Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate WP_057507967.1 ABB28_RS07090 MFS transporter
Query= TCDB::M1Q159 (468 letters) >NCBI__GCF_001431535.1:WP_057507967.1 Length = 445 Score = 199 bits (505), Expect = 2e-55 Identities = 126/395 (31%), Positives = 195/395 (49%), Gaps = 31/395 (7%) Query: 21 SAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAIVFGRIG 80 SAG ++EWYD Y++ A S+F++ + W G FA FL+RP GA FGR Sbjct: 29 SAGNLVEWYDVYVYSVFAKYFESQFFSADDKNSTMYIW-GIFAATFLMRPIGAWYFGRFA 87 Query: 81 DLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGGAAT 140 D GR+ +++++M +C+FLI + PT +G WA +IL+ R+LQG A GG+YG +AT Sbjct: 88 DRYGRRLALTVSVSVMAACSFLIAIAPTAASIGIWAAVILLFARLLQGFATGGEYGASAT 147 Query: 141 FVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMASILL 200 +++E A G RGF +S+ T G +++ V+L+ +S + +EWGWR+ F + Sbjct: 148 YMSEAAVPGWRGFLSSFHYVTLVGGHVLAQAVLLVMLLSWDTSHVSEWGWRVAFGIGGIG 207 Query: 201 VILSLWIRRALKES---PLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQGV 257 ++ W+RR + ES + KD KA + ++E F N + L+ F T G V Sbjct: 208 ALVVFWLRRTMDESLSAESIEAAKDGKAKASGSMRELFVNQWR---PLLLCFLITAGGTV 264 Query: 258 VWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFF-----GSLSDRIGRKKVM 312 +YT K+ T ++I G + L + F+ G LSDRIGRK ++ Sbjct: 265 AFYTYTING----PKMIQTAFAGDDVITGTWINLGVLTFLMLLQPLGGLLSDRIGRKSLL 320 Query: 313 LSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPI 372 + + VL Y Y + A T FL G+ + +T Sbjct: 321 VFFGVGGVL--YTWYLVTALPQQTSALSAFLILATGF-------------VILTGYTSIN 365 Query: 373 AAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMI 407 A ELFP IR + L Y + N +FGG P++ Sbjct: 366 AVVKAELFPAHIRALGVGLGYALANSLFGGTAPLL 400 Lambda K H 0.328 0.144 0.450 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: 42 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: 468 Length of database: 445 Length adjustment: 33 Effective length of query: 435 Effective length of database: 412 Effective search space: 179220 Effective search space used: 179220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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