GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Herbaspirillum aquaticum IEH 4430

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 WP_088755389.1 CEJ45_RS12295 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_002213425.1:WP_088755389.1
          Length = 381

 Score =  211 bits (536), Expect = 4e-59
 Identities = 135/370 (36%), Positives = 194/370 (52%), Gaps = 17/370 (4%)

Query: 3   KSLLSAVALTAMLAFSGNAWADVLIAVA--GPLTGPNAAFGAQLQKGAEQAAADINAAG- 59
           K +  A AL A  +F+G A A  +I +    PLTGPNA  G   + GA  A  ++NA G 
Sbjct: 5   KMIPVATALVAAFSFAGAAQAQEVIKIGHVAPLTGPNAHIGKDNENGARMAVDELNAKGF 64

Query: 60  GINGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGIL 117
            I G+++  +L   DD SDPKQ  +VA       VK V+GH NSG +IPAS++Y + GI 
Sbjct: 65  EIGGKKVTFQLVPQDDASDPKQATTVAQALVDAKVKGVVGHMNSGTTIPASKIYYDAGIP 124

Query: 118 RNHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLA 177
           +  P    P     G    FR    D Q G + G+Y  +  K   +AV+ D+T YGQG+A
Sbjct: 125 QISPSATNPKYTQQGFNTAFRVVANDGQLGGVLGRYAVNELKGKNVAVIDDRTAYGQGVA 184

Query: 178 DETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAAD 237
           +E +K+  AAG T V  +       DF+A++  +K     ++++GG+   AG ++RQ   
Sbjct: 185 EEFRKSALAAGATIVATQYTTDKATDFNAILTSVKSKKPDLVFFGGMDAVAGPMLRQMDQ 244

Query: 238 QGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAA---GFNP 294
            G+ A  + GDGI + EL S+AG  +  +            A K+ +E FKAA    FN 
Sbjct: 245 LGVAAKFMGGDGICTTELPSLAGAGLKDSEVVCAEAGGVTEAGKKPLEDFKAAYKKKFNQ 304

Query: 295 EA--YTLYSYAAMQTIAGAAKAAGSLDPEA---VAKAMKEKGPFPTVLGDISFDEKGDPK 349
           +   Y  Y+Y A+ T+A A K AGS DP+    V   +K KG    V G+I+FD KGD  
Sbjct: 305 DVVIYAPYTYDALMTLADAMKQAGSSDPKVYLPVLAKIKHKG----VTGEIAFDAKGDIL 360

Query: 350 IPGYIMYEWK 359
                +Y +K
Sbjct: 361 NGTLTLYTYK 370


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: 378
Number of extensions: 23
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: 381
Length adjustment: 30
Effective length of query: 351
Effective length of database: 351
Effective search space:   123201
Effective search space used:   123201
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 24 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