GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Enterococcus termitis LMG 8895

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_069664978.1 BCR25_RS17880 threonine synthase

Query= BRENDA::B1N2N4
         (423 letters)



>NCBI__GCF_001730305.1:WP_069664978.1
          Length = 352

 Score = 90.1 bits (222), Expect = 9e-23
 Identities = 89/297 (29%), Positives = 133/297 (44%), Gaps = 28/297 (9%)

Query: 50  NTISKKVGCKTYLKLENLQKTGSFKVRGAVNKIATLTEEEKKRGVVAASAGNHAQGVAFA 109
           +++SK++G   Y K E L  TGSFK RG V  +A   EE  K  +V AS GN +   A  
Sbjct: 35  HSLSKELGINLYGKYEGLNPTGSFKDRGMVMAVAKAVEEGAK-AIVCASTGNTSAAAAAY 93

Query: 110 STSAGCKATIVMPE-FASTAKVTATRGYGAEVVLHGKVFDESLAYAMQLCKEEGKTFVHP 168
           +T AG KA +V+P+   +  K+     YGA+++     FDE+L     + K E    V+ 
Sbjct: 94  ATRAGVKAYVVIPDGKIAMGKLAQAIIYGADIISIPGNFDEALKAVRDIAKTEAVALVNS 153

Query: 169 FNDPWVMAGQGTIALEILEQLEKC-DVIIGAIGGGGLMSGVAFAAKQIKPEIRIIGVQAA 227
            N P+ + GQ T A E+ EQL +  DV+   +G  G +S      K+         ++  
Sbjct: 154 VN-PYRLEGQKTAAFEVCEQLGQAPDVLAIPVGNAGNISAYWKGFKEWH------DLKGT 206

Query: 228 ECPSMAVSKAEHKICCVK-----TAKTMADGIAVKAPGDKTAPVLLKYVDE----IVTVD 278
             P M   +AE     VK       +T+A  I +  P   T     +  DE    I  V 
Sbjct: 207 SLPRMHGFEAEGAAAIVKGEAIDQPETIATAIRIGNPASWTLAEAAR--DESNGHIDAVT 264

Query: 279 EESIAQAMLLMLERCKIVSEGSGATPVAALL----SGKIKGLTEDTNVVCIVSGGNL 331
           +E I  A   +  +  +  E   A  +A ++    SGKIK       VV + +G  L
Sbjct: 265 DEEILNAYRKVAAQDGVFVEPGSAASLAGVIQHVKSGKIK---PGETVVAVFTGNGL 318


Lambda     K      H
   0.317    0.133    0.378 

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: 306
Number of extensions: 10
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: 423
Length of database: 352
Length adjustment: 30
Effective length of query: 393
Effective length of database: 322
Effective search space:   126546
Effective search space used:   126546
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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