Alignments for a candidate for ilvI in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Azospirillum lipoferum B510

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_086935435.1 AZL_RS17250 oxalyl-CoA decarboxylase

Query= BRENDA::P9WG39
         (547 letters)



>NCBI__GCF_000010725.1:WP_086935435.1
          Length = 580

 Score =  226 bits (576), Expect = 2e-63
 Identities = 169/551 (30%), Positives = 276/551 (50%), Gaps = 22/551 (3%)

Query: 4   DTAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFA 63
           + APA T    +L+   LK + I+ ++ + G  +  +    + EG+R++  RHEQ A  A
Sbjct: 13  EDAPALT-DGFQLVIDALKLNDINNLYVVPGIPISDLLRMAQAEGMRVVSFRHEQNAGNA 71

Query: 64  AEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQE 121
           A     +T+ PGV    + PG  NG++A+A A  N  P++++ G +    +    G  +E
Sbjct: 72  AAIAGFMTKKPGVCMTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYEE 131

Query: 122 IDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGR 181
           +D +    P+ + A     A++ G+ V +A++AAVS   G  ++D P    FS   D   
Sbjct: 132 MDQLAIAKPLCKAAFRILHAQDIGIGVARAIRAAVSGRPGGVYLDLPAK-LFSQVMDAAE 190

Query: 182 PGALTELPAGPTPA----GDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERH 237
                     PTPA     DA++RA  LL  A+RP+++ G    +  A+  +   VE+  
Sbjct: 191 GAKSLVKVVDPTPAQYPSADAVNRALDLLKGAKRPLVIFGKGAAYAQADETIRSFVEKSG 250

Query: 238 IPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFG--STT 293
           IP L   MA+G++P  H  +   ARS  L EADV ++VG  +++ L  G G  +G   + 
Sbjct: 251 IPFLQMSMAKGLLPDTHPQSAGAARSLVLQEADVVMLVGARLNWLLSHGKGKTWGKPGSK 310

Query: 294 QLIVADRVEPAREHPRPVAAGLYGDLTATLSAL---AGSGGTDHQGWIEELATAETMARD 350
           + I  D      +    + A L GD+ + +  L      G T    W+  +A        
Sbjct: 311 KFIQVDIEPREMDSNVEIHAPLVGDIASVMEVLLKGIEGGLTPPADWMATVAAKREQNVA 370

Query: 351 LEKAELVDDRIPLHPMRVYAELAALLER--DALVVIDAGDFGSYAGRMIDSYLPGCWLDS 408
               +L+ +  P++       L  +++   DA++V +  +    A  +ID Y P   LD 
Sbjct: 371 KMAPKLMSNASPMNFHGALGALRRVIKERPDAMLVNEGANTLDLARGIIDMYEPRKRLDV 430

Query: 409 GPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVI-GNNG 467
           G +G +G G GYA+AA +    + V+ ++GD AFGFSGME +T+ R+N+ V  VI  NNG
Sbjct: 431 GTWGVMGVGMGYAVAAAV-ESGKPVLAVEGDSAFGFSGMEVETICRYNLPVCIVIFNNNG 489

Query: 468 IW-GLEKHPMEALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGL 526
           I+ G + +P        +V    PG+RYD+++ A GG G  V+ P EL  A+  A  SG 
Sbjct: 490 IYRGTDTNPTGGADPSPMV--FVPGSRYDKMMEAFGGVGVHVTNPDELYRAVSEAMDSGR 547

Query: 527 PAVVNVLTDPS 537
           P ++N + DP+
Sbjct: 548 PTLINAVIDPA 558


Lambda     K      H
   0.319    0.135    0.405 

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: 722
Number of extensions: 39
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: 547
Length of database: 580
Length adjustment: 36
Effective length of query: 511
Effective length of database: 544
Effective search space:   277984
Effective search space used:   277984
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
the source code
instructions for running GapMind on your computer
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