Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate HSERO_RS05210 HSERO_RS05210 3-oxoacyl-ACP reductase
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >FitnessBrowser__HerbieS:HSERO_RS05210 Length = 261 Score = 335 bits (860), Expect = 5e-97 Identities = 165/253 (65%), Positives = 201/253 (79%), Gaps = 1/253 (0%) Query: 28 LAKFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPR 87 LA FPSL+G+ VF+TGGG+GIGAAIV AFA+QGA VAFVD+A EASEAL +A AG P+ Sbjct: 10 LASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPK 69 Query: 88 PWWRVCDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINE 147 P +R CD+RD+ A QA +A+ A+LG DF VLVNN A+D RH LE VT EY+++R+AIN+ Sbjct: 70 PLFRHCDLRDIPAFQATIAELQAQLG-DFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQ 128 Query: 148 RPAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQ 207 RP+FFA+Q+VV GM+R G GS+IN S W G G+P Y AK+S GLTRGLA+ LG Sbjct: 129 RPSFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGP 188 Query: 208 DRIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAM 267 +IR+NTV+PGWVMTERQIKLWLD EG+K +ARNQCL L P +ARMVLFLA+DD+AM Sbjct: 189 HKIRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAM 248 Query: 268 CTAQEFKVDAGWV 280 CTAQEF VDAGWV Sbjct: 249 CTAQEFIVDAGWV 261 Lambda K H 0.320 0.133 0.405 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: 216 Number of extensions: 2 Number of successful extensions: 2 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: 280 Length of database: 261 Length adjustment: 25 Effective length of query: 255 Effective length of database: 236 Effective search space: 60180 Effective search space used: 60180 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