Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BWI76_RS08460 BWI76_RS08460 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Koxy:BWI76_RS08460 Length = 435 Score = 246 bits (628), Expect = 1e-69 Identities = 133/364 (36%), Positives = 215/364 (59%), Gaps = 5/364 (1%) Query: 43 FIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQ 102 F++++KM+IAP++ T+V GIA M + K++G+ F S +++ +GLV+VN+ Q Sbjct: 47 FLRMVKMIIAPLVISTLVVGIAKMGDAKTLGRIFSKTFFLFICASLLSIALGLVIVNLFQ 106 Query: 103 PGNGMHIDVSTLDASKVAAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIF 162 PG G I+ DA VAA + ++ FI + +P +IV A A +ILQ+++FS+ Sbjct: 107 PGAG--INFVPHDAGAVAA--VQSEPFTLKVFISHAVPTSIVDAMARNEILQIVVFSIFL 162 Query: 163 GFALHRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLG 222 G +L +G +P++ +D HVM + +M AP+ A++ I G+G +V G Sbjct: 163 GCSLAAIGEKAEPIVKVLDSLVHVMLKLTGYVMLFAPLTVFAAISGLIAERGLGVMVSAG 222 Query: 223 QLMICFYITCVLFVLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKM 282 M FY+T + +++G G + +L + I E L+ TSSSE+A P L K+ Sbjct: 223 IFMGEFYLTLGMLWAILIGLSTVIVGPCISRLTKAIFEPALLAFTTSSSEAAFPGTLDKL 282 Query: 283 ERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSS 342 E+ G + V+P GYSFNL G+ Y + A VFIAQA + H+ + QIT+LL+L+L+S Sbjct: 283 EKFGVSSKIASFVLPIGYSFNLVGSMAYCSFATVFIAQACNVHLSMGEQITMLLILMLTS 342 Query: 343 KGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAK 402 KG AGV + +V+AATL+ ++P AGL L++G+D F+ R+ TN++ NA+ +V + Sbjct: 343 KGMAGVPRASMVVIAATLNQF-NIPEAGLILLMGVDPFLDMGRSATNVMSNAMGAAIVGR 401 Query: 403 WVKE 406 W E Sbjct: 402 WEGE 405 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: 451 Number of extensions: 33 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: 435 Length adjustment: 32 Effective length of query: 412 Effective length of database: 403 Effective search space: 166036 Effective search space used: 166036 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