Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate RR42_RS31670 RR42_RS31670 NAD-dependent dehydratase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS31670 Length = 254 Score = 181 bits (460), Expect = 1e-50 Identities = 110/251 (43%), Positives = 144/251 (57%), Gaps = 7/251 (2%) Query: 7 MPHILDLFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTF 66 MPH FRL G+ +VTGG GIG +A A AGARV + D N E A E+ Sbjct: 1 MPHPFPDFRLTGQVTVVTGGGSGIGKALAHTFAGAGARVVVLDTNGAAAEQVANEIGSMA 60 Query: 67 ERL--NVTDADAVA----DLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDG 120 + +V++ DA+ D+AR+ +DVL NNAG+ R + D DW AV++VN+ G Sbjct: 61 QHAVADVSNEDAIESVMEDVARQHGRIDVLFNNAGVNRRNTSFDLTIADWNAVVAVNMTG 120 Query: 121 VFWCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWAS 180 +F C R R M G G IV+TAS+ G IS P Y A+K AV+++TRS A EWA Sbjct: 121 MFLCARAAARHMRDGGGGRIVNTASILG-ISGGWYPNIVYQATKGAVVNMTRSWAVEWAP 179 Query: 181 RGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASF 240 +RVNAVAP TP+T P+ + TPLGRL EP ++ VL+LA+ A+S Sbjct: 180 YNIRVNAVAPSIIRTPMTEALTSQPDVVAKFEALTPLGRLCEPADMTGPVLFLATAASSM 239 Query: 241 VTGHTLVVDGG 251 VTGH L VDGG Sbjct: 240 VTGHILPVDGG 250 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: 205 Number of extensions: 10 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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