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 5207779 Shew_0300 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::O50649 (501 letters) >FitnessBrowser__PV4:5207779 Length = 452 Score = 171 bits (433), Expect = 5e-47 Identities = 137/462 (29%), Positives = 210/462 (45%), Gaps = 53/462 (11%) Query: 8 WKSRSGFIFATIGAAVGLGNFWRFPFMAYQNGGGAFLLPYFVALLTAGVPLMILEFGFGH 67 + SR GFI A G+AVG+GN W FP A +GGGAFLL Y V + G P+++ E G Sbjct: 9 FSSRIGFIMAAAGSAVGVGNIWGFPTQAATHGGGAFLLVYLVLIFLLGYPMLVAELMIGR 68 Query: 68 KMRTATITAF-----KKLNRRF-EWIGWWQITVPVVVVTFYSVIISWSLRYLIFSFTQAW 121 +T A KL+R + IG+ I ++ TFYS++ W + + + + Sbjct: 69 HGQTNPADAMAKLGSSKLSRNLGKTIGFASIITATLICTFYSILSGWFVSFTLAPIARLV 128 Query: 122 GDDPGTFFSSDFLGITSGPLELGGLRWGIFAAVAVVWFANYYISAQGISGGIEKACKIMT 181 G L +TS LE L IF + V+ + QG+ GIE K + Sbjct: 129 G------MQDIALWLTSFSLERNLLFTLIFILMVVL------VIRQGVQQGIEAWSKRLM 176 Query: 182 PFLIVAMLIFVIRGITLPGATYGLNYFLNPDFSKIMDPGVWVAAYSQVFFSTTLAVGVMI 241 P L+ +++ V +T PGA+ GLN L PDF +I +P V + A Q FFS T+ G M+ Sbjct: 177 PLLLAILILGVAYILTQPGASQGLNALLVPDFGRIWEPQVLIGALGQTFFSLTVGTGAMM 236 Query: 242 AYASYVPEDSDLANNAFITVFANSSFDFMAGLAVFSTLGYAAVTAGVPF---EEMAVAGP 298 Y +Y+ +LA ++S F+A L + + Y A GV + + Sbjct: 237 VYGAYLNRQENLAKLTAYVTLTDTSVAFLAALMIIPAM-YVAQHNGVQIFAADGSLLNAD 295 Query: 299 GVAFVAFPKAISMLPGPTWLQSLFGILFFSALLLAGISSSISQMESFASAVIDRFGVDRK 358 + F P L G L I+FF + +AG++S+IS +E S ++++ + R Sbjct: 296 TLVFTVLPALFDSLGG--LAGQLIAIVFFILMTIAGLTSAISIVEVPTSYMVEKTEIQR- 352 Query: 359 KLLGWFSLIGFAFSALFATGAGVHILD--IVDHFVGSYAIAILGLVEA----IVLGYIMG 412 SA + G G+ +L +V +F +A+ I E I LG + Sbjct: 353 ------------HSATYLVGGGIALLATIMVFNFDALFALVITLTTERAQPFIALGIALY 400 Query: 413 TARIREHVNLTSDIRV-------GMW---WDVLVKYVTPVLL 444 T + +L I G++ W V VKYV PVL+ Sbjct: 401 TGWVWHRNSLLKAIAAQEGAKLDGLFWRIWPVYVKYVCPVLI 442 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: 591 Number of extensions: 36 Number of successful extensions: 4 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: 501 Length of database: 452 Length adjustment: 33 Effective length of query: 468 Effective length of database: 419 Effective search space: 196092 Effective search space used: 196092 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: 51 (24.3 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