Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_028316775.1 G491_RS0127155 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000429905.1:WP_028316775.1 Length = 555 Score = 302 bits (773), Expect = 3e-86 Identities = 193/549 (35%), Positives = 285/549 (51%), Gaps = 23/549 (4%) Query: 9 QTMHAGRLIARRLKAS-GIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGW 67 Q ++ G L+AR LK + GIDTVF+LSGGH+ IYDG E G+RLID RHEQ AA AA W Sbjct: 2 QGIYGGHLVARHLKETEGIDTVFSLSGGHIDRIYDGFLEYGVRLIDVRHEQAAAMAAHAW 61 Query: 68 SKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPF 127 S + PG+ TAGPG TN ++ + A +PLV++ G W G+LQE++ Sbjct: 62 SIFSGKPGICIATAGPGFTNTLTGLVNAALENAPLVLISGATAVRDWQKGALQEMEQTAM 121 Query: 128 VAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDN----GRPG 183 V P ++AAT + + A++ AVS G F++ P D + +N G Sbjct: 122 VRPFVKWAATCHDVKRVPEYISAAIRHAVSGRPGPVFLELPPDVLNVSAQENEIVPAGSG 181 Query: 184 ALTELPAGPTPAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMN 243 A+ +GP PA A+ +AA +++ A++P+++AG+ + A L LVE+ IP + Sbjct: 182 AVV-YKSGPDPA--AVAKAAEMINQAKKPMLLAGSGIATDQAAELLTELVEKAGIPCGLT 238 Query: 244 GMARGVVPADHRLAF----SRARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQLIVAD 299 RG V + L+ + +AD+ + +G+ ++ L FG F +I AD Sbjct: 239 NNGRGAVSDLNPLSLWDGGQMGLMAGMPQADLVIALGIRFNWLLLFGEGFPQAC-VIRAD 297 Query: 300 RVEPAREHPRPVAAGLYGDLTATLSALAG-SGGTDHQGWIEELATAETMARDLEKAELVD 358 R GL GD+ TL AL D W+ EL + E+A Sbjct: 298 IDSSELSRNRACDVGLAGDMEMTLKALLPLVENKDRSQWLGELKESYLPLDAAEEAARTT 357 Query: 359 DRIPLHPMRVYAELAALLERDALVVIDAGD---FG--SYAGRMIDSYLPGCWLDSGPFGC 413 P+HP R+ ++ + DA+ ++D GD FG S+ L G GC Sbjct: 358 ASDPIHPARLAYQVRQAVGDDAIYIMDGGDTAYFGLTSFKATQRAHVLAA---SGGLLGC 414 Query: 414 LGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEK 473 LG+G +A+ AK A P ++VV+ GDG+FGF+ ME+DT RH++ ++ V+ N+ WG+ K Sbjct: 415 LGTGLPFAMGAKAALPHKKVVVFNGDGSFGFNAMEFDTFKRHDLPILCVVNNDQAWGMIK 474 Query: 474 HPMEALYGYSVVAELRPG-TRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNV 532 H E YG V G Y++V ALGG+GE V ++ PA++RA SG PA +N Sbjct: 475 HGQEICYGGERVIGSELGVVHYEQVAMALGGYGEFVDKDDQIIPAVQRALESGKPACINA 534 Query: 533 LTDPSVAYP 541 LTDP V P Sbjct: 535 LTDPCVTSP 543 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: 761 Number of extensions: 39 Number of successful extensions: 5 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: 555 Length adjustment: 36 Effective length of query: 511 Effective length of database: 519 Effective search space: 265209 Effective search space used: 265209 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