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_012755690.1 RLEG_RS26715 acetolactate synthase large subunit
Query= curated2:P37251 (574 letters) >NCBI__GCF_000023185.1:WP_012755690.1 Length = 548 Score = 259 bits (663), Expect = 1e-73 Identities = 165/542 (30%), Positives = 278/542 (51%), Gaps = 23/542 (4%) Query: 20 GALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILPRHEQGAIHAAEGYARVSG 79 G+ +L+ +L+ E V+ IFG PG L + + + S + +L RHEQ A A Y R++G Sbjct: 4 GSDLLVAALENEGVDRIFGIPGEENLDVVESIRKSSIELVLTRHEQAAAFMAATYGRLTG 63 Query: 80 KPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITMPVT 139 KPGV + T GPGA NL TG A A++ ++P+V+ TGQ FQ D++ P+T Sbjct: 64 KPGVCLTTLGPGALNLSTGAAYALLGAMPMVMITGQKGILSSRQARFQVVDVVASMKPLT 123 Query: 140 KHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGE---FSYDHEMNLPGY 196 K + Q+ P+ +P ++EAF IA RPGPV +++P+D+A E + H++ LP Sbjct: 124 KLARQIVSPQMIPTTVREAFRIAQEERPGPVHLELPEDIAAEECQEVALIAPHQLELPTA 183 Query: 197 QPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLG 256 + + +++AK+P+++ GA +++ ++ + + +IP T +G G Sbjct: 184 SDAA------LDRAAALIAAAKRPLLMFGAAASRPRSTSDIAQFVIRTRIPFFTTQMGKG 237 Query: 257 GFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDR---VTGNLKHFARNAKIAH 313 P L++G A + + A+ + DL+I+IG ++ + G K+ H Sbjct: 238 TVPGGTELYMGTAALSERDYVHEAIEQADLIITIGHDTIEKPPFIMGK-----SGPKVVH 292 Query: 314 IDIDPAEIGKIMKTQIPVVGDSKIVLQELI-KQDGKQSDSSEWKKQLAEWKEEYPLWYVD 372 I PA + ++ Q V+GD L+ L + +GK ++ E Sbjct: 293 IGYQPATVEQVYFPQSEVIGDIGPSLKALADRLEGKLPNAQALLHLRERILERIA---TR 349 Query: 373 NEEEGFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFG 432 E+ F PQ+L+ I + + I+A D G +++W A+ Y + A+ + L TMG G Sbjct: 350 ATEDRFTPQRLVHDIREVMPHDGILALDNGMYKIWFARNYRTRMANTLLLDNALATMGAG 409 Query: 433 LPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQE 492 LP+A+ A + + V+A+ GDGGF M QEL+ L L + V+++ + GM+R W++ Sbjct: 410 LPSAMVASMLYPERRVMAICGDGGFMMNSQELETAVRLKLNLVVLVIEDNAYGMIR-WKQ 468 Query: 493 IFYEERYSESKFASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVAS 552 E F + PDFVK +E+YG KG R+ + K+ LEEA +++V V Sbjct: 469 AVDEFPDFGMTFGN-PDFVKYAESYGAKGTRVDDIGQFKQVLEEAFAGGGVHLVNVPVDY 527 Query: 553 EE 554 E Sbjct: 528 SE 529 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: 684 Number of extensions: 34 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 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