GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Marinobacter adhaerens HP15

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 GFF3112 HP15_3055 high-affinity leucine-specific leucine-specific-binding periplasmic protein of high-affinity branched-chain amino acid ABC transporter transport system periplasmic binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__Marino:GFF3112 HP15_3055 high-affinity
           leucine-specific leucine-specific-binding periplasmic
           protein of high-affinity branched-chain amino acid ABC
           transporter transport system periplasmic binding protein
          Length = 370

 Score =  277 bits (708), Expect = 4e-79
 Identities = 147/357 (41%), Positives = 214/357 (59%), Gaps = 3/357 (0%)

Query: 3   KSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGIN 62
           K L++AV+ +  L  +G+A A++ I +AGP+TGP A +G     GA  A   INA GG+ 
Sbjct: 6   KKLVTAVSTSVALMGAGHAAAEIQIGIAGPMTGPVAQYGDMQFSGARMAIEQINANGGVM 65

Query: 63  GEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPG 122
           GE++     DDV DPKQ ++VAN    DGV+FVIGH  S  + PAS++Y + GIL   P 
Sbjct: 66  GEELVAVEYDDVCDPKQAVTVANSLVNDGVRFVIGHLCSSSTQPASDIYEDEGILMVTPA 125

Query: 123 RDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKK 182
              P++   G    FRT G D  QG +A +Y+A      ++A+VHDK  YG+G+A   + 
Sbjct: 126 STSPEITERGYELVFRTIGLDSMQGPVAARYIASQ-NPERVAIVHDKQQYGEGIATAVRD 184

Query: 183 AMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKA 242
            +  AGV   ++EGI  GDKDFS+L+ K+K+A V  +Y+GG H E GLI+RQA    L A
Sbjct: 185 TLKDAGVEIAMFEGITAGDKDFSSLVTKLKQADVDYVYYGGYHPELGLILRQANSADLDA 244

Query: 243 TLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYS 301
             +  +G+ + ++ +IAG+A  G L T  P       N+ LV+ F+  G +P   + L S
Sbjct: 245 RFMGPEGVGNKDINTIAGEAAEGLLVTLPPAFDQKAENQALVKAFEDKGEDPSGPFVLTS 304

Query: 302 YAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
           Y A+Q +A   +AAGS DP  VA A++E G F T +G + +D+ GD K   +++YEW
Sbjct: 305 YTAVQLVAEGIEAAGSTDPFDVAAALRE-GTFQTPIGTVEYDKAGDMKSFEFVVYEW 360


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: 395
Number of extensions: 25
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: 370
Length adjustment: 30
Effective length of query: 351
Effective length of database: 340
Effective search space:   119340
Effective search space used:   119340
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 preprint 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