Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Ac3H11_3445 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3445 Length = 257 Score = 159 bits (403), Expect = 4e-44 Identities = 95/253 (37%), Positives = 142/253 (56%), Gaps = 13/253 (5%) Query: 10 ILDLFRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGT-FER 68 + LF L G+ ALVTGG++G+G ++A L + GA++ I D A + L+ +E Sbjct: 3 VKQLFDLTGQVALVTGGSRGLGLQMAEALGEMGAKLAITARKADELAEAKKHLEAQGYEV 62 Query: 69 LNVTD--------ADAVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDG 120 L V + V + R +D+LVNNAG A AED PD W V+ +N+ Sbjct: 63 LTVVNDLQKTEDIPGLVDQVVERFGTIDILVNNAGATWGAKAEDYPDAAWHKVMDLNVSA 122 Query: 121 VFWCCREFG-RTMLARGRGAIVSTASMSGLISNHPQPQA-AYNASKAAVIHLTRSLAGEW 178 F+ RE G R M+ RG+G+I+ TAS++ L P AYN SKAA +H R+LA EW Sbjct: 123 PFFLSREVGKRCMIPRGKGSIIVTASVAALKGTPPGMNTIAYNTSKAAALHFARTLASEW 182 Query: 179 ASRGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAA 238 GVRVNA+ PG+ + + +E + ++ TPL R+ ++ AV++LAS+A+ Sbjct: 183 GHYGVRVNAICPGFFPSKMASGLIE--KLGPAMIERTPLRRIGGEEDLKGAVVFLASNAS 240 Query: 239 SFVTGHTLVVDGG 251 +TG ++VVDGG Sbjct: 241 RHITGESIVVDGG 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: 177 Number of extensions: 8 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: 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