GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tnaT in Shewanella loihica PV-4

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)



>lcl|FitnessBrowser__PV4:5207779 Shew_0300 sodium:neurotransmitter
           symporter (RefSeq)
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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