GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tnaT in Marinobacter adhaerens HP15

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 GFF878 HP15_857 sodium-dependent transporter family protein

Query= TCDB::O50649
         (501 letters)



>lcl|FitnessBrowser__Marino:GFF878 HP15_857 sodium-dependent
           transporter family protein
          Length = 460

 Score =  203 bits (517), Expect = 9e-57
 Identities = 148/473 (31%), Positives = 230/473 (48%), Gaps = 58/473 (12%)

Query: 8   WKSRSGFIFATIGAAVGLGNFWRFPFMAYQNGGGAFLLPYFVALLTAGVPLMILEFGFGH 67
           W SR  FI A  G+AVGLGN W+FP++  +NGGGAF+L Y   +   GVP++I E   G 
Sbjct: 15  WSSRMAFILAAAGSAVGLGNIWKFPYITGENGGGAFVLIYLACIFLIGVPVLIAETMIGR 74

Query: 68  K--------MRTATITAFKKLNRRFEWIGWWQITVPVVVVTFYSVIISWSLRYLIFSFTQ 119
           +        MRT T T  +   R +  IGW  +    +V++FY+VI  W+L Y+  + T 
Sbjct: 75  RGGQSPVATMRTLTKT--EGTARGWRAIGWNGVIASFLVLSFYAVIGGWALVYIGKAATG 132

Query: 120 AWGDDPGTFFSSDFLGITSGPLELGGLRWGIFAAVAVVWFANYYISAQGISGGIEKACKI 179
            +           F G+ + P EL  L W     V VV     +I  +GI  G+EKA  +
Sbjct: 133 LFTGADAEAIGGQFGGLLANPWEL--LMWHSVFMVIVV-----FIVGRGIRSGLEKAVNM 185

Query: 180 MTPFLIVAMLIFVIRGITLPGATYGLNYFLNPDFSKIMDPGVWVAAYSQVFFSTTLAVGV 239
           + P L V ++  VI  +        +++  +PDFSK+   GV + A     F+ ++ +GV
Sbjct: 186 LMPLLFVLLVAMVIYAMNSGSFGRAVSFMFSPDFSKLTTAGV-LTALGHAAFTLSIGIGV 244

Query: 240 MIAYASYVPEDSDLANNAFITVFANSSFDFMAGLAVFSTLGYAAVTAGVPFEEMAVAGPG 299
           ++AY SY+P+  ++A  A      ++S   +AGLA+F  +    +  G        AGPG
Sbjct: 245 LMAYGSYLPKTVNIARTAMTIAVVDTSVALLAGLAIFPLVFANGLEPG--------AGPG 296

Query: 300 VAFVAFPKAISMLPGPTWLQSLFGILFFSALLLAGISSSISQMESFASAVIDRFGVDRKK 359
           + FV  P A   + G     +LFG +FF+ LL+A I+S+IS +E     + +  GV R K
Sbjct: 297 LIFVTLPLAFGQMSG----GALFGTIFFALLLVAAITSAISMLEPVVEWLEEHKGVSRAK 352

Query: 360 ------LLGWFSLIGFAFSALFATGAGVH------------ILDIVDHFVGSYAIAILGL 401
                 L  WF  IG   S  F     VH            + D++D  V +  + + GL
Sbjct: 353 SAIGGGLAIWFIGIGTVLS--FNVWESVHPLGFIPFFEGKTVFDLLDFLVSNLMMPLGGL 410

Query: 402 VEAIVLGYIMGTARIREHVNLT-SDIRVGMWWDVLVKYVTP----VLLGYNIL 449
             A+  G+ M    +   + L  S  +  M+   +++Y+TP    V+  YN+L
Sbjct: 411 AIALFAGWAMKRESLPADIGLQGSSYKAFMF---VLRYLTPAGIAVVFLYNLL 460


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: 704
Number of extensions: 42
Number of successful extensions: 5
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: 460
Length adjustment: 34
Effective length of query: 467
Effective length of database: 426
Effective search space:   198942
Effective search space used:   198942
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