GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Acidovorax sp. GW101-3H11

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= curated2:Q7N9E5
         (403 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179
           Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase
           (EC 2.6.1.19)
          Length = 459

 Score =  218 bits (556), Expect = 2e-61
 Identities = 133/392 (33%), Positives = 203/392 (51%), Gaps = 34/392 (8%)

Query: 29  RGQGSRVWDQHGKEYIDFAGGIAVVALGHCHPTLVDVLKQQGEKLWHIS-NIFTNEPALI 87
           + + + +WD  G+ +IDFAGGIAV+  GH H  ++  +K Q +   H    +   EP + 
Sbjct: 59  KARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLYTHTCFQVVAYEPYVE 118

Query: 88  LAQKL---IDATFAERVFFANSGAEANEAAFKLARHYAIARHNPYKTKIIAFHQGFHGRT 144
           + ++L       FA++     +GAEA E A K+AR Y        +  +IAF  G+HGRT
Sbjct: 119 VCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYT------KRPGVIAFTGGYHGRT 172

Query: 145 LFTVSVGGQ-PKYADGFGPKPADIIHVPF-NDLDAVKA--------------VIDDHTCA 188
             T+ + G+   Y  GFGP P +  H  F N L  V                +  +   A
Sbjct: 173 NLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKNDIEPERVAA 232

Query: 189 VVLEPVQGEGGVTAAAPAFIHGVRELCDKHQVLLVFDEVQSGMGRTGKLFSYMHYDVTPD 248
            ++EPVQGEGG   A P FI G++ L D++ +LL+ DEVQ+G GRTG  F+   + V PD
Sbjct: 233 FIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWFASEQWPVAPD 292

Query: 249 IITTAKALGNGFPISAMLTTVNIASVMTPGAHGTTYGGNPLACAVANVAFDIINTPAVLA 308
           +ITTAK+L  GFP++ ++   ++     PG  G TY G+P+ACA +    +      +LA
Sbjct: 293 LITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVIEAFAQEKLLA 352

Query: 309 GVEKRHNLMVNFLNDINQKYSIFGEIRGKGLLIGAE------LKAPHQGKAKDILQLAAE 362
             +    L+V  L D+  +    G++RG G ++  E      L  P     K ++  AA 
Sbjct: 353 RSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFENGDLSRPDAALTKQVVAEAAR 412

Query: 363 NGLMLLSAG--GDVLRFTPSLIISEEEIAQGM 392
            GL+LLS G  G+V+R    L  S+E + +G+
Sbjct: 413 RGLILLSCGTHGNVIRILVPLTASDELLHEGL 444


Lambda     K      H
   0.321    0.138    0.410 

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: 450
Number of extensions: 24
Number of successful extensions: 6
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: 403
Length of database: 459
Length adjustment: 32
Effective length of query: 371
Effective length of database: 427
Effective search space:   158417
Effective search space used:   158417
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 (21.9 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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