GapMind for catabolism of small carbon sources

 

Aligments 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_RS04675 CA265_RS04675 L-fucose:H+ symporter permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS04675 CA265_RS04675 L-fucose:H+
           symporter permease
          Length = 436

 Score =  303 bits (776), Expect = 7e-87
 Identities = 157/406 (38%), Positives = 250/406 (61%), Gaps = 5/406 (1%)

Query: 25  YPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAGL 84
           Y   + ++TS+FF WGF+  L+ +LIPHL+  F+LN  E+ LV  + F AYFL++LPAG 
Sbjct: 21  YLFPLILVTSLFFFWGFVHNLDPVLIPHLRKAFQLNVFESTLVDSSVFIAYFLLALPAGY 80

Query: 85  LVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYVA 144
           ++ + GYK GI+ GL +  +G   F PAA    Y  FLGALF++A G+T L+ AAN YV 
Sbjct: 81  IMRKYGYKSGIILGLVLFAIGCLLFIPAANTAQYIFFLGALFIIACGLTFLETAANPYVT 140

Query: 145 LLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQE 204
           +LGP ++A+ RL  +Q+ N L  FLAP  GG  I +    +  Q+AK+ P E+ AY ++E
Sbjct: 141 VLGPPETATQRLNFSQSFNGLAAFLAPVLGGKFIFTEVKYTDAQLAKMLPLEKQAYMLEE 200

Query: 205 AQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHSLVSPLRHPHVLFGVLAI 264
           A TV+ PYL L I++ ++A+     +LP +  K E+ + ++ S    L H H+ + ++  
Sbjct: 201 ASTVKAPYLILGILIIVVAILFIFTKLPDI--KEEENAQEKSSFSHVLGHSHLRWAIIGQ 258

Query: 265 FFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKLSPRK 324
           FFYVG +V + S  +++++      +S+ AA  +     L  M+GRF G+  +  ++  K
Sbjct: 259 FFYVGAQVCVLSLFISFVT--SSAGISQDAAKWYAGAAGLAFMVGRFAGTFFMRYVAAHK 316

Query: 325 LLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGEASSL 384
           LL ++A I+  L L ++   G + +Y+++ +  F SIMFPTIFSLGI  +G  T   SSL
Sbjct: 317 LLMLYALISAVLTLVSIFASGMITVYALIGVSFFMSIMFPTIFSLGIAGLGKDTKLGSSL 376

Query: 385 LIMAIVGGAIVPFVQGLFADHI-GVQHAFFLPLLCYAYIVFYGLYG 429
           ++M+IVGGA +P V GL +D    +Q+ + +P +C+  + ++G  G
Sbjct: 377 IVMSIVGGAFLPPVLGLISDATHNIQYGYLVPFVCFLVVFYFGWKG 422


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: 496
Number of extensions: 26
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: 436
Length adjustment: 32
Effective length of query: 410
Effective length of database: 404
Effective search space:   165640
Effective search space used:   165640
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 paper from 2022 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