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_104485326.1 UN63_RS03140 sodium-dependent transporter
Query= TCDB::O67854 (513 letters) >NCBI__GCF_002936955.1:WP_104485326.1 Length = 445 Score = 181 bits (460), Expect = 4e-50 Identities = 140/475 (29%), Positives = 238/475 (50%), Gaps = 48/475 (10%) Query: 5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64 REH+ +R G I+A AG AVGLGN FP QAA NGGGAF+I Y++ +++ P++ +E A Sbjct: 2 REHFGSRFGFIMAAAGAAVGLGNIWGFPTQAASNGGGAFLIAYLVLVMMLAFPMLVMEVA 61 Query: 65 MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124 +GRYG A + + + A ++G G+ +P +V +Y + W L F + Sbjct: 62 IGRYGQANPVDSVRKLGRTPLQKTIASLVGYAGMLVPSLVLSFYAIVAGWLLAFLAAAVT 121 Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184 + +G E + L IV+ + ++ +++ Sbjct: 122 RI-------------------------LGWDAATEWLEAFGLGRNIVWTLVFYLLTILVV 156 Query: 185 R-GISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243 + G+ +GIER++ MP LF+L FL++ ++L T +G A GL PDF K+ +PG+ Sbjct: 157 QAGVRRGIERWSARLMPALFVL--FLLLFFYIL-TQDG-AMTGLKHYLVPDFSKVLEPGL 212 Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303 I+A+GQ FF+L++G +++ Y SY+ K+++I + TL + L G + +PA Sbjct: 213 LISAMGQAFFSLTIGGCSMLMYGSYLNKNENIPRTAF-QVTLLDTGVAFLAGLVILPA-- 269 Query: 304 AFFGVANAVAI-AKAGAF----NLGFITLPAIFSQTAG--GTFLGFLWFFLLFFAGLTSS 356 F + N V I A+ G+ L F+ LPA+F T G G + ++F L+ A LTSS Sbjct: 270 MFVAMKNGVTIFAEDGSLLSSDTLVFVVLPALF-DTMGPIGLVMALVFFVLMGIAALTSS 328 Query: 357 IAIMQPMIAFLEDELKLSRKHAV-LWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFF 415 I++++ +++ + K SR L A+ FS + + + + Sbjct: 329 ISMLEVPVSYTTERFKASRPLMTWLLGGALALFSVAICLNFGALFGFVIRLSTQNIQPLV 388 Query: 416 GLTELIIFFWIFGADKAWEEINRGGIIKVP----RIYYYVMRYITPAFLAVLLVV 466 GL ++ W++G K +EE+ +G RI+ + +R + P L VLLV+ Sbjct: 389 GLGFCVLGGWMWGRAKLFEELVQGSPELAGSVFWRIWPWYVRIVCP--LLVLLVI 441 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: 733 Number of extensions: 41 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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