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_004127101.1 RHSP_RS28500 ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_000359745.1:WP_004127101.1
          Length = 341

 Score =  211 bits (537), Expect = 2e-59
 Identities = 135/328 (41%), Positives = 189/328 (57%), Gaps = 20/328 (6%)

Query: 15  EGGIYVVLLVLLAII-----IFQDPTFL-SLLNLSNILTQSSVRIIIALGVAGLIVTQGT 68
           E GI++VL+ +  +      IF   +FL +L  L  ++ Q SV  II++GV  +I+T G 
Sbjct: 24  ELGIFLVLIGIALLCEILGWIFVGQSFLMNLQRLKIMILQVSVIGIISVGVTQVIITGGI 83

Query: 69  DLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIA 128
           DLS+G  VGL A+VAA+  QS   A  V+P +  MP  + I I   IG V G ING +I 
Sbjct: 84  DLSSGSVVGLTAMVAASFAQSSTWARAVYPALTDMPFFVPIGIGLLIGLVAGYINGQLIT 143

Query: 129 YLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITF 188
              + PFI TLG M+   G++ LY       PISG    F+    G           +  
Sbjct: 144 RTKIPPFIATLGMMVSARGLSKLY---TKGQPISGLTDQFNFIGSGIWP--------VVV 192

Query: 189 YALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGML 248
           + +IAV F  VL   TR+GK  +AIG N +AA+VSG+NV  +L+ +YA++G+     G++
Sbjct: 193 FLIIAVVFHIVL-RYTRYGKFTYAIGANVQAARVSGINVEGHLVKVYAIAGLLAGLAGII 251

Query: 249 EAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGV 308
            A R+ +A   +G  YELDAIAA V+GG S +GGVG + G V G II  V+  G T++ V
Sbjct: 252 TAARVQTAQAGMGVTYELDAIAAAVIGGTSLTGGVGRIAGTVIGTIILGVMISGFTFLNV 311

Query: 309 NPYWQYIIKGAIIIFAVALDSLKYARKK 336
           + Y+Q I KG III AVA+D   Y +KK
Sbjct: 312 DAYYQEIAKGVIIIAAVAID--VYRQKK 337


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: 334
Number of extensions: 22
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: 336
Length of database: 341
Length adjustment: 28
Effective length of query: 308
Effective length of database: 313
Effective search space:    96404
Effective search space used:    96404
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