Alignments for a candidate for ilvI in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Azospirillum brasilense Sp245

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS31945 AZOBR_RS31945 oxalyl-CoA decarboxylase

Query= BRENDA::P9WG39
         (547 letters)



>FitnessBrowser__azobra:AZOBR_RS31945
          Length = 585

 Score =  228 bits (582), Expect = 4e-64
 Identities = 181/560 (32%), Positives = 290/560 (51%), Gaps = 35/560 (6%)

Query: 2   STDTAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAA 61
           +TD  PA T    +L+   LK +GI+ ++ + G  +  +    + EG+R+I  RHEQ A 
Sbjct: 14  ATDAEPALT-DGFQLVIDALKLNGIENLYVVPGIPISDLLRMAQGEGLRVISFRHEQNAG 72

Query: 62  FAAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSL 119
            AA     +T+ PGV    + PG  NG++A+A A  N  P++++ G +    +    G  
Sbjct: 73  NAAAIAGFLTKKPGVCMTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDY 132

Query: 120 QEIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFS--MSS 177
           +E+D +    P+ + A     A++ G+ V +A++AAVS   G  ++D P    FS  M +
Sbjct: 133 EEMDQLAIAKPLCKAAFRVLHAQDIGIAVARAIRAAVSGRPGGVYLDLPAK-LFSQVMDA 191

Query: 178 DNGRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEE 235
             G    +  + A P   P+ D++ RA  +L  A+RP+I+ G    +  A+ A+  LVE+
Sbjct: 192 AEGARSLVKVVDAAPAQLPSPDSVARALEVLKGAKRPLIILGKGAAYAQADEAVRELVEK 251

Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFG-----GVFG 290
             IP L   MA+G++P  H  +   ARS  L +ADV ++VG  +++ L  G     G  G
Sbjct: 252 SGIPFLPMSMAKGLLPDTHPQSAGAARSMVLKDADVVVLVGARLNWLLSHGKGKTWGEPG 311

Query: 291 STTQLIVADRVEPAREHPRPVA--AGLYGDLTATLSALAGSGGTDHQGWI---EELATAE 345
           S T   +   +EP RE    VA  A L GD+ + +SAL        +GW     E   A 
Sbjct: 312 SKT--FIQIDIEP-REMDSNVAIVAPLVGDIGSCVSALTAGMA---KGWTPPPAEWTGAV 365

Query: 346 TMARDLEKAELVDDRIP-LHPMRVYAELAAL----LER-DALVVIDAGDFGSYAGRMIDS 399
           +  ++   A++    +    PM  +  L AL     ER +AL+V +  +    A  +ID 
Sbjct: 366 SARKEANIAKMAPKLMSNASPMNFHGALGALRRVVQERPEALLVNEGANTLDLARGIIDM 425

Query: 400 YLPGCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAV 459
           + P   LD G +G +G G G+A+AA +    + V+ ++GD AFGFSGME +T+ R+N+ V
Sbjct: 426 HQPRKRLDVGTWGVMGIGMGFAVAAAV-ESGKPVLAVEGDSAFGFSGMEVETICRYNLPV 484

Query: 460 -VSVIGNNGIW-GLEKHPMEALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPA 517
            + V  NNGI+ G + +P        +V    P +RYD+++ A GG G  V+ P EL  A
Sbjct: 485 CIVVFNNNGIYKGTDVNPTGGSDPSPMV--FVPDSRYDKMMEAFGGAGVNVTTPDELYRA 542

Query: 518 LERAFASGLPAVVNVLTDPS 537
           +  A  SG P ++N + DP+
Sbjct: 543 VSAAMDSGRPTLINAVIDPN 562


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: 759
Number of extensions: 50
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: 585
Length adjustment: 36
Effective length of query: 511
Effective length of database: 549
Effective search space:   280539
Effective search space used:   280539
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 09 2024. The underlying query database was built on Apr 09 2024.

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

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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
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