Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_013420232.1 RVAN_RS13305 acetolactate synthase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000166055.1:WP_013420232.1 Length = 603 Score = 321 bits (823), Expect = 4e-92 Identities = 204/562 (36%), Positives = 285/562 (50%), Gaps = 39/562 (6%) Query: 12 HAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVT 71 HAG +IA LKA G+ +FTL GGH+ I G ++ GIR++DTRHE TAAFAA+ ++++ Sbjct: 32 HAGDVIAASLKAQGVTAIFTLCGGHISPILIGAKDAGIRIVDTRHEATAAFAADAMARLS 91 Query: 72 RVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPFVAPV 131 VPGVAA+TAGPG+TN ++ + AQ QSPL++ GG AP + G G+LQ+ID P VAP Sbjct: 92 GVPGVAAVTAGPGLTNIVTPLKNAQLAQSPLILFGGAAPTMLQGRGALQDIDQRPVVAPH 151 Query: 132 ARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFS-------MSSDNGRPGA 184 + + + G ++ A A G AF++ P+D + + GR + Sbjct: 152 VKIVKQVRRVRDIGPALEDAFAVAREGVQGPAFIECPIDLLYPEALVRQWYAEAGGRGQS 211 Query: 185 L-------------------TELPAGP--------TPAGDALDRAAGLLSTAQRPVIMAG 217 L T+ PA P TPA +++ AA LS A+RP+ + G Sbjct: 212 LGARALRFYLHRHLEKMFGGTKAPATPRPRKIRIPTPASSSVNAAAAALSKAERPLAIIG 271 Query: 218 TNVW-WGHAEAALLRLVEERHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVG 276 + G AAL + IPV ++GMARG++ DH L R AL E+D ++ G Sbjct: 272 SQALATGTDAAALAEAITRLGIPVYLSGMARGLLGRDHPLQLRHQRRNALKESDCVILAG 331 Query: 277 VPMDFRLGFGGVFGSTTQLIVADRVEPAREHPRPVAAGLYGDLTATLSALAGSGGTDHQG 336 VP DFRL +G +T LI A+R R GD L ALA G Sbjct: 332 VPCDFRLDYGKQIRNTATLIAANRSRKDARLNRRATIEAIGDAALFLRALAERGRIHRDD 391 Query: 337 WIEELATAETMARDLEKAELVDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRM 396 W+ L + A+ + ++P+ + L +A+ V D GDF + A + Sbjct: 392 WLASLRARDAARETDIDAQAATEGAHVNPVAFFRALDREAGENAIFVADGGDFVATASYI 451 Query: 397 IDSYLPGCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHN 456 + P WLD G FG LG G G+AL A LARP ++ +L GDGA G+S E+DT VRH Sbjct: 452 VRPRRPLSWLDPGAFGTLGVGAGFALGAALARPDAEIWVLFGDGACGYSLAEFDTFVRHG 511 Query: 457 VAVVSVIGNNGIWGLEKHPMEALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRP 516 + V++V+GN+ W E + G V L T Y EV G G LV AE+ Sbjct: 512 IPVIAVVGNDAGWTQIAREQEKVLGDDVGTVL-ARTAYHEVAAGFGAEGILVKTNAEVPE 570 Query: 517 ALERAFA---SGLPAVVNVLTD 535 AL RA A +G P +VNV D Sbjct: 571 ALRRARAAAKAGRPVLVNVWLD 592 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: 841 Number of extensions: 34 Number of successful extensions: 4 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: 603 Length adjustment: 36 Effective length of query: 511 Effective length of database: 567 Effective search space: 289737 Effective search space used: 289737 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