Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Ac3H11_719 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_719 Length = 456 Score = 500 bits (1287), Expect = e-146 Identities = 246/413 (59%), Positives = 321/413 (77%) Query: 4 RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63 R P Y+ LYFQV++AI +G+LLGHF P G ALKPLGD FIKL+KM+IAP+IF T+V+GI Sbjct: 13 RLPFYRQLYFQVVLAIVLGVLLGHFEPSYGEALKPLGDAFIKLVKMIIAPVIFLTIVTGI 72 Query: 64 AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123 AGM + +VG+ G A+ YF ST+AL++GLVV NVVQPG GM+I+V+ LD S V YV Sbjct: 73 AGMSQLSTVGRVFGKAMAYFLFFSTLALVVGLVVANVVQPGAGMNINVADLDQSAVKGYV 132 Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183 + ++ GF L++IP T+V F +ILQVL+ +V+FG L +G G+PVL+F+D Sbjct: 133 AKSHEMTLTGFALDIIPKTLVSPFVGDNILQVLLVAVLFGVGLAMVGDAGRPVLNFLDAL 192 Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243 +F ++ ++MK AP+GA GAMAFTIG +G+GSLV L L+ FYIT +LFV+V+LG + Sbjct: 193 TTPVFKVVGIVMKAAPLGAFGAMAFTIGKFGLGSLVNLAWLVGSFYITSLLFVVVILGFV 252 Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303 R GFSV KL RY++ EL++VLGTSSSESALP ++ KME+ G KSVVGLV+PTGYSFN Sbjct: 253 ARLCGFSVFKLCRYLKAELMLVLGTSSSESALPSLMEKMEKAGCSKSVVGLVVPTGYSFN 312 Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363 LDGT+IY+T+AA+FIAQAT+T + + HQ+ LLLV +LSSKGAAGVTG+GFI LAATL+ V Sbjct: 313 LDGTNIYMTLAALFIAQATNTELTLGHQVALLLVAMLSSKGAAGVTGAGFITLAATLAVV 372 Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416 +PVAG+ALILG+DRFMSE R+LTN +GNAVATVVV++W LD ++L A L Sbjct: 373 PEVPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWENALDHERLDAAL 425 Lambda K H 0.326 0.142 0.402 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: 623 Number of extensions: 19 Number of successful extensions: 1 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: 444 Length of database: 456 Length adjustment: 33 Effective length of query: 411 Effective length of database: 423 Effective search space: 173853 Effective search space used: 173853 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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