Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_013644168.1 METBO_RS02890 thiamine pyrophosphate-binding protein
Query= metacyc::MONOMER-11900 (599 letters) >NCBI__GCF_000191585.1:WP_013644168.1 Length = 536 Score = 411 bits (1057), Expect = e-119 Identities = 227/557 (40%), Positives = 333/557 (59%), Gaps = 35/557 (6%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 A+A++K E V+ +FG+PG +LP YDAL S++ H+L RHEQ AAHAADG+ARAS Sbjct: 9 ADALVKVFEKFGVKFIFGHPGEQILPLYDALKESEIEHVLMRHEQGAAHAADGFARASSN 68 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GVCI T GPGA NLV GVATA+ DS PM+ +TG VP KL G FQ+ID G+F PI Sbjct: 69 TGVCIATGGPGAMNLVMGVATAYKDSVPMIVVTGDVPLKLKGKHGFQDIDINGVFQPITI 128 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 +FQIQ + +AF I + R GPVH++ PKDV LE ++ + S ++ N Sbjct: 129 ESFQIQNAEEGVLALINAFNILKYKRKGPVHLNFPKDV--LESLVEDSLVDSILE--NNN 184 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 +P ++++KLI ++++P+I+AG GVL S ++++LL E IPV +T +G Sbjct: 185 IKNFINPLITEESLKLIENSEKPLIIAGAGVLWSKSSDKLLNFAEKHKIPVASTYHSRGV 244 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 + E+H L++GM+G+ GTK ANY SD+++++GCR S+R I AKIIH+++D Sbjct: 245 LPEDHDLSVGMIGLRGTKAANYAGKNSDLILALGCRLSERTCQGI----GEAKIIHVNLD 300 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 + ++ D+ I GD L E IN NN+ +W N+ K+ Sbjct: 301 E----RVLDGDLKIQGDVNQFLDE--------INNVQLLNNE-----EWRSNIFKHPKTF 343 Query: 364 IPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFLS 423 ++ IPIKPQ+ +KE++ +D ++I D G + W+ +TP S L Sbjct: 344 TVKTNFSTIPIKPQRAIKEILDAAED------SVIVNDAGTHTTWVTLLKNVKTPASLLF 397 Query: 424 SGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDNR 483 SGG G MG+G P+AIGA +A P V+ I GDG F M QELGTI E +P+VICI +N Sbjct: 398 SGGFGPMGYGVPAAIGASLANPGKPVVAIVGDGDFQMTLQELGTIHELKLPIVICIINNS 457 Query: 484 TLGMVYQWQNLFYGKR-QCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCD 542 +L ++ QWQ ++YGK Q + PDF KLAESY + + + SP E+ +A+++A+ Sbjct: 458 SLRIIKQWQEMYYGKSYQVELE---NPDFKKLAESYHVNSLGVNSPGEVIKAVRKALTMQ 514 Query: 543 EPYLLDFAIDPSSALSM 559 +PYLLD +D + + + Sbjct: 515 KPYLLDIEVDQTECIPL 531 Lambda K H 0.319 0.137 0.405 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: 852 Number of extensions: 38 Number of successful extensions: 5 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: 599 Length of database: 536 Length adjustment: 36 Effective length of query: 563 Effective length of database: 500 Effective search space: 281500 Effective search space used: 281500 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 (21.7 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