GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Acidovorax sp. GW101-3H11

Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate Ac3H11_1907 Acetylglutamate kinase (EC 2.7.2.8)

Query= curated2:Q6LMZ6
         (441 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1907
          Length = 317

 Score =  111 bits (278), Expect = 3e-29
 Identities = 84/284 (29%), Positives = 134/284 (47%), Gaps = 16/284 (5%)

Query: 14  QSAPYVNAHSGKTVVIMLGGEAIADPNF-ANIVNDIALLNSLGLQIVVVYGARPQISHLL 72
           Q+ PY+    GKT+VI  GG A+ DP   A+   D+ LL  +G+  VVV+G  PQI   L
Sbjct: 39  QALPYIRKFHGKTMVIKYGGNAMTDPALQADFAEDVVLLKLVGMNPVVVHGGGPQIETAL 98

Query: 73  TSQGYTTPYHKGIRVTDARALELVKQA-AGQLQLDITARFSMGLNNTPMAGAQINVISGN 131
              G    + +G+RVTDA  +E+V+   AG++Q DI       +N        +    G 
Sbjct: 99  NRLGKKGEFIQGMRVTDAETMEVVEWVLAGEVQQDIVGL----INQAGGKAVGLTGRDGG 154

Query: 132 FIIAQPLGIDDG------IDYYHTGRIRRIDIDGIQRQLNQHSIVLLGPVASSVTGECFN 185
            I AQ L + D        D    G I  ID   ++   +   I ++ P+      E +N
Sbjct: 155 MIRAQKLKMVDNKNPAIEHDVGQVGDIVSIDPSVVKALQDDAFIPVISPIGFGENNESYN 214

Query: 186 LTSEEVATQLAIRLKADKLIGFCSEQGVIDLDGEVASEMLPNEAETALQRLIEAQEDDCG 245
           + ++ VA++LA  LKA+KL+   +  GV+D  G + +++        +  L        G
Sbjct: 215 INADVVASKLAEVLKAEKLMLLTNTPGVLDKAGNLLTDLTARR----IDELFADGTISGG 270

Query: 246 TARFLRGAVSACRAGVPRSHLISYKEDGALIQELFSLDGIGTQI 289
               + GA+ A +AGV   H+I  +   A++ E+ +    GT I
Sbjct: 271 MLPKIAGALDAAKAGVNAVHIIDGRVPHAMLLEILTEQAYGTMI 314


Lambda     K      H
   0.321    0.138    0.391 

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: 257
Number of extensions: 13
Number of successful extensions: 4
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: 441
Length of database: 317
Length adjustment: 30
Effective length of query: 411
Effective length of database: 287
Effective search space:   117957
Effective search space used:   117957
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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