GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Pseudovibrio axinellae Ad2

Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate WP_068002937.1 PsAD2_RS04500 sugar ABC transporter permease

Query= reanno::Phaeo:GFF1304
         (288 letters)



>NCBI__GCF_001623255.1:WP_068002937.1
          Length = 307

 Score =  137 bits (345), Expect = 3e-37
 Identities = 85/281 (30%), Positives = 149/281 (53%), Gaps = 6/281 (2%)

Query: 1   MATQHSRSAARIMMAPAVILLLGWMLVPLTMTLYFSFKKYLPL-RGGDLGWVGFDNYARF 59
           +A + +R    + + PA I+++  +L P+   +Y SF  + P  R G   ++G  NY   
Sbjct: 3   LAIKANRLTPYMFLLPAGIVMILALLYPIGYMIYASFLDWSPSQRIGQAEFIGIRNYINL 62

Query: 60  LSSSAFWPSVQATLVIVGGVLAITVILGVFLALLLNQPMWGQGIVRILVIAPFFVMPTVS 119
           L  +AF  S   T+     V+ + +I+GV LA+LL++ + G  ++R + I P  + P V 
Sbjct: 63  LGDAAFRESFWVTIRFAAIVVTLEMIVGVGLAMLLDRNIRGMVLLRTVFILPMMIAPIVV 122

Query: 120 ALVWKNMFMDPVNGLFAHLWKAFGAEPVSWLSEASLQSIILIVS--WQWLPFATLILLTA 177
            L+W+ MF  P  G+F  + K+FG E + WL++++   I ++++  WQW PF  ++ L A
Sbjct: 123 GLMWRYMF-HPTVGIFNRMLKSFGFEGIPWLADSTWAFIAIVIADVWQWTPFIFILALAA 181

Query: 178 IQSLDSEQLEAAEMDGAPPVARFGYITLPHLSRAITVVVLIQTIFLLSIFAEIFVTTQGS 237
            QSL    LEAAE+DGA    +   I LP +   + V ++++ I +  +   I V T G 
Sbjct: 182 TQSLPRSALEAAEIDGANEWQKIVMIKLPLMMPVLIVTLMLRLIDVFKVLEVILVLTNGG 241

Query: 238 FG--TKTLTYLIYQRVLESQNVGLGSAGGVYAIILANIVAI 276
            G  T+ L   I++   E Q +G  +A     +++  ++ I
Sbjct: 242 PGLSTEILALRIFRTAQEFQELGEAAAMSNMLLMMLMVLTI 282


Lambda     K      H
   0.328    0.140    0.430 

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: 233
Number of extensions: 18
Number of successful extensions: 3
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: 288
Length of database: 307
Length adjustment: 26
Effective length of query: 262
Effective length of database: 281
Effective search space:    73622
Effective search space used:    73622
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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