Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate AO353_04405 AO353_04405 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04405 Length = 438 Score = 228 bits (581), Expect = 3e-64 Identities = 145/448 (32%), Positives = 230/448 (51%), Gaps = 40/448 (8%) Query: 15 KVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 +V AS GT IE+YDFY++ A A + F+ + +++ TF + FL RP G+ Sbjct: 21 RVATASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQMLSAFLTFGIAFLARPLGS 80 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 +FG GD +GRK T + ++ +MG CT LIG+LP + +GAWA I+L +R QGL LGG Sbjct: 81 ALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYESIGAWAPILLCVLRFGQGLGLGG 140 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGAA E+AP+GKR ++ + Q + G L + G+ L ++L + F WGWR+P Sbjct: 141 EWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTLAMTLNDEQFRSWGWRIP 200 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATM 253 F+ S +LV++ L++R L E+P+F + K PL E F+ W + L A M Sbjct: 201 FLLSAVLVMVGLYVRLKLHETPVFANAMARQERVKIPLVELFSQ----YWAPMLLGAAAM 256 Query: 254 GQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLS-MPFFVFFGS--------LSD 304 VV YALFY+ +F+ S L L + F V F + SD Sbjct: 257 ---VV-----CYALFYISTVFSLSYGVSTLGYSRETFLGLLCFAVLFMAAATPLSAWASD 308 Query: 305 RIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIY 364 R GRK V++ G +LA+L+ + + L+ + L + I++ Sbjct: 309 RFGRKPVLIIGGVLAILSGFTMEPLLTHGTTWG----------------VALFLCIELFL 352 Query: 365 VTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWW 424 + + + P+ A L ELFPT++RYT S Y++G V P L+ G + G + Sbjct: 353 MGVTFAPMGALLPELFPTRVRYTGASAAYNLGGIVGASAAPFFAQKLVAMGGLSWVGGY- 411 Query: 425 PMAIAGICLVVGFLLIKETNKVDISDAS 452 ++ A + ++ L +KET D++ + Sbjct: 412 -VSAAAVISLIAVLCLKETRHNDLNQVA 438 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: 629 Number of extensions: 39 Number of successful extensions: 5 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: 438 Length adjustment: 33 Effective length of query: 435 Effective length of database: 405 Effective search space: 176175 Effective search space used: 176175 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