Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate BPHYT_RS27425 BPHYT_RS27425 C4-dicarboxylate ABC transporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS27425 Length = 433 Score = 432 bits (1110), Expect = e-125 Identities = 217/423 (51%), Positives = 299/423 (70%), Gaps = 4/423 (0%) Query: 1 MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60 M +PL +SLY QV++ + +GI LGHF P+ G L+P D F+ L+KM+IAPI+FCT+V Sbjct: 1 MRVAKPL-RSLYVQVLLGVVLGIALGHFLPEVGARLRPFSDAFVGLVKMMIAPIVFCTIV 59 Query: 61 SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVA 120 SGI + + K++ +T AL F +++ +AL +GLV V+QPG GMHID LD S +A Sbjct: 60 SGITSLASGKAIARTIFQALGLFYLLTAVALALGLVTAFVLQPGAGMHIDAQHLDTSILA 119 Query: 121 AYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI 180 Y + + +V F LNVIP T++GA G++L VL+ S++FGF+L+ G+PVL I Sbjct: 120 QYGKHAQPRGLVAFALNVIPETMLGALDKGEVLPVLLLSLLFGFSLNAYPKAGRPVLALI 179 Query: 181 DRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVL 240 D A +F I+ MIM+LAP+GA GAMAFT+G +G+ S+ LG LM+ FY+ C+LFV +VL Sbjct: 180 DGIAQTLFRILAMIMRLAPLGAFGAMAFTVGRFGIRSVGSLGMLMVSFYVACLLFVALVL 239 Query: 241 GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300 + R HGF++ +L+RY+REELLIVL TSS+E LPR++ K+E LG K VVGLV+P GY Sbjct: 240 APLARLHGFALWRLLRYLREELLIVLATSSTEPVLPRLIAKLEALGCDKGVVGLVLPAGY 299 Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360 SFNLDGT+IYLT+A+VFIAQA D + +L V+LL+SKGAAGV+GSG + L ATL Sbjct: 300 SFNLDGTAIYLTLASVFIAQACDVPLTAPQIAIMLAVMLLTSKGAAGVSGSGLVALVATL 359 Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDED---QLQAELA 417 + + LPVAG+AL++GIDRFMSEARALT+++ NA A + V+ W D Q+ +A Sbjct: 360 TVIPDLPVAGVALLVGIDRFMSEARALTSVISNACAVIFVSMWEGACDRTRLAQMLGAMA 419 Query: 418 SGG 420 GG Sbjct: 420 PGG 422 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: 556 Number of extensions: 31 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: 444 Length of database: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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