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_029328972.1 ON01_RS03645 acetolactate synthase
Query= curated2:P37251 (574 letters) >NCBI__GCF_000224785.1:WP_029328972.1 Length = 545 Score = 298 bits (764), Expect = 3e-85 Identities = 180/538 (33%), Positives = 281/538 (52%), Gaps = 10/538 (1%) Query: 18 MSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILP-RHEQGAIHAAEGYAR 76 M+ A ++E +K E + F PG + LP+ D LY+ + ++ RHE GA A+GYA+ Sbjct: 1 MTAAQAIVECMKTEGISDAFCVPGESYLPLMDALYDESSIRLISARHESGAAFMADGYAK 60 Query: 77 VSGKPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITM 136 S KPGVV+AT G GA+NL G+ A DS P++VF GQV + G + FQE D+ Sbjct: 61 SSLKPGVVMATRGVGASNLSIGVHTAYQDSTPMIVFLGQVHSKFRGREGFQEIDLEQYFR 120 Query: 137 PVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGY 196 K + +V+ PE + I++ AF IA TGRPGPV++ +P+DV E E ++ P Sbjct: 121 HTAKWAVEVKAPERVAEIVQRAFRIAQTGRPGPVVVSLPEDVLPAEAEMTF----GPPAV 176 Query: 197 QPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLG 256 +P P +I+ + E +++++KP+I+AG GV +A + L ++AE+ +PV Sbjct: 177 KPKPVPAQEEIKLVEELLATSEKPLIIAGGGVKTSEAEDALVSFAEKYSLPVIAAFRRQD 236 Query: 257 GFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFARNAKIAHIDI 316 FP +H L+ G G+ + E +++IG R + T + + A K+ HIDI Sbjct: 237 VFPNNHRLYAGHLGLGTNANILQTVKEAGTILAIGTRLSEVTTQDYQILAPEKKLIHIDI 296 Query: 317 DPAEIGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVDNEEE 376 IGK+ I +V D+K L+ L + + K + S W EE V +++ Sbjct: 297 SYDVIGKVYSPDIGIVADAKKALKALERMEIKSTWKS-WVNSRRRAFEEISSLGVSHKDA 355 Query: 377 GFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPAA 436 K ++ + A+V D G W FYPF+ +V G MG+GLP A Sbjct: 356 INK--HIVSVMAGMLPDNALVTNDAGNFAGWLHAFYPFKGKHTYVGPTS-GAMGYGLPGA 412 Query: 437 IGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFYE 496 +GA+LA D V+A+ GDGGF MT+QEL+ +PV ++ NN G +R QE+ Y Sbjct: 413 LGAKLALPDKPVIALAGDGGFMMTMQELETAVRYKIPVISLVFNNDMYGTIRMHQEMHYP 472 Query: 497 ERYSESKFASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVASEE 554 E+ + + F L+E+ G +G + S E E + AL + P VI++ E+ Sbjct: 473 EKVIGTDL-GRISFKNLAESVGAEGYLVKSADEFSEAFDAALQNNVPAVIEIMTEKEQ 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: 809 Number of extensions: 45 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: 545 Length adjustment: 36 Effective length of query: 538 Effective length of database: 509 Effective search space: 273842 Effective search space used: 273842 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