GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Lutibaculum baratangense AMV1

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 WP_023430731.1 N177_RS02905 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_000496075.1:WP_023430731.1
          Length = 375

 Score =  133 bits (334), Expect = 9e-36
 Identities = 112/350 (32%), Positives = 163/350 (46%), Gaps = 9/350 (2%)

Query: 6   LSAVALTAMLAF-SGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGE 64
           ++A+AL A++A  + +A   V I   GPL+G N+  G   + G + A    NA   + G 
Sbjct: 13  VAAIALAAVVATGAADAQETVKIGFIGPLSGGNSQQGLTARNGFQLAIDQANAREDL-GF 71

Query: 65  QIKIELGDDVSDPKQGISVANKFAAD-GVKFVIGHFNSGVSIPASEVYAENGILRNHPGR 123
           +I+  + DD S+P+ G+S A K   D  V  V GH+NS V++  + V    GI     G 
Sbjct: 72  KIEGVIQDDASNPQTGVSAALKLTNDPAVIAVTGHWNSPVALATAPVITRAGIPFVIWGA 131

Query: 124 DEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKA 183
             P +  T      R              + A+      IA+V D + YG       +K 
Sbjct: 132 ISPKITETNNPLLARVVPTLVNTNEPLAAWAAEEIGQ-NIAIVSDTSDYGMANVAAFRKP 190

Query: 184 MNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAT 243
              AG T    E   VG  DF A + K+K      IY+GG+ TEAGL+ +Q  + GL   
Sbjct: 191 FEEAGGTITSVETAPVGTTDFRATLTKIKSDNPDAIYFGGVVTEAGLVRQQMKEVGLDVP 250

Query: 244 LVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPE--AYTLYS 301
           ++  DG    E   IAGDA  GT++    + T N    E+ E + AAGF      YT  +
Sbjct: 251 MIGVDGFHDPEFIKIAGDAAEGTISGIMKE-TENEKLVEMNEAYAAAGFAEPVGTYTKNA 309

Query: 302 YAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIP 351
           Y A   I  A + AG+ D  AV +A++    +   +G  SFDE G  K+P
Sbjct: 310 YDAANIIIAAIEEAGT-DRAAVGEAIRAM-EYDGAMGHTSFDENGQTKLP 357


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: 336
Number of extensions: 17
Number of successful extensions: 5
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: 375
Length adjustment: 30
Effective length of query: 351
Effective length of database: 345
Effective search space:   121095
Effective search space used:   121095
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 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