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.
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