GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysY in Rhizorhabdus wittichii RW1

Align [amino group carrier protein]-6-phospho-L-2-aminoadipate reductase (EC 1.2.1.103); [amino-group carrier protein]-5-phospho-L-glutamate reductase (EC 1.2.1.106) (characterized)
to candidate WP_011950947.1 SWIT_RS00480 N-acetyl-gamma-glutamyl-phosphate reductase

Query= BRENDA::O50146
         (344 letters)



>NCBI__GCF_000016765.1:WP_011950947.1
          Length = 313

 Score = 68.6 bits (166), Expect = 2e-16
 Identities = 80/289 (27%), Positives = 115/289 (39%), Gaps = 37/289 (12%)

Query: 63  EKLEPADILVLALPHGVFAREFDRYSALAPILIDLSADFRLKDPELYRRYYGEHPRPDLL 122
           E L  AD +VL LP           +  A  +ID S   R                    
Sbjct: 46  EALNAADAVVLCLPDDAAREAVALIANPAVRVIDASTAHRTAAD---------------- 89

Query: 123 GCFVYAVPEL---YREALKGADWIAGAGCNATATLLGLYPLLKAGVLKP-TPIFVTLLIS 178
             + Y   EL    REAL GA  I+  GC  T  L  + PL++AG+L   TP+ V  +  
Sbjct: 90  --WAYGFAELDPGQREALAGATRISNPGCYPTGFLALVRPLVRAGLLPADTPLSVNAVSG 147

Query: 179 TSAAGAEASPASHHPERAGS----IRVYK-PTGHRHTAEVVENLP-GRPEVHLTAIATDR 232
            S  G         P    +     R Y    GH+H  E+ +      P + L ++A   
Sbjct: 148 YSGGGKSMIAMFEDPASPDATDTAFRAYALGLGHKHVPEMQKRAGLAHPPIFLPSVART- 206

Query: 233 VRGILMTAQCFVQDGWSERDVWQAYRE----AYAGEPFIRLVKQKKGVHRYPDPRFVQGT 288
            RG+L+     +      R    A RE    AY G   +R+    + V          GT
Sbjct: 207 YRGMLVEVPLHLHL-LPGRPTGAAIRELLAAAYEGSRIVRVATDDRPVLTIEQ---AAGT 262

Query: 289 NYADIGFELEEDTGRLVVMTAIDNLVKGTAGHALQALNVRMGWPETLGL 337
           +  ++    +E  G+  ++ A+DNL KG AG A+Q LN+ +G  ET GL
Sbjct: 263 DRLELFVHADEKAGQARLIAALDNLGKGAAGAAVQNLNIALGLDETEGL 311


Lambda     K      H
   0.321    0.140    0.431 

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: 290
Number of extensions: 16
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: 344
Length of database: 313
Length adjustment: 28
Effective length of query: 316
Effective length of database: 285
Effective search space:    90060
Effective search space used:    90060
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 Jul 25 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