GapMind for catabolism of small carbon sources

 

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

Align Glucose/galactose transporter (characterized, see rationale)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Pedo557:CA265_RS08575
          Length = 422

 Score =  278 bits (711), Expect = 2e-79
 Identities = 170/424 (40%), Positives = 240/424 (56%), Gaps = 18/424 (4%)

Query: 11  TSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFG 70
           T   S +G   Y    + + SLFF+WG    L+ ILIPHLK   +LN  Q+ LI    F 
Sbjct: 3   TEGDSSSGK-KYLLPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFF 61

Query: 71  AYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGIT 130
           AYFL++IPAG ++K+ GY+  +++GL+  + G  LF PAA+  +Y  FL ALF++  G+T
Sbjct: 62  AYFLMAIPAGMILKKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLT 121

Query: 131 ILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQAN 190
           +L+ +ANPY   LG    A+SRLNL  +FN L   VAP  G + ILS  +    ELA   
Sbjct: 122 MLETSANPYAAVLGDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMT 181

Query: 191 ---------AEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTS 241
                     EA  VK PY+ L   L V+A IF  + LP I+  S    E   +  G   
Sbjct: 182 DAGRNSYFLEEAASVKTPYITLGIVLLVIAAIFYFIHLPEIKTKS-IDGEAKGSFFG--- 237

Query: 242 ALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGR 301
           AL+  HL    V  F YVGA+V + SF +    +    G  E+ AA Y+A Y     VGR
Sbjct: 238 ALRHKHLKWAVVAQFFYVGAQVCVTSFFIRMAQQGG--GFDEKTAASYLAIYGLLFTVGR 295

Query: 302 FIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLA 361
           F G+A++Q + +  +LA  A ++ LL LVA+   GS  ++A+  +G F SIMFPTIF+L 
Sbjct: 296 FAGTAILQFVSSHKLLAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALG 355

Query: 362 LRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLG--IQLAFILPVVCYGFILFYGAK 419
           +  +G  T  GS  L ++IVGGAI+P   G L D  G  IQ+ + +P+VC+  IL++G +
Sbjct: 356 IDGIGDDTKPGSSWLIMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYFGLR 415

Query: 420 GSKM 423
           G K+
Sbjct: 416 GYKI 419


Lambda     K      H
   0.326    0.138    0.402 

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: 475
Number of extensions: 23
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: 423
Length of database: 422
Length adjustment: 32
Effective length of query: 391
Effective length of database: 390
Effective search space:   152490
Effective search space used:   152490
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: 50 (23.9 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