Align tonoplast dicarboxylate transporter (characterized)
to candidate Echvi_4197 Echvi_4197 anion transporter
Query= CharProtDB::CH_091173 (540 letters) >FitnessBrowser__Cola:Echvi_4197 Length = 491 Score = 271 bits (693), Expect = 4e-77 Identities = 166/492 (33%), Positives = 261/492 (53%), Gaps = 30/492 (6%) Query: 44 KNCYIALGPLLCAVVCLCVDLGGDETTTARNMLGVLVWMFAWWLTEAVPMPITSMTPLFL 103 K + LGP++ + L +D + A +L V +WM WW+ EAVP+ +T++ P+ L Sbjct: 7 KKWSLILGPMVFIGLIL-LDPPSGMSEEALKVLAVTLWMAIWWIAEAVPIAVTALLPIVL 65 Query: 104 FPLFGISAADDVANSYMDDVISLVLGSFILALAVEHYNIHRRLALNITLVFCVEPLNAPL 163 FP+ G +Y I L +G FILALA+E + +H+R+AL ++ + N Sbjct: 66 FPITGAVEIGITTEAYGHKYIFLYMGGFILALAIERWGLHQRIAL---IIISLIGSNMNS 122 Query: 164 LLLGICATTAFVSMWMHNVAAAVMMMPVATGILQRLPSSSST-TEVVHPAVGKFSRAVVL 222 ++LG TAF+SMW+ N A AVMM+P+ I+ + S + VGK A++L Sbjct: 123 IMLGFMLATAFLSMWISNTATAVMMLPIGMAIVNQFAKVSDIYPDNREKEVGK---ALML 179 Query: 223 GVIYSAAVGGMSTLTGTGVNLILVGMWKSYFPEADPISFSQWFFFGFPLALCIFVVLWCV 282 + YSA++GG +TL GT NL+L G+ + + +SF W FGFPL++ + ++ W Sbjct: 180 AIAYSASIGGFATLIGTPPNLVLAGIIEELYDVK--LSFLDWMKFGFPLSMLLLIICWKY 237 Query: 283 LCVMY--CPKGAGQALSPYLHKSHLRRELDLLGPMNFAEKMVLAVFGGLVVLWMTRNITD 340 L C K K + + L LG ++F EK VL +F W+ R+ Sbjct: 238 LTTYAFDCKKVDFPG-----GKQEINKMLKALGKISFEEKWVLIIFALTAAAWILRSFIQ 292 Query: 341 DIPGWGRIFAGRAGDGTVSVMMATLLFIIPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGF 400 R+ G D +++M A LF++PS K KL++W + KLPW I+LL G G Sbjct: 293 ------RLLPG-IDDAVIALMAAITLFVLPSKSGK-RKLINWEEAVKLPWGIILLFGGGM 344 Query: 401 AIADGVRTSGLAEVLSKGLVFLETAPYWAIAPTVCLIAATITEFTSNNATTTLLVPLLIE 460 A+A G +GLAE ++ + + + + + +TE TSN ATT +++P+L Sbjct: 345 ALAKGFGITGLAEWIAGKMGQMNGMSMILMILILVAMVNFLTEITSNLATTAMILPVLAP 404 Query: 461 IAKNMGIHPLLLMVPGAIGAQFAFLLPTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTI 520 +A + HP +LMVP + A AF+LP TP N V F +G+++I DM+K G + I Sbjct: 405 LAMSFNAHPFMLMVPVTVAASCAFMLPVATPPNAVVFGSGYLKIPDMVKAGFWMNI---- 460 Query: 521 FLSILMPTLGAY 532 SIL+ T+ +Y Sbjct: 461 -FSILLVTIVSY 471 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: 774 Number of extensions: 40 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: 491 Length adjustment: 35 Effective length of query: 505 Effective length of database: 456 Effective search space: 230280 Effective search space used: 230280 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