GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Lentibacillus jeotgali Grbi

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_010529905.1 ON01_RS04970 ornithine--oxo-acid transaminase

Query= curated2:Q58131
         (398 letters)



>NCBI__GCF_000224785.1:WP_010529905.1
          Length = 398

 Score =  301 bits (771), Expect = 2e-86
 Identities = 161/389 (41%), Positives = 240/389 (61%), Gaps = 5/389 (1%)

Query: 7   IDLEKKYHLQIYGRLPVVLVEGKGMEVYDIDGKKYLDFLAGIGVNNVGHCHPKVVEAIKK 66
           ID  ++Y  + Y  LPVV+ + +G+ V D +G +Y+D L+     N GH HPK+++A+KK
Sbjct: 9   IDQTQEYGAKNYHPLPVVINKAEGVWVEDPEGNRYMDMLSSYSALNQGHRHPKIIDALKK 68

Query: 67  QAETLIHTSNIYYTIPQIKLAKKLVELSGLDRAFFCNSGAEANEGAIKFARKYVSKVLG- 125
           QA+ +  TS  ++        +K+ +L+  +     N+GAEA E A+K AR++   V G 
Sbjct: 69  QADAVTLTSRAFHNDQLGPWYEKICKLTNKEMTLPMNTGAEAVETAVKAARRWAYDVKGV 128

Query: 126 -REGGEIISMYNAFHGRTLTTLAATPKPKYQDGFYPLPPGFKYVPFNDIEALKEAITDKT 184
                EII     FHGRT+T ++ + + +YQ GF PL PG K +P+ D++ALKEAI + T
Sbjct: 129 AENKAEIIVAEGNFHGRTMTAVSLSSESEYQRGFGPLLPGIKIIPYGDVDALKEAINENT 188

Query: 185 AAIMIEPVQGEGGIHVADKDYLKAVRDLCDDKNIVLIFDEVQCGMGRTGRMFAFEHYGVE 244
           AA + EP+QGE GI++  + +LK   D+C + N++ + DE+Q G+ RTG+MFA +  GV 
Sbjct: 189 AAFLFEPIQGEAGINIPPEGFLKEAYDVCAENNVLYMADEIQSGLARTGKMFACDWEGVT 248

Query: 245 PDILTLAKALGGGV-PIGAVVLKEEIAKALSYGDHGTTFGGNPLACSAALASVEVIEELI 303
           PD+L L KALGGGV PI AVV  ++I    + G HG+TFGGNPLAC+ +  S+EV+EE  
Sbjct: 249 PDVLILGKALGGGVFPISAVVANKDILGVFNPGSHGSTFGGNPLACAVSTVSLEVLEEEK 308

Query: 304 KDDKVIEKGKYFIRKLENLIEKYNFIKEVRGLGLMIGAELEFNGADIVKKMLEKGFLINC 363
             D+  E G Y + +L+ +  K   IKEVRG GL IG EL        + + EKG L   
Sbjct: 309 LADRSNELGNYMMGELKKI--KNPKIKEVRGKGLFIGVELTEAARPYCEALKEKGLLCKE 366

Query: 364 TSDTVLRFLPPLIVEKEHIDALINALDEV 392
           T + V+RF PPL+++K  ++  +  + EV
Sbjct: 367 THENVIRFAPPLVIDKPDLEWAVGHIKEV 395


Lambda     K      H
   0.320    0.141    0.409 

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: 411
Number of extensions: 17
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: 398
Length of database: 398
Length adjustment: 31
Effective length of query: 367
Effective length of database: 367
Effective search space:   134689
Effective search space used:   134689
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 (21.7 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