Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Dsui_3158 Dsui_3158 Na+/H+ dicarboxylate symporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__PS:Dsui_3158 Length = 448 Score = 538 bits (1387), Expect = e-157 Identities = 276/411 (67%), Positives = 330/411 (80%), Gaps = 1/411 (0%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 +K LY QVL AIA+G+ LG F+PE G MKPLGD F+KLIKM+IAP+IF TVV GIA M Sbjct: 7 YKRLYVQVLFAIALGVALGAFFPETGATMKPLGDAFIKLIKMMIAPIIFATVVVGIAKMG 66 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 MK VGR G AL+YFE+VST+AL IGLI+VN++QPGAGMNVDP+TLD KA+A YA A Sbjct: 67 DMKEVGRVGLKALIYFEVVSTVALAIGLIVVNILQPGAGMNVDPSTLDTKAIANYAAAAH 126 Query: 126 DQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 +Q F+M++IP SV+ AFA G ILQVLLF+VLFG AL RLG K + + +++ FS + Sbjct: 127 NQSTTDFLMNIIPNSVVDAFAKGEILQVLLFSVLFGLALSRLGDKAKPLVKILDEFSHGL 186 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 FG+I MIM APIGAFGAMAFTIGKYG+G+L QLG L+ YITC LFV +VLG IAK T Sbjct: 187 FGVIGMIMHFAPIGAFGAMAFTIGKYGIGSLKQLGFLMANVYITCALFVFVVLGLIAKFT 246 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFS+ KF+ YI+EELLIVLGTSSSESALPRM+ K+E LGC K VVG+VIPTGYSFNLDGT Sbjct: 247 GFSLLKFLAYIKEELLIVLGTSSSESALPRMMTKLENLGCHKPVVGMVIPTGYSFNLDGT 306 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAV-GHL 364 SIYLTMAA+FIAQA N + + Q+T+L VLLL+SKGAA VTG GFI LAATL+ + G L Sbjct: 307 SIYLTMAAIFIAQALNVPLTLTEQLTILGVLLLTSKGAAAVTGGGFITLAATLATLGGKL 366 Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 PV GLAL+LG+DRFMSEARA+TNL+GNGVATIVV+KW L+ ++ VLN Sbjct: 367 PVEGLALLLGVDRFMSEARAITNLIGNGVATIVVSKWENALNTDRMTRVLN 417 Lambda K H 0.327 0.142 0.401 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: 611 Number of extensions: 25 Number of successful extensions: 2 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: 428 Length of database: 448 Length adjustment: 32 Effective length of query: 396 Effective length of database: 416 Effective search space: 164736 Effective search space used: 164736 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 (21.7 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