Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_171817373.1 SUTH_RS13830 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000828635.1:WP_171817373.1 Length = 602 Score = 273 bits (699), Expect = 1e-77 Identities = 201/577 (34%), Positives = 293/577 (50%), Gaps = 31/577 (5%) Query: 27 LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86 LM L G+D +F PGG + + D L E + I HEQA AA+A+ R G Sbjct: 7 LMSHLAGLGIDHVFVLPGGGAMHLNDGL---ACEPRITAIPCHHEQACGIAAEAWGRVAG 63 Query: 87 KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTD------AFQETDIFG 140 K GV T+GPGATN+VT + A ++SVPM+VI+GQV RP + D QE DI Sbjct: 64 KFGVAMVTTGPGATNVVTPVTGAWIESVPMLVISGQVKRPDLLRDRPLRQGGVQEVDIVP 123 Query: 141 ITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVEPGSV 200 I I K++ V+DPA + + +A GR GPV +DIP DV Q VP E Sbjct: 124 IVRSITKYAVTVQDPATIRYHLERALHQMQDGRAGPVWLDIPLDVQAAQI--VPAELTGY 181 Query: 201 IPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTT 260 IP + +P LD + L+LI A+RPL+ G G A A LAE+ +PV TT Sbjct: 182 IPEA--EVQPGLDEPIQQTLELIAAAERPLILAGHGVRLAGAAKRFLALAEKLDIPVVTT 239 Query: 261 LMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDT-FAPRAR 319 L VG G+ ANFAV CDLLI++G R D+ +T FA AR Sbjct: 240 WNALDLIPWAHPLCVGRPGVVALRAANFAVQNCDLLISIGCRLDNIITAYNPRGFARTAR 299 Query: 320 VVHFEIDPAEIGK-NRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKDRY 378 + ++DP EI K + D+ + D G S + ++ P AW +R + WK RY Sbjct: 300 KIVVDVDPEEIAKLDMDIDLRLPVDAG-SFIDALAAHTGSSSLPDRPAWRQRCSDWKRRY 358 Query: 379 PLTIPP---AEGAIYPQEVLLAVRDLAP-DAIVTTD---VGQHQMWAAQHLRNGPRGWIS 431 + +G I + A+ D AP + +V+T +G + + G R +++ Sbjct: 359 AVGEGKPFHTDGPISHYHFVSALSDAAPPETLVSTGSSGLGVEAFYTVFRNKPGQRVFLT 418 Query: 432 SAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNH 491 S GLG MG+G+PAA+GA +A R + I D S+ +N+QEL T+ A LP+ +VI++N Sbjct: 419 S-GLGAMGYGLPAAIGACLAGNRRPAIAIESDGSLQLNLQELATVKAQKLPICLVIMDNG 477 Query: 492 WQGMVRQWQESFYDERYSASDMLNG--MPDFIALARSFGVDGVKITDRELLHRDLAAALQ 549 +R Q +++ ERY D +G +PD +A ++G+ ++I D + L AL Sbjct: 478 GYCSIRNTQRNYFQERYLGIDPASGLWLPDLEKIAAAYGLPFLRIDDPGNIDAALKEALA 537 Query: 550 SPTPTMIDVHVRRGENCYP---MVPPGKSNAQMVGLP 583 P P +IDV + + E P VP + + M+ +P Sbjct: 538 LPRPCLIDVRLMKDETLAPKSAAVP--QPDGSMISMP 572 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: 981 Number of extensions: 53 Number of successful extensions: 9 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: 602 Length adjustment: 37 Effective length of query: 580 Effective length of database: 565 Effective search space: 327700 Effective search space used: 327700 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