Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 200848 SO1683 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__MR1:200848 Length = 252 Score = 119 bits (297), Expect = 8e-32 Identities = 89/253 (35%), Positives = 128/253 (50%), Gaps = 23/253 (9%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFE----RLNV 71 L + ++TGGA G+G +A AQAGA++ + D++ D E A +L + E L++ Sbjct: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDI 62 Query: 72 TD-ADAVADLARRLPD---VDVLVNNAGIVRNAPAEDTPD---------DDWRAVLSVNL 118 TD D VA A L D ++VLVNNAGI+R+ D D +++V++VNL Sbjct: 63 TDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNL 122 Query: 119 DGVFWCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEW 178 G F C RE M+ G+ ++ ++S L Q+ Y ASKA V ++ A E Sbjct: 123 TGTFLCGREAAAAMIESGQAGVI--VNISSLAKAGNVGQSNYAASKAGVAAMSVGWAKEL 180 Query: 179 ASRGVRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAA 238 A +R AVAPG AT +T PE E K P+GRL EIA V ++ + Sbjct: 181 ARYNIRSAAVAPGVIATEMT--AAMKPEALERLEKLVPVGRLGHAEEIASTVRFIIEN-- 236 Query: 239 SFVTGHTLVVDGG 251 +V G VDGG Sbjct: 237 DYVNGRVFEVDGG 249 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: 142 Number of extensions: 10 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: 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