Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate WP_039104627.1 FPB0191_RS05845 SDR family oxidoreductase
Query= SwissProt::A9CES4 (256 letters) >NCBI__GCF_000807275.1:WP_039104627.1 Length = 295 Score = 96.7 bits (239), Expect = 5e-25 Identities = 82/263 (31%), Positives = 121/263 (46%), Gaps = 30/263 (11%) Query: 2 RLNNKVALITGAARGIGLGFAQAFAAEGAKVIIADI--------DIARATTSAAAIGPAA 53 RL L+TG GIG A A+A EGA V I + D+A+ S +G A Sbjct: 47 RLEGLKMLVTGGDSGIGRAAAIAYAKEGADVAINYLPHEQKDAEDVAKVIES---VGRKA 103 Query: 54 KAVKLDVTDLAQIDAVVKAVDEEFGGID----ILVNNAAIFDMAPINGITEESYERVFDI 109 + D++D A +V E+ GG+D + A+ D I +T E ++ F+I Sbjct: 104 VLIPGDLSDEAFCKKLVDQAHEKLGGLDNVTFVAGKQTAVED---IMKLTTEQIKKTFEI 160 Query: 110 NLKGPMFMMKAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALA 169 N+ ++ KA + A G II +S + A + Y +K AII+ T+ A Sbjct: 161 NVFSLFWVTKAALGYLKA---GSTIITTSSIQAYQPSANLLDYACTKTAIIAFTRGLAKQ 217 Query: 170 LVKHGINVNAIAPGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKG 229 + K GI VN++APG + W + G +P E K P+ R P ++ Sbjct: 218 VAKKGIRVNSVAPGPI----WTPLQIC-----GGQPSEVIPEFGKQAPLMRAGQPVELAS 268 Query: 230 LAVFLASADSDYILAQTYNVDGG 252 L VFLAS +S YI A T+ V GG Sbjct: 269 LYVFLASEESSYITADTFGVTGG 291 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: 151 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: 295 Length adjustment: 25 Effective length of query: 231 Effective length of database: 270 Effective search space: 62370 Effective search space used: 62370 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 24 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