GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Dyella japonica UNC79MFTsu3.2

Align N-acetyl-L-citrulline deacetylase; Short=ACDase; Short=Acetylcitrulline deacetylase; EC 3.5.1.- (characterized, see rationale)
to candidate N515DRAFT_3767 N515DRAFT_3767 acetylornithine deacetylase

Query= uniprot:A0A1I2DJB5_9GAMM
         (366 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3767
          Length = 366

 Score =  734 bits (1896), Expect = 0.0
 Identities = 366/366 (100%), Positives = 366/366 (100%)

Query: 1   MSQLLDDTLRHLRALVSHDTRNPPREIGTGGIFDYLREQLAGFEVTVTDFGAGAVNLYAV 60
           MSQLLDDTLRHLRALVSHDTRNPPREIGTGGIFDYLREQLAGFEVTVTDFGAGAVNLYAV
Sbjct: 1   MSQLLDDTLRHLRALVSHDTRNPPREIGTGGIFDYLREQLAGFEVTVTDFGAGAVNLYAV 60

Query: 61  RGKPKYLFNVHLDTVPDSPHWSADPHVLRVEGDRAIGLGACDIKGAAAALVAVANATQGD 120
           RGKPKYLFNVHLDTVPDSPHWSADPHVLRVEGDRAIGLGACDIKGAAAALVAVANATQGD
Sbjct: 61  RGKPKYLFNVHLDTVPDSPHWSADPHVLRVEGDRAIGLGACDIKGAAAALVAVANATQGD 120

Query: 121 MALLLSTDEEANDARCIAGFLKDHPVYEAVIVAEPTKGEAVLAHRGIHSVQMRFSGKAGH 180
           MALLLSTDEEANDARCIAGFLKDHPVYEAVIVAEPTKGEAVLAHRGIHSVQMRFSGKAGH
Sbjct: 121 MALLLSTDEEANDARCIAGFLKDHPVYEAVIVAEPTKGEAVLAHRGIHSVQMRFSGKAGH 180

Query: 181 ASGEQKPSDSAVHQAVRWGVAALDYVESQAHERFGGLTGLRFNIGKVEGGIKANVIAPTA 240
           ASGEQKPSDSAVHQAVRWGVAALDYVESQAHERFGGLTGLRFNIGKVEGGIKANVIAPTA
Sbjct: 181 ASGEQKPSDSAVHQAVRWGVAALDYVESQAHERFGGLTGLRFNIGKVEGGIKANVIAPTA 240

Query: 241 DVRFGFRPLPSMDADRMLETFRTLVEPQPVEFGETFRGDSLPAGDTATAETRRLAARDLA 300
           DVRFGFRPLPSMDADRMLETFRTLVEPQPVEFGETFRGDSLPAGDTATAETRRLAARDLA
Sbjct: 241 DVRFGFRPLPSMDADRMLETFRTLVEPQPVEFGETFRGDSLPAGDTATAETRRLAARDLA 300

Query: 301 DELGIPVGNAVNFWTEAALFSAAGYISFVYGPGDIAQAHAADEWVALEQLDHYAQTIYRI 360
           DELGIPVGNAVNFWTEAALFSAAGYISFVYGPGDIAQAHAADEWVALEQLDHYAQTIYRI
Sbjct: 301 DELGIPVGNAVNFWTEAALFSAAGYISFVYGPGDIAQAHAADEWVALEQLDHYAQTIYRI 360

Query: 361 VDRGSA 366
           VDRGSA
Sbjct: 361 VDRGSA 366


Lambda     K      H
   0.319    0.136    0.405 

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: 604
Number of extensions: 15
Number of successful extensions: 1
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: 366
Length of database: 366
Length adjustment: 30
Effective length of query: 336
Effective length of database: 336
Effective search space:   112896
Effective search space used:   112896
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 (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