Align The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized)
to candidate WP_043768573.1 U743_RS11885 sodium-dependent transporter
Query= TCDB::O67854 (513 letters) >NCBI__GCF_000733765.1:WP_043768573.1 Length = 445 Score = 194 bits (492), Expect = 7e-54 Identities = 150/475 (31%), Positives = 236/475 (49%), Gaps = 53/475 (11%) Query: 5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64 RE+W +RLG ++A AG+AVGLGN RFP A ENGGGAF+I Y+ + G+ ++ E Sbjct: 4 RENWGSRLGFVMAAAGSAVGLGNIWRFPYTAGENGGGAFLIIYLGIIAIFGVSVLLAEIV 63 Query: 65 MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124 +GR G + +WR G+ G+ V+ +YV + WTL + + Sbjct: 64 LGRATQRNPVGAFGQLGGRIWRP-----AGLLGVITGFVILSFYVVVAGWTLAY-----L 113 Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGD-EPILKPSLFAYIVFLITMFINVSIL 183 GL ++TDPD + F + + G P+ +LF +V + + Sbjct: 114 GLSLAGGLDSTDPDLLGAQF-------VALSGGIWAPLALAALFMALV--------GATV 158 Query: 184 IRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243 GI++GIER ++ MP LF+L V L V+ + P G A G+ FL PDF K+ Sbjct: 159 GGGITRGIERANRVLMPLLFLLLVGLA--VYAMTLPGGGA--GVAFLLQPDFSKISG-AT 213 Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303 + AA+ Q FF+LSLG G ++TY SY+R + + ++ +L+ A ++ G ++I V Sbjct: 214 FTAALAQAFFSLSLGMGCMLTYGSYLRPHERLGVATGAIISLDVVAALLAG--LAIMPVV 271 Query: 304 AFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPM 363 FGV+ +AG L FITLPA F+ GG +G +F LL A LTS+I+I++P Sbjct: 272 FAFGVS-----PEAGP-GLTFITLPAAFAAMPGGAIVGPAFFLLLSVAALTSAISILEPA 325 Query: 364 IAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKS------------LDEMDFWAGTIG 411 I++L DE SR V W A + + + L+ + MDF A + Sbjct: 326 ISWLTDEHGWSRGRTV-WVCASICLALGVPSSLSMGAAPGLQIAGMSFFNAMDFAATNVM 384 Query: 412 VVFFGLTELIIFFWIFGADKAWEEINRGGIIKV-PRIYYYVMRYITPAFLAVLLV 465 + L + W +G E N G+ + R + ++R++ P L ++L+ Sbjct: 385 MPVGALITAVFVGWFWGQGALEELSNTSGVAPIWARGWLLLLRFVAPPALVLILL 439 Lambda K H 0.330 0.146 0.463 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: 722 Number of extensions: 52 Number of successful extensions: 6 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: 513 Length of database: 445 Length adjustment: 34 Effective length of query: 479 Effective length of database: 411 Effective search space: 196869 Effective search space used: 196869 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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