Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Synpcc7942_1596 Synpcc7942_1596 short chain dehydrogenase
Query= reanno::WCS417:GFF2259 (257 letters) >FitnessBrowser__SynE:Synpcc7942_1596 Length = 245 Score = 97.8 bits (242), Expect = 2e-25 Identities = 70/212 (33%), Positives = 104/212 (49%), Gaps = 7/212 (3%) Query: 1 MKRLEGKSALITGSARGIGRAFAQAYIAEGATVAIADIDLQRAQATAAELGPQAYAV--- 57 M L LITG++ GIG A A A+ G ++ + D R Q+ A Q A Sbjct: 4 MSFLPSPFVLITGASSGIGAATAHAFAQAGWSLLLLGRDRGRLQSVAESARSQGAAAVAT 63 Query: 58 -AMDVTDQASIDGAITAVVAQAGKLDILINNAALFDLAPIVDITRDSYDRLFSINVAGTL 116 ++D+T+ +I AI +V Q G D+LINNA P+ ++ + +F++NV L Sbjct: 64 YSLDLTNLTAIGPAIAQLVEQFGVPDVLINNAGTAQTGPLATLSLSDLECIFALNVHSPL 123 Query: 117 FTLQAAARQMIRQGHGGKIINMASQAGRRGEPLVAIYCATKAAVISLTQSAGLNLIKQGI 176 +QA M RQ G I+N+AS A ++ P YCA+K+A+ + ++ GI Sbjct: 124 LVVQALLPGM-RQRQRGLILNVASIAAQQAFPDWGAYCASKSALAAWSRVLAAEERSHGI 182 Query: 177 NVNAIAPGVVDGEHWD--GVDALFAKHEGLAP 206 V+ I PG VD WD V A F + L P Sbjct: 183 RVSLICPGSVDTALWDQPSVGANFDRQAMLRP 214 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: 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: 257 Length of database: 245 Length adjustment: 24 Effective length of query: 233 Effective length of database: 221 Effective search space: 51493 Effective search space used: 51493 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