Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 3609507 Dshi_2891 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Dino:3609507 Length = 242 Score = 169 bits (427), Expect = 6e-47 Identities = 102/241 (42%), Positives = 144/241 (59%), Gaps = 7/241 (2%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTDA 74 RL+G+ A+VTGG G G I R A GA+V +AD+N E A E GT +++V+DA Sbjct: 2 RLEGKTAIVTGGGSGFGAGIVRKFAAEGAQVIVADINKGAAEAVAEEYGGTAAQVDVSDA 61 Query: 75 DAVADLARRLPDVDVLVNNAGIVR-NAPAEDTPDDDWRAVLSVNLDGVFWCCREFGRTML 133 D++A LA D+LVNNAGI P E+ ++++ VL+VN V+ R F M Sbjct: 62 DSMAALAEAHGAPDILVNNAGITHLPKPMEEVTEEEFDRVLAVNAKSVYLSARVFVPAMK 121 Query: 134 ARGRGAIVSTASMSGLISNHPQPQAA-YNASKAAVIHLTRSLAGEWASRGVRVNAVAPGY 192 ARG GAI++ AS +G+ P+P+ YNASK +I T+++A E A G+RVNA+ P Sbjct: 122 ARGSGAILNIASTAGV---SPRPKLNWYNASKGWMITATKAMAVELAPFGIRVNALNPVA 178 Query: 193 TATPL--TRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLVVDG 250 TPL + G +TPE R +L PLGR ++P ++ A +L SD AS +TG + VDG Sbjct: 179 GETPLLASFMGEDTPEMRAKFLATIPLGRFSQPEDLGNAAAFLCSDEASMITGVAMEVDG 238 Query: 251 G 251 G Sbjct: 239 G 239 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: 167 Number of extensions: 10 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: 255 Length of database: 242 Length adjustment: 24 Effective length of query: 231 Effective length of database: 218 Effective search space: 50358 Effective search space used: 50358 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: 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