Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_106717515.1 CU100_RS15595 acetolactate synthase large subunit
Query= curated2:P37251 (574 letters) >NCBI__GCF_003010935.1:WP_106717515.1 Length = 548 Score = 254 bits (648), Expect = 8e-72 Identities = 159/523 (30%), Positives = 272/523 (52%), Gaps = 19/523 (3%) Query: 20 GALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILPRHEQGAIHAAEGYARVSG 79 G+ +L+ +L+ E + IFG PG L + + + NS + IL RHEQ A A Y R++G Sbjct: 4 GSDLLVAALENEGTDRIFGIPGEENLDVVESIRNSSIQLILTRHEQAAAFMAATYGRLTG 63 Query: 80 KPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITMPVT 139 KPGV + T GPGA NL TG A A++ ++P+++ TGQ FQ D++ P+T Sbjct: 64 KPGVCLTTLGPGALNLSTGAAYALLGAMPMIMITGQKGILSSRQARFQIVDVVASMKPLT 123 Query: 140 KHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPT 199 K S Q+ P +P +++EAF +A RPGPV +++P+D+A E E + + P Sbjct: 124 KLSRQIVSPLMIPTMVREAFRVAQEERPGPVHLELPEDIAAEECE---NVALIAPHPVDL 180 Query: 200 TEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLGGFP 259 + + + E + A++P+++ GA +++ +L + + +IP T +G G P Sbjct: 181 ATASDQALDRAAEIILRARRPLLMLGAAASRPRSTSDLAQFVLRTRIPFFTTQMGKGTVP 240 Query: 260 ADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFARNAKIAHIDIDPA 319 L++G A + + A+ + DL+I+IG D K+ H+ PA Sbjct: 241 GGTELYMGTAALSERDYVHEAIEQADLIITIG--HDTIEKPPFLMGEGGPKVVHVGYQPA 298 Query: 320 EIGKIMKTQIPVVGDSKIVLQELIKQ-DGKQSDSS---EWKKQLAEWKEEYPLWYVDNEE 375 + ++ Q VVGD L+ L + +GK +++ +K++ E E Sbjct: 299 SVEQVYFPQCEVVGDIGPSLKALADRIEGKLTNADALLHLRKRILE------RIGARATE 352 Query: 376 EGFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPA 435 + F PQ+L+ + + + I+A D G +++W A+ Y + A+ + L TMG GLP+ Sbjct: 353 DRFTPQRLVRAVREVMPHDGILALDNGMYKIWFARNYRTEMANTLLLDNALATMGAGLPS 412 Query: 436 AIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFY 495 A+ A + V+A+ GDGGF M QEL+ L L + V+++ + GM+R Q + Sbjct: 413 AMTAAMLYPGRRVMAICGDGGFMMNSQELETAVRLKLNLVVLVIEDKAYGMIRWKQAV-- 470 Query: 496 EERYSESKFA-SQPDFVKLSEAYGIKGIRISSEAEAKEKLEEA 537 +R+ + + PDFVK +++Y KG R+S + K+ LE+A Sbjct: 471 -DRFPDFGMTFNNPDFVKYAQSYAAKGTRVSDIGDFKDVLEKA 512 Lambda K H 0.317 0.135 0.391 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: 664 Number of extensions: 32 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: 574 Length of database: 548 Length adjustment: 36 Effective length of query: 538 Effective length of database: 512 Effective search space: 275456 Effective search space used: 275456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 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