GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens GW456-L13

Align L-amino acid N-acyltransferase MnaT; L-methionine N-acyltransferase; L-methionine sulfoximine/L-methionine sulfone N-acetyltransferase; L-phenylglycine N-acetyltransferase; EC 2.3.1.- (characterized)
to candidate PfGW456L13_88 GCN5-related N-acetyltransferase

Query= SwissProt::P76112
         (172 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_88
          Length = 177

 Score =  221 bits (562), Expect = 7e-63
 Identities = 110/169 (65%), Positives = 124/169 (73%), Gaps = 1/169 (0%)

Query: 3   IRFARKADCAAIAEIYNHAVLYTAAIWNDQTVDADNRIAWFEARTLAGYPVLVS-EENGV 61
           IR A  AD  AI +IYN AVL T AIWN+Q VD  NR AWF AR    YP+LV  + +  
Sbjct: 5   IRDAVHADLPAIRDIYNDAVLNTTAIWNEQAVDLGNRQAWFSARQSQAYPILVIVDADDT 64

Query: 62  VTGYASFGDWRSFDGFRHTVEHSVYVHPDHQGKGLGRKLLSRLIDEARDCGKHVMVAGIE 121
           V GYASFGDWR FDGFRHTVEHSVYV  D +G GLG KL+  LI+ ARDCGKHVMVA IE
Sbjct: 65  VLGYASFGDWRPFDGFRHTVEHSVYVRSDQRGNGLGPKLMDVLIERARDCGKHVMVAAIE 124

Query: 122 SQNQASLHLHQSLGFVVTAQMPQVGTKFGRWLDLTFMQLQLDERTEPDA 170
           S N AS+ LH+ +GF+ T QMPQVGTKFGRWLDLTFMQL L+   +P A
Sbjct: 125 SGNAASIRLHERIGFITTGQMPQVGTKFGRWLDLTFMQLTLNPGAQPPA 173


Lambda     K      H
   0.322    0.136    0.420 

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: 121
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: 172
Length of database: 177
Length adjustment: 19
Effective length of query: 153
Effective length of database: 158
Effective search space:    24174
Effective search space used:    24174
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 (21.9 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