Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate GFF2780 HP15_2724 short-chain dehydrogenase/reductase SDR
Query= SwissProt::A9CES4 (256 letters) >FitnessBrowser__Marino:GFF2780 Length = 286 Score = 134 bits (337), Expect = 2e-36 Identities = 95/263 (36%), Positives = 138/263 (52%), Gaps = 22/263 (8%) Query: 2 RLNNKVALITGAARGIGLGFAQAFAAEGAKVIIADIDIARATTSAAAIGPAAKAVKLDVT 61 RL+ K ALITGAARGIG A FA +GA VI++DID + + LDV+ Sbjct: 22 RLDGKTALITGAARGIGEAIAIQFAEQGATVIVSDIDDQMGQALVDSSKLDMHYLHLDVS 81 Query: 62 DLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPING------ITEESYERVFDINLKGPM 115 D +Q K+++++FGG+DILVNNA I G + S+E V NL G Sbjct: 82 DESQWITCAKSIEDQFGGLDILVNNAGITGFLESAGPHDPEHLDLASWETVHATNLNGVA 141 Query: 116 FMMKAVSNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHG- 174 K +M +R I+N++S++G G Y +SKA + + T+S AL + G Sbjct: 142 LGCKYGIKLM-KSSRSASIVNISSRSGLVGIPGAAAYASSKAGVRNHTKSVALHCAEKGY 200 Query: 175 -INVNAIAPGVVDGEHWEVVDAHFAKWEGLKPGE-KKAAVAK---SVPIGRFATPDDIKG 229 I N+I PG + WE + L GE ++AA+A+ VPIGR P+D+ Sbjct: 201 PIRCNSIHPGAIMSPMWEAM---------LGEGEAREAAIAEVEAGVPIGRMGKPEDVAY 251 Query: 230 LAVFLASADSDYILAQTYNVDGG 252 A++LAS +S+Y+ N+DGG Sbjct: 252 AALYLASDESNYVTGIELNIDGG 274 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: 189 Number of extensions: 11 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: 286 Length adjustment: 25 Effective length of query: 231 Effective length of database: 261 Effective search space: 60291 Effective search space used: 60291 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