Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate H281DRAFT_03703 H281DRAFT_03703 NADP-dependent 3-hydroxy acid dehydrogenase YdfG
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_03703 Length = 257 Score = 143 bits (361), Expect = 3e-39 Identities = 101/250 (40%), Positives = 131/250 (52%), Gaps = 17/250 (6%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAAREL-----DGTFERLN 70 L G+HA+VTGG GIG IA L AGARVT+ N + A RE D ++ Sbjct: 8 LAGQHAVVTGGGSGIGAAIAEALLHAGARVTLMGRNSE-RLAAQREKCRAWGDVACITVD 66 Query: 71 VTDADAVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWCCREFGR 130 VT ++VA VD+L+NNAG + AP T W+ +L VNL GVF R Sbjct: 67 VTQEESVAKAFNEAGAVDILINNAGQAQAAPFTHTDMTLWQRMLDVNLTGVFLGTRAVLP 126 Query: 131 TMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVRVNAVAP 190 ML R G IV+ AS +G I AAY A+K VI LTRSLA E A++GV VNAV P Sbjct: 127 GMLERRHGRIVNVASTAGQIGY--AYVAAYCAAKHGVIGLTRSLALEVATKGVTVNAVCP 184 Query: 191 GYTATPLTRRGLE---------TPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFV 241 GYT T L L+ + RE+ L+ P R P ++A AVL+L + + Sbjct: 185 GYTETELLHASLQQITSKTSRTEEQARESLLRSNPQHRFVSPEQVANAVLWLCQPGSDAI 244 Query: 242 TGHTLVVDGG 251 TG ++ + GG Sbjct: 245 TGQSVSISGG 254 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: 166 Number of extensions: 7 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: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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