Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate HSERO_RS15670 HSERO_RS15670 major facilitator transporter
Query= TCDB::Q7X4L6 (552 letters) >FitnessBrowser__HerbieS:HSERO_RS15670 Length = 427 Score = 182 bits (462), Expect = 2e-50 Identities = 104/337 (30%), Positives = 178/337 (52%), Gaps = 22/337 (6%) Query: 8 AAP-APITSEE-RRVIFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLG 65 AAP A IT + RR I +SS+G EW+D + G+ A+ I++ FF + + + T Sbjct: 6 AAPGADITHPQARRAIISSSIGNALEWFDILIYGAFAVVIAKQFFPTGDDSVSLLLTFAT 65 Query: 66 FAAGFAVRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFI 125 F F +RP GA+V G D GRK + +I+LM + T ++ +P Y +IG+ AP Sbjct: 66 FGVSFFMRPLGAVVLGAYSDRAGRKAALMLSIMLMTVGTAMIAFMPSYASIGLLAPAGIA 125 Query: 126 AMRMLQGLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLN 185 +M+QG + GGE+G + ++ EHAP ++RG +++W + + L ++ L + ++L Sbjct: 126 LGKMIQGFSAGGEFGSSTAFLVEHAP-HRRGFFSSWQVASQGISLLLAALFGAVLNNMLT 184 Query: 186 EDTFAAWGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNL 245 + A+WGWRVPF+ +++ ++IR L E+P F K + + APL + F K Sbjct: 185 PEQLASWGWRVPFIFGLLIAPAGIYIRRHLDEAPEF---KESSEKTNAPLRDTFAHQK-- 239 Query: 246 KIVLLALFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGT------SANMLVAVALLIGTPF 299 + L G AG ++ + +L+ T +K G +A + + + IG+P Sbjct: 240 ---MRLLIG--AGSVIMATVSVYLSLYIPTYAVKQLGLPAWSSFAAMSVAGLIMFIGSP- 293 Query: 300 FLFFGSLSDKIGRKPIIMAGCLIAALTYFPLFKALAH 336 G+LSDKIGR P ++ + + +P+F L + Sbjct: 294 --LVGALSDKIGRTPFMITSSALYIVLTYPMFVFLTN 328 Score = 43.5 bits (101), Expect = 2e-08 Identities = 26/84 (30%), Positives = 46/84 (54%), Gaps = 1/84 (1%) Query: 455 ILILTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPYHIGNGWFGGFLPATAFAIIAA 514 +L+ T++ + +TM + + A+L ++FP R T MSL Y+I FGGF +I Sbjct: 336 LLLQTVIGVLMTMYFAAMPALLADIFPVATRGTGMSLAYNIAVTIFGGFAGLIITWLIDF 395 Query: 515 RGNIYSGLWYPIVIASVAFVIGTL 538 G+ S + Y ++ +V +I +L Sbjct: 396 TGDKLS-VSYFVIFGAVLSLIASL 418 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: 561 Number of extensions: 21 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: 427 Length adjustment: 34 Effective length of query: 518 Effective length of database: 393 Effective search space: 203574 Effective search space used: 203574 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