Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate AO356_06425 AO356_06425 MFS transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_06425 Length = 437 Score = 226 bits (576), Expect = 1e-63 Identities = 147/445 (33%), Positives = 227/445 (51%), Gaps = 40/445 (8%) Query: 15 KVIFASSAGTVIEWYDFYIFG-ALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 +V AS GT IE+YDFY++ A A + F+ + +++ TF + FL RP G+ Sbjct: 20 RVATASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQMLSSFLTFGIAFLARPLGS 79 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 +FG GD +GRK T + ++ +MG CT LIG+LP +GAWA I+L +R QGL LGG Sbjct: 80 ALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYASIGAWAPILLCLLRFGQGLGLGG 139 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGAA E+AP+GKR ++ + Q + G L + G+ L +SL + F +WGWR+P Sbjct: 140 EWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTLAMSLDDEQFRDWGWRIP 199 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATM 253 F+ S +LVI+ L++R L E+P+F + K PL E F+ W L A M Sbjct: 200 FLLSAVLVIVGLYVRLKLHETPVFANAMARQERVKVPLVELFSQ----YWAPTLLGAAAM 255 Query: 254 GQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLS-MPFFVFFGS--------LSD 304 VV YALFY+ +F+ S L L + F V F + SD Sbjct: 256 ---VV-----CYALFYISTVFSLSYGVSTLGYSRETFLGLLCFAVLFMAAATPLSAWASD 307 Query: 305 RIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIY 364 R GRK +++ G LLA+ + + + L+ + + L + I++ Sbjct: 308 RYGRKPILIIGGLLAIASGFLMEPLLTHGSTGG----------------VALFLCIELFL 351 Query: 365 VTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWW 424 + + + P+ A L ELFPT +RYT S Y++G V P L+ G + G + Sbjct: 352 MGVTFAPMGALLPELFPTHVRYTGASAAYNLGGIVGASAAPFFAQKLVAMGGLSYVGGY- 410 Query: 425 PMAIAGICLVVGFLLIKETNKVDIS 449 ++ A + V+ L +KET D++ Sbjct: 411 -VSAAALLSVIAVLCLKETRHNDLN 434 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: 609 Number of extensions: 37 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: 437 Length adjustment: 33 Effective length of query: 435 Effective length of database: 404 Effective search space: 175740 Effective search space used: 175740 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