Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BWI76_RS19175 BWI76_RS19175 dicarboxylate/amino acid:cation symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__Koxy:BWI76_RS19175 Length = 424 Score = 246 bits (627), Expect = 1e-69 Identities = 137/413 (33%), Positives = 242/413 (58%), Gaps = 15/413 (3%) Query: 15 VIVAIAIGILLG---HFYP-QTGVA-----LKPLGDGFIKLIKMVIAPIIFCTVVSGIAG 65 +++ + +GIL G H Y QT + + L D F++LIKMVIAP++F T+ GI Sbjct: 11 IVIFMLLGILSGAAIHAYAGQTTITAWSENITLLTDVFLRLIKMVIAPLVFSTLTVGIMR 70 Query: 66 MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125 + ++G+ GG A+++F S +++L+GLV+V + PG G+++ + A Sbjct: 71 LGETATIGRVGGKAMVWFITSSILSILVGLVIVTLEHPGAGLNLAIPKESVDTGLAV--- 127 Query: 126 GKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKPVLDFIDRFA 184 S+ GF+ + IP +I A A+ +ILQ+++FS+ FG A LG + P++ ++ + Sbjct: 128 -SGMSLKGFLTHTIPTSITEAMASNEILQIVVFSMFFGIAGASLGEKFNAPLVAALNVVS 186 Query: 185 HVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAIC 244 H+M + +M +AP+ A++ I + G+G L+ + +Y+ +L V+L Sbjct: 187 HIMLKVTGYVMYVAPLAIFAAISSVIASQGLGILLNYASFIGGYYVAILLTSAVLLAVGY 246 Query: 245 RAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNL 304 V +L+ +++ +L+ TSSSE+A P+ L ++ G +++ V+P GYSFNL Sbjct: 247 MVLKKEVFRLLNMLKDPVLVAFTTSSSEAAYPKTLERLVEFGCSRNIASFVLPIGYSFNL 306 Query: 305 DGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVG 364 G+ +Y + AA+FIAQA + + + ++L L+L+SKG AGV S +VLAAT+ + Sbjct: 307 VGSMVYCSFAAMFIAQAYNVQLSFSEITVMMLTLMLASKGIAGVPRSALVVLAATIPSF- 365 Query: 365 HLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELA 417 ++PVAG+ L++GID F+ R+ N++GN +AT +++K +L E+ L+AE A Sbjct: 366 NIPVAGILLLMGIDHFLDMGRSAINVLGNGIATAMLSKNEGQLQEEVLEAEAA 418 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: 448 Number of extensions: 24 Number of successful extensions: 5 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: 424 Length adjustment: 32 Effective length of query: 412 Effective length of database: 392 Effective search space: 161504 Effective search space used: 161504 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