Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate 200106 SO0922 proton/glutamate symporter (NCBI ptt file)
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__MR1:200106 Length = 424 Score = 260 bits (665), Expect = 5e-74 Identities = 145/408 (35%), Positives = 233/408 (57%), Gaps = 10/408 (2%) Query: 11 LYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70 L+ Q+ V + +GIL+G + LKP+G F+ IKM+I P++FC+++ G+ M++ Sbjct: 5 LWLQIFVGMVLGILVGVTLGEQASYLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMEDTA 64 Query: 71 SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTAGKDQS 130 +G+ G + ++ + IA+ +GLVV V+QPG G+ + + A TA + S Sbjct: 65 KMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPL-------LQHEAVNTAKEVPS 117 Query: 131 IVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAHVMFNI 190 ++ +++++P V A A+G ILQV++F+V G AL +G +GKP + + A M+ + Sbjct: 118 VMQTLIDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKL 177 Query: 191 INMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICRAHG-F 249 +M+MKLAP G G MA+ G YG+ L L +++I YI C++ VL + R Sbjct: 178 TDMVMKLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFAKL 237 Query: 250 SVLKLIRYIREELLIVLGTSSSESALP-RMLIKMERLGAKKSVVGLVIPTGYSFNLDGTS 308 + L + I + + TSSS LP M E LG K + V+P G + N+DGT+ Sbjct: 238 NPLHFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTA 297 Query: 309 IYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 368 +Y + A+F+AQA + +T++L L+S G AGV G+G ++L LS VG LP+ Sbjct: 298 LYQGVTALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVG-LPL 356 Query: 369 AGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAEL 416 G+ALI GIDR + AR + N+ G+ VAT V+AK ELD + A++ Sbjct: 357 EGVALIAGIDRILDMARTVVNVSGDLVATTVIAKSENELDVEHYNADM 404 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: 446 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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