GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Azospirillum brasilense Sp245

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase

Query= curated2:Q7W8Y3
         (379 letters)



>FitnessBrowser__azobra:AZOBR_RS31030
          Length = 398

 Score = 92.4 bits (228), Expect = 2e-23
 Identities = 117/395 (29%), Positives = 165/395 (41%), Gaps = 54/395 (13%)

Query: 7   LDLVKDLIARPSVTPD-DVDCQMLLAQRLERIGFQCETIARGGVT--NLWARRGAGAPL- 62
           L+L++DLIA  + + + ++D    +   L  +G     +     T  NL+A  G   P+ 
Sbjct: 18  LELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEERTKANLYATIG---PMD 74

Query: 63  ---TVFAGHTDVVPPGPRDKWDSDPFVPTERDGFLYGRGAADMKSSIAAFVVAAEEFVAA 119
                 +GHTDVVP   +D W SDPF  TERDG L+GRG ADMK  IAA +  A +F+AA
Sbjct: 75  RGGVCLSGHTDVVPVDDQD-WSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAA 133

Query: 120 HPEHPGSIALLITSDEEGPAVDGTVIVCDELRQRGEQLDYCIVGEPTSTEALGDVCKNGR 179
           +   P  +    + DEE   + G   +  +L     +   CIVGEPT    +      G 
Sbjct: 134 NLTTP--VHYAFSYDEELGCL-GVPGLLTQLAGMAVKPRLCIVGEPTRMRVI-----VGH 185

Query: 180 RGSLSGRLLVKGVQGHVAYPHLARNPVHQLAPALTELVAIEWDQGNEY-----------F 228
           +G ++ R     V GH  +  LA   V+ +  A  ELV+     G  +            
Sbjct: 186 KGKVALRC---RVHGHACHSSLAPQGVNAVEYA-AELVSFLRGMGRRFAEQGPFDHDYDI 241

Query: 229 PPTTFQVSNLHAGTGATNVVPGEAVALFNFRFSTASTPDQLKARVHEVLDRHGLEYQ--- 285
           P TT     +  GT A N+VP +A   F  R         +   + +       E +   
Sbjct: 242 PYTTVHTGVMEGGT-ARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVR 300

Query: 286 ----LDWE-LGGEPFL-TPRGSLTDALVSAIQAETGLQAELSTTGG---TSDGRFIARIC 336
                 WE L   P L TP  S    LV  +  + G       T G   TS     A +C
Sbjct: 301 PDAGFSWETLSDSPALDTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVC 360

Query: 337 -PQVIEFGPCNATIHKVNERIELSSLAPLKNIYRR 370
            P  IE        HK +E +ELS LA  +    R
Sbjct: 361 GPGDIE------QAHKPDEYVELSELARAERFLHR 389


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: 402
Number of extensions: 21
Number of successful extensions: 3
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: 398
Length adjustment: 30
Effective length of query: 349
Effective length of database: 368
Effective search space:   128432
Effective search space used:   128432
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:

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