Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate Ga0059261_3350 Ga0059261_3350 Na+/H+-dicarboxylate symporters
Query= uniprot:A1S570 (437 letters) >FitnessBrowser__Korea:Ga0059261_3350 Length = 436 Score = 272 bits (696), Expect = 1e-77 Identities = 147/404 (36%), Positives = 238/404 (58%), Gaps = 16/404 (3%) Query: 24 LIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVCGTCSLSEPSK 83 ++G L+ G W + + IG +F+ ++MLVVPLVF+++ G +L++P + Sbjct: 35 ILGALVLGAIAGVAWGPGATSIAW---IGELFVRLIRMLVVPLVFLTIAAGVAALADPKR 91 Query: 84 LGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQYSAKEAPSLADVLINIV 143 LG +G KTLA Y+FTT +A+ + A L+ PG + ++++ + P A + + I+ Sbjct: 92 LGSIGVKTLAMYVFTTTLAVTTGLIVATLIGPGIGASFADAVPRAMGTPPDTARMFMEII 151 Query: 144 PSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLNEVIMRVVTLIMQLAP 203 P NP+ A+++G L +I FA++ G + G+ V A + ++V++++V +M+ AP Sbjct: 152 PDNPVGAMADGKTLSVIFFAILVGAGVIAAGKGAEPVRAFLNGASDVMLKIVGFVMETAP 211 Query: 204 YGVFALMGKLALTLGMETLESVIKYFMLV-----LVVLLFHGFVVYPTLLKLFSGLSPLM 258 +GVFAL+ + T G + +++K + V +V LL HG +V ++L + LSPL Sbjct: 212 FGVFALIAVVMGTSGPASFLAILKLAICVVAGSAVVTLLIHGLIV----VRLMAWLSPLP 267 Query: 259 FIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATINMDGTAIMQG 318 F R + D + FST+SS+ATLPV + +++ LG VAS LPLGATI MDG A+ Sbjct: 268 FFRGIADAIMVGFSTSSSSATLPVAIRVAQNNLGISKPVASTVLPLGATIGMDGAAMYVA 327 Query: 319 VATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIAL 378 + T+F AQ FG+DLT DY ++ T T+ ++G A VP L +LA VL+ +G+ E AL Sbjct: 328 MLTLFSAQAFGLDLTWADYLVIAATTTIVAMGVAPVPSGSLFVLAAVLHAIGITPEQTAL 387 Query: 379 ILG----VDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFN 418 ++G DR+LDM RT NVT D +A+ EG ++ V+N Sbjct: 388 VVGFVLPFDRILDMTRTVPNVTSDLAIATAVARWEGEMDVTVYN 431 Lambda K H 0.325 0.139 0.388 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: 396 Number of extensions: 12 Number of successful extensions: 3 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: 437 Length of database: 436 Length adjustment: 32 Effective length of query: 405 Effective length of database: 404 Effective search space: 163620 Effective search space used: 163620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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