Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= SwissProt::A9CES4 (256 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 146 bits (368), Expect = 5e-40 Identities = 94/254 (37%), Positives = 130/254 (51%), Gaps = 16/254 (6%) Query: 3 LNNKVALITGAARGIGLGFAQAFAAEGAKVIIADIDI----ARATTSAAAIGPAAKAVKL 58 L+ K A++TGAARGIG A FAAEGA + D+ I + A+G AK Sbjct: 4 LDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYAS 63 Query: 59 DVTDLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMM 118 + + VV+ + ++FG IDILVNNA I + ++E+ ++ V ++NLK + Sbjct: 64 NAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFI 123 Query: 119 KAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINVN 178 A + VM+ R + G IINMAS G G A Y ASKA +I+ +S A L GI N Sbjct: 124 HACTPVMM-RQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIRAN 182 Query: 179 AIAPGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASAD 238 AIAPG + E +A AK +P+ R TP+D+ +A FLAS Sbjct: 183 AIAPGFI-----------LTDMTAALSDEVRAEWAKKIPLRRGGTPEDVANIATFLASDM 231 Query: 239 SDYILAQTYNVDGG 252 S Y+ Q VDGG Sbjct: 232 SSYVSGQVIQVDGG 245 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: 158 Number of extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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