GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapE in Dyella japonica UNC79MFTsu3.2

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate N515DRAFT_3767 N515DRAFT_3767 acetylornithine deacetylase

Query= curated2:A5FYQ7
         (371 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3767 N515DRAFT_3767
           acetylornithine deacetylase
          Length = 366

 Score = 62.8 bits (151), Expect = 1e-14
 Identities = 91/333 (27%), Positives = 131/333 (39%), Gaps = 50/333 (15%)

Query: 38  GFSIEWLRFGEVS-NLVARRGSGSPHFGFAGHTDVVPPGEGWRHDPFAAVIEDGLLFGRG 96
           GF +    FG  + NL A RG   P + F  H D VP    W  DP    +E     G G
Sbjct: 42  GFEVTVTDFGAGAVNLYAVRGK--PKYLFNVHLDTVPDSPHWSADPHVLRVEGDRAIGLG 99

Query: 97  AVDMKGAIAAFVAALAARPANHAGTISLLITGDEEGDAVDGTRRILDHLAASGALPEFCL 156
           A D+KGA AA VA   A      G ++LL++ DEE +      R +        + E  +
Sbjct: 100 ACDIKGAAAALVAVANAT----QGDMALLLSTDEEAN----DARCIAGFLKDHPVYEAVI 151

Query: 157 VGEPTCRARLGDTIKIGRRGSISAHVTVRGVQGHVAYPHL-ADNPLHRL----IPALEAL 211
           V EPT     G+ + +  RG  S  +   G  GH +     +D+ +H+     + AL+ +
Sbjct: 152 VAEPT----KGEAV-LAHRGIHSVQMRFSGKAGHASGEQKPSDSAVHQAVRWGVAALDYV 206

Query: 212 RATTLDEGTAWFEPSSLQITSVDTGNKAGNVIPASASARLNIRFNDRHTGPDLAAWIRDT 271
            +    E           I  V+ G KA NVI  +A  R                     
Sbjct: 207 ESQA-HERFGGLTGLRFNIGKVEGGIKA-NVIAPTADVRFGF------------------ 246

Query: 272 VARHAPGAACDIGISGEAFLTEPGPVTTLFSEAVAAVTGITPKLDTGGGTSDARFIAAHC 331
             R  P    D  +     L EP PV   F E     +   P  DT   T++ R +AA  
Sbjct: 247 --RPLPSMDADRMLETFRTLVEPQPVE--FGETFRGDS--LPAGDT--ATAETRRLAARD 298

Query: 332 PVAEFGL-VGTSMHRVDEAVPVSELRALAEIYG 363
              E G+ VG +++   EA   S    ++ +YG
Sbjct: 299 LADELGIPVGNAVNFWTEAALFSAAGYISFVYG 331


Lambda     K      H
   0.320    0.137    0.412 

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: 397
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 371
Length of database: 366
Length adjustment: 30
Effective length of query: 341
Effective length of database: 336
Effective search space:   114576
Effective search space used:   114576
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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