GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Burkholderia phytofirmans PsJN

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate BPHYT_RS31715 BPHYT_RS31715 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__BFirm:BPHYT_RS31715
          Length = 380

 Score =  206 bits (524), Expect = 9e-58
 Identities = 131/362 (36%), Positives = 186/362 (51%), Gaps = 12/362 (3%)

Query: 6   LSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GINGE 64
           ++A++     AF+ +    + I  A P TG  A  G + + GA  A  D+N  G  ING+
Sbjct: 11  VAALSAACNAAFAADDITVIKIGSAAPTTGAIANLGKENENGARLAVEDVNRRGLVINGK 70

Query: 65  QIKIELG--DDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPG 122
           +IK+EL   DD +DP+QG  VA +   DGV  V+GH NSGVSI AS +Y +  IL+  P 
Sbjct: 71  KIKLELDAVDDQADPRQGTQVAQRLVDDGVVAVVGHLNSGVSIAASRIYHDAQILQISPD 130

Query: 123 RDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKK 182
              P     G   T+R    D QQ  +   Y  +  K  K+A+V D T YGQGLAD+   
Sbjct: 131 STNPKFTQQGFNTTYRLVATDAQQSPVLAHYALETLKAKKVAIVDDSTAYGQGLADQFSS 190

Query: 183 AMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKA 242
           A+ + G T V  E  N    DF  +I K+K     +I++GG+   AG  I+Q A  GL A
Sbjct: 191 AVKSGGATVVAREATNDKTIDFKGVITKIKGQSPDVIFYGGMDATAGPFIKQVAQLGLNA 250

Query: 243 TLVSGDGIVSNELASIAGDAVAGTLNTFGPDP----TANPA-NKELVEKFKAAGFNPEAY 297
            ++ GDG  S+E+ ++AG AV   + +    P     A PA  KE  ++F   G   + Y
Sbjct: 251 KVLGGDGTCSDEVIALAGPAVDRLVCSIAGLPLSRMKAGPAFEKEYQQRF---GMPVQIY 307

Query: 298 TLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYE 357
             Y+Y A+  I  A K +GS D  A   A      +  + G I FD+KGD + P   +Y 
Sbjct: 308 APYAYDAVMVIVDAMKKSGSTD-HAKILAAASATDYQGLTGQIQFDDKGDVRSPRLTLYG 366

Query: 358 WK 359
           +K
Sbjct: 367 YK 368


Lambda     K      H
   0.314    0.132    0.383 

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: 356
Number of extensions: 15
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: 381
Length of database: 380
Length adjustment: 30
Effective length of query: 351
Effective length of database: 350
Effective search space:   122850
Effective search space used:   122850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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