Align tonoplast dicarboxylate transporter (characterized)
to candidate Echvi_3555 Echvi_3555 anion transporter
Query= CharProtDB::CH_091173 (540 letters) >FitnessBrowser__Cola:Echvi_3555 Length = 485 Score = 270 bits (690), Expect = 9e-77 Identities = 157/490 (32%), Positives = 266/490 (54%), Gaps = 25/490 (5%) Query: 44 KNCYIALGPLLCAVVCLCVDLGGDETTTARNMLGVLVWMFAWWLTEAVPMPITSMTPLFL 103 K + LGP+ ++ L + G T A+ +L + VWM WW+ EA+P+ T++ PL + Sbjct: 7 KRSGLVLGPVAFLLIVLFFNPDG-LTYEAQAVLALAVWMAIWWILEAIPIAATALLPLVI 65 Query: 104 FPLFGISAADDVANSYMDDVISLVLGSFILALAVEHYNIHRRLALNITLVFCVEPLNAPL 163 PL G + D+ A Y D + L +G F++A+ +E +N+H+R+AL+I + + Sbjct: 66 LPLTGALSMDESAAPYADPKVLLYMGGFMIAVTIEKWNLHKRIALSIISLIGTD---MRF 122 Query: 164 LLLGICATTAFVSMWMHNVAAAVMMMPVATGILQRLPSSSSTTEVVHPAVGKFSRAVVLG 223 ++LG TA +SMW+ N A ++MM+P+A ++ +L S + +A++LG Sbjct: 123 IVLGFMLATALLSMWISNTATSLMMLPIAVAVIHQLADGSDEISAT-----RIGQALMLG 177 Query: 224 VIYSAAVGGMSTLTGTGVNLILVGMWKSYFPEADPISFSQWFFFGFPLALCIFVVLWCVL 283 + YSA++GG++T+ GT N++LVG+ K + I F++W G P++L + + W L Sbjct: 178 IAYSASIGGLATIIGTPTNIVLVGIVKELY--GIEIGFAEWMLVGLPISLGLLGICWWYL 235 Query: 284 CVMYCPKGAGQALSPYLHKSHLRRELDLLGPMNFAEKMVLAVFGGLVVLWMTRNITDDIP 343 + P +L+ K ++R+L +GP++ E VL VF + W+TR D+ Sbjct: 236 VSVAYPFPKNMSLAG--GKVEIQRQLAAIGPISKPEIRVLLVFLLVSFSWITRVFLQDLL 293 Query: 344 GWGRIFAGRAGDGTVSVMMATLLFIIPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIA 403 + D ++++ LLF++PS+ K ++L+DW + +PW I+LL G G A+A Sbjct: 294 PF-------LNDTIIALVGVLLLFMLPSSRGK-KRLLDWKTAEDIPWGILLLFGGGLALA 345 Query: 404 DGVRTSGLAEVLSKGLVFLETAPYWAIAPTVCLIAATITEFTSNNATTTLLVPLLIEIAK 463 G + +GLA L L+ + + +TE TSN AT ++L+P+L +A Sbjct: 346 AGFKETGLAAWLGSHFEALQGVHFLLFILIIVASVNFLTEITSNVATASMLLPILGAVAL 405 Query: 464 NMGIHPLLLMVPGAIGAQFAFLLPTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAG----T 519 +G+HP LMV + A AF+LP TP N V F +G++ I M K GL + I T Sbjct: 406 ALGVHPYGLMVAATMAASCAFMLPVATPPNAVVFGSGYLTIPAMAKAGLWMNILSIFFIT 465 Query: 520 IFLSILMPTL 529 +F+ +MP L Sbjct: 466 LFVYYIMPFL 475 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: 866 Number of extensions: 65 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: 540 Length of database: 485 Length adjustment: 35 Effective length of query: 505 Effective length of database: 450 Effective search space: 227250 Effective search space used: 227250 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 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