GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhizobium freirei PRF 81

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_004124021.1 RHSP_RS23175 ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_000359745.1:WP_004124021.1
          Length = 350

 Score =  199 bits (507), Expect = 7e-56
 Identities = 115/326 (35%), Positives = 188/326 (57%), Gaps = 12/326 (3%)

Query: 15  EGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGR 74
           EG  +  L+V++A+  F  P + +L N   + +  ++  I+A+G+  +I+  G DLS G 
Sbjct: 28  EGRAFFALIVIIAVFSFLSPNYFTLGNFLTMSSHVAIFGILAIGMLLVILNGGIDLSVGS 87

Query: 75  QVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTP 134
            +GLA  VA  L+Q +  ++  F  +   P+  V+++ CA GA+IG +NG+++AYL V  
Sbjct: 88  TLGLAGCVAGFLMQGVTLSS--FGVILYPPVWAVVVLTCAFGAIIGAVNGVLVAYLRVPA 145

Query: 135 FITTLGTMIIVYGI-----NSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFY 189
           F+ +LG + +  GI     N L Y+ +G  P  G ++GF     GF  L    +S I   
Sbjct: 146 FVASLGVLYVARGIALLMTNGLTYNNLGGRPELG-NTGFGWL--GFNRLAGIPISVIVLA 202

Query: 190 ALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLE 249
           AL  +    ++ ++T FG+ ++A GGN  AA +SGV V    +++Y LSGV  A  G++ 
Sbjct: 203 ALAIIC--GLVLSRTAFGRWLYASGGNERAADLSGVPVKRVKIIVYVLSGVCAAIAGLVL 260

Query: 250 AGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVN 309
           + ++ SA    G  YEL AIAA V+GG + +GG GT  G + G  +   ++ GL  IGV+
Sbjct: 261 SSQLTSAGPTAGTTYELTAIAAVVIGGAALTGGRGTTRGTMLGAFVIGFLSDGLVIIGVS 320

Query: 310 PYWQYIIKGAIIIFAVALDSLKYARK 335
            YWQ +  GA+I+ AV ++S++Y R+
Sbjct: 321 AYWQTVFTGAVIVLAVLMNSIQYGRR 346


Lambda     K      H
   0.327    0.143    0.415 

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: 337
Number of extensions: 16
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: 336
Length of database: 350
Length adjustment: 29
Effective length of query: 307
Effective length of database: 321
Effective search space:    98547
Effective search space used:    98547
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: 49 (23.5 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