Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate Ga0059261_0617 Ga0059261_0617 Na+/H+-dicarboxylate symporters
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Korea:Ga0059261_0617 Length = 445 Score = 487 bits (1254), Expect = e-142 Identities = 243/410 (59%), Positives = 309/410 (75%) Query: 6 FKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGME 65 + LY QVL AIA G+ +G+F+P+ G +KPLGD F+KL+KMIIAPVIF T+VTGIAGM Sbjct: 19 YGQLYVQVLVAIAAGVSVGYFWPDAGASLKPLGDAFIKLVKMIIAPVIFLTLVTGIAGMT 78 Query: 66 SMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAK 125 +K+VGR A YF ST+AL++GLI+ N VQPGAGMNVDPA+LD AV Y +A Sbjct: 79 ELKSVGRVAGKAFAYFLFFSTLALVVGLIVANTVQPGAGMNVDPASLDTGAVKDYVAKAH 138 Query: 126 DQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVI 185 D IV F+M +IP +++ A ++LQVLL ++LFG AL +G + +++E V+ Sbjct: 139 DSSIVGFLMAIIPTTLVSALTGESLLQVLLVSILFGIALSMVGEPAAPVRDLLEKTGLVV 198 Query: 186 FGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKAT 245 F ++ ++MR AP+GAFGAMAFTIGKYG+ +L L L+ FY+T +FVV+VLG +AK Sbjct: 199 FKLVGILMRAAPVGAFGAMAFTIGKYGIESLANLAGLVATFYLTSAIFVVVVLGVVAKLA 258 Query: 246 GFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGT 305 GFSIFK IRY+R ELL+VLGTSSSESALP ++DKME+ GC K VVGLV+PTGYSFNLDGT Sbjct: 259 GFSIFKLIRYLRAELLLVLGTSSSESALPSLMDKMERAGCAKPVVGLVVPTGYSFNLDGT 318 Query: 306 SIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLP 365 +IY+T+AA+FIAQA N + + QI LL + ++SSKGAAGVTG+GFI LAATLS V +P Sbjct: 319 NIYMTLAALFIAQACNVDLSLGDQIALLAIAMISSKGAAGVTGAGFITLAATLSIVPDVP 378 Query: 366 VAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415 VAG+ALILGIDRFMSE R+LTN +GN VATIVVA+W LD L LN Sbjct: 379 VAGMALILGIDRFMSECRSLTNFIGNAVATIVVARWDNALDTAALHHALN 428 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: 583 Number of extensions: 17 Number of successful extensions: 1 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: 445 Length adjustment: 32 Effective length of query: 396 Effective length of database: 413 Effective search space: 163548 Effective search space used: 163548 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