GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Allochromatium vinosum DSM 180

Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein

Query= BRENDA::B1XNF8
         (418 letters)



>NCBI__GCF_000025485.1:WP_043795594.1
          Length = 392

 Score =  346 bits (888), Expect = e-100
 Identities = 184/387 (47%), Positives = 250/387 (64%), Gaps = 11/387 (2%)

Query: 24  VMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHH 83
           +M TY R PV   +GEG  LWDT GK YLD ++GIA C LGHAHPA+  A+  Q  +L H
Sbjct: 5   LMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLIH 64

Query: 84  ISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVIL 143
            SN+Y + EQ  L   + E +  D+VFF NSGAEANEAAIKL R +AH     +E P IL
Sbjct: 65  TSNIYGVAEQERLGALLTEQAGMDRVFFANSGAEANEAAIKLARLHAHRRG--IENPAIL 122

Query: 144 SAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVAA 203
            A+ SFHGRTLAT++ATG  K Q  F+PL  GF  VPY+D+ A+E A T+       + A
Sbjct: 123 VAEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRVPYDDLDAIETAATN----RPNIVA 178

Query: 204 IMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEPD 263
           I++E +QGEGG+R    +Y   +R ICD +G LL+LDE+Q G+GRTG+ + +++ GI+PD
Sbjct: 179 ILIEPIQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGRTGRLFAFQHAGIQPD 238

Query: 264 IFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLLE 322
           + T AKGL  G+PIGA + + + A VF+PG H STFGGNP +C    AV+ETL  ENL E
Sbjct: 239 VVTLAKGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRVGRAVLETLIDENLTE 298

Query: 323 NVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLLA 382
           N  A+G  L   L+    +     ++RG GL+ G+E    L+    E+V  A++ GLL+ 
Sbjct: 299 NAAAQGAYLLDSLRAALGETHGLVEIRGRGLMVGIE----LDRPCGELVGRALDAGLLIN 354

Query: 383 PAGPKVLRFVPPLIVSAAEINEAIALL 409
               +V+R +PPLI+  A+I+E +A L
Sbjct: 355 VTAERVIRLLPPLIIDRAQIDELVATL 381


Lambda     K      H
   0.319    0.136    0.406 

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: 435
Number of extensions: 20
Number of successful extensions: 5
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: 418
Length of database: 392
Length adjustment: 31
Effective length of query: 387
Effective length of database: 361
Effective search space:   139707
Effective search space used:   139707
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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