Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 6939300 Sama_3393 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::WCS417:GFF2259 (257 letters) >FitnessBrowser__SB2B:6939300 Length = 241 Score = 116 bits (291), Expect = 4e-31 Identities = 81/251 (32%), Positives = 126/251 (50%), Gaps = 18/251 (7%) Query: 7 KSALITGSARGIGRAFAQAYIAEGATVAIA-DIDLQRAQATAAE---LGPQAYAVAMDVT 62 K L+TGS+RGIG+A A ++G VA+ +L A+ATA+E LG + + DV Sbjct: 3 KRVLVTGSSRGIGKAIALRLASQGYDVAVHYHSNLTAAEATASEIADLGVKVSLLKFDVA 62 Query: 63 DQASIDGAITAVVAQAGKLDILINNAALFDLAPIVDITRDSYDRLFSINVAGTLFTLQAA 122 D+A++ AI A + G ++ NA + +T D +D + N+ G +Q Sbjct: 63 DRAAVRAAIEADIEANGAYYGVVLNAGINRDTAFPAMTDDDWDSVIHTNLDGFYNVVQPT 122 Query: 123 ARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGINVNAIA 182 MI+ GG+II +AS +G G Y A+KA +I T++ L L K+ I VN IA Sbjct: 123 VMPMIQSRKGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELAKRKITVNCIA 182 Query: 183 PGVVDGEHWDGVDALFAKHEGLAPGEKKQRVGAEVPFGRMGTAEDLTGMAIFLASKEADY 242 PG+++ + + + V VP RMG E++ +A FL S +A Y Sbjct: 183 PGLIETD--------------MVSEFPSEMVDQLVPMRRMGKPEEIAALAGFLMSDDAAY 228 Query: 243 VVAQTYNVDGG 253 + Q +V+GG Sbjct: 229 ITRQVISVNGG 239 Lambda K H 0.318 0.133 0.374 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: 141 Number of extensions: 10 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: 257 Length of database: 241 Length adjustment: 24 Effective length of query: 233 Effective length of database: 217 Effective search space: 50561 Effective search space used: 50561 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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