Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate WP_057508837.1 ABB28_RS11900 MFS transporter
Query= TCDB::Q7X4L6 (552 letters) >NCBI__GCF_001431535.1:WP_057508837.1 Length = 408 Score = 189 bits (480), Expect = 2e-52 Identities = 107/317 (33%), Positives = 171/317 (53%), Gaps = 10/317 (3%) Query: 21 IFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLGFAAGFAVRPFGAIVF 80 ++ ++L TV EWYDF L A +SR FF G A + TL GFA + +RP GA+ F Sbjct: 1 MWVAALSTVVEWYDFTLYLYFATVLSRVFFGGGETA--LLATLAGFAVSYLMRPLGALCF 58 Query: 81 GRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALGGEYG 140 G LGD +GR++ LA++ LM + LLP Y IG +A V+ +A+R + ++GGEY Sbjct: 59 GHLGDRLGRRWMLLASMALMAAAMLATALLPTYAQIGASAGVLLLALRCVMAFSVGGEYT 118 Query: 141 GAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAAWGWRVPFLV 200 G Y+ E AP +RG T+ + +G +++ + +LL WGWR+PF V Sbjct: 119 GVVAYLLESAPPRRRGLVTSLASAASEVGALLAVALSALTVALLPAPALDTWGWRIPFFV 178 Query: 201 SIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLKIVLLALFGLTAGQA 260 L + + R +HESP FER + EG AP+ + ++ + F ++A + Sbjct: 179 GAGLALLILLARSGMHESPEFERQQREGSVPSAPIRQIL---RSHPGAVARTFAISALGS 235 Query: 261 VVWYTGQFYTLFFLTQTLKVDGTS--ANMLVAVALLIGTPFFLFFGSLSDKIGRKPIIMA 318 + +Y G Y FL + +G + + + AVA+++ TP FG LSD+ GR+P+++ Sbjct: 236 ITYYVGITYVPAFLHANGRGEGEALWLSTIAAVAVILATP---LFGLLSDRFGRRPLLLG 292 Query: 319 GCLIAALTYFPLFKALA 335 L++AL +F +A Sbjct: 293 LTLLSALLPLSMFGWMA 309 Lambda K H 0.325 0.139 0.420 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: 556 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 552 Length of database: 408 Length adjustment: 33 Effective length of query: 519 Effective length of database: 375 Effective search space: 194625 Effective search space used: 194625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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