GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argJ in Sphingomonas indica Dd16

Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_085218902.1 B9N75_RS11360 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ

Query= BRENDA::Q59280
         (388 letters)



>NCBI__GCF_900177405.1:WP_085218902.1
          Length = 407

 Score =  280 bits (715), Expect = 7e-80
 Identities = 163/388 (42%), Positives = 235/388 (60%), Gaps = 10/388 (2%)

Query: 6   ITAPKGFVASATTAGIKASGNPDMALVVNQ-GPEFSAAAVFTRNRVFAAPVKVSRENVA- 63
           +TA +GFVA+   AG+K    PDMAL+  + G     AAVFT+N+ FA PV VSRE +A 
Sbjct: 24  VTAAEGFVAAGLHAGVKQR-RPDMALLATEDGKPVPCAAVFTQNKFFAPPVGVSRERLAA 82

Query: 64  -DGQIRAVLYNAGNANACNGLQGEKDARESVSHLAQNLGLEDSDIGVCSTGLIGELLPMD 122
             G+  A++ N+GNANA  G QG +DA    +  A  LG+   D+ VCSTG+IG  LPM+
Sbjct: 83  NGGRAAAIIVNSGNANAGTGAQGRRDADAMCTETAAALGIAVDDVLVCSTGIIGTHLPME 142

Query: 123 KLNAGIDQLTAEGALGDNGAAAAKAIMTTDTVDKETVVFADGWTVGGMGKGVGMMAPSLA 182
           K+   I +L  + ++ +    AA+ I+TTD+  K+ V+    +T+GGM KG GM+AP++A
Sbjct: 143 KIAPAIPKLARQRSV-EGAQDAARGILTTDSKPKQAVISGSTFTLGGMAKGCGMIAPNMA 201

Query: 183 TMLVCLTTDASVTQEMAQIALANATAVTFDTLDIDGSTSTNDTVFLLASGASGITPTQDE 242
           TML  LTTDA++ ++  Q  LA+A+  TF+TL++DG+TSTND+ FLL SG  G     +E
Sbjct: 202 TMLAFLTTDAALDRDTLQRVLADASDRTFNTLNVDGATSTNDSAFLLTSGRRG-PADPEE 260

Query: 243 LNDAVYAACSDIAAKLQADAEGVTKRVAVTVVGTTNNEQAINAARTVARDNLFKCAMFGS 302
             DAV+  C D+  ++  DAEG+TK V +TV G  ++ +A  AA+ +A +NL KC+ +GS
Sbjct: 261 FADAVHRLCEDLTLQMAHDAEGMTKMVRLTVSGAASDAEARAAAKAIAENNLVKCSWYGS 320

Query: 303 DPNWGRVLAAVGMADADMEPEKISVFFNGQAVCLDSTGA---PGAREVDLSGADIDVRID 359
           DP WGR+LAA G A    E +  +V + G  V     G     G     +   +I + + 
Sbjct: 321 DPYWGRLLAAAGSAGIGFEADSATVAYGGTIVSRGGEGVDHDAGKVAAHMQHKEIAIEVA 380

Query: 360 LGTSGEGQATVRTTDLSFSYVEINSAYS 387
           LG  G G+A V   DL   Y++ NS  S
Sbjct: 381 LGL-GRGRAQVIGIDLGPGYIKENSVTS 407


Lambda     K      H
   0.313    0.128    0.357 

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: 398
Number of extensions: 19
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: 388
Length of database: 407
Length adjustment: 31
Effective length of query: 357
Effective length of database: 376
Effective search space:   134232
Effective search space used:   134232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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