Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate GFF2310 Psest_2358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__psRCH2:GFF2310 Length = 252 Score = 144 bits (362), Expect = 2e-39 Identities = 101/246 (41%), Positives = 132/246 (53%), Gaps = 12/246 (4%) Query: 15 RLDGRHALVTGGAQGIGFEIARGLAQAGARVTIA-----DL-NPDVGEGAARELDGTFER 68 R G+ AL+TG A GIG A LA GARV I DL N V + A D Sbjct: 5 RFAGQTALITGAATGIGRATALALAAEGARVWINHRDQHDLANQLVEQITANGGDAWAIE 64 Query: 69 LNVTDADAVADLARRLP---DVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCC 125 +V+D AVA + + +D+LVNNAG++ P +T + DW VL V+L GV+ CC Sbjct: 65 ADVSDPAAVAAMFETIEAQGSLDLLVNNAGVILEKPFLETSEADWAMVLGVDLGGVYRCC 124 Query: 126 REFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRV 185 R M R GAIV+ AS G + + AY +KA VI LTRSLA E+A+ G+RV Sbjct: 125 RHALAQMQPRRSGAIVNVASDLGFLGR--EQYVAYCTAKAGVIGLTRSLAREFAADGIRV 182 Query: 186 NAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGHT 245 N VAPG AT + + EW L P+ RL P E+A A+++L S AS+ TG Sbjct: 183 NGVAPGPIATAMVSPEHMSDEWMAKEL-AIPMARLGTPEEVAAAIVFLLSPQASYFTGQL 241 Query: 246 LVVDGG 251 L +GG Sbjct: 242 LGPNGG 247 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: 183 Number of extensions: 9 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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