Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SMc04455 SMc04455 thiamine pyrophosphate protein
Query= curated2:Q7U5G1 (617 letters) >FitnessBrowser__Smeli:SMc04455 Length = 548 Score = 258 bits (658), Expect = 6e-73 Identities = 179/553 (32%), Positives = 272/553 (49%), Gaps = 42/553 (7%) Query: 22 SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81 +G +++AL +GV I PG + L + DAL+ A+ ++ ++ R E ADA+ Sbjct: 3 TGGQLVVEALAANGVKRISCVPGESYLAVLDALYDAD----IEVVVCRQEGGAAMMADAW 58 Query: 82 ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141 R TG+ G+C T GPGATN G+ A+ DSVPM++ GQV R A +AFQE + Sbjct: 59 GRLTGEPGICMVTRGPGATNASAGLHVARQDSVPMILFIGQVQREAREREAFQEIEYRRA 118 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFN------YVPV 195 + K + DPA + V +AF +A SGRPGPV++ +P+D+ + Y PV Sbjct: 119 FTEVAKWVGEIDDPARIPEFVTRAFAVATSGRPGPVVLTLPEDMLTQSTEAPAARAYQPV 178 Query: 196 EPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQL 255 E P + +A +L+ A+RP+ +GG SA + + AER+QL Sbjct: 179 E------------SHPGPSQIAKLAELLSTAKRPIAILGGTRWSAESVAGFQSFAERWQL 226 Query: 256 PVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTG---KLD 312 PV + + FD G +G+ + E DL++ VG RF + + +D Sbjct: 227 PVGCSFRRQMLFDHLHPNYAGDVGIGINPSLAGEIREADLVLLVGGRFSEMPSSGYTLID 286 Query: 313 TFAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERIN 372 PR +VH DP E+G+ + D+A+ +A + +L +AEP W R Sbjct: 287 VPYPRQTLVHVHPDPGELGRVYRPDLAIAASPRDFVAAL--SNLTPSAEPH---WSARTG 341 Query: 373 TWKDRY-PLTIPPAEGAIYPQEVLLA------VRDLAPDAIVTTDVGQHQMWAAQHLRNG 425 Y + PP +G P +V + + P+ I T G + W + R Sbjct: 342 EMHAAYLKWSTPPEKG---PGDVQMGPIVNWLEANTGPETIFTNGAGNYATWLHRFHRFR 398 Query: 426 PRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKV 485 G ++ G+MG+G+PAA+ A+ PDR+VVC AGD LM+ QE T Y LP+ V Sbjct: 399 RYGTQAAPASGSMGYGLPAAVAAKHLHPDREVVCFAGDGCFLMHGQEFATAVRYELPIIV 458 Query: 486 VIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLA 545 ++VNN G +R QE Y R SA+D+ N PDF ALAR++G G + E Sbjct: 459 LVVNNGIYGTIRMHQEREYPGRVSATDLTN--PDFAALARAYGGHGETVARTEEFAGAFL 516 Query: 546 AALQSPTPTMIDV 558 A +S P +I++ Sbjct: 517 RARESGKPAIIEI 529 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: 934 Number of extensions: 54 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: 548 Length adjustment: 36 Effective length of query: 581 Effective length of database: 512 Effective search space: 297472 Effective search space used: 297472 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