Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010960298.1 MCA_RS04880 thiamine pyrophosphate enzyme family decarboxylase
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000008325.1:WP_010960298.1 Length = 549 Score = 157 bits (397), Expect = 1e-42 Identities = 177/560 (31%), Positives = 245/560 (43%), Gaps = 65/560 (11%) Query: 27 LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86 L+ L + GV IFG PG +L YD + ++G V+HI E AAD YAR G Sbjct: 13 LLACLYQAGVGHIFGVPGDYVLGFYDLM----AKGPVRHIGTTREDTAAFAADGYARCRG 68 Query: 87 KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITG------QVPRPAI----GTDAFQET 136 +G T G GA N V +A A +S P+VVI+G Q P I G FQ Sbjct: 69 -MGALAVTYGVGALNTVNAVAGAYAESSPVVVISGAPGVREQREDPLIHHRFGPFRFQRE 127 Query: 137 DIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196 IT V V+ DP V +A L AA PV I+IP D + Sbjct: 128 IFERITCAAV----VLDDPVIAFRQVERA-LAAARQHCKPVYIEIPADR--------VMA 174 Query: 197 PGSVIPGGFHQPEPP------LDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLA 250 PG IP PE P L AVA A +L+ +A P++ G D+L L Sbjct: 175 PGYPIPQ--ETPETPSSDDSALAEAVAEAAELLGRAVSPVILAGVELHRRGLQDALVGLV 232 Query: 251 ERYQLPVTTTLMGKGAFDENDALSVGML-GMHGTAYANFAVTECDLLIAVGARFDDRVTG 309 E+ +LPV TL GK F E +G+ G T A + V + DLL+ +G +D TG Sbjct: 233 EQARLPVAATLTGKSVFAERHPAYLGVYEGAMSTENARYMVEQSDLLLMLGVTLNDVDTG 292 Query: 310 KLDTFAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLE 369 R+V + I +R V +L D +LAR V+ + P A E Sbjct: 293 IYTARLDPQRIVRAAQNEVVIRHHRYPRV-LLADFVTALARSVKARGEAFPMP---AGPE 348 Query: 370 RINTWKDRYPLTIPPAEGAIYPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLRNGPRG- 428 + P+TI + V R L D IV DVG ++AA LR R Sbjct: 349 PWDFPAPDRPMTIA--------RLVERLDRALTSDMIVVCDVGDC-LFAATDLRVHERSE 399 Query: 429 WISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIV 488 +++SA +MGF +PAA+GAQ+A PD + + + GD + M EL T A GL VV++ Sbjct: 400 FLASAFYTSMGFAVPAALGAQIARPDHRALILVGDGAFQMTGTELSTHARLGLAPIVVVL 459 Query: 489 NNHWQGMVRQWQESFYDERYSASDMLNGMPD--FIALARSFG-VDGVKITDRELLHRDLA 545 +N + ER+ N + D F L FG + G D L+ Sbjct: 460 DN----------RGYSTERFILDGAFNDIADWRFHRLGEVFGPLQGYDAPDEAAFENALS 509 Query: 546 AALQSPT-PTMIDVHVRRGE 564 AL + P++I+V + G+ Sbjct: 510 EALVNRNMPSLINVRLSPGD 529 Lambda K H 0.320 0.136 0.414 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: 851 Number of extensions: 62 Number of successful extensions: 6 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: 617 Length of database: 549 Length adjustment: 36 Effective length of query: 581 Effective length of database: 513 Effective search space: 298053 Effective search space used: 298053 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