GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Paraburkholderia bryophila 376MFSha3.1

Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate H281DRAFT_02211 H281DRAFT_02211 N-acetylglutamate kinase

Query= curated2:Q9JXU9
         (436 letters)



>FitnessBrowser__Burk376:H281DRAFT_02211
          Length = 299

 Score =  105 bits (261), Expect = 2e-27
 Identities = 85/288 (29%), Positives = 130/288 (45%), Gaps = 11/288 (3%)

Query: 3   APDLFVAHFREAVPYIRQMRGKTLVAGIDDRLLEGDTLNK-LAADIGLLSQLGIRLVLIH 61
           AP L      EA+PYIRQ  GKT+V       +  + L +  A D+ LL  +GI  V++H
Sbjct: 11  APTLKAEILAEALPYIRQYHGKTVVIKYGGNAMTEERLKQGFARDVILLKLVGINPVIVH 70

Query: 62  GARHFLDRHAAAQGRTPHYCRGLRVTDETSLEQAQQFAGTVRSRFEAALCGSVSGFARAP 121
           G    +D+     G+   + +G+RVTDE ++E  +   G    +    L     G   A 
Sbjct: 71  GGGPQIDQALKKVGKQGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVTLINHFGG--HAV 128

Query: 122 SVPLVSGNFLTARPIGVIDG------TDMEYAGVIRKTDTAALRFQLDAGNIVWLPPLGH 175
            +    G  + AR + + D        D+   G +   + A ++   D   I  + P+G 
Sbjct: 129 GLTGKDGGLIHARKMLMPDRDNPGQYVDIGQVGEVEAINPAVVKALQDDAFIPVISPIGF 188

Query: 176 SYSGKTFYLDMLQTAASAAVSLQAEKLVYLTLSDGISRPDGTLAETLSAQEAQSLAEHA- 234
              G ++ ++    A   AV L AEKLV +T   G+   +G L   LSA+E   L     
Sbjct: 189 GEDGLSYNINADLVAGKLAVVLNAEKLVMMTNIPGVMDKEGNLLTDLSAREIDGLFADGT 248

Query: 235 -GGETRRLISSAVAALEGGVHRVQILNGAADGSLLQELFTRNGIGTSI 281
             G     ISSA+ A + GV  V I++G  + S+L E+ T    GT I
Sbjct: 249 ISGGMLPKISSALDAAKSGVRSVHIIDGRIEHSVLLEILTEQPFGTMI 296


Lambda     K      H
   0.320    0.136    0.391 

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: 324
Number of extensions: 20
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: 436
Length of database: 299
Length adjustment: 29
Effective length of query: 407
Effective length of database: 270
Effective search space:   109890
Effective search space used:   109890
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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