Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate PP_3365 PP_3365 Acetolactate synthase
Query= curated2:O08353 (599 letters) >FitnessBrowser__Putida:PP_3365 Length = 547 Score = 269 bits (688), Expect = 2e-76 Identities = 173/552 (31%), Positives = 273/552 (49%), Gaps = 27/552 (4%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 A+ +++ LE E VE +FG PG L ++L S + +LTRHEQ+A A Y R +GK Sbjct: 5 ADVVVQCLENEGVEYVFGIPGEENLDLLESLRKSKIKLVLTRHEQSAGFMAATYGRLTGK 64 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GV + T GPGATNLVT A A+ PM+ +TGQ P K FQ ID G+ PI K Sbjct: 65 TGVSLSTLGPGATNLVTASAYAYLGGMPMMMITGQKPIKKSKQGRFQIIDVCGMMDPITK 124 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 + Q IP R AF +A+ +PG VH++LP+D+ + D PIP + + Sbjct: 125 YTHQFASADNIPARMREAFRLAEEEKPGAVHLELPEDIAAEQ--TDALPIPRSL-----H 177 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 + I+ A++ + +A+ PI++ G G + L +L++ IP TT MGKG Sbjct: 178 RRPLAEHVAIEAAVEKLQNARNPILVIGAGANRKMTAKVLKQLIDKTGIPFITTQMGKGV 237 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 + E HP LG + + + +D++I+IG ++ + T ++IHI+ Sbjct: 238 VDERHPRFLGNAALSSGDFVHRAVEAADLIINIGHDVIEKPPFFMVRGGT--EVIHINFR 295 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 AE+ V ++GD + + Q+ +N S + + + + ++ Sbjct: 296 SAEVDAVYFPQVEVIGD----IANAVWQISEALNDTSHWDFTR------LMAIREANEAQ 345 Query: 364 IPV-MDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFL 422 I D D P+ PQ++V ++ V+ I+ D G ++W A +K P + L Sbjct: 346 IAEGADDDRFPVYPQRMVADIRRVLP-----SEGIVALDNGIYKIWFARNYKAHKPNTVL 400 Query: 423 SSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDN 482 L TMG G PSA+ A + PD VI + GDGGFMMN QEL T + + + I + Sbjct: 401 LDNALATMGAGLPSAMAAHLVHPDRPVISVCGDGGFMMNSQELETAVRLGMHITVVILRD 460 Query: 483 RTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCD 542 GM+ +W+ G +++G PDF+K AE+YG R+ES + L+ I Sbjct: 461 DGYGMI-RWKQANMGFTDFGLDYGN-PDFVKYAEAYGANGHRVESAEGLLPLLEHCIKTP 518 Query: 543 EPYLLDFAIDPS 554 +++D +D S Sbjct: 519 GVHVIDCPVDYS 530 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: 747 Number of extensions: 29 Number of successful extensions: 4 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: 547 Length adjustment: 36 Effective length of query: 563 Effective length of database: 511 Effective search space: 287693 Effective search space used: 287693 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 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