GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pseudomonas putida KT2440

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate PP_5185 PP_5185 acetylglutamate kinase-like protein (regulatory domain)/amino acid N-acetyltransferase

Query= curated2:Q2KU83
         (300 letters)



>FitnessBrowser__Putida:PP_5185
          Length = 432

 Score =  121 bits (303), Expect = 3e-32
 Identities = 93/283 (32%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 20  LSEALPYIRRFHGKTIVVKYGGNAMTEERLQRSFAHDVVLLKLVGLNPVVVHGGGPQIDD 79
           L  A PYI      T VV   G+ +       +  HD+VLL  +G+  V+VHG  PQI+ 
Sbjct: 8   LRHASPYINAHRDCTFVVMLPGDGVEHPNFG-NIVHDLVLLHSLGVRLVLVHGSRPQIES 66

Query: 80  ALRRLGKQGTFVQGMRVTDAETMEVVEWVLGG---QVQQDIVMMINEAGGKAVGLTGKDG 136
            L   G    + +GMR+TDA T++ V   +G     ++  + M I  +  +   L    G
Sbjct: 67  RLADRGLTPHYHRGMRITDAATLDCVIDAVGALRLAIEARLSMDIAASPMQGSRLRVASG 126

Query: 137 MLLQARKKLMADKEKPGELLDIGLVGDVTRVEPAVVKALQDDQFIPVISPIGYGEDGTAY 196
            L+ AR   +       E +D    G+V RV+   +  L D++ I ++SP+GY   G  +
Sbjct: 127 NLVTARPIGVL------EGVDYHHTGEVRRVDRKGISRLLDERSIVLLSPLGYSPTGEIF 180

Query: 197 NINADVVAGKIAEVLGAEKLLMMTNTPGVLDKSGKLLRSLSAQTI-DELFADGTISGGML 255
           N+  + VA + A  LGA+KLL+    PG+LD  G+L+R L  Q +   L   G+   G L
Sbjct: 181 NLACEDVATRAAIELGADKLLLFGAEPGLLDADGRLVRELRPQQVAPHLQRLGSDYQGEL 240

Query: 256 PKISSALDAAKNGVPSVHVVDGRVPHCLLLELLTDQGVGTMIS 298
             + +A +A K GV   H+V       LL EL T  G GT++S
Sbjct: 241 --LDAAAEACKGGVARSHIVSYAEDGALLTELFTRGGGGTLVS 281


Lambda     K      H
   0.317    0.137    0.386 

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: 323
Number of extensions: 15
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: 300
Length of database: 432
Length adjustment: 29
Effective length of query: 271
Effective length of database: 403
Effective search space:   109213
Effective search space used:   109213
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 (21.6 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