GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argA in Pedobacter sp. GW460-11-11-14-LB5

Align Acetyltransferase, N-acetylglutamate synthase (characterized, see rationale)
to candidate CA265_RS18550 CA265_RS18550 N-acetyltransferase

Query= uniprot:L0G3H4_ECHVK
         (224 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS18550 CA265_RS18550
           N-acetyltransferase
          Length = 232

 Score =  276 bits (706), Expect = 2e-79
 Identities = 138/218 (63%), Positives = 168/218 (77%), Gaps = 3/218 (1%)

Query: 1   MTKSQFIIQTAGVQHCKYAETIVDEMALSAKARGTGIAKRSPDYIIQKMMEGKAVIALSK 60
           M  ++FI+Q A  +H  +AE IV EMA SAKARGTGIAKRSP+YI  KM EGK+VIA  K
Sbjct: 1   MDINEFIVQVALPEHRVFAEEIVTEMAESAKARGTGIAKRSPEYISNKMQEGKSVIAFHK 60

Query: 61  EGEWAGFCYIEAWGHGKFVANSGLIVSPNFRKSGLAREIKKAVFKLSRSKFPHAKIFGLT 120
           +G WAGFCYIE W HG+FVANSGL+VSP +RK+GLA+ IK  +F LSR  +P AKIFGLT
Sbjct: 61  DGSWAGFCYIETWSHGQFVANSGLVVSPKYRKAGLAKAIKNEIFGLSRKLYPKAKIFGLT 120

Query: 121 TGAAVMKINSELGYVPVSYSDLTDDEEFWKGCQSCVNYEILKSKNRQNCLCTAMLYVPKD 180
           TG AVMKINS+LGY PV+YS+LT DEEFWKGCQSCVN+EILK K R+NC+CTAMLY P  
Sbjct: 121 TGLAVMKINSDLGYEPVTYSELTQDEEFWKGCQSCVNFEILKMKERKNCMCTAMLYDPA- 179

Query: 181 QKKKEVAMK--KDFGKNLNLFERLVRMKRAVFTGIKKK 216
           +KK EVA +  ++  K   L+ER +R+K+ +    K K
Sbjct: 180 EKKHEVAKQFAEELQKKPKLYERFMRIKQRLVVKPKPK 217


Lambda     K      H
   0.320    0.134    0.395 

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: 206
Number of extensions: 10
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: 224
Length of database: 232
Length adjustment: 23
Effective length of query: 201
Effective length of database: 209
Effective search space:    42009
Effective search space used:    42009
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: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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