Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate RR42_RS29140 RR42_RS29140 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >FitnessBrowser__Cup4G11:RR42_RS29140 Length = 558 Score = 259 bits (663), Expect = 2e-73 Identities = 181/551 (32%), Positives = 264/551 (47%), Gaps = 27/551 (4%) Query: 18 PQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHA 77 P SG L+DALR HG IF PG + L + DALH + + I+ +HE A + Sbjct: 10 PAARSGGRVLVDALRIHGAQRIFCVPGESFLDVLDALH---DQPAIDLIVCKHEGAAANM 66 Query: 78 ADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETD 137 A+A + TG+ G+CF T GPGAT+ G+ A DS PM++ GQ+ R G +AFQE D Sbjct: 67 AEADGKLTGRPGICFVTRGPGATHASIGVHIAAQDSTPMLLFVGQIARGHKGREAFQEVD 126 Query: 138 IFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEP 197 + I K + DPA + +VA+AF A SGRPGPV+I +P+DV + Sbjct: 127 YGAMFGSIAKWVVEIEDPARIPELVARAFQCATSGRPGPVVISLPEDVLDGLCEV--ADT 184 Query: 198 GSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPV 257 G P DA AA + A+RPL+ GG SA A +R+ LPV Sbjct: 185 GRYRPVAAAPRAADADALAAA----LAGAERPLVIAGGANWSAQAAADFAAFVQRWNLPV 240 Query: 258 TTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTG---KLDTF 314 + FD D VG L + V D+++A G R D T L+ Sbjct: 241 ACAFRRQDVFDNRDPHYVGHLSLGVNPALAERVRTADVILAFGTRLGDIATDGYTLLEAP 300 Query: 315 APRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTW 374 PR R+ H D AE+G+ + ++A+ + A + ++ P W + + Sbjct: 301 QPRQRLFHLHADSAELGRVYQPELAIHAGIEPGAAMLAALT-----PPAAVRWGDWTSAA 355 Query: 375 KDRYPLTIPPAE------GAIYPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLR-NGPR 427 + + + PA+ G V R L DA++T G + +W ++ PR Sbjct: 356 RAAHGAFVAPAKPHPQLTGVDMGAVVAHLDRILPDDAVLTNGAGNYTVWLHRYYAYRQPR 415 Query: 428 GWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVI 487 ++ G MG+G+PAA+ A++ P R VVC AGD LM QEL T A YG + VV+ Sbjct: 416 TELAPT-CGAMGYGLPAAVAAKLRDPQRTVVCFAGDGCFLMYPQELATAAQYGANLIVVV 474 Query: 488 VNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAA 547 VNN G +R QE Y R S +D+ + PDF+A+ARS G ++T E A A Sbjct: 475 VNNGMYGTIRMHQEKRYPGRVSGTDIPS--PDFVAMARSCGAWAERVTQTEDFAAAFARA 532 Query: 548 LQSPTPTMIDV 558 + P ++++ Sbjct: 533 QAAGKPAVLEL 543 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: 1013 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: 558 Length adjustment: 37 Effective length of query: 580 Effective length of database: 521 Effective search space: 302180 Effective search space used: 302180 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