Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate YP_002823812.1 NGR_b16080 acetolactate synthase large subunit-like protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000018545.1:YP_002823812.1 Length = 600 Score = 310 bits (794), Expect = 1e-88 Identities = 190/576 (32%), Positives = 303/576 (52%), Gaps = 31/576 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDAL--HHSDLIHLLTRHEQAAAHAADGYA 58 + G + + KAL+ VE + G PG + +DA S++ + HEQ+A H ADGY Sbjct: 3 LTGGQVVAKALKEYGVEYVAGVPGHGIWSLFDAFLEEGSEIPFIQVMHEQSAVHMADGYF 62 Query: 59 RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALG-- 116 RASG+ C + GPGA N + G+ATA+ DS+ + ++G T + G+ QE++ Sbjct: 63 RASGRPMACSTSVGPGAANTIIGLATAYCDSTSLFYVSGSPQTYMHGHGTMQELERQQDN 122 Query: 117 ----LFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHP 172 + + K +Q +P I AF TGRPGPVH+++P DVQ D+ HP Sbjct: 123 AFPRITEQVTKRAWQANSVQVLPSIMHRAFNAMVTGRPGPVHVEVPMDVQVEAADVTIHP 182 Query: 173 IPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232 + ++ + P P+ I+ AIK++ +A+RP+I+AGGG + + A+ EL +L E L Sbjct: 183 LEKRLPIGVAYPD----PKAIEAAIKVLLNAERPVIVAGGGAITANASTELTRLAEKLGA 238 Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSD----RITGDI 288 V T GKG ISE+H L +G VG GT N + +DV++S+GCRF+D + Sbjct: 239 AVSITWNGKGAISEDHALFIGAVGQTGTTCGNKITASADVVVSVGCRFTDWSASSYAKGV 298 Query: 289 KSFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKEN 348 +AK+IHID+DP EIGKN +V IV DAK+ L+ ++ + +K K + +E Sbjct: 299 SFSIPSAKLIHIDLDPREIGKNYETEVGIVSDAKVALEALLAMISDAESK--KMLSRRET 356 Query: 349 ISQWIENVNSLKKSSI-PVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQM 407 ++ + ++ + P + + P Q+ + L V+D +N I+ G Q Sbjct: 357 FLADVQKAKADWRAQVEPRENSRETPFTSQRPLMALRKVLD-----RNGIVVVGSGNTQG 411 Query: 408 WMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGT 467 + F PR+ L+SG MG+ P+A+GAK+A PD +V+ I GDG FMM+ E+GT Sbjct: 412 SVKQSFPVYEPRTHLTSGSYSPMGWAVPAALGAKLACPDRQVVAIVGDGDFMMSLPEMGT 471 Query: 468 IAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSV----NFGGAP---DFIKLAESYGI 520 A I VV + +N+ + Q F G+ S G P D A ++G+ Sbjct: 472 AAMNGINVVFLVLNNQGYMSIRGGQRKFMGRHIASEFNRHAGNGQPYSADIAASARAFGL 531 Query: 521 KARRIESPNEINEALKEAINCDEPYLLDFAIDPSSA 556 +A ++E ++ ++LK A+ C P L++ + +A Sbjct: 532 EAWKVEKDEDLEKSLKAALECGGPALVEVIVSRDAA 567 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: 715 Number of extensions: 34 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: 599 Length of database: 600 Length adjustment: 37 Effective length of query: 562 Effective length of database: 563 Effective search space: 316406 Effective search space used: 316406 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