GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Hydrogenovibrio halophilus DSM 15072

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_019895362.1 A377_RS0106195 diaminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P18335
         (406 letters)



>NCBI__GCF_000384235.1:WP_019895362.1
          Length = 417

 Score =  156 bits (395), Expect = 9e-43
 Identities = 124/410 (30%), Positives = 190/410 (46%), Gaps = 47/410 (11%)

Query: 23  PAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQ--GETLWHISNV 80
           PA F  VKGQ ++ WD+ GKEY+DF  G  V   GH +P L  A+      + + H  ++
Sbjct: 19  PAVF--VKGQNAKQWDETGKEYIDFYAGAGVLNFGHNNPKLKAAMMDYLAEDGVLHSLDM 76

Query: 81  FTNEPALRLGRKLIEATFAERVV----------FMN-SGTEANETAFKLARHYACVRHSP 129
            T        R  I+  F E ++          FM  +GT A E A KLAR         
Sbjct: 77  MTAAK-----RDFIQG-FVETILQPRKMDYKLQFMGPTGTNAVEAALKLARKVTG----- 125

Query: 130 FKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFND--------LHAVKA 181
            +  +IAF   FHG +L  ++      +    G     + H PF          L  ++A
Sbjct: 126 -RQNVIAFAQGFHGMTLGALACTANGYFRQAAGVPLNHVSHCPFETNVGGGLAMLDTLRA 184

Query: 182 VMDDHT------CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRT 235
           + D+ +       A++VEPIQ EGGV  A+ E+LQGL +L     ALL+ D++Q G GRT
Sbjct: 185 LYDNTSGGAEKPAAILVEPIQAEGGVNVASAEWLQGLDKLAKDLGALLIVDDIQAGCGRT 244

Query: 236 GDLFAYMHYGVTPDILTSAKALGG-GFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAV 294
           G  F++   G+ PDI+T AK LGG G PI+  L   E    + PG H  T+ G  L+   
Sbjct: 245 GQYFSFDEAGIDPDIITLAKGLGGLGTPIAMNLVKPEHDQHWQPGEHTGTFRGQNLSFVA 304

Query: 295 AGAAFDIINTPEVLEGIQAKRQRFVDHLQKIDQQY-DVFSDIRGMGLLIGAEL--KPQYK 351
              A       +++  +  K +  V  L+++ Q Y D    +RG G++   ++      K
Sbjct: 305 GREALRYFEDDQLMNAVHDKGEIMVGALEQMAQTYPDAGFSVRGKGMMQALDVGDGALAK 364

Query: 352 GRARDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVA 401
             AR+    G   G      G  V++  P L + + ++  G++  + A+A
Sbjct: 365 AVARECFERGMLFG--PCGVGGSVIKLIPPLTIPEDELVAGLEILSEALA 412


Lambda     K      H
   0.322    0.138    0.415 

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: 440
Number of extensions: 24
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: 406
Length of database: 417
Length adjustment: 31
Effective length of query: 375
Effective length of database: 386
Effective search space:   144750
Effective search space used:   144750
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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