Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate Echvi_1862 Echvi_1862 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= uniprot:Q8EGC1 (252 letters) >FitnessBrowser__Cola:Echvi_1862 Length = 246 Score = 123 bits (308), Expect = 4e-33 Identities = 86/249 (34%), Positives = 124/249 (49%), Gaps = 18/249 (7%) Query: 7 VVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQDKLERACADLGSSTEVQGYALDITDEE 66 + ++TGGA GLGLA A F +I ++ KL +A +LG + YA D+ D Sbjct: 5 IALVTGGASGLGLATAKKFCDHDITTIIIGRNESKLAKAQEELGPNCHY--YAFDLNDLP 62 Query: 67 DVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQFQSVINVNLTGTF 126 ++ I + GKI++LVNNAGI ++ D ++FQ +I N+ F Sbjct: 63 NIPDLINTITTEHGKIDILVNNAGINMKKPFIEVTD---------EEFQQIITTNVFAVF 113 Query: 127 LCGREAAAAMIESGQAGVIVNISSLAKAGNVGQS-NYAASKAGVAAMSVGWAKELARYNI 185 RE A M S + G IVNISS+A + + Y ASK+ + M+ A EL+ I Sbjct: 114 SLSREIAKTMA-SQKHGAIVNISSMASQYGIPKVIAYTASKSAIEGMTKAMAVELSPLGI 172 Query: 186 RSAAVAPGVIATEMTAAM---KPEALERLEKLVPVGRLGHAEEIASTVRFIIEN--DYVN 240 R VAPG IATEM+A PE +++ P+G LG IA V ++ Y+ Sbjct: 173 RVNCVAPGFIATEMSAKALNGDPERKQKVLSRTPMGALGTPANIADAVYYLASESASYIT 232 Query: 241 GRVFEVDGG 249 G + VDGG Sbjct: 233 GTILPVDGG 241 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: 112 Number of extensions: 4 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: 252 Length of database: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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: 46 (22.3 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