GapMind for Amino acid biosynthesis

 

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

Align Acetyltransferase (GNAT) family protein; SubName: Full=L-amino acid N-acyltransferase YncA (characterized, see rationale)
to candidate CA265_RS00200 CA265_RS00200 N-acetyltransferase

Query= uniprot:H1XRZ0_9BACT
         (202 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS00200 CA265_RS00200
           N-acetyltransferase
          Length = 201

 Score =  197 bits (500), Expect = 1e-55
 Identities = 93/180 (51%), Positives = 130/180 (72%), Gaps = 1/180 (0%)

Query: 1   MDKNKVTIVTASQEHFKYAEKICETIEDAAKIRGTGIAKRKPEYIRSKMREGKAVIALTS 60
           MD + + +  A Q+   YAE+I +  E +A  RG+GIAKR    +  KM  GKAVIALT+
Sbjct: 1   MDNHIIFVRIADQDDAHYAEEIIQETEQSAIARGSGIAKRTLASVIEKMAAGKAVIALTN 60

Query: 61  DGRLAGFCYIESWGKEKNYVANSGLIVVPEFRELGLGKMIKKAAFELSRKKYPHAKLFGI 120
            G   GF Y+E+W  E+ +V+NSGLIV P+FR  G+ + IK   F++SR+ YPH+K+F I
Sbjct: 61  TGEWVGFSYLETWEDER-FVSNSGLIVAPKFRNSGVARSIKNRIFKMSRRLYPHSKIFSI 119

Query: 121 TTSPAVMKINYQLGYRPVTFAQLTDDEEFWKGCESCVNFDILQRTNRKHCLCTAMLFDPE 180
           T+ PA+M++N +LG+ PV+FA++T DE FW+GC+SCVN+DIL R  + +CLCTAMLFDPE
Sbjct: 120 TSGPAIMRMNAKLGFLPVSFAEITHDEHFWEGCKSCVNYDILTRKKKCNCLCTAMLFDPE 179


Lambda     K      H
   0.317    0.133    0.389 

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: 142
Number of extensions: 4
Number of successful extensions: 2
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: 202
Length of database: 201
Length adjustment: 21
Effective length of query: 181
Effective length of database: 180
Effective search space:    32580
Effective search space used:    32580
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 (21.7 bits)
S2: 45 (21.9 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, 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