Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Ga0059261_2720 Ga0059261_2720 Arabinose efflux permease
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Korea:Ga0059261_2720 Length = 558 Score = 692 bits (1787), Expect = 0.0 Identities = 343/539 (63%), Positives = 425/539 (78%), Gaps = 10/539 (1%) Query: 15 KEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRP 74 + E++VI ASSLGTVFEWYDFYL G LA IS FFSGVN T AFI L FAAGFAVRP Sbjct: 10 RNERKVIIASSLGTVFEWYDFYLYGLLATVISAKFFSGVNETTAFILALGAFAAGFAVRP 69 Query: 75 FGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLA 134 FGALVFGRLGD+VGRKYTFL+T+ +MGLST VG LP YA+IG+A+P+I +A+RL+QGLA Sbjct: 70 FGALVFGRLGDVVGRKYTFLVTMGLMGLSTFAVGILPSYASIGVAAPIILVALRLVQGLA 129 Query: 135 LGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGW 194 LGGEYGGAATYVAEHAP +RG +T+WIQTTATLGLF +LLV++G+RTA+GE AF WGW Sbjct: 130 LGGEYGGAATYVAEHAPEGKRGLFTSWIQTTATLGLFAALLVVIGIRTAIGEAAFADWGW 189 Query: 195 RIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIG 254 R+PF+ S++LL +S+WIR+QL ESP F+++K EG TSKAP +EAFGQW+NL+ V++ L+G Sbjct: 190 RLPFLVSILLLAVSLWIRLQLAESPVFQKMKEEGTTSKAPFTEAFGQWRNLRTVLIVLLG 249 Query: 255 VTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKP 314 AGQAVVWYTGQFYALFFL +TLKVDGA+ANILIAIAL + TPFF+ FG+LSDRIGRK Sbjct: 250 AVAGQAVVWYTGQFYALFFLEKTLKVDGATANILIAIALALATPFFVIFGALSDRIGRKK 309 Query: 315 IILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKF-T 373 IIL GC +AA++YFP F ALT ANPAL AA +++P+ ++++ D CS QF+P+G +KF Sbjct: 310 IILTGCALAAISYFPTFHALTQAANPALAAAQRQAPVTIMSSNDICSVQFDPIGGNKFDQ 369 Query: 374 SSCDIAKSALSKAGLNYDNV------AAPAGTLAQIKVGDTTIDTYDGKA-ADAKDAG-- 424 S CDIAK+ L+K+G+ Y +V AP ++VG+ D A A+ A Sbjct: 370 SGCDIAKAYLAKSGIPYKSVPATLPPGAPTLKFTTVRVGEEDHPAPDPVGIAPAERAAVI 429 Query: 425 KAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRI 484 A+ L TAL A YP KADP+ +N P+ V +L LV+ VT VYGPIAA+LVE+FPTRI Sbjct: 430 AAYQAELKTALTRAGYPAKADPAAMNKPLIVALLFWLVLLVTAVYGPIAALLVEIFPTRI 489 Query: 485 RYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRET 543 RYT+MSLPYHIGNGWFGGFLP AFA+VAA G+IY GLWYPII+A+ T ++GLLF+ ET Sbjct: 490 RYTAMSLPYHIGNGWFGGFLPTIAFAMVAATGDIYYGLWYPIIVAVLTLILGLLFLPET 548 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: 868 Number of extensions: 38 Number of successful extensions: 6 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: 552 Length of database: 558 Length adjustment: 36 Effective length of query: 516 Effective length of database: 522 Effective search space: 269352 Effective search space used: 269352 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: 53 (25.0 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