Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_020176835.1 A3OQ_RS0118060 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000385335.1:WP_020176835.1 Length = 566 Score = 238 bits (608), Expect = 3e-67 Identities = 173/539 (32%), Positives = 281/539 (52%), Gaps = 28/539 (5%) Query: 16 LIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTRVPG 75 L+ LK +GIDT+F ++G + + + EG+ + RHEQ+A AA +T+ PG Sbjct: 13 LVVDALKLNGIDTIFGVAGIPITDLARLAQAEGMNYVGFRHEQSAGNAAAISGYLTQKPG 72 Query: 76 VAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQEIDHVPFVAPVAR 133 + + PG NGM A+A A N P++++ G + + G +E+D + P A+ Sbjct: 73 ICLTVSAPGFLNGMVALANATTNCFPMILISGSSDRAIVDLEQGDYEELDQMNAAKPYAK 132 Query: 134 FAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFP-MDHAFSMSSDNGRPGALTELPAGP 192 A AE+ G+ + +A+ AAVS G ++D + + + ++ GR + + P Sbjct: 133 AAFRINKAEDIGIGIARAIHAAVSGRPGGVYLDITAVTLSEVIDAEIGRKSLVKIVDPAP 192 Query: 193 T--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGVV 250 PA + + RA LL++A+RP+I+ G + A+ + +E IP L MA+G++ Sbjct: 193 KQIPAPENISRALALLASAKRPLIILGKGAAYAQADKDIRSFIETTGIPFLPMSMAKGLL 252 Query: 251 PADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTTQLIVADRVEPAREHP 308 P +H + + ARS A+G+ADV +++G +++ L G G ++ TTQ + D + Sbjct: 253 PDNHPQSAATARSFAIGQADVVMLIGARLNWLLSHGKGPLWSDTTQFVQLDVSPTEIDSN 312 Query: 309 RPVAAGLYGDLTATLSAL--AGSGGTDHQG--WIEELATAETMARDLEKAELVDDRIPLH 364 RP+AA + GD+ ++++AL A G G W+ LA E D L D H Sbjct: 313 RPIAAPVVGDIKSSIAALLTALKPGQIKAGAEWLAALAEHEKKNIDSMTKRLAADP---H 369 Query: 365 PMRVYAELAALLERDAL-------VVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGSG 417 PM + L A+ RDAL +V + + +A +ID Y P LDSG +G +G G Sbjct: 370 PMNFSSALRAV--RDALAGRPDIYIVNEGANTLDFARNIIDMYEPRKRLDSGTWGVMGIG 427 Query: 418 PGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEKHPME 477 GYA+ A + + VV ++GD AFGFSGME +T+ R+++ VV VI NNG G+ + + Sbjct: 428 MGYAIGAAVV-SGKPVVAIEGDSAFGFSGMEIETICRYHLPVVIVILNNG--GI--YHGD 482 Query: 478 ALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTDP 536 A P RYD+++ A GG V + L AL A A+G PA+++ + DP Sbjct: 483 APDAPPSPTGFIPHARYDKLIEAFGGAAYHVEDTSSLTKALTGALAAGRPAIIDCVIDP 541 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: 795 Number of extensions: 45 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: 566 Length adjustment: 36 Effective length of query: 511 Effective length of database: 530 Effective search space: 270830 Effective search space used: 270830 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.
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:
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