Align tonoplast dicarboxylate transporter (characterized)
to candidate WP_017600457.1 D471_RS0121060 DASS family sodium-coupled anion symporter
Query= CharProtDB::CH_091173 (540 letters) >NCBI__GCF_000341125.1:WP_017600457.1 Length = 533 Score = 274 bits (700), Expect = 7e-78 Identities = 178/546 (32%), Positives = 276/546 (50%), Gaps = 40/546 (7%) Query: 5 DVTVAGSDDLKSPLLPVVHNDEPFERQTVGQQLRTIFTPKNCYIALGPLLCAVVC-LCVD 63 D V D P PV P ++ T P+ + LGP+L +V L D Sbjct: 5 DPAVNAPDSASVPRQPV-----PQDKDRASGNRETNPLPRRIGLVLGPVLGLLVYFLLPD 59 Query: 64 LG---------GDETTTARNMLGVLVWMFAWWLTEAVPMPITSMTPLFLFPLF--GISAA 112 + GD R + G+ V++ WW TEA+P+P+TS+ PL FP+ G+ A Sbjct: 60 MPLPLPDGEGMGDLAVNGRAVAGITVFIATWWATEAIPIPVTSLVPLVAFPILVDGV-AV 118 Query: 113 DDVANSYMDDVISLVLGSFILALAVEHYNIHRRLALNITLVFCVEPLNAPLLLLGICATT 172 DVA SY I L +G F+LALA++ +N+H+R+AL T+V V N L+ G T Sbjct: 119 GDVAPSYGSPTIFLFMGGFMLALAMQRWNLHKRIAL--TIVSKVGS-NTVGLIGGFMVAT 175 Query: 173 AFVSMWMHNVAAAVMMMPVATGILQRLPS-SSSTTEVVHPAVGKFSRAVVLGVIYSAAVG 231 AF+SMW+ N A VMM+PV ++ + T+ F+ A++LG+ Y+A++G Sbjct: 176 AFISMWVSNTATTVMMLPVGLSVVALITQFRGGRTDA------NFATALMLGIAYAASIG 229 Query: 232 GMSTLTGTGVNLILVGMWKSYFPEADPISFSQWFFFGFPLALCIFVVLWCVLCVMYCPKG 291 ++TL GT N+++V + I F QW G P+A+ + W VL + G Sbjct: 230 SVATLIGTPPNVLMVAYLSEFHDIT--IGFGQWMMVGLPIAVAFLFLAWVVLARLLFRPG 287 Query: 292 AGQALSPYLHKSHLRRELDLLGPMNFAEKMVLAVFGGLVVLWMTRNITDDIP--GWGRIF 349 + + +R EL +GP++ EK+VLAVF + W+ + D G + Sbjct: 288 VKRVEGA---QELIRDELREMGPISRPEKLVLAVFVTAALSWIFVPMRADSQTIGGALPW 344 Query: 350 AGRAGDGTVSVMMATLLFIIPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIADGVRTS 409 G D +++ +A LF+IP+ G +L+DW+ KLPW I+LL G G AI+ S Sbjct: 345 LGGISDPVIAMAVAVALFLIPAERGTGTRLLDWDTAVKLPWGILLLFGGGIAISGQFTAS 404 Query: 410 GLAEVLSKGLVFLETAPYWAIAPTVCLIAATITEFTSNNATTTLLVPLLIEIAKNMGIHP 469 GL+ + + L P W + V + +TE TSN ATT+ +P+L +A + + Sbjct: 405 GLSVWIGGQVSVLGGVPIWVLVLCVTAVVLLLTELTSNTATTSTFLPVLGGVAAGLDVDV 464 Query: 470 LLLMVPGAIGAQFAFLLPTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTIFLSILMPTL 529 L+L+VP + A AF+LP TP N + F +GHI I M++ G+ L +A ++ + L Sbjct: 465 LVLVVPAVLAASMAFMLPVATPPNAIVFGSGHITINQMMRGGVLLNLA-----ALFVVLL 519 Query: 530 GAYVFA 535 G Y A Sbjct: 520 GMYALA 525 Lambda K H 0.326 0.140 0.441 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: 928 Number of extensions: 52 Number of successful extensions: 7 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: 540 Length of database: 533 Length adjustment: 35 Effective length of query: 505 Effective length of database: 498 Effective search space: 251490 Effective search space used: 251490 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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