GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Sinorhizobium meliloti 1021

Align glucose transporter, ATPase component (characterized)
to candidate SM_b20904 SM_b20904 sugar uptake ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>FitnessBrowser__Smeli:SM_b20904
          Length = 261

 Score =  357 bits (915), Expect = e-103
 Identities = 178/246 (72%), Positives = 209/246 (84%)

Query: 13  TPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72
           TPLVEMK+ISISFGGI AVD  SVDLYPGEVV LLGHNGAGKSTLIK+LSGAY+ DAGEI
Sbjct: 6   TPLVEMKNISISFGGIHAVDDASVDLYPGEVVALLGHNGAGKSTLIKILSGAYKRDAGEI 65

Query: 73  RVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAE 132
            +NG+  EI NPRDA+ + IETIYQTLA+ADN+DAA+NL+LGREL TP+G +DD AMEA+
Sbjct: 66  LINGEPAEINNPRDAKKYGIETIYQTLAVADNVDAAANLYLGRELRTPWGTLDDVAMEAK 125

Query: 133 CRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMV 192
            R++M RLNPNFQ+F EPV ALSGGQRQSVAIARA+ F+A+ILIMDEPTAALGP ET  V
Sbjct: 126 AREVMGRLNPNFQRFKEPVKALSGGQRQSVAIARAILFDARILIMDEPTAALGPQETAQV 185

Query: 193 AELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMIILG 252
            ELI+QLK +GIGIFLI HD++ V +L DR SVMKNGQ+VG    +DVT D++L MII+G
Sbjct: 186 GELIKQLKREGIGIFLISHDIHDVFDLADRVSVMKNGQVVGHARTEDVTKDEVLGMIIMG 245

Query: 253 KRPGEA 258
           K P +A
Sbjct: 246 KVPPKA 251


Lambda     K      H
   0.317    0.135    0.373 

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: 252
Number of extensions: 8
Number of successful extensions: 1
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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