GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Pseudomonas stutzeri RCH2

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 GFF1279 Psest_1312 ABC-type branched-chain amino acid transport systems, periplasmic component

Query= TCDB::Q9L3M3
         (381 letters)



>lcl|FitnessBrowser__psRCH2:GFF1279 Psest_1312 ABC-type
           branched-chain amino acid transport systems, periplasmic
           component
          Length = 372

 Score =  282 bits (722), Expect = 9e-81
 Identities = 153/361 (42%), Positives = 216/361 (59%), Gaps = 3/361 (0%)

Query: 8   AVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIK 67
           A+ALT   +++  A   + I +AGP+TGP A +G     GAE A   IN AGG+NG Q+K
Sbjct: 13  AMALTGAASYTLAA-DTIRIGLAGPVTGPVAQYGDMQFIGAEMAIEQINKAGGVNGAQLK 71

Query: 68  IELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPD 127
               DD  DPKQ ++VANK   D VKFV+GH  S  + PAS++Y + GIL        PD
Sbjct: 72  GVRYDDACDPKQAVAVANKIVNDNVKFVVGHLCSSSTQPASDIYEDEGILMITAASTSPD 131

Query: 128 LHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAA 187
           +   G    FRT G D  QG  AG ++ADH K   +AV+HDK  YG+G+A   K+ +   
Sbjct: 132 ITSRGYELIFRTIGLDSLQGPTAGNFIADHVKPKNVAVIHDKQQYGEGIATAVKQTLEGK 191

Query: 188 GVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSG 247
            +   ++EGIN GDKDFS+LIAK+K  GV  +Y+GG H E GL++RQ+ ++GL    +  
Sbjct: 192 NIKVGLFEGINAGDKDFSSLIAKLKREGVDFVYYGGYHPELGLLLRQSKEKGLNVRFMGP 251

Query: 248 DGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSYAAMQ 306
           +G+ ++E+++IAG A  G   T       +P NKELV+ FKA   +P   +   +YAA+Q
Sbjct: 252 EGVGNSEISAIAGPASEGMYVTLPKSFDQDPRNKELVDGFKAKKQDPSGPFVFPAYAAVQ 311

Query: 307 TIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKKVRTAST 366
            IA   + AGS D + VA+A++    F T  G +SFDEKGD K   +++YEW +  T + 
Sbjct: 312 VIAEGIEKAGSTDTDKVAEALR-SNTFDTPTGMLSFDEKGDLKDFNFVVYEWHQDGTKTE 370

Query: 367 A 367
           A
Sbjct: 371 A 371


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: 420
Number of extensions: 20
Number of successful extensions: 3
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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