GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguB in Phaeobacter inhibens BS107

Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF3640 PGA1_262p00440 xylose transport system permease protein XylH

Query= TCDB::O05177
         (398 letters)



>FitnessBrowser__Phaeo:GFF3640
          Length = 433

 Score =  215 bits (547), Expect = 2e-60
 Identities = 144/415 (34%), Positives = 211/415 (50%), Gaps = 47/415 (11%)

Query: 23  NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDL 82
           ++R  GM+ A V + + F   T G    P N+ NL +Q   + IMA GM+ VIV  HIDL
Sbjct: 24  DVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDL 83

Query: 83  SVGSIVAFVGAIAAILTVQ-------WGMNP----FLAALICLVIGGIIGAAQGYWIAYH 131
           SVG+++A   A+ A++           G+N      +   + L IG +IGA QG+ + + 
Sbjct: 84  SVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFL 143

Query: 132 RIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILT 191
            IP+FIVTL G LV+R +  ++  G+ IGP  + F V         GG  G   T++   
Sbjct: 144 TIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVF--------GGTSGTLGTTLSWV 195

Query: 192 VLITVALFYLA--WRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYR----- 244
           V I   L  LA  W  R     HG  V+P     V    I+ +IL     L+ Y+     
Sbjct: 196 VGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPARR 255

Query: 245 --------------------GLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATK 284
                               GLP  +++++    + + + RRT +GR ++A GGN  A +
Sbjct: 256 LKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAE 315

Query: 285 LSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASG 344
           LSGINT  L+   F  MG L  L+ ++ + RL + +   G   EL VIAA  IGG + SG
Sbjct: 316 LSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSG 375

Query: 345 GVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDV-YNKNKG 398
           G G I GA++GA IM  + +GM++VG+   FQ +V G VL+AAV+ D+ Y K  G
Sbjct: 376 GFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKRVG 430


Lambda     K      H
   0.329    0.145    0.422 

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: 553
Number of extensions: 36
Number of successful extensions: 6
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: 398
Length of database: 433
Length adjustment: 31
Effective length of query: 367
Effective length of database: 402
Effective search space:   147534
Effective search space used:   147534
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 (21.8 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