Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Korea:Ga0059261_0201 Length = 455 Score = 273 bits (697), Expect = 1e-77 Identities = 146/364 (40%), Positives = 224/364 (61%), Gaps = 11/364 (3%) Query: 43 FIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQ 102 F++LIKM+IAP++F T+V+GIA M + ++G+ GG A+ +F S ++L +GL++VN+ Q Sbjct: 56 FLRLIKMIIAPLVFATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQ 115 Query: 103 PGNGMHIDVSTLDASKVAAYVTAGKDQS---IVGFILNVIPNTIVGAFANGDILQVLMFS 159 PG G++ + +DA T+G +++ + F +V P + + A A +ILQ+++FS Sbjct: 116 PGVGLNFPLPPVDA-------TSGVEKAAFNLKDFFTHVFPASGIEAMAKNEILQIVIFS 168 Query: 160 VIFGFALHRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLV 219 + G A+ +G KP++ ++ HVM + N +M+ API A+A T+ G + Sbjct: 169 LFIGVAITAVGEKAKPLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIG 228 Query: 220 QLGQLMICFYITCVLFVLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRML 279 L M FYI +++G G L+RYIR+ LL+ T+SSE+A PR L Sbjct: 229 NLAYFMGTFYIAMFTLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTL 288 Query: 280 IKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLL 339 ++R G + V+P GYSFNLDG+ IY+T A +FIAQA + + +IT+LLVL+ Sbjct: 289 EALDRFGVPPRIASFVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLM 348 Query: 340 LSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVV 399 ++SKG AGV + +V+AATL +P AGL LILGID F+ R+ TN+VGNAVA+ V Sbjct: 349 ITSKGIAGVPRASLVVIAATLGFF-DIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAV 407 Query: 400 VAKW 403 VAKW Sbjct: 408 VAKW 411 Lambda K H 0.326 0.142 0.402 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: 519 Number of extensions: 29 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: 444 Length of database: 455 Length adjustment: 33 Effective length of query: 411 Effective length of database: 422 Effective search space: 173442 Effective search space used: 173442 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