Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Dsui_3482 Dsui_3482 Na+/H+ dicarboxylate symporter
Query= TCDB::Q848I3 (444 letters) >FitnessBrowser__PS:Dsui_3482 Length = 437 Score = 285 bits (730), Expect = 2e-81 Identities = 163/400 (40%), Positives = 246/400 (61%), Gaps = 11/400 (2%) Query: 39 LGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVV 98 L D F++LIKM+IAP+IF T+V+G+A M + K+VG+ GG AL +F S +L IGL+ Sbjct: 44 LTDIFLRLIKMIIAPLIFATLVAGLANMGDAKAVGRVGGRALGWFICASFCSLFIGLLFA 103 Query: 99 NVVQPGNGMHIDVSTLDASKVAAYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMF 158 NV+QPG+ + + + A ++ FI +V P +I+ A A ++LQ+L+F Sbjct: 104 NVLQPGHALSVPLP----ESAAGLNLKTSALNLKDFITHVFPKSIMEAMAGNEVLQILVF 159 Query: 159 SVIFGFAL-HRLGAYGKPVLDFIDRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGS 217 +V FG AL H + +++ +D HVM + + +M+ AP G GA+A I G+G Sbjct: 160 AVFFGLALGHLHNQAARSLVNTMDEVVHVMLKVTDYVMRFAPFGVFGAVAGAITTNGLGM 219 Query: 218 LVQLGQLMICFYIT-CVLFVLVVLGAICRAHGFSVLKLIRYIREELLIVLGTSSSESALP 276 L+ G+ M+ FY+ L+ L++L G V +LI+ +R LL+ T+SSES P Sbjct: 220 LLVFGKFMLSFYVALAALWALLILAGFI-VLGKDVFRLIKLVRGPLLVGFSTASSESVYP 278 Query: 277 RMLIKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLL 336 +++ ++E+ G K V G V+P GYSFNLDG+ +Y T A+FIAQA D M +T QIT+LL Sbjct: 279 KLMEQLEKFGIKTRVTGFVLPLGYSFNLDGSMMYTTFLALFIAQAYDIPMSLTAQITMLL 338 Query: 337 VLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVA 396 VL++SSKG AGV + +V+AA L + +LP AGL L+LGID F+ R +TN++GN++A Sbjct: 339 VLMVSSKGIAGVPRASLVVVAAVL-PMFNLPEAGLLLVLGIDHFLDMGRTVTNVLGNSIA 397 Query: 397 TVVVAKWVKELDEDQLQAELASGGRAISDTREEDDLGVAE 436 T VVAKW + D + ELA ++ E+D L A+ Sbjct: 398 TAVVAKWEGAI--DPVSEELAEAEESL-PVPEDDSLVTAK 434 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: 484 Number of extensions: 24 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 412 Effective length of database: 405 Effective search space: 166860 Effective search space used: 166860 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