Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_043879696.1 AZC_RS21420 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000010525.1:WP_043879696.1 Length = 560 Score = 267 bits (683), Expect = 8e-76 Identities = 190/548 (34%), Positives = 274/548 (50%), Gaps = 28/548 (5%) Query: 18 PQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHA 77 P+ +G ++D L+ GV+ I PG + L + DALH A + ++ R+E Sbjct: 4 PKPRTGGQLIVDQLKAQGVERITCVPGESYLAVLDALHDAA----IDVLVCRNEGGAAMM 59 Query: 78 ADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETD 137 ADAY + TG+ G+CF T GPGATN G+ A DS P+++ GQV R +AFQE D Sbjct: 60 ADAYGKLTGRPGICFVTRGPGATNASHGLHIAAQDSTPLILFVGQVERGMREREAFQELD 119 Query: 138 IFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEP 197 G I K + + DPA + IVA+AF +A GRPGPV+I +P+D V +E Sbjct: 120 YRGAFGSIAKWAVEIDDPARIPEIVARAFRVAMQGRPGPVVIALPED--------VLIET 171 Query: 198 GSVIPGGFHQPEP--PLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQL 255 SV + P P A +A +L+E A+RPL+ +GG + A L +ERY L Sbjct: 172 ASVPDAPYVAPAESYPHPADMARFAELLEGAERPLMILGGSRWTDEAQAGLIAFSERYSL 231 Query: 256 PVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGK---LD 312 PV T+ F + G +G+ V E D+LI +GAR + + +D Sbjct: 232 PVATSFRRGHLFPSDHPNYAGDVGIGPNPKLAKRVKEADVLILLGARMSEMPSSSYTLID 291 Query: 313 TFAPRARVVHFEIDPAEIGKNRKADVAVLGD---LGLSLARMVEISLQRTAEPRTAAWLE 369 APR R+VH E+GK + ++A+ +LA + R A+ A + Sbjct: 292 IPAPRQRLVHIHPGAEELGKVYQPEIAIEASPAGFAKALADLSPGQTPRWAQDTATAHSD 351 Query: 370 RINTWKDRYPLTIPPAEGAIYPQEVLLAVRD-LAPDAIVTTDVGQHQMWAAQHLRNGPRG 428 + W + P T+P GA E +L +R+ L P+AIV G + W ++ R RG Sbjct: 352 YL-AWTET-PATLP---GAFQYGEAMLHLRNTLPPEAIVCNGAGNYATWLHRYYRLRKRG 406 Query: 429 WISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIV 488 + G+MG+G+PAA+ A+ PD VV AGD LMN QE T YG+P+ VV+V Sbjct: 407 TQLAPTSGSMGYGVPAAIMAKRHKPDVPVVAFAGDGCFLMNGQEFATAVQYGIPLIVVVV 466 Query: 489 NNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAAL 548 +N G +R QE Y R SA+ + N PDF A AR+FG G + E A A Sbjct: 467 DNGMYGTIRMHQEREYPGRISATKLKN--PDFAAYARAFGGHGETVERTEDFAPAFARAQ 524 Query: 549 QSPTPTMI 556 S P ++ Sbjct: 525 ASGLPAIL 532 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: 970 Number of extensions: 44 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: 617 Length of database: 560 Length adjustment: 37 Effective length of query: 580 Effective length of database: 523 Effective search space: 303340 Effective search space used: 303340 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