GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:209486
          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:

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