Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate N515DRAFT_3073 N515DRAFT_3073 Arabinose efflux permease
Query= TCDB::F8SVK1 (552 letters) >FitnessBrowser__Dyella79:N515DRAFT_3073 Length = 551 Score = 777 bits (2007), Expect = 0.0 Identities = 377/534 (70%), Positives = 446/534 (83%), Gaps = 3/534 (0%) Query: 18 KRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGFAAGFAVRPFGA 77 +RVI ASSLGTVFEWYDFYL GSLA I K FFSG+N T+AFIF LL FAAGFAVRPFGA Sbjct: 16 RRVILASSLGTVFEWYDFYLYGSLAVLIGKHFFSGLNETSAFIFALLAFAAGFAVRPFGA 75 Query: 78 LVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIAMRLLQGLALGG 137 +VFGRLGD+VGRKYTFLITI+IMGLST +VG LP Y+ +GM +PV+ I +RLLQGLALGG Sbjct: 76 IVFGRLGDLVGRKYTFLITIIIMGLSTFLVGVLPSYSTVGMIAPVLLIVLRLLQGLALGG 135 Query: 138 EYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGEDAFGAWGWRIP 197 EYGGAATYVAEHAP +RG YT++IQ TAT GLFLSLLVILG R A+G+ F WGWRIP Sbjct: 136 EYGGAATYVAEHAPDGKRGLYTSFIQITATFGLFLSLLVILGTRMALGDKVFEDWGWRIP 195 Query: 198 FVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLKIVILALIGVTA 257 F+ S VL+ +SV+IR+QL ESP F+++KAEGK SKAPL+EAFG WKNLK+VILAL+G TA Sbjct: 196 FLISSVLVAVSVYIRLQLQESPVFQQMKAEGKHSKAPLTEAFGHWKNLKVVILALLGATA 255 Query: 258 GQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSLSDRIGRKPIIL 317 GQAVVWYTGQFYAL+FLTQ+LK+DG +AN+LIA AL+IGTPFF+FFG LSDRIGRK I+L Sbjct: 256 GQAVVWYTGQFYALYFLTQSLKIDGTTANLLIAAALIIGTPFFVFFGWLSDRIGRKSIVL 315 Query: 318 AGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNPVGTSKFTSSCD 377 AGCL+AALTYFP+FK LTH+ NPA+E A +P+ VIA+P+ CSFQF+PVG SKFTSSCD Sbjct: 316 AGCLLAALTYFPIFKGLTHFGNPAIETAAASAPVTVIADPNACSFQFDPVGKSKFTSSCD 375 Query: 378 IAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADAKD---AGKAFDKNLGTA 434 +AK+ L+K G+ Y N AAPAG +AQ+ +G TI++++G D+ KAF +G A Sbjct: 376 VAKTVLAKKGIPYRNEAAPAGAVAQVTIGTGTIESFEGGGLDSATFAAQSKAFGTKIGDA 435 Query: 435 LKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTRIRYTSMSLPYH 494 LKAA YP KADP+Q N M V++L ILV+YVTMVYGPIAA LVEMFPTRIRYTSMSLPYH Sbjct: 436 LKAAGYPEKADPAQRNDVMLVILLAILVLYVTMVYGPIAAWLVEMFPTRIRYTSMSLPYH 495 Query: 495 IGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRETKDSNI 548 IGNGWFGGF+P F +VA KG+IY GLWYPII+A+ TF IGLLF++ETKD NI Sbjct: 496 IGNGWFGGFVPTIGFMLVAWKGDIYYGLWYPIIVAVGTFFIGLLFLKETKDVNI 549 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: 899 Number of extensions: 33 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: 551 Length adjustment: 36 Effective length of query: 516 Effective length of database: 515 Effective search space: 265740 Effective search space used: 265740 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