Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_057507470.1 ABB28_RS04410 SDR family oxidoreductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_001431535.1:WP_057507470.1 Length = 258 Score = 154 bits (389), Expect = 2e-42 Identities = 101/251 (40%), Positives = 138/251 (54%), Gaps = 15/251 (5%) Query: 14 FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTF--ERLNV 71 +RLDG+ AL+TG + GIG IAR L GA V I + D+ E A +L + + ++ Sbjct: 6 WRLDGQTALITGASAGIGLAIARELLGFGADVMIVGRDIDMLESARDDLADEYPAQAIHA 65 Query: 72 TDADAVADLARR---------LPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVF 122 AD D RR + +LVNNAG PA D +D+WR + NL F Sbjct: 66 LAADVSDDEDRREILDWVEDHADGLHILVNNAGGNITRPAIDYTEDEWRNIFETNLFSAF 125 Query: 123 WCCREFGRTMLAR-GRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASR 181 R + +LAR AIV+ S+SGL H + A Y +KAA+ +TR+LA EWA Sbjct: 126 ELSR-YAHPLLARHAASAIVNVGSVSGL--THVRSGAVYGMTKAAMHQMTRNLAVEWAED 182 Query: 182 GVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFV 241 G+RVNAVAP Y T T L P++ E ++ TP+ R+ EP E+A AV +L AAS+V Sbjct: 183 GIRVNAVAPWYIRTRRTSGPLSDPDYYEQVIERTPMRRIGEPEEVASAVGFLCLPAASYV 242 Query: 242 TGHTLVVDGGY 252 TG + VDGG+ Sbjct: 243 TGECIAVDGGF 253 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: 203 Number of extensions: 9 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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 Apr 09 2024. 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