Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_012402930.1 BPHY_RS18290 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000020045.1:WP_012402930.1 Length = 579 Score = 238 bits (606), Expect = 6e-67 Identities = 172/549 (31%), Positives = 284/549 (51%), Gaps = 29/549 (5%) Query: 8 AQTMHAG-RLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEG 66 AQ M G L+ LKA+ IDT+F L G + + + EG+R I RHEQ A AA Sbjct: 17 AQQMTDGFHLVIDALKANDIDTIFGLVGIPITDLARLAQAEGMRFIGFRHEQHAGHAAAI 76 Query: 67 WSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQEIDH 124 +T+ PG+ + PG NG++A+A A N P++++ G + + G +E+D Sbjct: 77 AGYMTQKPGICLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYEEMDQ 136 Query: 125 VPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDH-AFSMSSDNGRPG 183 + P A+ A AE+ G+ + +A++AAVS G ++D P A ++ + + Sbjct: 137 LNAAKPYAKAAYRVLHAEDIGIGLARAIRAAVSGRPGGVYLDLPAKLLAQTIDAAKAKQS 196 Query: 184 ALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVL 241 + + A P PA D++ RA LL +A+RP+++ G + A+ + +E+ IP L Sbjct: 197 IVRVIDAAPRQLPAPDSVKRAIDLLKSAKRPLVLLGKGASYSQADKEIRAFIEKTGIPYL 256 Query: 242 MNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTTQLIVAD 299 MA+G++P H + S ARS L E+DV +++G +++ L G G +G Q + D Sbjct: 257 PMSMAKGLLPDTHEQSASAARSFVLAESDVVVLIGARLNWLLAHGKGKTWGKPKQFVQID 316 Query: 300 RVEPAREHPRPVAAGLYGDLTATLSALAGSGGTDH----QGWIEELATAETMARDLEKAE 355 + +AA + GD+ + +++L G D + W++ A ++ +LEK Sbjct: 317 ISAQEMDSNVAIAAPIVGDIGSCVASLLDQVGDDFPQPPKEWLD--AVSQKKNTNLEKMA 374 Query: 356 LVDDRIPLHPMRVYAELAALLE-----RDALVVIDAGDFGSYAGRMIDSYLPGCWLDSGP 410 + P PM ++ L L + D VV + + YA +ID Y P DSG Sbjct: 375 ATLAKNP-SPMNFHSALRVLRDIVKENPDINVVNEGANTLDYARAIIDMYQPRKRFDSGT 433 Query: 411 FGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVI-GNNGIW 469 +G +G G G+A+ A + +QV+ ++GD AFGFSGME +T+ R+ + V ++I NNG++ Sbjct: 434 WGVMGIGMGFAIGAAVT-SGKQVLAIEGDSAFGFSGMELETICRYELPVCTIIFNNNGVY 492 Query: 470 -GLEKHPMEALYGYSVVAE--LRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGL 526 G + +P G VA RYD+++ A GG G V+ P EL A++ A ASG Sbjct: 493 RGTDVNPT----GGKDVAPTVFVKDARYDKMIEAFGGIGYNVTTPEELEKAVKEAIASGK 548 Query: 527 PAVVNVLTD 535 P ++N + D Sbjct: 549 PTLINAVID 557 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: 691 Number of extensions: 35 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: 579 Length adjustment: 36 Effective length of query: 511 Effective length of database: 543 Effective search space: 277473 Effective search space used: 277473 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.
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