Align sodium:C4-dicarboxylate symporter (dctA) (characterized)
to candidate Dsui_3482 Dsui_3482 Na+/H+ dicarboxylate symporter
Query= reanno::pseudo5_N2C3_1:AO356_18980 (450 letters) >FitnessBrowser__PS:Dsui_3482 Length = 437 Score = 290 bits (742), Expect = 6e-83 Identities = 165/400 (41%), Positives = 244/400 (61%), Gaps = 9/400 (2%) Query: 41 DGFIKLIKMVIAPIIFCTVVSGIGGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNV 100 D F++LIKM+IAP+IF T+V+G+ M + K+VG+ GG AL +F S +L IGL+ NV Sbjct: 46 DIFLRLIKMIIAPLIFATLVAGLANMGDAKAVGRVGGRALGWFICASFCSLFIGLLFANV 105 Query: 101 VQPGAGMHIDVSTLDTSKIAGFISAGKDQSIIAFILNVIPNTIVGAFANGDILQVLMFSV 160 +QPG + + + AG ++ FI +V P +I+ A A ++LQ+L+F+V Sbjct: 106 LQPGHALSVPLP----ESAAGLNLKTSALNLKDFITHVFPKSIMEAMAGNEVLQILVFAV 161 Query: 161 LFGFAL-HRLGAYGKPVLDFIDRFAHVMFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLV 219 FG AL H + +++ +D HVM + + +M+ AP G FGA+A I G+G L+ Sbjct: 162 FFGLALGHLHNQAARSLVNTMDEVVHVMLKVTDYVMRFAPFGVFGAVAGAITTNGLGMLL 221 Query: 220 QLGQLMICFYITCVVFVLVVLGAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRML 279 G+ M+ FY+ +++ A G V +LI+ +R LL+ T+SSES P+++ Sbjct: 222 VFGKFMLSFYVALAALWALLILAGFIVLGKDVFRLIKLVRGPLLVGFSTASSESVYPKLM 281 Query: 280 IKMERLGAKKSVVGLVIPTGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLL 339 ++E+ G K V G V+P GYSFNLDG+ +Y T A+FIAQA D PM LT QIT+LLVL+ Sbjct: 282 EQLEKFGIKTRVTGFVLPLGYSFNLDGSMMYTTFLALFIAQAYDIPMSLTAQITMLLVLM 341 Query: 340 LSSKGAAGVTGSGFIVLAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATIV 399 +SSKG AGV + +V+AA L + +LP AGL L+LGID F+ R +TN++GN++AT V Sbjct: 342 VSSKGIAGVPRASLVVVAAVL-PMFNLPEAGLLLVLGIDHFLDMGRTVTNVLGNSIATAV 400 Query: 400 VAKWVKELDEDQLQTELASGGRGISDVREDDEQIAAAQIA 439 VAKW + D + ELA + V EDD + A A Sbjct: 401 VAKWEGAI--DPVSEELAEAEESL-PVPEDDSLVTAKAAA 437 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: 494 Number of extensions: 27 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: 450 Length of database: 437 Length adjustment: 32 Effective length of query: 418 Effective length of database: 405 Effective search space: 169290 Effective search space used: 169290 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 (21.7 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