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_088754101.1 CEJ45_RS04945 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_002213425.1:WP_088754101.1
          Length = 373

 Score =  284 bits (727), Expect = 2e-81
 Identities = 155/363 (42%), Positives = 222/363 (61%), Gaps = 4/363 (1%)

Query: 8   AVALTAMLAFSGNAWAD-VLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQI 66
           A+A     AF+G A A+ V IA+AGPLTG  A +G  ++ GA  A   INAAGG NG + 
Sbjct: 11  ALAAATFAAFAGVAHAETVKIAIAGPLTGAVAQYGDMVKAGALTAIEQINAAGGANGNKF 70

Query: 67  KIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEP 126
           +  + DD  +PKQ ++VANK  + G+K+VIGH  SG +IPAS++Y   G++   P    P
Sbjct: 71  EAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATAP 130

Query: 127 DLHGTGLWN-TFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMN 185
            L         FRT GRDDQQG  A +Y+ +  K  K+AV+HDK  YGQG+A   K A++
Sbjct: 131 QLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKSALD 190

Query: 186 AAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLV 245
           AA V  V++EGIN GD D+SA++ K+K  GV  +Y+GG H E GLI+RQA +QG+KA  +
Sbjct: 191 AAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGVKAVFM 250

Query: 246 SGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEA-YTLYSYAA 304
             +G+ + ++ +IAG A  G L T   D  A+PAN  LV+ F AA  +    + + +Y+A
Sbjct: 251 GPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDANGPFQMPAYSA 310

Query: 305 MQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWKKVRTA 364
           ++ IA A   A S DP+ VA A      F T +G++ +D+KGD K   ++++ W K  T 
Sbjct: 311 VKIIADAITGAKSTDPDKVA-AYIHGNSFKTPIGNVEYDKKGDLKAFKFVVFTWHKDATK 369

Query: 365 STA 367
           + A
Sbjct: 370 TEA 372


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: 487
Number of extensions: 26
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: 373
Length adjustment: 30
Effective length of query: 351
Effective length of database: 343
Effective search space:   120393
Effective search space used:   120393
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