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 353168 BT3642 Na+-dependent transporter (NCBI ptt file)
Query= TCDB::O67854 (513 letters) >FitnessBrowser__Btheta:353168 Length = 456 Score = 201 bits (511), Expect = 5e-56 Identities = 144/482 (29%), Positives = 232/482 (48%), Gaps = 54/482 (11%) Query: 2 EVKREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWI 61 ++ R ++ ++LG+ILA AG+AVGLGN RFP + +GG AF++ Y+ L+G+P++ Sbjct: 3 KIDRANFGSKLGVILASAGSAVGLGNIWRFPYETGNHGGAAFILIYLGCVFLLGLPILIA 62 Query: 62 EWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIK 121 E+ +GR + T + L + +G G+ ++ YY + WTL + + Sbjct: 63 EFLIGR----RSRANTAGAYQKLAPGTHWRWVGRMGVLAAFLILSYYSVVAGWTLEYVYE 118 Query: 122 FLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVS 181 L P + F++F S +P L+ + L+T F Sbjct: 119 ALTNGF-----TGKTPTEFISSFQQFSSS----------PWRPVLWLVLFLLVTHF---- 159 Query: 182 ILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDP 241 I+++G+ KGIE+ +KI MPTLFI+ + LVI L A G+ FL PDF K+ D Sbjct: 160 IIVKGVEKGIEKSSKIMMPTLFIIILILVICSVTLP----GAGAGIEFLLKPDFSKV-DG 214 Query: 242 GVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPA 301 V+++A+GQ FF+LSLG G + TYASY K+ ++ + + + + +L G I PA Sbjct: 215 NVFLSAMGQAFFSLSLGMGCLCTYASYFSKETNLTKTAFSVGII-DTFVAVLAGFIIFPA 273 Query: 302 AVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGT-----FLGFLWFFLLFFAGLTSS 356 A +V I +L FITLP +F Q G +++ LL A LTS+ Sbjct: 274 AF-------SVGIQPDAGPSLIFITLPNVFQQAFSGVPILAYIFSVMFYVLLAMAALTST 326 Query: 357 IAIMQPMIAFLEDELKLSR-KHAVLWTAAIVFFSAHLVMFLNKS----------LDEMDF 405 I++ + + A+L +E +R K A L T +F + L D DF Sbjct: 327 ISLHEVVTAYLHEEFNFTRGKAARLVTGGCIFLGILCSLSLGVMKGFTIFGLGIFDLFDF 386 Query: 406 WAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVP--RIYYYVMRYITPAFLAVL 463 I + GL I W W EI G +KVP ++ +++RYI P ++++ Sbjct: 387 VTAKIMLTLGGLCISIFTGWYLDKKIVWSEITNDGSLKVPVYKLIIFILRYIAPIAISLI 446 Query: 464 LV 465 + Sbjct: 447 FI 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: 691 Number of extensions: 45 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: 456 Length adjustment: 34 Effective length of query: 479 Effective length of database: 422 Effective search space: 202138 Effective search space used: 202138 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