Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 3607861 Dshi_1269 thiamine pyrophosphate protein central region (RefSeq)
Query= curated2:O08353 (599 letters) >FitnessBrowser__Dino:3607861 Length = 621 Score = 152 bits (383), Expect = 5e-41 Identities = 147/587 (25%), Positives = 262/587 (44%), Gaps = 58/587 (9%) Query: 4 AEAMIKALEAEKVEI-------------LFGYPGGALLPFYDALH-HSDLIHLLT-RHEQ 48 A+A+I+ L A+ +E +FG+ G + +ALH H + + L ++EQ Sbjct: 11 AQAIIRYLNAQFIETDGTRQRVCGGGFGIFGH--GNVTCLGEALHDHRETLPLYRGQNEQ 68 Query: 49 AAAHAADGYAR--ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGN 106 + AA YA+ + C ++GPG NL+T A AH++ PM+ L G + + Sbjct: 69 SMGFAAAAYAKYHLRRRFMFCTASAGPGTANLLTASALAHANRLPMLMLCGDTFLTRLPD 128 Query: 107 DAFQEID-----ALGL---FMPIVKHNFQIQKTCQIPEIFRSAFE-IAQTGRPGPVHIDL 157 Q+++ ALGL F + ++ +I Q+ + +A + GP + L Sbjct: 129 PVLQQLEHYGNPALGLNDAFHAVTRYWDRITHPAQVIQSLPAALATMLDPADCGPAFLAL 188 Query: 158 PKDVQELELDIDKHPIPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLS 217 P+DVQ D + K I ++ +A L+ SA+RP+I+AGGGV S Sbjct: 189 PQDVQGWAYDYPRAFFEEKTHRIR---RITPDADEVAEAAALLRSAERPVIIAGGGVQYS 245 Query: 218 GANEELLKLVELLNIPVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIG 277 GA EL E IPV T+ G+ + +HPL +G VG+ G+ AN ++DV++++G Sbjct: 246 GAVAELTGFAEAHGIPVIETIAGRANLLADHPLNIGPVGVTGSDSANAIAEQADVILAVG 305 Query: 278 CRFSDRITGDIKSFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIIN 337 R D TG +FA A+ I ++ + GK + +PIVGDAKL L + L Sbjct: 306 TRLQDFTTGSWTAFAQEARFIALNAARHDAGK--HRALPIVGDAKLGLVALEAAL----- 358 Query: 338 KDSKENNDKENISQWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTI 397 D W + +K + + P + + V++ L ++ + Sbjct: 359 ------GDYRCPEAWRNYAQTERKGWDAYVADNVRPGNRPNSYAQAIGVVNALCEPRDRV 412 Query: 398 ITTDVGQNQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVA----KPDSKVICIT 453 + G A++ +T + G MG+ GA++A +P++ I Sbjct: 413 VAAAGGLPAEVTANW-RTLDIGTVDVEFGFSCMGYEIAGGWGARIAQTEVEPEADTIVFC 471 Query: 454 GDGGFMMNCQELGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAP---- 509 GDG +++ ++ + +++ + DN ++ + QN G + AP Sbjct: 472 GDGSYLLMNSDIYSSVLTRKKMIVLVLDNGGFAVINKLQN-NTGNESFNNLLADAPTIPE 530 Query: 510 ----DFIKLAESYGIKARRIESPNEINEALKEAINCDEPYLLDFAID 552 DF+ A + G +A ++ + +E+ EA K A D+ ++ ++D Sbjct: 531 AFGVDFVAHAAAMGAEATQVANADELAEAFKAAKASDKTTVIVMSVD 577 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: 775 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 599 Length of database: 621 Length adjustment: 37 Effective length of query: 562 Effective length of database: 584 Effective search space: 328208 Effective search space used: 328208 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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