GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pseudomonas stutzeri RCH2

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate GFF3930 Psest_4000 amino-acid N-acetyltransferase

Query= curated2:Q2KU83
         (300 letters)



>FitnessBrowser__psRCH2:GFF3930
          Length = 432

 Score =  114 bits (286), Expect = 3e-30
 Identities = 88/284 (30%), Positives = 140/284 (49%), Gaps = 15/284 (5%)

Query: 20  LSEALPYIRRFHGKTIVVKYGGNAMTEERLQRSFAHDVVLLKLVGLNPVVVHGGGPQIDD 79
           L ++ PYI     +T VV   G+ +       +  HD+VLL  +G+  V+V G  PQI+ 
Sbjct: 8   LRDSSPYINSHRDRTFVVMLPGDGLEHANFA-NIVHDLVLLHSLGVRLVLVFGSRPQIEA 66

Query: 80  ALRRLGKQGTFVQGMRVTDAETMEVVEWVLGG-----QVQQDIVMMINEAGGKAVGLTGK 134
            L   G +  F + +RVTDA TME V   +G      + +  + M  +   G  + + G 
Sbjct: 67  RLAARGIEPRFHRDLRVTDAPTMECVIDAVGQLRIALEARLSMDMAASPMQGARLRVAG- 125

Query: 135 DGMLLQARKKLMADKEKPGELLDIGLVGDVTRVEPAVVKALQDDQFIPVISPIGYGEDGT 194
            G  + AR   + D       +D+   G+V R++   +  L D++ I ++SP+GY   G 
Sbjct: 126 -GNFVTARPIGVLDG------VDLHHTGEVRRIDRKGIGRLLDERTIVLLSPLGYSPTGE 178

Query: 195 AYNINADVVAGKIAEVLGAEKLLMMTNTPGVLDKSGKLLRSLSAQTIDELFADGTISGGM 254
            +N+  + VA + A  L A+KL++    PG+LD+SGKL+R L  Q I   + +   S   
Sbjct: 179 IFNLACEDVATRAAIDLQADKLVLYGAEPGLLDESGKLVRELRPQQI-PAYVERLGSQYQ 237

Query: 255 LPKISSALDAAKNGVPSVHVVDGRVPHCLLLELLTDQGVGTMIS 298
              + +A  A + GV   HVV       LL EL T  G GT+++
Sbjct: 238 AELLDAAAQACRGGVRRSHVVSYADDGALLNELFTRDGGGTLVT 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: 331
Number of extensions: 17
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