Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_035235448.1 Q366_RS00780 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000745975.1:WP_035235448.1 Length = 597 Score = 226 bits (575), Expect = 3e-63 Identities = 167/529 (31%), Positives = 256/529 (48%), Gaps = 34/529 (6%) Query: 27 LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86 +++ L GV +F G IL + DA A +K I V HEQA + AA AY + Sbjct: 8 MIERLYALGVKHLFLVTGRGILFLSDA---AARHKELKSICVHHEQAASFAAMAYTQCNE 64 Query: 87 KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQ-----------VPRPAIGTDAFQE 135 +G C ++G ATN +TG+ A D VP V ++GQ +P G QE Sbjct: 65 TIGACLVSTGCAATNALTGLLCAWQDDVPCVFVSGQNKLAQTTRFSGIPLRTFGQ---QE 121 Query: 136 TDIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPV 195 DI + PI K++ ++ DP +G + +AF +A SGR GPV ID+P D+ + P Sbjct: 122 ADIISLVSPITKYAVMITDPGKIGYEMDKAFFMAQSGRNGPVWIDVPLDI--QNMRVAPE 179 Query: 196 EPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISAC-AHDSLRMLAERYQ 254 + +P P + + A+D E AQRP+L +G G S+ A L E + Sbjct: 180 KLERFVPDTHVSCFNPQGSDIEYAIDCFENAQRPVLLIGSGVRSSSGALAQLEAFVEMFP 239 Query: 255 LPVTTTLMGKGAFDENDALSVGMLG-MHGTAYANFAVTECDLLIAVGARFDDRVTGK-LD 312 +PVT T + E + LS+G +G + GT N A+ DLLIA+G+R TG+ Sbjct: 240 VPVTFTASAADVYGEANKLSMGAVGSIGGTRAGNMALQNADLLIALGSRLSPITTGETYS 299 Query: 313 TFAPRARVVHFEIDPAEIGKNR-KADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERI 371 FA +A ++ +ID E KN K D ++ D G L + R P W+++ Sbjct: 300 KFARKALIIAVDIDNVEHSKNTVKIDRLIVSDAGCFLKALG----NRGIRPADPGWIDKC 355 Query: 372 NTWKDRYPLTIPPAEGAIYPQEVLLAV---RDLAPDAIVTTDVGQHQMWAAQHLRNG-PR 427 WK +P + + LA R L ++ TD G ++ + G + Sbjct: 356 LHWKQVFPKCEEKYKQSEKVDLHYLAACLSRLLPEKGVLITDAGLEELIIPSTVSFGKSQ 415 Query: 428 GWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVI 487 I A G MG+ +PAA+G A ++ + GD SI+MN+QEL T+ +PVK+++ Sbjct: 416 RCIHPASQGAMGYALPAAIGVYYA-HGTDIIAVIGDGSIMMNLQELQTIKYNKIPVKILV 474 Query: 488 VNNHWQGMVRQWQESFYDERYSASDMLNGM--PDFIALARSFGVDGVKI 534 VNN+ ++R Q+ + R +D NG+ PDF +AR F + +KI Sbjct: 475 VNNNVYSVIRTRQQELFRTRTIGTDPGNGVSCPDFENVARCFDIPYLKI 523 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: 835 Number of extensions: 59 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: 597 Length adjustment: 37 Effective length of query: 580 Effective length of database: 560 Effective search space: 324800 Effective search space used: 324800 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