GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Marivita geojedonensis DPG-138

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_085640565.1 MGEO_RS17020 acetylglutamate kinase

Query= BRENDA::Q87EL2
         (421 letters)



>NCBI__GCF_002115805.1:WP_085640565.1
          Length = 289

 Score =  112 bits (279), Expect = 2e-29
 Identities = 87/283 (30%), Positives = 143/283 (50%), Gaps = 19/283 (6%)

Query: 1   MASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDVDALTS---SLSFLQEVGLTPIVLH 57
           +A+A+ +S+ L  + Q  A    VVK GG  + DD DA+      +  +++VG+ P+V+H
Sbjct: 11  IATARTLSEALP-YMQRYAGAIVVVKFGGNAMGDD-DAMAEFARDIVLMRQVGINPVVVH 68

Query: 58  GAGPQLDEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSI 116
           G GP +++ LT +GI+   V G RVT   T+ +V  V     N ++++A+   G RA  +
Sbjct: 69  GGGPMINDMLTKLGIKSDFVRGKRVTDKATVQVVEMVLTGLVNKRIVQAIMDEGGRAVGL 128

Query: 117 TGG-----VFEAHYLDQETYGLVGGISAVNIAPIEASLRAASIPVIA--SLGETPSGQIL 169
           +G      V EA   D    G VG    +N   +    +A  IPV+A  + G  P+ +  
Sbjct: 129 SGKDDDLMVCEA---DDPELGFVGRPVEMNPQVLRDLFKAGIIPVVAPVATGMQPN-ETF 184

Query: 170 NINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMK 229
           N+N D AA  +   L+  +++ LT   G+ D DG ++ ++    + E +I    + GGM 
Sbjct: 185 NVNGDTAAGAIAGALKADRLLLLTDVSGVKDRDGNVVTAMT-PEDVEAMIADGTIAGGMI 243

Query: 230 LKIE-QIKHLLDRLPLESSVSITRPADLAKELFTHKGSGTLIR 271
            K E  +K + D +     +    P     ELFT  G+G+LIR
Sbjct: 244 PKTETALKAIEDGVRAVVILDGRVPNACLLELFTEHGAGSLIR 286


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: 227
Number of extensions: 10
Number of successful extensions: 3
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: 289
Length adjustment: 29
Effective length of query: 392
Effective length of database: 260
Effective search space:   101920
Effective search space used:   101920
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 Jul 26 2024. The underlying query database was built on Jul 25 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