GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Pedobacter sp. GW460-11-11-14-LB5

Align Glucose/galactose porter (characterized)
to candidate CA265_RS04675 CA265_RS04675 L-fucose:H+ symporter permease

Query= TCDB::P0C105
         (412 letters)



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

 Score =  312 bits (800), Expect = 1e-89
 Identities = 170/426 (39%), Positives = 252/426 (59%), Gaps = 17/426 (3%)

Query: 1   MATSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQS 60
           M+ +  TN  +     + K Y F L  +T LFF WGF+  L+ +LIPHL+  FQLN  +S
Sbjct: 1   MSHTPSTNFQVSDTPKNGKGYLFPLILVTSLFFFWGFVHNLDPVLIPHLRKAFQLNVFES 60

Query: 61  MLIQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGA 120
            L+    F AYF+++LPAG ++++  YK GI++GL++ AIGC LFIPAA+   Y  FLGA
Sbjct: 61  TLVDSSVFIAYFLLALPAGYIMRKYGYKSGIILGLVLFAIGCLLFIPAANTAQYIFFLGA 120

Query: 121 LFVLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAA-- 178
           LF++A G+T L+ AANPYVT+LG PETA  RL  +Q+FN L   +APV G   I +    
Sbjct: 121 LFIIACGLTFLETAANPYVTVLGPPETATQRLNFSQSFNGLAAFLAPVLGGKFIFTEVKY 180

Query: 179 TDATVN------------AEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDK 226
           TDA +              EA  V+ PYL+L +   V+AI+F   K PD++E+E A    
Sbjct: 181 TDAQLAKMLPLEKQAYMLEEASTVKAPYLILGILIIVVAILFIFTKLPDIKEEENAQEKS 240

Query: 227 KEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGA 286
                  + HL    IG F YVGA+V V S  ++F++  + AG+S+  A  +        
Sbjct: 241 SFSHVLGHSHLRWAIIGQFFYVGAQVCVLSLFISFVT--SSAGISQDAAKWYAGAAGLAF 298

Query: 287 MVGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTI 346
           MVGRF G+  MRY+   K L   A ++ +L  +++  +G I +++++ +  F SIMFPTI
Sbjct: 299 MVGRFAGTFFMRYVAAHKLLMLYALISAVLTLVSIFASGMITVYALIGVSFFMSIMFPTI 358

Query: 347 FSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAI-GIHLAFLMPIICYAYIAFY 405
           FSL + GLG  T  GS ++ ++IVGGA +P + G ++DA   I   +L+P +C+  + ++
Sbjct: 359 FSLGIAGLGKDTKLGSSLIVMSIVGGAFLPPVLGLISDATHNIQYGYLVPFVCFLVVFYF 418

Query: 406 GLIGSK 411
           G  G K
Sbjct: 419 GWKGWK 424


Lambda     K      H
   0.328    0.141    0.420 

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: 613
Number of extensions: 34
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: 412
Length of database: 436
Length adjustment: 32
Effective length of query: 380
Effective length of database: 404
Effective search space:   153520
Effective search space used:   153520
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