GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens FW300-N2C3

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate AO356_25850 AO356_25850 GNAT family acetyltransferase

Query= BRENDA::Q9I3W7
         (177 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25850
          Length = 165

 Score =  234 bits (596), Expect = 7e-67
 Identities = 117/163 (71%), Positives = 134/163 (82%), Gaps = 2/163 (1%)

Query: 7   TIRLERYSERHVEGLTALYNDPAVARQVLQMPYQSVEQRRKRLHDSADDDRLLILVALHQ 66
           +I L R++E H+ G+TALYNDPAV RQVLQMP+QS E  RKRL  + DD+RLL LVALH 
Sbjct: 5   SITLARFTEAHIAGVTALYNDPAVTRQVLQMPFQSTEVWRKRL--ATDDERLLKLVALHT 62

Query: 67  GDVIGSASLEQHPRIRRSHSGSIGMGVAVAWQGKGVGSRLLGELLDIADNWMNLRRVELT 126
           GDVIG+  LEQ  R+RR+H GS+GMGVAVAWQGKGVGS LL   LD+ADNWMNLRRVELT
Sbjct: 63  GDVIGNLGLEQFSRVRRAHCGSLGMGVAVAWQGKGVGSMLLAAALDVADNWMNLRRVELT 122

Query: 127 VYTDNAPALALYRKFGFETEGEMRDYAVRDGRFVDVYSMARLR 169
           VY DN  A+ LYRKFGFE+EG MRDYAVRDGR+VD  +MARLR
Sbjct: 123 VYADNEAAIGLYRKFGFESEGLMRDYAVRDGRWVDTLAMARLR 165


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: 157
Number of extensions: 5
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: 165
Length adjustment: 18
Effective length of query: 159
Effective length of database: 147
Effective search space:    23373
Effective search space used:    23373
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: 43 (21.2 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