Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_050461056.1 AKL27_RS02420 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_001189915.1:WP_050461056.1 Length = 567 Score = 229 bits (584), Expect = 2e-64 Identities = 172/536 (32%), Positives = 259/536 (48%), Gaps = 29/536 (5%) Query: 22 SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81 +G LM LR HGV +F PG + LP DAL+ E + ++ I+ R E + A+AY Sbjct: 10 NGGQILMQQLRVHGVKRVFLVPGESYLPCIDALN--EHQDAMESIVCRQEGGAAYMAEAY 67 Query: 82 ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141 + TG+ G+CF T GPGATN G+ TA DS PM++ GQV +AFQE D + Sbjct: 68 GKLTGEPGICFVTRGPGATNASIGVHTAYQDSTPMILFVGQVGNDFYEREAFQEIDYRRM 127 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDV--GQEQFNYVPVEPGS 199 + K + + +A+AF +A SGRPGPV++ +P+D G Q +P + Sbjct: 128 FGQMTKWVAQIDRTERIPEFIARAFAVATSGRPGPVVLALPEDTLWGTAQVADMPRYRRA 187 Query: 200 VIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTT 259 Q P + A VA +LIE A+RP + VGG + A L+ AER+ LPV Sbjct: 188 -------QSNPGV-ADVAQMRELIEAAERPFMIVGGHGWTQQASARLQAFAERFDLPVGV 239 Query: 260 TLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFA---P 316 FD+ G +G + V DL+++V R + T A P Sbjct: 240 AWRRLECFDQRHPNFAGHVGWGMSPELRARVANADLILSVCTRLGEATTEGYSVIASPLP 299 Query: 317 RARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKD 376 + +++H DP E+G+ A++ D ++ + LQ T R +A NT Sbjct: 300 QQKLIHVYPDPEELGRVFMPTQAIVADPAGFAEQVAD--LQPTRAIRWSAATRSANT--- 354 Query: 377 RYPLTIPP--AEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLRNGPRGWISSA 433 Y T+ P A GA+ + + P DA +T G + ++ ++ + G + Sbjct: 355 EYLSTLQPLDAPGAMNLNAAAAHLNTVLPADACITVGAGNYALYPHRYRQFSGVGSSLAP 414 Query: 434 GLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQ 493 LG MG+G+PAA+ A++ DR VVC AGD MN+QELG Y L + V++ NN Sbjct: 415 ALGAMGYGLPAAISAKLEKRDRTVVCYAGDGCFQMNLQELGVAMQYRLGIIVLVFNNGMW 474 Query: 494 GMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQ 549 G +R QE + R A + N P+F + R++ G +I D+ D AAA + Sbjct: 475 GTIRAHQERDFPARAIALNFDN--PEFTEIVRAYRGYG-EIVDKT---EDFAAAFE 524 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: 873 Number of extensions: 49 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: 567 Length adjustment: 37 Effective length of query: 580 Effective length of database: 530 Effective search space: 307400 Effective search space used: 307400 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