Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate BPHYT_RS30290 BPHYT_RS30290 MFS transporter
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__BFirm:BPHYT_RS30290 Length = 452 Score = 216 bits (549), Expect = 2e-60 Identities = 117/323 (36%), Positives = 182/323 (56%), Gaps = 7/323 (2%) Query: 14 TSEERRVIFASSLGTVFEWYDFYLAGSLAIYI-SRTFFS-GVNPAAGFVFTLLGFAAGFA 71 TS+ RR + + LG V EWYDF+L G+ A + + FF G +P G + GF GF Sbjct: 18 TSKVRRAVTTAVLGQVLEWYDFFLYGTAAALVFGKLFFPVGSDPLTGTIAAFGGFTVGFI 77 Query: 72 VRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQ 131 RP G ++ G +GD GRK + T+L+MG +T +GLLP Y +G+ AP++ + +R+LQ Sbjct: 78 ARPIGGVLCGHIGDRYGRKTVMMLTLLVMGTATVCMGLLPTYQQVGIAAPIMLVLLRVLQ 137 Query: 132 GLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAA 191 GLA GGE+ G+ + E AP+++RGA AW A G +S L V++L D F + Sbjct: 138 GLAAGGEWSGSILLIHESAPASRRGALAAWSPCGAAFGFVLSTAAFLLVQTLSPAD-FHS 196 Query: 192 WGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLKIVLLA 251 WGWRVPFL S L+A+ +W+R + ES F +KA + ++ P+ E Q +L Sbjct: 197 WGWRVPFLCSAALVALGLWMRRSVDESAEFAAVKATHRDARMPVVEVLRQCPR---QVLT 253 Query: 252 LFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFFLFFGSLSDKIG 311 +FGL G+ Y +++ + Q + + + + V++L+ P L G L+D++G Sbjct: 254 VFGLRFGEGAASYIFFAFSIAY-GQFIGLKSSWVLGGLTVSMLLMIPVSLLMGRLTDRVG 312 Query: 312 RKPIIMAGCLIAALTYFPLFKAL 334 RKP+ +AG + L +P F L Sbjct: 313 RKPVYLAGAVAMVLVAYPYFTLL 335 Score = 32.3 bits (72), Expect = 4e-05 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 4/79 (5%) Query: 77 AIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALG 136 +++ GRL D +GRK +LA + M L + L G G + V A+ + + LG Sbjct: 301 SLLMGRLTDRVGRKPVYLAGAVAMVLVAYPYFTLLGSGVLWK----VITALVLANSITLG 356 Query: 137 GEYGGAATYVAEHAPSNKR 155 G +++E P + R Sbjct: 357 ILEGAQPAFISELLPVHLR 375 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: 594 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 552 Length of database: 452 Length adjustment: 34 Effective length of query: 518 Effective length of database: 418 Effective search space: 216524 Effective search space used: 216524 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: 52 (24.6 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