Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012336155.1 M446_RS31550 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000019365.1:WP_012336155.1 Length = 561 Score = 246 bits (629), Expect = 1e-69 Identities = 175/524 (33%), Positives = 253/524 (48%), Gaps = 44/524 (8%) Query: 22 SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81 + A L+D L +GV +F PG + LP+ DAL + + R E A A+A+ Sbjct: 9 TAARVLVDQLVANGVRHVFTVPGESFLPVLDALR----DSGIAVTTCRQEGAAAMMAEAH 64 Query: 82 ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141 +ATG G+CF T GPGATN G+ AQ DS PM++ GQ+ R +AFQE D + Sbjct: 65 GKATGMPGICFVTRGPGATNASAGLHVAQQDSTPMILFVGQIERRFREREAFQELDYRAV 124 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSVI 201 P+ K + + DP + VA+AF A +GRPGPV++ +PKD+ E P+ P Sbjct: 125 FGPMAKWATEIDDPDRVPEFVARAFATATAGRPGPVVVALPKDMLSEA-TAAPLAP---- 179 Query: 202 PGGFHQPEPPLDAA-----VAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256 P P++AA VA DL+ A+RPLL +GG S A ++ AE + LP Sbjct: 180 ------PFRPVEAAPGEEDVARLADLVASAERPLLLLGGSRWSEGACAAIARFAEAFDLP 233 Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDD---RVTGKLDT 313 V T+ FD G LG+ DLL+ +G R + + LD Sbjct: 234 VATSYRRSPLFDALHPNYAGDLGLAPNPKLVARARAADLLVLLGGRLGEIPSQGYSLLDV 293 Query: 314 FAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERIN- 372 PR R+VH P E+G+ + +A+ S AR +L R P W E Sbjct: 294 PGPRTRLVHIHAGPEELGRVYQPFLAI----NASPAR-TAAALARLPAPARIPWREETRA 348 Query: 373 ------TWKDRYPLTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLR-N 424 W +R P G + EV++ +R++ P DA++ G + W + R Sbjct: 349 AHAEFLAWGER----ATPQPGGVNLGEVIIHLREVLPRDAVLCNGAGNYAAWIHRFYRFR 404 Query: 425 GPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVK 484 G I+ +MG+G+PAA+ + P R VV I GD LMN QE T Y LP+ Sbjct: 405 GLASHIAPTS-ASMGYGVPAAVAMKRLWPQRTVVSINGDGDFLMNGQEFATAVQYRLPLV 463 Query: 485 VVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFG 528 V++ +N G +R QE + +R A+D++N PDF A AR+FG Sbjct: 464 VIVADNASYGTIRMHQEREFPDRVVATDLVN--PDFAAYARAFG 505 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: 961 Number of extensions: 60 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: 561 Length adjustment: 37 Effective length of query: 580 Effective length of database: 524 Effective search space: 303920 Effective search space used: 303920 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 09 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