Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_011882845.1 thiamine pyrophosphate protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000016205.1:WP_011882845.1 Length = 567 Score = 246 bits (628), Expect = 2e-69 Identities = 166/538 (30%), Positives = 264/538 (49%), Gaps = 20/538 (3%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD--GGVEHLLCRHEQGAAMAAIGYARA 60 GA+ +V AL A V VF PG + + V DAL D ++ ++CRHE AA A + Sbjct: 14 GARLLVDALLANHVERVFCVPGESFLAVLDALADDTARIQTVVCRHEAAAANMAEAVGKL 73 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLA 120 TG+ G+ T GPGAT+ G+ A DS P++ GQ + + +AFQE+D + Sbjct: 74 TGRPGIAFVTRGPGATHASIGVHTAFQDSTPMILFVGQCAREHLDREAFQEIDYRRMFGQ 133 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 K + +P ++ AF V SGRPGPV++ +P+D+ + +P + Sbjct: 134 MAKWVAQIDDPRRIPEYLSHAFHVTTSGRPGPVVLALPEDVLSEACAPQPAVPAAKRIAA 193 Query: 181 FPH-AEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239 P A++++ R+ LA+A++P + VGG A LR F+ ++P C + + Sbjct: 194 SPSAAQLDELRERLARAERPFVIVGGSGWTPDACANLRTFVERWQLPVACAFRFQDTFDN 253 Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTG---KLNTFAPHASVIHMDID 296 +P Y G +G+ A +++ DLL+ +G R + TG L+ + ++IH+ Sbjct: 254 AHPNYAGDVGLGINPALGRRIRDADLLLVLGPRLGEATTGGYTLLDIPKTYQTLIHVHQG 313 Query: 297 PAEMNKLRQAH---VALQGDLNALLPALQQPLNQYDWQQHCAQL-RDEHSWR--YDHPGD 350 E+ ++ VA ++ A L AL+ P Q W A R W PGD Sbjct: 314 ADELGRVYAPDLPIVAGMPEIAAPLAALEPP-QQRPWAGTVADAHRAYREWHAPLPMPGD 372 Query: 351 AIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIA--HTRPENFITSSGLGTMGFGLP 408 +++ QL +R P D ++T G + +W +H A H R + TS G MG+GLP Sbjct: 373 VQLGDVMV-QLRERLPHDAILTNGAGNYAIWLHRHFAYRHFRSQLAPTS---GAMGYGLP 428 Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468 AA+ A+ P VV ++GDG FMM EL T + L + +++++N G +R Q+ Sbjct: 429 AALAAKSLYPTRAVVALAGDGCFMMAGNELATAMQYGLNIVVIVVNNGHFGTIRMHQERN 488 Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526 + R T LT NPDF A AFG HG+ + + AL+ L P L+ + I + Sbjct: 489 YPGRVHGTGLT-NPDFAAYARAFGAHGETVAHTAEFAPALERALGCGLPALIEIRIPQ 545 Lambda K H 0.320 0.135 0.410 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: 789 Number of extensions: 45 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: 548 Length of database: 567 Length adjustment: 36 Effective length of query: 512 Effective length of database: 531 Effective search space: 271872 Effective search space used: 271872 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