Align High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed (characterized)
to candidate 5210455 Shew_2896 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::O50649 (501 letters) >FitnessBrowser__PV4:5210455 Length = 503 Score = 420 bits (1079), Expect = e-122 Identities = 202/487 (41%), Positives = 302/487 (62%), Gaps = 13/487 (2%) Query: 4 QRDQWKSRSGFIFATIGAAVGLGNFWRFPFMAYQNGGGAFLLPYFVALLTAGVPLMILEF 63 +R+QW SR GFI A +G+A+GLGN WRFP+MAY NGGGAF +PY A++TAG+P MI+EF Sbjct: 2 KREQWNSRVGFILAAVGSAIGLGNIWRFPYMAYDNGGGAFFIPYLFAMITAGIPFMIMEF 61 Query: 64 GFGHKMRTATITAFKKLNR----RFEWIGWWQITVPVVVVTFYSVIISWSLRYLIFSFTQ 119 GHK++ + F +L R EW+GW+Q+ + V+ +Y II W+L YL FSF+Q Sbjct: 62 SLGHKIKKTSPRIFAQLGHTLGFRLEWLGWFQVFIAAVIAVYYVAIIGWTLSYLGFSFSQ 121 Query: 120 AWGDDPGTFFSSDFLGI-TSGPLELGGLRWGIFAAVAVVWFANYYISAQGISGGIEKACK 178 AWGD+P FF + +L + + P LG + GI A+++ W + G+ GGIE+A K Sbjct: 122 AWGDNPNDFFFNHYLKLGNNSPSHLGEFQIGIAIAMSIAWLMTFMAVFTGVKGGIERANK 181 Query: 179 IMTPFLIVAMLIFVIRGITLPGATYGLNYFLNPDFSKIMDPGVWVAAYSQVFFSTTLAVG 238 IM P L + +L+ + R + LPGA GLNY PDFS+++D VW AAY Q+FF+ ++ Sbjct: 182 IMMPMLFIMVLVLIGRIMFLPGALSGLNYLFEPDFSRLLDAQVWSAAYGQIFFTLSVGFA 241 Query: 239 VMIAYASYVPEDSDLANNAFITVFANSSFDFMAGLAVFSTLGYAAVTAGVPFEEMAVAGP 298 +M+AY+SY+P +D+ NNAF+TV N F +AG+ +F LGY A P E+ +G Sbjct: 242 IMLAYSSYLPTKADINNNAFMTVLINCGFSILAGILIFGVLGYMAEEQMKPLTEVVSSGI 301 Query: 299 GVAFVAFPKAISMLPGPTWLQSLFGILFFSALLLAGISSSISQMESFASAVIDRFGVDRK 358 G+AFV P AI+++P P + G LFF AL++AG+SS IS +E+ SAVID+F V RK Sbjct: 302 GLAFVTIPTAINLMPAP----YILGPLFFIALVIAGLSSHISIIEAVTSAVIDKFHVRRK 357 Query: 359 KLLGWFSLIGFAFSALFATGAGVHILDIVDHFVGSYAIAILGLVEAIVLGYIMGTARIRE 418 +G+ S FAT G+ +LD+VD+F+ + A+ + L+E +++ +++ I + Sbjct: 358 PAAVLVCSLGYLVSMAFATNGGLLLLDLVDYFINNIALLLSCLLELVIITWLLKVTVIHQ 417 Query: 419 HVNLTSDIRVGMWWDVLVKYVTPVLLGYNILSNFISEFREPYAGYPTGALVLFGWVVAIA 478 H N S+ RVG W+ V +++++P +L + N + Y YP + GW Sbjct: 418 HANENSEFRVGGWFVVCLRFISPAILATILAKNLYNTLVNGYGDYPIADQLFLGW----G 473 Query: 479 MFGTSLF 485 + GT LF Sbjct: 474 LVGTMLF 480 Lambda K H 0.328 0.142 0.450 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: 832 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 503 Length adjustment: 34 Effective length of query: 467 Effective length of database: 469 Effective search space: 219023 Effective search space used: 219023 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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