GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Desulfovibrio vulgaris Hildenborough

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 209486 DVU0547 high-affinity branched chain amino acid ABC transporter, periplasmic branched chain amino acid-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|MicrobesOnline__882:209486 DVU0547 high-affinity branched chain
           amino acid ABC transporter, periplasmic branched chain
           amino acid-binding protein
          Length = 372

 Score =  176 bits (445), Expect = 1e-48
 Identities = 111/354 (31%), Positives = 175/354 (49%), Gaps = 7/354 (1%)

Query: 9   VALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIKI 68
           VA+ A   F+G+    + + V G  +G  A++G      A+  A   N  GGING+ +++
Sbjct: 15  VAVMAGPVFAGDT---IKLGVPGAHSGDLASYGLPSANAAKIVAKMFNDKGGINGKMVEV 71

Query: 69  ELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPDL 128
              DD   P+   + A K  +DGV  V+GH  SG +  A  +Y E   +   P    P L
Sbjct: 72  IPQDDQCKPEMATNAATKLVSDGVDIVLGHICSGATKAALPIYKEANKVVMSPSATTPAL 131

Query: 129 HGTGLWNT-FRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187
             +G +   FRT   DDQQ  +   +  D     KIAV+HDK  YG+G A+  K+ +  +
Sbjct: 132 TQSGDYPMFFRTISSDDQQAKLGVDFAIDKLGAKKIAVLHDKGDYGKGYAEYAKQFIEQS 191

Query: 188 G-VTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVS 246
           G  T V++EG+  G  D+SA++ K++  G   + +GG H EA  I+ Q   + +    +S
Sbjct: 192 GKATVVLFEGVTPGAVDYSAVVQKVRSEGADAVMFGGYHPEASKIVAQMRKKRMTTPFIS 251

Query: 247 GDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA-GFNPEAYTLYSYAAM 305
            DG+  +    +AG    G   +   D +  P  KE +E  K   G  P A+   ++AA 
Sbjct: 252 DDGVKDDTFIKVAGKDAEGVYASSSKDVSMLPMYKEAIELHKKEFGTEPGAFYKEAFAAA 311

Query: 306 QTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
           Q +  A + AGS +   V  A++      T +G I FD++GD +  G+ MY+ K
Sbjct: 312 QALLTAVQRAGSTETPKVVDALRNNF-VETAIGKIKFDKRGDAEGTGFSMYQVK 364


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: 374
Number of extensions: 32
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: 372
Length adjustment: 30
Effective length of query: 351
Effective length of database: 342
Effective search space:   120042
Effective search space used:   120042
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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