Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__PV4:5210421 Length = 255 Score = 137 bits (344), Expect = 3e-37 Identities = 95/252 (37%), Positives = 137/252 (54%), Gaps = 12/252 (4%) Query: 13 LFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL---DGTFERL 69 LF L GR ALVTG ++GIG IA LA GA V +A + + A ++ G+ E + Sbjct: 6 LFDLSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAM 65 Query: 70 --NVTDADAVADLARRLPD----VDVLVNNAGIVRN-APAEDTPDDDWRAVLSVNLDGVF 122 +V D +A+ ++ +D+LVNNA DT + + + VNL G F Sbjct: 66 ACHVGDLEAIQATFEQIQAKHGRLDILVNNAATNPYFGHILDTDLNAFNKTMEVNLRGYF 125 Query: 123 WCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRG 182 + GR M +G G I++TAS++ L + Q Y+ SKAAV+ +T++ A E A G Sbjct: 126 FMSVTAGRMMREQGHGVILNTASVNALQPG--EMQGIYSISKAAVVSMTKAFAKECAPLG 183 Query: 183 VRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVT 242 +R NA+ PG+T T + + + P+GR A P E+A AVLYL SDA+S+ T Sbjct: 184 IRCNALLPGFTKTQFAGALFNNDKIYQQLIARIPMGRHAVPSEMAGAVLYLVSDASSYTT 243 Query: 243 GHTLVVDGGYTV 254 G TLVVDGG T+ Sbjct: 244 GETLVVDGGLTL 255 Lambda K H 0.319 0.134 0.408 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: 166 Number of extensions: 7 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: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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