GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruP in Bacteroides thetaiotaomicron VPI-5482

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate 353142 BT3616 fucose permease (NCBI ptt file)

Query= uniprot:A0A1I2JXG1
         (442 letters)



>lcl|FitnessBrowser__Btheta:353142 BT3616 fucose permease (NCBI ptt
           file)
          Length = 418

 Score =  249 bits (636), Expect = 1e-70
 Identities = 145/414 (35%), Positives = 230/414 (55%), Gaps = 9/414 (2%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y + + ++ S+FF+W   + L   +I  L    +LN  EA   +  ++ AYF+  +P  +
Sbjct: 6   YTIPLALVFSLFFLWAISSNLLPTMIRQLMKTCELNTFEASFTETAYWLAYFIFPIPIAM 65

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
            + R  YK GI+ GL +A VG   F+PAA +  Y A+L   F++ATG+  L+ AAN YV 
Sbjct: 66  FMKRYSYKAGIIFGLLLAAVGGLLFFPAAMLKEYWAYLCIFFIIATGMCFLETAANPYVT 125

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE 204
           +LG  ++A  RL LAQ+ N LG F+A  F   LILS    + E +    P    AY   E
Sbjct: 126 VLGAPETAPRRLNLAQSFNGLGAFIAAMFLSKLILSGTHYTRETLPVDYPGGWQAYIQLE 185

Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPAL-TEKTEQASVKQHSLV--SPLRHPHVLFGV 261
              ++ PYL LA++L  +AV     +LP +  E  E AS K+  L+    L+  H+ +GV
Sbjct: 186 TDAMKLPYLILALLLLAIAVVFVFSKLPKIGDEGAEPASGKKEKLIDFDVLKRSHLRWGV 245

Query: 262 LAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLS 321
           +A FFY GG+ AI S  + Y        + E  A  +   Y L  ++GR+IG+ L+ K  
Sbjct: 246 IAQFFYNGGQTAINSLFLVYCC--TYAGLPEDTATTFFGLYMLAFLLGRWIGTGLMVKFR 303

Query: 322 PRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEA 381
           P+ +L ++A +N+ L    M+  G + +Y++++I  F SIM+PT FSL ++ +G  T   
Sbjct: 304 PQGMLLVYALMNILLCGVVMLWGGMIGLYAMLAISFFMSIMYPTQFSLALKGLGNQTKSG 363

Query: 382 SSLLIMAIVGGAIVPFVQGLFA---DHIGVQHAFFLPLLCYAYIVFYGLYGSRI 432
           S+ L+MAIVG A +P +   F    +HI    A+ +P++C+A+  +YG  G ++
Sbjct: 364 SAFLVMAIVGNACLPQLTAYFMHVNEHI-YYVAYGIPMICFAFCAYYGWKGYKV 416


Lambda     K      H
   0.327    0.140    0.414 

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: 489
Number of extensions: 17
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: 442
Length of database: 418
Length adjustment: 32
Effective length of query: 410
Effective length of database: 386
Effective search space:   158260
Effective search space used:   158260
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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