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_024850572.1 N745_RS0102550 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000526715.1:WP_024850572.1 Length = 592 Score = 228 bits (581), Expect = 5e-64 Identities = 167/559 (29%), Positives = 269/559 (48%), Gaps = 28/559 (5%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARA 60 M + +V +G VF GG M + D+L + + HEQ A+AA GY R Sbjct: 1 MRLSDYVADFFVKKGCEHVFMVTGGGAMHLNDSLGKSDLTCVFNHHEQACAIAAEGYYRV 60 Query: 61 TGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSA-------PFIGTDAF--QE 111 + K + TSGPG TN ITG+ A +DS ++ I+GQV P + QE Sbjct: 61 SNKVPLVNVTSGPGGTNAITGVYGAWVDSASMIVISGQVKRETMVGYYPDLNLRQLGDQE 120 Query: 112 VDVLGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEP- 170 +D++ L + TK++ V ++ ++ +A+ +GRPGPV +DIP DIQ A D E Sbjct: 121 LDIIPLVDSITKYAVTVWDKNQIRYVLEKAWFEVTNGRPGPVWIDIPLDIQGAQIDPETL 180 Query: 171 -WFTTVENE-VTFPHAEVEQARQMLAK---AQKPMLYVGGGVGMAQAVPALREFLAATKM 225 F V+++ V QA+++ +K +++P+LY+G GV ++ + F + Sbjct: 181 VGFEVVQHKNAQTKQRLVTQAKEVFSKIKNSKRPLLYLGTGVHISGQKENVLNFSRKHNI 240 Query: 226 PATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDR-VTGKLNTF 284 P V +P Y+G G G +A NFAVQ D L+ +G+R + R ++ F Sbjct: 241 PVVTAWNNNDLVPDSHPCYVGRPGTVGDRAGNFAVQASDCLVVLGSRLNIRQISYNWENF 300 Query: 285 APHASVIHMDIDPAEMNK-LRQAHVALQGDLN---ALLPALQQPLNQYDWQQHCAQLRDE 340 AP+A VI +DID E+ K + DL A LP +QP+ +W C + RD+ Sbjct: 301 APNAHVIMVDIDSNELFKPTLNVDFPINADLKNFMACLPGGEQPIGNEEWLNWCIERRDK 360 Query: 341 HSWRYD----HPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFIT 396 + + +A+ + +LS D + T G + + Q + + T Sbjct: 361 YKMANEEHLPEKSNAVNPYRFMHELSKYLSEDQITITGDGTACVASFQAMQVKENQRLFT 420 Query: 397 SSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQ 456 +SG +MG+ +PA++GA A N TV C++GDGS MMN+QEL T+ ++P+KI +L+N Sbjct: 421 NSGCASMGYDVPASIGAYYA-SNRTVNCLAGDGSIMMNIQELATIAGNKIPIKIFVLNNN 479 Query: 457 RLGMVRQWQQLFF---QERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLN 513 +RQ Q +F + + PDF +A + + + VE + Sbjct: 480 GYHSIRQTQNNYFPSGKMGFQPDNGVKLPDFEKIAYGYSLPYFAVKELGAVEQVYKEIQR 539 Query: 514 SDGPYLLHVSIDELENVWP 532 +GP L V +D + P Sbjct: 540 CEGPVLCEVFLDVEQEFMP 558 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: 762 Number of extensions: 44 Number of successful extensions: 8 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: 592 Length adjustment: 36 Effective length of query: 512 Effective length of database: 556 Effective search space: 284672 Effective search space used: 284672 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