GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens FW300-N2E3

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate AO353_22845 AO353_22845 GNAT family acetyltransferase

Query= BRENDA::Q9I3W7
         (177 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_22845
          Length = 173

 Score =  232 bits (591), Expect = 3e-66
 Identities = 117/171 (68%), Positives = 139/171 (81%), Gaps = 2/171 (1%)

Query: 1   MTAESPTIRLERYSERHVEGLTALYNDPAVARQVLQMPYQSVEQRRKRLHDSADDDRLLI 60
           M+A  P I +ER SE H+EG+TALYNDPAVARQVLQMP+QS E  RKRL  + +++R++ 
Sbjct: 1   MSAIDPVISIERMSEAHIEGITALYNDPAVARQVLQMPFQSTEVWRKRL--APENERVVQ 58

Query: 61  LVALHQGDVIGSASLEQHPRIRRSHSGSIGMGVAVAWQGKGVGSRLLGELLDIADNWMNL 120
           LVALHQG VIG+  LEQ  RIRRSH  +IGMGVAVAWQGKGVGSRLL  +LD+ADNWMN+
Sbjct: 59  LVALHQGQVIGNVGLEQVSRIRRSHCANIGMGVAVAWQGKGVGSRLLAAVLDLADNWMNV 118

Query: 121 RRVELTVYTDNAPALALYRKFGFETEGEMRDYAVRDGRFVDVYSMARLRRV 171
           +RVEL+VY DN  A+ LYRKFGF+TEG  R+YAVRDG  VD  SMARLRR+
Sbjct: 119 QRVELSVYADNEAAIGLYRKFGFDTEGLFREYAVRDGVLVDALSMARLRRL 169


Lambda     K      H
   0.320    0.136    0.394 

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: 163
Number of extensions: 7
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: 177
Length of database: 173
Length adjustment: 19
Effective length of query: 158
Effective length of database: 154
Effective search space:    24332
Effective search space used:    24332
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: 44 (21.6 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