Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate N515DRAFT_0378 N515DRAFT_0378 acetolactate synthase, large subunit (EC 2.2.1.6)
Query= curated2:O08353 (599 letters) >FitnessBrowser__Dyella79:N515DRAFT_0378 Length = 547 Score = 266 bits (681), Expect = 1e-75 Identities = 175/562 (31%), Positives = 266/562 (47%), Gaps = 40/562 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN A +KALEAE V +FG PG L +AL S + ++TRHEQAA A + R Sbjct: 1 MNAAALFVKALEAEGVRRIFGVPGEENLDLVEALRDSKIELIVTRHEQAAGFMAATWGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GV + T GPGATNLVT A A + PM+ +TGQ P + FQ +D + + P Sbjct: 61 TGEAGVALSTLGPGATNLVTAAAYAQLGAMPMLMITGQKPIRTHKQGLFQLVDVVDMMQP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQE--------LELDIDKHP 172 + K+ QI IP R AF A+ RPG VH++LP+D+ L + + P Sbjct: 121 LTKYTRQIVSAPTIPARVREAFRRAEEERPGAVHLELPEDIARDSVDEAILLPTEYARRP 180 Query: 173 IPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232 P L+ +A + I +AK PI++ G L ++ L I Sbjct: 181 SPDDAALV--------------QAGEAITAAKHPILMIGAAANRQRTAVALRTFIDKLGI 226 Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFA 292 P TT MGKG + E+HPL LG + + + +DV++++G ++ Sbjct: 227 PFFTTQMGKGVVDEDHPLWLGNAALSDGDFVHRAIDAADVIVNVGHDVVEK--PPFFMHK 284 Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352 +IHI+ AE+ + +VGD + +++L D+ N + Sbjct: 285 GRRTVIHINFSSAEVDTVYFPQIEVVGD----IAHTVERL-----TDALTPQAHWNFKYF 335 Query: 353 IENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412 + + + D PI P ++V + + D + ++ D G ++W A Y Sbjct: 336 DQVREAFHRQLAEHADDPRFPIHPVRLVADTRRYMPD-----DGVLCLDNGMYKIWYARY 390 Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472 ++ + P + L L TMG G PSA+ AK+ P+ KV+ I GDGGFMMN QEL T Sbjct: 391 YRARQPNTVLLDNALATMGAGLPSAMAAKLVYPERKVLAICGDGGFMMNAQELETAVRLK 450 Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532 + +VI + + GM+ +W+ G + F PDF+K AE++G R ES + Sbjct: 451 MDLVILLLRDDAYGMI-RWKQAEMGYADFGMQFSN-PDFVKFAEAHGAHGHRPESADAFL 508 Query: 533 EALKEAINCDEPYLLDFAIDPS 554 LK A +L+D AID S Sbjct: 509 PTLKRAFEQGGVHLIDLAIDYS 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: 667 Number of extensions: 32 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: 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