GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Sinorhizobium meliloti 1021

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate SMc02358 SMc02358 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Smeli:SMc02358
          Length = 235

 Score =  219 bits (557), Expect = 5e-62
 Identities = 113/235 (48%), Positives = 161/235 (68%), Gaps = 2/235 (0%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           ML    +S  YG I+A+  +S  ++KGE+V+L+GANGAGKS+ +  + G+ +A+ G+I  
Sbjct: 1   MLDVTDLSVSYGAIRAVRSISFTLRKGELVSLLGANGAGKSSTIKCIAGALKASGGTITL 60

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDY--QVQMDKVLE 118
           EG+++       ++R  +A VPE R VF  LTV ENL +G F   +D    +  ++K+  
Sbjct: 61  EGKDITAASPEQVVRAGLATVPETRDVFPDLTVAENLMLGAFIHRRDQAGNRDNLEKLNT 120

Query: 119 LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQ 178
           LFPRL ER +Q AGT+SGGEQQML I RALM++P++LLLDEPSLGLAP I+++IFE+IE 
Sbjct: 121 LFPRLAERSKQAAGTLSGGEQQMLVIARALMARPRVLLLDEPSLGLAPAIVERIFEMIET 180

Query: 179 LRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233
           L++ G+T+ LVEQN NQAL +ADRA+V+  G IV   T   + +   +   YLGG
Sbjct: 181 LKKSGLTILLVEQNVNQALAVADRAFVMRLGAIVASGTAEEIRSTSDLSAHYLGG 235


Lambda     K      H
   0.318    0.136    0.374 

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: 8
Number of successful extensions: 2
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: 233
Length of database: 235
Length adjustment: 23
Effective length of query: 210
Effective length of database: 212
Effective search space:    44520
Effective search space used:    44520
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: 46 (22.3 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