GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Pedobacter sp. GW460-11-11-14-LB5

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__Pedo557:CA265_RS08575
          Length = 422

 Score =  306 bits (785), Expect = 6e-88
 Identities = 169/410 (41%), Positives = 252/410 (61%), Gaps = 5/410 (1%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y +   ++ S+FF+WG    L+ ILIPHLK    LN  ++ L+  + F AYFLM++PAG+
Sbjct: 13  YLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFLMAIPAGM 72

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
           ++ + GYK  +++GL     GA  F PAA    Y  FL ALF++  G+T+L+ +AN Y A
Sbjct: 73  ILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLETSANPYAA 132

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE 204
           +LG    A+SRL LA + N L   +AP  GGL ILS    + E++A ++ A + +Y ++E
Sbjct: 133 VLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMTDAGRNSYFLEE 192

Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264
           A +V+ PY+ L IVL ++A   Y   LP +  K+     K  S    LRH H+ + V+A 
Sbjct: 193 AASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKSIDGEAK-GSFFGALRHKHLKWAVVAQ 251

Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324
           FFYVG +V + SF +        G   E+ AA+++A Y L   +GRF G+A+L  +S  K
Sbjct: 252 FFYVGAQVCVTSFFIRMAQQG--GGFDEKTAASYLAIYGLLFTVGRFAGTAILQFVSSHK 309

Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSL 384
           LLAI+A I++ L L  ++ KG+  +Y++ +IG F SIMFPTIF+LGI+ +G  T   SS 
Sbjct: 310 LLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGIGDDTKPGSSW 369

Query: 385 LIMAIVGGAIVPFVQGLFADHIG--VQHAFFLPLLCYAYIVFYGLYGSRI 432
           LIM+IVGGAI+PF  G   D  G  +Q  + +PL+C+  I+++GL G +I
Sbjct: 370 LIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYFGLRGYKI 419


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: 24
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: 422
Length adjustment: 32
Effective length of query: 410
Effective length of database: 390
Effective search space:   159900
Effective search space used:   159900
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:

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