GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Pseudomonas simiae WCS417

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate GFF3695 PS417_18910 acetylornithine deacetylase

Query= curated2:B2FIC0
         (375 letters)



>FitnessBrowser__WCS417:GFF3695
          Length = 385

 Score = 88.2 bits (217), Expect = 3e-22
 Identities = 73/238 (30%), Positives = 108/238 (45%), Gaps = 20/238 (8%)

Query: 49  NLWATHGLG-APVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAF 107
           NL AT G    P +VL GHTDVVP    + W+  PF    +DG LYGRG ADMKG +A  
Sbjct: 51  NLLATIGPAEVPGIVLSGHTDVVPV-EGQRWSVAPFDLTEKDGKLYGRGTADMKGYIACV 109

Query: 108 VVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTA 167
           +      V      P  + + L+ DEE   + GVR +   F  +  +   C+ GEP+   
Sbjct: 110 LACVPALVKASLRMP--VHIALSYDEEVGCL-GVRSLIERFHEQPVKPLLCVIGEPTELK 166

Query: 168 TLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAEL--------CARRW 219
            +     +G +G L+ +  V G   H AY     N I  AA  ++EL          +  
Sbjct: 167 PV-----LGHKGKLAMRCHVHGAACHSAYAPAGVNAIEYAACLISELVRLGETLKAPQHL 221

Query: 220 DDGYESFPPTSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEAEITALLER 277
           D  +   P  S   + +  G  A N++P +   DF +R  P  D  ++  ++ A  E+
Sbjct: 222 DQRFA--PAFSTVQTGLINGGKALNIVPQDCSFDFEVRSLPAQDPWQVARQLQAYAEQ 277


Lambda     K      H
   0.319    0.137    0.421 

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: 321
Number of extensions: 18
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: 375
Length of database: 385
Length adjustment: 30
Effective length of query: 345
Effective length of database: 355
Effective search space:   122475
Effective search space used:   122475
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. The underlying query database was built on Apr 09 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