Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Korea:Ga0059261_3091 Length = 430 Score = 216 bits (550), Expect = 1e-60 Identities = 145/434 (33%), Positives = 221/434 (50%), Gaps = 32/434 (7%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74 K I SAG ++EWYD+Y + A A F+ G ++ FAVGFL+RP G Sbjct: 15 KSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAAVFAVGFLMRPIGGW 74 Query: 75 VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134 + G D GRK +++++M + + LI + P + +GA A +L+ R++QGL++GG+ Sbjct: 75 LMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALLVFARLMQGLSIGGE 134 Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194 YG +AT+++E A + +RGF++S+ T G LI+LGV+LI + S+ EA WGWR+PF Sbjct: 135 YGASATYLSEMAGRKRRGFFSSFQYVTLISGQLIALGVLLILQASMSEAALESWGWRIPF 194 Query: 195 MASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMG 254 L ++ W+RR L E+ F+ K + L +P V+ G T+ Sbjct: 195 FIGGALAVIVFWLRRGLSETQSFENAK-AEGRKTGALALLREHPGEFLLVMALTAGGTLA 253 Query: 255 QGVVWYTGQFYAL-FYLQK-IFNTPLID---SNLIVGAALLLSMPFFVFFGSLSDRIGRK 309 FYA YLQK + NT D ++ I AAL + M G+LSDRIGRK Sbjct: 254 ---------FYAYSIYLQKFLVNTSGFDRETASEINAAALFVFMCIQPLAGALSDRIGRK 304 Query: 310 KVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVY 369 +M+ +L VL YPI+ + + +A G ++LG LV VT Sbjct: 305 PLMIGFGVLGVLCTYPIFTALEQVSSA-------WAAFG---LMLGALVI-----VTGYT 349 Query: 370 GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIA 429 A ELFP IR ++LPY + N +FGG + L G + W+ + Sbjct: 350 SINAVVKAELFPAHIRTLGVALPYALANAIFGGTAEYVAL-WFKDQGMERGFYWYVTGMI 408 Query: 430 GICLVVGFLLIKET 443 GI L+V +L +++T Sbjct: 409 GISLIV-YLRMRDT 421 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: 565 Number of extensions: 22 Number of successful extensions: 3 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: 430 Length adjustment: 33 Effective length of query: 435 Effective length of database: 397 Effective search space: 172695 Effective search space used: 172695 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 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