GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapE in Magnetospirillum magneticum AMB-1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_011384771.1 AMB_RS11990 acetylornithine deacetylase

Query= curated2:Q7W8Y3
         (379 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384771.1 AMB_RS11990
           acetylornithine deacetylase
          Length = 404

 Score =  104 bits (260), Expect = 4e-27
 Identities = 111/342 (32%), Positives = 149/342 (43%), Gaps = 30/342 (8%)

Query: 51  NLWARRG-AGAPLTVFAGHTDVVPPGPRDKWDSDPFVPTERDGFLYGRGAADMKSSIAAF 109
           N++A  G +  P  V +GHTDVVP   +D W  DPF   + DG LYGRG ADMKS IA  
Sbjct: 75  NIFATIGPSDVPGIVLSGHTDVVPVDGQD-WSRDPFHLVQADGKLYGRGTADMKSFIAIC 133

Query: 110 VVAAEEFVAAHPEHPGSIALLITSDEEGPAVDGTVIVCDELRQRGEQLDYCIVGEPTSTE 169
           +  A +F AA    P  +    + DEE   V G   + D+L     +   CIVGEPT  +
Sbjct: 134 LAMAPQFAAAPLRMP--VHFAFSYDEEVGCV-GVRRLIDDLAHLPVRPALCIVGEPTDMK 190

Query: 170 ALGDVCKNGRRGSLSGRLLVKGVQGHVAYPHLARNPVHQLAPALTELVAIE--------W 221
           A+      G +G  S R  V+G + H A  H   N +   A  +T L A++        +
Sbjct: 191 AV-----IGHKGKKSVRCHVEGHECHSALNHQGVNAIEIAAEMVTRLRALQRRIREQGPF 245

Query: 222 DQGNEYFPP-TTFQVSNLHAGTGATNVVPGEAVALFNFRFSTASTPDQLKARVHEVLDRH 280
           D G  Y PP TT     +  GT A N+VP      F  R      P+ L A V       
Sbjct: 246 DLG--YQPPYTTVHTGTMQGGT-ALNIVPKSCSFEFEIRNLPDHDPETLMAEVRGWAQDL 302

Query: 281 GLEYQLDWELGG----EPFLTPRGSL--TDALVSAIQAETGLQAELSTTGGTSDGRFIAR 334
             E     E  G    E   TP   +   DA V  + A +G          T  G F   
Sbjct: 303 VPEMLAVSEASGITLDEHNSTPGLGMDEMDAAVRLVCALSGANQTSKVAFTTEAGLFQQA 362

Query: 335 ICPQVIEFGPCNAT-IHKVNERIELSSLAPLKNIYRRTLENL 375
             P V+  GP + T  H+ +E I L  +A  ++  RR L ++
Sbjct: 363 GIPAVV-IGPGSITQAHRPDEFITLEQVAQCEDFLRRLLAHM 403


Lambda     K      H
   0.318    0.136    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: 359
Number of extensions: 21
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: 379
Length of database: 404
Length adjustment: 31
Effective length of query: 348
Effective length of database: 373
Effective search space:   129804
Effective search space used:   129804
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 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