Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate 352759 BT3232 gluconate 5-dehydrogenase (NCBI ptt file)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Btheta:352759 Length = 267 Score = 121 bits (303), Expect = 2e-32 Identities = 83/260 (31%), Positives = 133/260 (51%), Gaps = 22/260 (8%) Query: 3 LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSS-TEVQGYALD 61 LK KV ++TG + G+G A+A +A+ GA + D++Q+ +++ A + GY D Sbjct: 9 LKGKVALVTGASYGIGFAIASAYAEQGATVCFNDINQELVDKGMAAYAEKGIKAHGYVCD 68 Query: 62 ITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVN 121 +TDE V A A I ++ G I++LVNNAGI+R + M F+ VI+++ Sbjct: 69 VTDEPAVQAMVATIEKEVGTIDILVNNAGIIRRVPM---------HEMEAADFRRVIDID 119 Query: 122 LTGTFLCGREAAAAMIESGQAGVIVNISSL-AKAGNVGQSNYAASKAGVAAMSVGWAKEL 180 L F+ + AM++ +AG I+NI S+ ++ G S YAA+K G+ ++ E Sbjct: 120 LNAPFIVSKAVLPAMMKK-RAGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEY 178 Query: 181 ARYNIRSAAVAPGVIATEMTAAMKPEALER--------LEKLVPVGRLGHAEEIASTVRF 232 YNI+ + PG IAT TA ++ + + + P GR EE+ F Sbjct: 179 GEYNIQCNGIGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVF 238 Query: 233 IIE--NDYVNGRVFEVDGGI 250 + ++ VNG V VDGGI Sbjct: 239 LASEASNAVNGHVLYVDGGI 258 Lambda K H 0.317 0.134 0.369 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: 163 Number of extensions: 6 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: 252 Length of database: 267 Length adjustment: 24 Effective length of query: 228 Effective length of database: 243 Effective search space: 55404 Effective search space used: 55404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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