GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS18550
          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 (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