Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate Echvi_1519 Echvi_1519 Na+/H+-dicarboxylate symporters
Query= TCDB::P96603 (421 letters) >FitnessBrowser__Cola:Echvi_1519 Length = 444 Score = 222 bits (566), Expect = 2e-62 Identities = 143/425 (33%), Positives = 228/425 (53%), Gaps = 29/425 (6%) Query: 7 LTVQVITAVIIGVIVGLVW------PDVGKE-MKPLGDTFINAVKMVIAPIIFFTIVLGI 59 L Q+I +++G++ GL+ PD + +KP+G FIN +KM+ P++ ++++G+ Sbjct: 7 LHTQIIIGLVLGLVFGLIVIKTQMSPDFTMDYIKPIGTIFINGLKMIAVPLVLASLIVGV 66 Query: 60 AKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEK--------- 110 + +GD+ K+G++GGK + + T +A+ +GL +VN+ PG L E+ Sbjct: 67 SNLGDITKLGRIGGKTIGAYMMTTVIAVTVGLLLVNVFAPGKSLPIETRERLMEQFDDVV 126 Query: 111 GDVSQYTQNGGQGIDWIEFITHIVPSNMVDAFA-KGDILQVLFFSILFGVGLAALGE-KG 168 GD S + ++ + +VP N+ A A G +LQV+FF+I+ G+ L + + K Sbjct: 127 GDKSSQAAELKEQTP-LKPLVDMVPENVFLAAADNGSMLQVVFFAIIVGIALLEIPKSKA 185 Query: 169 KSVIDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMF 228 VI FFD ++ V KI+GYIM AP G F MA I D+ L+ ++ Sbjct: 186 SPVIAFFDGLNDVIIKIVGYIMLIAPYGVFALMASLIVEIAGDNPDSAIELLFALLKYSL 245 Query: 229 LFVFVALNIICKLYG-----FSLWNYLRF---IKDELLIVLGTSSSESVLPRMMDKMER- 279 L V L +I +Y F+ Y F ++ L+ TSSS + LP M ++E Sbjct: 246 LVVAGLLLMIVLVYPTILKLFTKVKYKDFFAALRPAQLLAFSTSSSSATLPVTMKQVEEE 305 Query: 280 YGCSKSVVGLVIPTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKG 339 G S+ V V+P G + N+DGT +Y +A VF+AQ G+DLS+ QQ+ I+L L S G Sbjct: 306 IGVSEEVSSFVLPLGATINMDGTCLYQGVAAVFIAQALGLDLSLTQQLMIVLTATLASIG 365 Query: 340 AAGVTGSGFIVLASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSE 399 AGV G+G I+L L ++ V P GLAL+L DR + R +VN+ G+ +VA +E Sbjct: 366 TAGVPGAGLIMLLIVLESIGV-PSAGLALILAPDRILDMFRTVVNVTGDATVCTVVASTE 424 Query: 400 NEFDE 404 E + Sbjct: 425 GELPD 429 Lambda K H 0.326 0.143 0.408 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: 457 Number of extensions: 21 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: 421 Length of database: 444 Length adjustment: 32 Effective length of query: 389 Effective length of database: 412 Effective search space: 160268 Effective search space used: 160268 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