GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Methylovulum miyakonense HT12

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_019867255.1 METMI_RS0115735 acetylglutamate kinase

Query= BRENDA::Q87EL2
         (421 letters)



>NCBI__GCF_000384075.1:WP_019867255.1
          Length = 299

 Score =  117 bits (293), Expect = 5e-31
 Identities = 90/284 (31%), Positives = 141/284 (49%), Gaps = 24/284 (8%)

Query: 6   EISQYLKRFSQLDAKRFAVVKVGGAVLRDDV--DALTSSLSFLQEVGLTPIVLHGAGPQL 63
           E   Y++RF      +  VVK GG  + D+   ++    +  ++ VG  PIV+HG GPQ+
Sbjct: 16  EALPYIQRFKG----KTVVVKFGGNAMVDESLKNSFARDIVLMKLVGFNPIVVHGGGPQI 71

Query: 64  DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG--GV 120
            + L  +G     V+G R+T  ETM +V  V     N +++  +  NG +A  +TG  G 
Sbjct: 72  GQLLEKLGKTTGFVDGMRITDSETMDVVEMVLGGLVNKEIVNLINMNGGKAVGLTGKDGD 131

Query: 121 F--------EAHYLDQET-----YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQ 167
           F        +   LD E       G VG +S+++ + +E   R+  IPVIA +G    G 
Sbjct: 132 FIRAKKINLKRSSLDAEASEIIDLGHVGEVSSIDPSVVEMLGRSDFIPVIAPIGVGADGH 191

Query: 168 ILNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGG 227
             NINAD+ A ++  VL+  K+I LT T G+LD  G ++  +++ T+ + LI    + GG
Sbjct: 192 SYNINADLVAGKIAEVLKAEKLILLTNTAGILDKQGSLLTGLSV-TDIDSLIADGTISGG 250

Query: 228 MKLKIEQIKHLLDRLPLESSVSITRPAD-LAKELFTHKGSGTLI 270
           M  K       L+       +   R A  +  ELFT +G GTL+
Sbjct: 251 MIPKTRCATDALNGGVHSVHIIDGRVAHAVLLELFTDQGVGTLL 294


Lambda     K      H
   0.320    0.136    0.399 

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: 259
Number of extensions: 16
Number of successful extensions: 4
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: 421
Length of database: 299
Length adjustment: 29
Effective length of query: 392
Effective length of database: 270
Effective search space:   105840
Effective search space used:   105840
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: 49 (23.5 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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