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_009121821.1 BUB52_RS13665 sodium-dependent transporter
Query= TCDB::O67854 (513 letters) >NCBI__GCF_900129655.1:WP_009121821.1 Length = 455 Score = 204 bits (519), Expect = 5e-57 Identities = 151/480 (31%), Positives = 238/480 (49%), Gaps = 54/480 (11%) Query: 4 KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEW 63 +R ++ ++LG+ILA AG+AVGLGN RFP + +GG AF++ Y++ L++GIP+M E+ Sbjct: 5 ERANFGSKLGVILASAGSAVGLGNIWRFPFETGNHGGAAFILIYLVCVLILGIPIMIAEF 64 Query: 64 AMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFL 123 +GR + T + L + +G G+ ++ YY + WTL F Sbjct: 65 LIGR----RSRANTAGAYQKLAPGTQWRWVGRMGVLAGFLILGYYSVVAGWTLEF----- 115 Query: 124 VGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSIL 183 + E N+ S EF+ S+ G +P ++ + L+T F I+ Sbjct: 116 ---IGEAATNSFAGKSA----AEFIASFNGFVSNP---WRPVIWLIVFLLVTHF----II 161 Query: 184 IRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243 I+G+ KGIE+ AKI MP LFIL + L I L A++G+ FL PDF K+ D V Sbjct: 162 IKGVEKGIEKSAKIMMPMLFILLIVLAICSVSLP----GASEGIEFLLKPDFSKV-DGNV 216 Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303 ++ A+GQ FF+LSLG G + TYASY R D ++ + L A + + IL G I PAA Sbjct: 217 FLGAMGQAFFSLSLGMGCLCTYASYFRNDTNLPKTALNVAGI-DTLVAILAGFIIFPAAF 275 Query: 304 AFFGVANAVAIAKAGAFNLGFITLPAIFSQTAG-----GTFLGFLWFFLLFFAGLTSSIA 358 +V I +L FITLP +F Q G L +++ LL A LTS+I+ Sbjct: 276 -------SVGIQPDAGPSLLFITLPNVFQQAFGNIPWLAIVLSIMFYVLLALAALTSTIS 328 Query: 359 IMQPMIAFLEDELKLSR-KHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGL 417 + + + A+L +E K +R K A L TA + + L D F + F Sbjct: 329 LHEVVTAYLHEEFKFTRGKAARLVTAGCIILGVLCSLSLGVGKDYTIFGLNLFDLFDFVT 388 Query: 418 TELII----FF------WIFGADKAWEEINRGGI--IKVPRIYYYVMRYITPAFLAVLLV 465 ++++ FF W WEE++ G I + R+ ++++YI P + ++ + Sbjct: 389 AKIMLPLGGFFISLFTGWYLDKKIVWEEVSNNGTLNIHIYRLLIFILKYIAPIGIGLIFI 448 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: 677 Number of extensions: 32 Number of successful extensions: 9 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: 455 Length adjustment: 34 Effective length of query: 479 Effective length of database: 421 Effective search space: 201659 Effective search space used: 201659 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 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