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_015934192.1 MNOD_RS37675 thiamine pyrophosphate-binding protein
Query= curated2:P37251 (574 letters) >NCBI__GCF_000022085.1:WP_015934192.1 Length = 596 Score = 273 bits (698), Expect = 1e-77 Identities = 181/568 (31%), Positives = 276/568 (48%), Gaps = 35/568 (6%) Query: 18 MSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLY--NSGLVHILPRHEQGAIHAAEGYA 75 M G ++ E L K+KV +FG G + I D ++ + + PRHEQ A H A+ Y Sbjct: 4 MKGGEVIAEYLVKQKVPYVFGICGHGNVGILDAMHAVRDEVTLVSPRHEQCAGHMADAYF 63 Query: 76 RVSGKPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQE------A 129 R+ +P + ++GPG+ N+V LA A+ DS + T V TS FQE A Sbjct: 64 RIRHQPVATLTSTGPGSANMVMSLATALSDSSAFLAITANVPTSQANRAPFQELYAHNQA 123 Query: 130 DILGITMPVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDH 189 D + PV K S+Q + + LP +++AF TGRPGPV +DIP +V E E Sbjct: 124 DFAQVLRPVVKRSFQPSRVDMLPLALRQAFDTMVTGRPGPVNLDIPYNVFQEEAETEVPP 183 Query: 190 EMNLPG-YQPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPV 248 ++ G ++P + + +E +++A+KPV G G A E+ ++ IPV Sbjct: 184 LSHVHGAHRPAASE--ADVARALELLAAARKPVFFIGQGTTLADAGPEISALQQRLGIPV 241 Query: 249 AHTLLGLGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVT-----GNLK 303 + G+G PAD PL LG G +G Y AN A DL++ IG RFDDR + G Sbjct: 242 ITSPNGMGCVPADDPLTLGFIGRNGAYPANQAGRHADLVLCIGTRFDDRSSSTWHPGYSW 301 Query: 304 HFARNAKIAHIDIDPAEIGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSE-----WKKQ 358 +F K+ +DIDPAE+G+ + ++ D+K +L +SD S W+ + Sbjct: 302 NFP-TTKLIQVDIDPAELGRNYPPTLGIIADAKAFAGQLNDALVSRSDLSPETWATWRAE 360 Query: 359 LAEWKEEYPLWYVDNEEE---GFKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQ 415 +A W+ E+ + N +P+ ++ + + I++ D G H W QF+ + Sbjct: 361 IAGWQAEWDAFVRPNFSAITTPIRPEYVVGTLQAALPDDVILSLDSGVHHNWFMQFWRPR 420 Query: 416 KADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVK 475 + + S G +MGFG+ +GAQLA D VAVVGDGGF M + E NLP Sbjct: 421 RPRSMLNSWGYSSMGFGVCGVLGAQLAAPDRPCVAVVGDGGFMMAPYVVATAVEYNLPCV 480 Query: 476 VVILNNACLGMVRQWQEIFYEERYSESKFAS----------QPDFVKLSEAYGIKGIRIS 525 ++ NN G +R Q +E R + F PDF + A G G+ ++ Sbjct: 481 WIVWNNFAWGAIRDLQYGLFEGREHGTAFYKGNQGPGGERYNPDFAAWARACGADGVTVT 540 Query: 526 SEAEAKEKLEEALTSREPVVIDVRVASE 553 + +E A+ +R P VIDV V +E Sbjct: 541 RSQDLAGAVEAAVRNRRPCVIDVHVDAE 568 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: 808 Number of extensions: 43 Number of successful extensions: 7 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: 596 Length adjustment: 37 Effective length of query: 537 Effective length of database: 559 Effective search space: 300183 Effective search space used: 300183 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