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_040912231.1 ON01_RS05315 diaminobutyrate--2-oxoglutarate transaminase

Query= curated2:O66442
         (376 letters)



>NCBI__GCF_000224785.1:WP_040912231.1
          Length = 425

 Score =  201 bits (510), Expect = 4e-56
 Identities = 142/404 (35%), Positives = 219/404 (54%), Gaps = 41/404 (10%)

Query: 5   MNNYAR-LPVKFVRGKGVYLYDEEGKEYLDFVSGIGVNSLGHAYPKLTEALKEQVEK--L 61
           + +Y+R  P  F + KG  L+D +GKEYLDF +G G  + GH    +   + E ++   +
Sbjct: 22  VRSYSRGWPTVFEKAKGYKLWDTDGKEYLDFFAGAGGLNYGHNDDAMQAKMIEYIQNNGI 81

Query: 62  LH---VSNLYENPWQEELAHKLVKHFWTEGKVFFAN-SGTESVEAAIKLARKYWRDKGKN 117
           LH   +       + E     ++K    + KV F   +GT SVE+A+K+ARK        
Sbjct: 82  LHSLDMGTTSRKEFLERFKEVILKPRNLDYKVMFPGPTGTNSVESALKIARKV-----TG 136

Query: 118 KWKFISFENSFHGRTYGSLSATGQP-KFHKGFEPL-----VPGFSYAK-LNDIDSVYKLL 170
           +   ISF N+FHG T GSLS T    K H    PL     +P   Y +  N I  + + L
Sbjct: 137 RDTVISFTNAFHGMTIGSLSVTANSFKRHGAGVPLHHSVSMPFDEYVEDQNTIAYLERFL 196

Query: 171 DEETAG------IIIEVIQGEGGVNEASEDFLSKLQEICKEKDVLLIIDEVQTGIGRTGE 224
           ++  +G      II+E +QGEGG+N AS D+L K++++CK+ D+LLI+D++Q G GRTG 
Sbjct: 197 EDRGSGVALPAAIILETVQGEGGINAASMDWLKKVEDLCKQWDILLIVDDIQAGCGRTGT 256

Query: 225 FYAYQHFNLKPDVIALAKGLGG-GVPIGAILAREEVAQSFTPGSHGSTFGGNPLACRAGT 283
           F++++   + PD++ L+K +GG G+P+   L + E  Q + PG H  TF GN LA    T
Sbjct: 257 FFSFEPAGIDPDIVCLSKSIGGAGLPMALTLIKPEHDQ-WGPGEHNGTFRGNNLAFIGAT 315

Query: 284 VVVD--EVEKLLPHVREVGNYFKEKLKELG------KGKVKGRGLMLGLELERE--CKDY 333
             +   E +     +RE G   +E ++EL           +GRGLM G+ L +     D 
Sbjct: 316 QALSYWENDDFGKSIREKGELLREGIEELVAKYPELDAHHRGRGLMQGIALGKPELTDDI 375

Query: 334 VLKALEKGLLINCTAG---KVLRFLPPLIIQKEHIDRAISVLRE 374
             +A ++GL++  TAG   +V++FLPPLII KE +   + +L E
Sbjct: 376 CAEAFQRGLIVE-TAGPDDEVVKFLPPLIIDKEALKEGLKILDE 418


Lambda     K      H
   0.318    0.139    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: 385
Number of extensions: 19
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: 376
Length of database: 425
Length adjustment: 31
Effective length of query: 345
Effective length of database: 394
Effective search space:   135930
Effective search space used:   135930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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