Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_03336 H281DRAFT_03336 Na+/H+-dicarboxylate symporter
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_03336 Length = 438 Score = 428 bits (1100), Expect = e-124 Identities = 207/412 (50%), Positives = 299/412 (72%) Query: 7 KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66 +SLY QVL + +G+ +GHF P+ G +KP D FV L++M+IAP++FCT+V+GI + S Sbjct: 8 RSLYVQVLLGMVLGVAVGHFLPQAGALLKPFSDAFVGLVRMMIAPIVFCTIVSGITSLAS 67 Query: 67 MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126 KA+GRT AL F +++ +AL GL+ V++PGAGM++D LD +A Y A+ Sbjct: 68 GKAIGRTIFKALALFYLLTVVALAFGLVTAIVLRPGAGMHIDAHGLDTSILAQYVKHAQP 127 Query: 127 QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIF 186 G+VAF + VIP +++GAF G++L VLL ++LFGF+L+ G+ + +I+ + V+F Sbjct: 128 GGLVAFALSVIPETMLGAFEKGDVLPVLLLSLLFGFSLNSCPKAGRPVLALIDGVAHVLF 187 Query: 187 GIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATG 246 I+ MIMRLAP+GAFGAMAFT+G++G+ ++ LG L++CFY+ C+LF+ LVL S+A+ G Sbjct: 188 RILAMIMRLAPLGAFGAMAFTVGRFGIRSVGSLGMLMVCFYVACLLFIALVLASLARLHG 247 Query: 247 FSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTS 306 F++++ +RY+REELLIVL TSS+E LPR++ K+E LGC K VVGLV+P GYSFNLDGT+ Sbjct: 248 FALWRLLRYMREELLIVLATSSTEPVLPRLIVKLEALGCDKGVVGLVLPAGYSFNLDGTA 307 Query: 307 IYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 366 IYLT+A++FIAQA + + +L V+LL+SKGAAGV+GSG + L ATL+ + LPV Sbjct: 308 IYLTLASMFIAQACDVPLSASQIAMMLAVMLLTSKGAAGVSGSGLVALVATLTVIPDLPV 367 Query: 367 AGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRA 418 AG+AL++GIDRFMSEARALT+++ N A I V+ W D +L +L A Sbjct: 368 AGVALLVGIDRFMSEARALTSVISNACAVIFVSMWEGACDRARLAQMLGAAA 419 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: 539 Number of extensions: 25 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: 438 Length adjustment: 32 Effective length of query: 396 Effective length of database: 406 Effective search space: 160776 Effective search space used: 160776 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