Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012114786.1 XAUT_RS14070 thiamine pyrophosphate-binding domain-containing protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000017645.1:WP_012114786.1 Length = 572 Score = 259 bits (663), Expect = 2e-73 Identities = 179/547 (32%), Positives = 268/547 (48%), Gaps = 21/547 (3%) Query: 22 SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81 SG L+DAL+ HGVDT++ PG + LP DAL A + G ++ I+ RHE A + A+AY Sbjct: 9 SGGEILVDALKIHGVDTVYCLPGESFLPAIDAL--AGATGRIRTIVTRHEAAAANMAEAY 66 Query: 82 ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141 + TG+ G+CF T GPGA++ GI TA DS P+++ GQV G +A+QE D + Sbjct: 67 GKLTGRPGICFVTRGPGASHAAIGIHTAAQDSTPLILFIGQVDTAIRGREAWQEVDYPAM 126 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVI 201 + K V P L +V++AF +A SGRPGPV++ +P+DV + I Sbjct: 127 FGGMAKWVVEVDRPERLPELVSRAFHVAVSGRPGPVVVALPEDVLGASAQVADAQAYKRI 186 Query: 202 PGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTL 261 H L+ A ++E ++RPL+ VGGG SA A + E + LPV Sbjct: 187 AA--HPGADDLNRLTA----MLEASERPLVIVGGGGWSARACRDFQHFVEDFDLPVAAAF 240 Query: 262 MGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTF---APRA 318 + D + VG G+ + DL++A+G R + T F P Sbjct: 241 RRQDILDNHHPNYVGHAGLGPNPKLVARIRAADLIVAIGPRLGETTTAGYTLFELPRPAQ 300 Query: 319 RVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKDRY 378 R VH DP E+G+ +AD+ + + A + R A A W + + Y Sbjct: 301 RFVHVHADPLELGRVYQADLPINAGMPEFAAAAAALK-PRGAAGWHAPWSAAVKAARADY 359 Query: 379 PLTIPPA--EGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLRNGPRGWISSAGL 435 P G + V++ +R+ P DAI+T G + +W + R G + Sbjct: 360 LADQTPGAMPGRLDLGAVMVHLRESLPRDAILTNGAGNYAIWVHRFHRYGGFRTQLAPTS 419 Query: 436 GTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGM 495 G MG+G+PAA+ A++ P R V+C AGD M+ QEL T YG V V++VNN G Sbjct: 420 GAMGYGLPAAIAAKLHQPARDVICFAGDGCFQMSGQELATGCQYGAGVVVLLVNNGIYGS 479 Query: 496 VRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITD----RELLHRDLAAALQSP 551 +R QE Y R A+ + N PDF ALAR++G G ++ + E +R A A Sbjct: 480 IRMHQEREYPGRVFATTLEN--PDFPALARAYGAFGERVEETAAFAEAFNRARAFAADRN 537 Query: 552 TPTMIDV 558 P ++++ Sbjct: 538 KPALLEL 544 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: 1008 Number of extensions: 53 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: 572 Length adjustment: 37 Effective length of query: 580 Effective length of database: 535 Effective search space: 310300 Effective search space used: 310300 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