-----AAAMQNRIPLKRYGKPEDIAELVAFLASDRASFI 233 Query: 243 LAQTYNVDGG 252 YN+DGG Sbjct: 234 TGAEYNIDGG 243 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: 134 Number of extensions: 5 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: 256 Length of database: 252 Length adjustment: 24 Effective length of query: 232 Effective length of database: 228 Effective search space: 52896 Effective search space used: 52896 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: 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