Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_022530640.1 L248_RS12645 SDR family oxidoreductase
Query= BRENDA::Q1J2J0 (255 letters) >NCBI__GCF_000469325.1:WP_022530640.1 Length = 246 Score = 165 bits (418), Expect = 7e-46 Identities = 106/246 (43%), Positives = 149/246 (60%), Gaps = 12/246 (4%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDG-TFERLNVTD 73 RL+ +HA+VTGGAQGIG I + A GA+V IAD+N D G A ++ G F L+VT Sbjct: 4 RLESKHAIVTGGAQGIGLAITKRFAAEGAQVIIADVNADEGAKVAADIPGAAFHVLDVTS 63 Query: 74 ADA----VADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFG 129 ++ AD ++L +D+LVNNAGI R A E T DW+AV++VNL G F ++G Sbjct: 64 EESWQALFADAEKQLGRIDILVNNAGIARMADIEHTTLADWQAVIAVNLTGNF-LGNKYG 122 Query: 130 RTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASR--GVRVNA 187 + GAIV+ +S++GL+ + AAY ASK V LT+S+A A + +RVN+ Sbjct: 123 VIHMKDHGGAIVNMSSIAGLVGD--PNSAAYTASKGGVRLLTKSVASYCAEQHYNIRVNS 180 Query: 188 VAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHTLV 247 V PG ATP+ G+ + + P+GR+A+P EIA VL++ASD AS+ TG + Sbjct: 181 VHPGVVATPMV-AGIPKAIVAKV-AAQNPMGRIAQPEEIANMVLFVASDEASYSTGSEFI 238 Query: 248 VDGGYT 253 VDGG T Sbjct: 239 VDGGTT 244 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: 196 Number of extensions: 11 Number of successful extensions: 5 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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 24 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