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_072904866.1 BUB13_RS00910 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_900142125.1:WP_072904866.1 Length = 591 Score = 219 bits (559), Expect = 2e-61 Identities = 173/582 (29%), Positives = 284/582 (48%), Gaps = 49/582 (8%) Query: 4 AQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD----GGVEHLLCRHEQGAAMAAIGYAR 59 A +V L GV +FG PGG+I P+Y+A+ GG+ ++ RHE GAA A GYAR Sbjct: 19 ADLIVEQLEKLGVEYIFGVPGGSIEPLYNAMARSQRAGGLRPVVARHEAGAAFMADGYAR 78 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQE-----VDV 114 TGK GVC +T+GPGATNL+TG+A A ++ +PV+AIT Q G QE VD Sbjct: 79 ETGKLGVCCSTTGPGATNLLTGVASAHIEQVPVLAITAQTVLHSFGRQTLQESTCSAVDT 138 Query: 115 LGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPW--- 171 + + ACT++S LV +L +A A GP + IP DI S + + Sbjct: 139 VAIFKACTRYSSLVSHRGQLENKLAAAIAATQGAPAGPAHLSIPMDIMADSRRMNSYQPM 198 Query: 172 ----FTTVENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPA 227 F + VT A E + + +A++ +L +G G G A+ + F ++P Sbjct: 199 ASLDFLLKKPAVTDAAAVAELVLE-IQQAKRMVLLLGDGCG--SAIDEIIRFAERLQVPI 255 Query: 228 TCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQE--CDLLIAVGARFDDRVTGKLNTFA 285 G + +P Y G+LG G K+A+ +++ DL++AVG RF + + L Sbjct: 256 ITGPSGKRWISQRHPLYHGVLGFAGHKSASDRLKDERNDLVLAVGTRFSEMMYPNLEKDK 315 Query: 286 -PHASVIHMDIDPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQ-----HCAQLRD 339 ++ ++H+D A + + G L + L L + +Q H A + Sbjct: 316 WLNSKLVHIDDVLENFCHSPMARLHVCGALPLIFSTLLNSLPDRERKQPVAVNHTAPTGE 375 Query: 340 -EHSWRYDHP------GDAIYA---PL----LLKQLSDRKPADCVVTTDVGQHQMWAAQH 385 + + Y P D+ Y+ PL ++++LS R P D V D G WA + Sbjct: 376 GDKTIIYTAPRVRLDDEDSCYSSAVPLKPQRVMRELSLRLPEDARVFVDAGNSWAWATHY 435 Query: 386 IAHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQ 445 + + + + G G+M + + AA+G+ VA +C++GDGS++M+ QE+ ++ Sbjct: 436 LHLQKGGLYRIAIGFGSMTWAIGAAIGSAVASKGVPTICLTGDGSYLMSGQEITVAVEEK 495 Query: 446 LPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVE 505 LP+ ++L+++ LGMV+ Q+L E + DF+ LA + G + + +++E Sbjct: 496 LPVVFIVLNDRALGMVKHGQRLGGAESIAHE--LPPVDFVGLAHSLGAQAEVVRTPEELE 553 Query: 506 AA-LDTMLNSDGPYLLHVSIDELENVWPLVPPGASNSEMLEK 546 + L ++ GP L+ V ID E VPP + + LE+ Sbjct: 554 SLDLISICERPGPTLIEVQIDGEE-----VPPIGARMKTLER 590 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: 767 Number of extensions: 31 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 548 Length of database: 591 Length adjustment: 36 Effective length of query: 512 Effective length of database: 555 Effective search space: 284160 Effective search space used: 284160 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