GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Klebsiella michiganensis M5al

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 BWI76_RS26350 BWI76_RS26350 branched chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__Koxy:BWI76_RS26350
          Length = 369

 Score =  259 bits (663), Expect = 6e-74
 Identities = 141/360 (39%), Positives = 212/360 (58%), Gaps = 3/360 (0%)

Query: 1   MKKSLLSAVALTAMLAFSGNAWA-DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG 59
           MK++  + +A    LA S  A+A D+ +AV G ++GP A +G     GA QA  DINA G
Sbjct: 1   MKRNAKTVIAGLVALAMSQAAFAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINAQG 60

Query: 60  GINGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRN 119
           GI G+++     DD  DPKQ ++VANK   DG+++VIGH  S  + PAS++Y + GIL  
Sbjct: 61  GIKGDKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMI 120

Query: 120 HPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADE 179
            PG   P+L   G     RT G D  QG  A KY+ +  K  +IA++HDK  YG+GLA  
Sbjct: 121 SPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYIMETVKPQRIAIIHDKQQYGEGLARS 180

Query: 180 TKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQG 239
            ++++   G   V ++GI  G+KDFSAL+A++K+  +  +Y+GG + E G ++RQA   G
Sbjct: 181 VQESLKKGGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVG 240

Query: 240 LKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YT 298
           LK   +  +G+ +  L++IAGDA  G L T       +PAN  +V+  KA   +P   Y 
Sbjct: 241 LKTVFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANSAIVDALKAEKKDPSGPYV 300

Query: 299 LYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
             +YAA+Q++A A   A S +P  + K +K  G   TV+G +++DEKGD K   + +++W
Sbjct: 301 WITYAAVQSLAQAMDRAASQEPLDLIKDLKAHGA-KTVIGPLNWDEKGDLKGFEFGVFQW 359


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: 391
Number of extensions: 20
Number of successful extensions: 2
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: 369
Length adjustment: 30
Effective length of query: 351
Effective length of database: 339
Effective search space:   118989
Effective search space used:   118989
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.

Links

Downloads

Related tools

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