GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Azohydromonas australica DSM 1124

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_084150484.1 H537_RS0106500 oxalyl-CoA decarboxylase

Query= BRENDA::P9WG39
         (547 letters)



>NCBI__GCF_000430725.1:WP_084150484.1
          Length = 597

 Score =  238 bits (608), Expect = 4e-67
 Identities = 167/537 (31%), Positives = 274/537 (51%), Gaps = 20/537 (3%)

Query: 16  LIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTRVPG 75
           L+   LK +GIDT++ L G  +  +    + EG+R+I  RHEQ A  AA     +T+ PG
Sbjct: 42  LVIDALKLNGIDTIYGLPGIPITDLTRLAQAEGLRVISFRHEQNAGHAAAAAGFLTQKPG 101

Query: 76  VAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQEIDHVPFVAPVAR 133
           +    + PG  NG++A+A A  N  P++++ G +    +    G  +E+D +    P  +
Sbjct: 102 ICLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYEEMDQLNAAKPFCK 161

Query: 134 FAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD-HAFSMSSDNGRPGALTELPAGP 192
            A     A++ G+ + +A++AAVS   G  ++D P    + +M ++ GR   +      P
Sbjct: 162 AAFRVLHAQDIGIGIARAIRAAVSGRPGGVYLDLPAKLFSQTMEAEAGRRSLVEVRDPAP 221

Query: 193 T--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGVV 250
              PA D + RA  LL  A+RP+I+ G    +  A+A + +L+E   IP L   MA+G++
Sbjct: 222 RQLPAPDTVARALDLLKGAKRPLILLGKGAAYAQADAEIRQLIERTGIPYLPMSMAKGLL 281

Query: 251 PADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTTQLIVADRVEPAR-EH 307
           P  H  + + ARS  L EADV ++VG  +++ L  G G  +G+  +  +   + P   + 
Sbjct: 282 PDTHVQSAAAARSYVLAEADVVMLVGARLNWLLSHGKGKTWGAEPKKFIQIDISPTEIDS 341

Query: 308 PRPVAAGLYGDLTATLSALAGSGGTDHQGWIEELATAETMARD--LEKAELVDDRIPLHP 365
             P++A L GD+ + +SAL    G   Q    E  +A    +D  L K     +     P
Sbjct: 342 NVPISAPLIGDIGSCVSALLDGVGAGWQKPPSEWTSAIAQRKDKNLSKMAQTLEATTTGP 401

Query: 366 MRVYAELAALLE-----RDALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGSGPGY 420
           M  ++ L  + +      DA+VV +  +   +A  ++D Y P   LD G +G +G G G+
Sbjct: 402 MNFHSALGVIRKVVQERPDAMVVNEGANTLDFARSIVDMYEPRKRLDVGTWGVMGIGMGF 461

Query: 421 ALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAV-VSVIGNNGIW-GLEKHPMEA 478
           A+AA +    + V+ ++GD AFGFSGME +T+ R+ + V + V  NNG++ G + +    
Sbjct: 462 AVAAAVT-TGKPVIAIEGDSAFGFSGMEVETICRYELPVCIVVFNNNGVYKGTDVNQSGG 520

Query: 479 LYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTD 535
                 V       RYD ++ A GGHG  V  P EL  A+  A ASG P ++N + D
Sbjct: 521 ADPAPTV--FVKNARYDLMMTAFGGHGVTVVTPDELGRAMREAVASGRPTLINAVID 575


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: 766
Number of extensions: 38
Number of successful extensions: 7
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: 597
Length adjustment: 36
Effective length of query: 511
Effective length of database: 561
Effective search space:   286671
Effective search space used:   286671
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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