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 206527 DVU1092 sodium-dependent symporter family protein
Query= TCDB::O67854 (513 letters) >MicrobesOnline__882:206527 Length = 453 Score = 192 bits (489), Expect = 2e-53 Identities = 142/475 (29%), Positives = 235/475 (49%), Gaps = 49/475 (10%) Query: 5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64 R+ +ATRLG++ A G+AVGLGN +FP +NGG F++ YIIA LLVG+P+M E Sbjct: 8 RDGFATRLGVLAATLGSAVGLGNIWKFPALTGQNGGATFLLVYIIATLLVGLPVMISEIM 67 Query: 65 MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124 +GR A T L + + ++G+ G+ +++ +Y + W + K + Sbjct: 68 LGRKAKANAVRTYRE---LGPKGQPWSLIGISGVIAAVLIMGFYTDVAGWVFAYIFKAMS 124 Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184 G + TDP KE + +G P + ++ +IV + +I++ Sbjct: 125 GSIA-----TTDP----AVAKEAFVALVGSP------TQSLMWQWIVLALVS----AIIL 165 Query: 185 RGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVW 244 G+S GIER KI MP L +L + R L AA+GL FL+TPDF K+ GV Sbjct: 166 GGVSSGIERTTKILMPVLLLLLCVVCARSLTLP----KAAEGLAFLFTPDFSKITG-GVI 220 Query: 245 IAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVA 304 + A+G FF LS+G G + TY SY R DQ+I +TAA + ++ SISI A VA Sbjct: 221 LMALGLAFFKLSIGMGTMTTYGSYFRDDQNI---PVTAARV-----MLCDLSISILAGVA 272 Query: 305 FFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMI 364 F + +L F+T+PA+F+ GG ++F L A + +++ + + Sbjct: 273 IFPAVFNFGFEPSAGPSLLFMTIPAVFASMPGGQLFTVIFFCLTAIAATGAMLSLFEVPV 332 Query: 365 AFLEDELKLSRKHAVLWTAAI-----------VFFSAHLVMFLNKSLDEMDFWAGTIGVV 413 A+L +E K+SR A + TA + + MF D DF + I + Sbjct: 333 AWLVEEFKMSRAKATIGTALVLGVMGAPATLSMSVLGDFKMFGLNMFDLYDFVSSNILLP 392 Query: 414 FFGLTELIIFFWIFGADKAWEEINRGGIIKVPRI---YYYVMRYITPAFLAVLLV 465 G+ I W++G+ + E ++ GG + + + +V+++++P + ++L+ Sbjct: 393 VGGIFICIFAGWVWGSKRTRELLSNGGHLDNAAVVSGFLFVVKWVSPVLVTIVLL 447 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: 612 Number of extensions: 32 Number of successful extensions: 7 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: 453 Length adjustment: 34 Effective length of query: 479 Effective length of database: 419 Effective search space: 200701 Effective search space used: 200701 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: 52 (24.6 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