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 GFF3976 HP15_3916 sodium-dependent transporter family protein
Query= TCDB::O67854 (513 letters) >FitnessBrowser__Marino:GFF3976 Length = 465 Score = 170 bits (431), Expect = 9e-47 Identities = 139/478 (29%), Positives = 221/478 (46%), Gaps = 60/478 (12%) Query: 8 WATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGR 67 W++RL ILA G+AVGLGN +FP ENGGGAF++ Y++ ++GIP+M E +GR Sbjct: 19 WSSRLAFILAATGSAVGLGNIWKFPYVTGENGGGAFVLVYLLCIAVIGIPIMMAEVFIGR 78 Query: 68 YGGAQGHGTTPAIFYLLWRNRFA---KILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124 G H ++ + RN A +I + G+ V+ +Y I W + V Sbjct: 79 NG---RHNPITSMRLVAERNLSAPGWRISAIIGMIAAFVILSFYSVIGGWAASY-----V 130 Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184 G DSI F L S + +L ++F +V L ++ Sbjct: 131 GHAAMGDFTGGTADSIGELFGGLLAS------PGQLLLWHTIFMALVIL--------VVS 176 Query: 185 RGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVW 244 +G+ G+ER I MP LF+L + V T G + ++FL+TPDF L GV Sbjct: 177 QGLKGGLERAVTILMPALFLLLLVAV----GYATTTGHFGEAVSFLFTPDFGALTINGVL 232 Query: 245 IAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVA 304 I A+G FFTLSLG ++ Y SY+ +D I G TA ++ I+ +++ A +A Sbjct: 233 I-ALGHAFFTLSLGMAIMMAYGSYLGRDVSI---GRTAVSV-----AIMDTVVALLAGLA 283 Query: 305 FFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMI 364 F V A + L F TLP F G G L+F LL FA TS I++++P++ Sbjct: 284 IFPVVFANGLEAGAGPGLIFQTLPLAFGNMPMGGLFGTLFFILLLFAAWTSGISLLEPVV 343 Query: 365 AFLEDELKLSRKHA------VLWTAAIVFF--------SAHLVMFL----NKSLDEMDFW 406 ++E++ L+R + + W I A L MF D +DF+ Sbjct: 344 EWVEEKTSLARTGSSILVGVLCWALGIASILSLNVWADVAPLAMFERFEGKTIFDLLDFF 403 Query: 407 AGTIGVVFFGLTELIIFFWIFGADKAWEEIN-RGGIIKVPRIYYYVMRYITPAFLAVL 463 + + GL + W + ++ +GG ++Y ++R++TP +A++ Sbjct: 404 TANVLLPLSGLLTAVFVGWFVAKESLKSDLALQGGAF---TLWYNLIRFVTPIAVAIV 458 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: 740 Number of extensions: 41 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: 465 Length adjustment: 34 Effective length of query: 479 Effective length of database: 431 Effective search space: 206449 Effective search space used: 206449 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