Aligments for a candidate for dapE in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments 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_RS18740 AZOBR_RS18740 succinyl-diaminopimelate desuccinylase

Query= curated2:B9JZL9
         (404 letters)



>FitnessBrowser__azobra:AZOBR_RS18740
          Length = 427

 Score =  115 bits (288), Expect = 2e-30
 Identities = 121/401 (30%), Positives = 165/401 (41%), Gaps = 55/401 (13%)

Query: 20  LIRCPSVTPAEG---GALSALAAMLEPLGFTVERMVAREEGTPDVENLYARLGT------ 70
           LIR P+V P           L   L   GF VE +  R +G P   + Y R         
Sbjct: 27  LIRIPTVNPPGDVYTDCAEFLGRRLAGRGFAVEYV--RADGAPGDSDRYPRTNVIARVEG 84

Query: 71  --EGPHLMFAGHTDVVPVGNEADWTYPPFSAEIAGGELYGRGAVDMKGGIACFVAAIARH 128
              GP + F GH DVVP G    WT  PF   +  G +YGRGA DMKGGIA  + A+   
Sbjct: 85  REPGPCVHFNGHIDVVPAGQ--GWTVDPFEGVVKDGRVYGRGACDMKGGIAASIIAVEAI 142

Query: 129 IESQGAPKGSISFLITGDEEGPSINGTTKLLEWAAAKGERWDACLVGEPTNPDQLGDMIK 188
           +E+     G++    T DEE     G   L         R D  ++ EP N D+    + 
Sbjct: 143 LEAGIPFPGALEISGTVDEESGGYGGVGHLATLGYFSRPRVDHVIIPEPLNVDR----VC 198

Query: 189 IGRRGSLSGEIIVKGVQGHAAYPHLADNPVRGMIKLAE----------ALMHPAFDAGTE 238
           IG RG    EI  KG   H + P L +  VR M  +            A    A     E
Sbjct: 199 IGHRGVWWAEIETKGRVAHGSMPFLGNCAVRHMGAVLHRIETELIPRLAAKRTAMPVVPE 258

Query: 239 NFQPSNLEVTTI------DVGNAATNVIPARASAKFNIRFNDTWTAETLRTEIIARLDTA 292
             + S L +  I      D G   + ++P R     + R+      E +R EI+  L+  
Sbjct: 259 GARQSTLNINAIHGGQPEDHGGLPSPMVPDRCRMVIDRRYLIEEDPEEVRAEIVGILED- 317

Query: 293 SADPLLRPGRPPIAYEL--VWADRPSQVFLTRNNA-LISSLSAAIEKMTGKTPALSTTGG 349
                LR  RP   YEL  V A  P+   LT  +A ++ ++ AAIE + G+  A   + G
Sbjct: 318 -----LRRERPGFDYELREVLAFLPT---LTDADAPVVRAVGAAIETVLGRPAAQVVSPG 369

Query: 350 TSDARFI------KDYCPVVEFGLVGQTMHMVDERVAVSDL 384
           T D + I      KD C     G++    H  DE V + D+
Sbjct: 370 TYDQKHIARVGHLKD-CIAYGPGIL-DLAHQPDEYVGIDDM 408


Lambda     K      H
   0.316    0.133    0.399 

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: 448
Number of extensions: 30
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: 404
Length of database: 427
Length adjustment: 31
Effective length of query: 373
Effective length of database: 396
Effective search space:   147708
Effective search space used:   147708
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 (21.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis