GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRIC in Brucella inopinata BO1

Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate WP_002965418.1 BIBO1_RS10685 trimeric intracellular cation channel family protein

Query= reanno::ANA3:7023996
         (213 letters)



>NCBI__GCF_000182725.1:WP_002965418.1
          Length = 218

 Score =  128 bits (322), Expect = 7e-35
 Identities = 64/189 (33%), Positives = 110/189 (58%), Gaps = 1/189 (0%)

Query: 14  GILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLAIA 73
           G+   A TGALAA R+Q+D+ G + +   TAIGGGT+RD++L + P+ WV    YL    
Sbjct: 11  GVFVFAATGALAASRRQLDIIGFIFLANITAIGGGTMRDLVLAS-PVFWVVQPLYLFVGT 69

Query: 74  FASLLTVAIAPVMRYLSKLFLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFG 133
            A++     A  +    +  L +DA+G+A ++++GA K L LGF P++A+V G+ T  FG
Sbjct: 70  LAAIAVYFTAHKVESRYRTLLWLDAIGMAAYTVMGAAKGLALGFGPSVAIVTGIFTATFG 129

Query: 134 GVIRDILCNQVPLIFKKELYAVISLFTAGLYITLNAYQLAEWINLVVCLTLGFSLRMLAL 193
           G++RD++  +  ++ ++E+Y   ++  A LY+ L    +   I+        F +R  AL
Sbjct: 130 GILRDMVVGEPSVLMRREIYVTAAVAGACLYVVLEYLGINPVISAGAAAFAAFFVRGGAL 189

Query: 194 RYHWSMPTF 202
            + W++P +
Sbjct: 190 YFGWTLPVY 198


Lambda     K      H
   0.330    0.143    0.438 

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: 149
Number of extensions: 10
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: 213
Length of database: 218
Length adjustment: 22
Effective length of query: 191
Effective length of database: 196
Effective search space:    37436
Effective search space used:    37436
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: 45 (21.9 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