Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate CCNA_01031 CCNA_01031 transporter, major facilitator superfamily
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Caulo:CCNA_01031 Length = 550 Score = 740 bits (1910), Expect = 0.0 Identities = 361/541 (66%), Positives = 438/541 (80%), Gaps = 3/541 (0%) Query: 11 APMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGF 70 AP + V+ ASSLGTVFEWYDFYL GSLA I+ FFSGVN T FI LL FAAGF Sbjct: 8 APAKGRDTMVVGASSLGTVFEWYDFYLYGSLAPIITSHFFSGVNETTGFILALLAFAAGF 67 Query: 71 AVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLL 130 A+RP GAL+FGRLGD+ GRK TFLIT+++MG+ST VVG LP YA IG+A+P+ + MRL+ Sbjct: 68 AIRPLGALIFGRLGDLWGRKNTFLITMLLMGVSTFVVGLLPSYAQIGVAAPIALVLMRLV 127 Query: 131 QGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFG 190 QGLALGGEYGGAATYVAEHAP +RGFYT+WIQTTAT+GLFLSL VIL R +GE+AF Sbjct: 128 QGLALGGEYGGAATYVAEHAPPGKRGFYTSWIQTTATIGLFLSLAVILVARIQLGEEAFK 187 Query: 191 AWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVIL 250 AWGWRIPF+ SL+LLG+S+WIR++LHESP FER+ AEGK SK PL+EAFG W NLKIV+L Sbjct: 188 AWGWRIPFLVSLLLLGVSLWIRLKLHESPTFERMIAEGKGSKKPLTEAFGNWPNLKIVLL 247 Query: 251 ALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRI 310 AL+G+T GQAVVWYTGQFYALFFL +TLK+DGA AN L+A+ALLIGTPFF+ G LSD+I Sbjct: 248 ALVGLTMGQAVVWYTGQFYALFFLEKTLKLDGALANTLVAVALLIGTPFFVICGWLSDKI 307 Query: 311 GRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTS 370 GRKPII+ GCL+AALTYFP+FKA+T YANPAL A +P+VV A+ C+FQF+ +G + Sbjct: 308 GRKPIIILGCLLAALTYFPIFKAITTYANPALAKAEATAPVVVTADTATCAFQFDLIGKA 367 Query: 371 KFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAK---DAGKAF 427 KF + CD+AK+ L+KAG++Y AAPAGT +KVGD T++ D K A + DA KA+ Sbjct: 368 KFNTPCDVAKAYLAKAGVSYSVQAAPAGTPTAVKVGDVTLEGLDSKGATGQAFADARKAW 427 Query: 428 DKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYT 487 + +LG LKAA YP KAD + +N P + +L +LVIYVTMVYGPIAAMLVE+FPTRIRYT Sbjct: 428 EADLGAQLKAAGYPAKADAALVNKPAVIGLLALLVIYVTMVYGPIAAMLVELFPTRIRYT 487 Query: 488 SMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSN 547 +MSLPYHIGNGWFGGFLP TAFAIVAA G+IYSGLWYP+IIA T V+G LF+++T+ + Sbjct: 488 AMSLPYHIGNGWFGGFLPTTAFAIVAATGDIYSGLWYPVIIAAITAVVGGLFLKDTRHNR 547 Query: 548 I 548 + Sbjct: 548 L 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: 893 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: 552 Length of database: 550 Length adjustment: 36 Effective length of query: 516 Effective length of database: 514 Effective search space: 265224 Effective search space used: 265224 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