Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate Ac3H11_3022 putative sugar transport protein
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3022 Length = 543 Score = 796 bits (2055), Expect = 0.0 Identities = 392/543 (72%), Positives = 457/543 (84%), Gaps = 3/543 (0%) Query: 13 MTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAV 72 M+ EE++VIFASSLGTVFEWYDFYL GSLAA I+K FFSG++ +AFIF LL FAAGF V Sbjct: 1 MSPEERKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDSGSAFIFALLAFAAGFIV 60 Query: 73 RPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQG 132 RPFGA+ FGRLGDM+GRKYTFL+TI+IMGLST +VG LP YA+IG+A+P+I I +RLLQG Sbjct: 61 RPFGAIFFGRLGDMIGRKYTFLVTILIMGLSTFIVGILPTYASIGVAAPIILIVLRLLQG 120 Query: 133 LALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAW 192 LALGGEYGGAATYVAEHAP RRG YTAWIQTTATLGLFLSL+VILG RT +GE+AF W Sbjct: 121 LALGGEYGGAATYVAEHAPHGRRGAYTAWIQTTATLGLFLSLMVILGTRTIVGEEAFADW 180 Query: 193 GWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILAL 252 GWR+PF+ S+VLL ISVWIR+ ++ESPAF+++KAEGKTSKAPL E+FG+WKNLKIVILAL Sbjct: 181 GWRVPFIVSIVLLAISVWIRLAMNESPAFQKMKAEGKTSKAPLKESFGEWKNLKIVILAL 240 Query: 253 IGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGR 312 +G+TAGQAVVWY+GQFYALFFLTQ LKVDGA+ANIL+A++LLIGTPFF+ FGSLSD+IGR Sbjct: 241 VGLTAGQAVVWYSGQFYALFFLTQALKVDGATANILVAVSLLIGTPFFIVFGSLSDKIGR 300 Query: 313 KPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKF 372 KPIILAGCL+AALTYFP+F ALT ANPAL A K+ +VV+A+ +ECSFQFNP GT KF Sbjct: 301 KPIILAGCLLAALTYFPVFGALTKAANPALAEAQAKNKVVVVADANECSFQFNPTGTVKF 360 Query: 373 TSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKDAGK---AFDK 429 TSSCDIAK L+ A ++Y+N AGT A IK+G+T I Y K A +A K F K Sbjct: 361 TSSCDIAKQVLAGASVSYENAPGAAGTPAVIKIGETAITGYSSKGLPADEAKKKDGEFKK 420 Query: 430 NLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSM 489 + ALKAA YP KADP++++ M IL LV+ VTMVYGPIAAMLVEMFPTRIRYTSM Sbjct: 421 AVADALKAAGYPTKADPARIDKVMVTAILVYLVLLVTMVYGPIAAMLVEMFPTRIRYTSM 480 Query: 490 SLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNIY 549 SLPYHIGNGWFGG LP TAFAIVA GN+Y+GLWYPIIIA AT VIG LF++ETKD +IY Sbjct: 481 SLPYHIGNGWFGGLLPTTAFAIVAQTGNMYNGLWYPIIIAAATVVIGGLFIKETKDVDIY 540 Query: 550 AQD 552 A D Sbjct: 541 AND 543 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: 889 Number of extensions: 33 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: 543 Length adjustment: 36 Effective length of query: 516 Effective length of database: 507 Effective search space: 261612 Effective search space used: 261612 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