Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate AO353_05775 AO353_05775 MFS transporter
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05775 Length = 446 Score = 230 bits (586), Expect = 1e-64 Identities = 120/341 (35%), Positives = 196/341 (57%), Gaps = 9/341 (2%) Query: 15 KEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRP 74 ++ +R ++ G + EWYD+ + G LA +I K+FF +PT++ + + FA F +RP Sbjct: 10 RQRRRAFIGATSGHLIEWYDYGVYGFLAVYIGKAFFVSDDPTSSLLASFAAFALSFFIRP 69 Query: 75 FGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLA 134 G L FG L D +GR+ T + +V+M ST ++G LP YA +G+A+P++ + +R +QG + Sbjct: 70 LGGLFFGPLADKIGRRKTLITVLVMMAGSTVLLGLLPTYATLGIAAPILLVLIRCVQGFS 129 Query: 135 LGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGW 194 GGE G ++++E+A RRGF T W+ TA LGL L V G+ MG D AWGW Sbjct: 130 AGGEIGTITSFISEYAGPGRRGFATCWLMVTAVLGLLLGGAVANGMTWVMGADLMQAWGW 189 Query: 195 RIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIG 254 RIPF+ + L IS++IR++L +SP F ++ G+TSKAPL E + QWK ++ +I Sbjct: 190 RIPFLIAAPLGLISMYIRLKLEDSPEFLALQRAGETSKAPLREVW-QWKRAIALVFFIIT 248 Query: 255 VTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKP 314 + + ++Y +A +++ LK D + + + +A L F G+ +D+ GRKP Sbjct: 249 L---HSSIFYLVLTFASTYMSSILKFDSGTTLLYVFVASLSAAVVMPFGGAFTDKYGRKP 305 Query: 315 IILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIA 355 +L +A L + LFK+ P A+ P++ +A Sbjct: 306 FLLVVGTLATLAMYWLFKSA-----PTATPASFIYPLMTVA 341 Score = 48.1 bits (113), Expect = 7e-10 Identities = 43/134 (32%), Positives = 63/134 (47%), Gaps = 13/134 (9%) Query: 415 GKAADAKDAGKAFDKNLGTALKAASY-----PPKADPSQLNWP-MTVVILTILVIYVTMV 468 G A K K F +GT A Y P A P+ +P MTV IL +Y + Sbjct: 294 GGAFTDKYGRKPFLLVVGTLATLAMYWLFKSAPTATPASFIYPLMTVAIL--FGLYASST 351 Query: 469 YGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIII 528 Y A++ E+ PTRIR T +++ Y+I FGG P + ++ G+I S WY I Sbjct: 352 Y----ALMSELLPTRIRSTGIAVAYNIPVAVFGGSAPLISTWLIKVTGDITSP-WYFYIG 406 Query: 529 ALATFVIGLLFVRE 542 +I L+ +R+ Sbjct: 407 TGVVSLIALVLLRK 420 Lambda K H 0.325 0.139 0.422 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: 634 Number of extensions: 34 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: 446 Length adjustment: 34 Effective length of query: 518 Effective length of database: 412 Effective search space: 213416 Effective search space used: 213416 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