Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011021953.1 MA_RS10205 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000007345.1:WP_011021953.1 Length = 583 Score = 317 bits (812), Expect = 9e-91 Identities = 203/568 (35%), Positives = 302/568 (53%), Gaps = 25/568 (4%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 A+ M++ LE E VE +FG PG + F DAL S + ++ RHEQ A+ AD Y R +GK Sbjct: 40 AQLMVQCLENEGVEYIFGLPGEENIRFVDALGDSTIRFIVVRHEQGASFMADIYGRVTGK 99 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GVCI T GPGA NL+ G A A +DS+P+VA++ QV I + Q +D L +F P+ K Sbjct: 100 AGVCISTLGPGAINLLLGTADAFTDSTPLVAISAQVSLNRIYKETHQVVDLLNMFKPVTK 159 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 I + IPE+ R AFE AQT RPG V++ +P+DV+ + P+ + Sbjct: 160 WAEMIIGSAAIPEMMREAFEKAQTSRPGAVYLCVPEDVESISGLTGLRPLARSDE----- 214 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 ++ QI +A +++ A +PIILAG G + A + L++ E L IPV TT MGKG Sbjct: 215 ADSMPGSAQITRAAQVLQEATKPIILAGHGAVRDYAGDALVRFSERLRIPVATTFMGKGI 274 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 ++HP +LG +G N+ E+DV++ +G + I A + KI+H+ Sbjct: 275 FPDDHPNSLGTIGFMQHDYVNFGFDEADVIVCVGYDLQEFDPVRINPNA-DKKILHLHRY 333 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 PAEI + V V + G+ L + L II KE D E+ + +L + Sbjct: 334 PAEIDAHYPVTVSVEGN----LSAALDGLAAIIT--PKEGLDAED-----RKIRNLLREE 382 Query: 364 IPV-MDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFL 422 + D P+KPQ++V ++ A + D + I D G +MWMA + T P + + Sbjct: 383 LEYGARADAYPVKPQRLVSDIRAAMGD-----SDIALVDTGALKMWMARLYPTYQPNTCV 437 Query: 423 SSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDN 482 S GL TM F P AIGAK+A PD KV+ +TGDG F+MN QEL T IP V+ ++ + Sbjct: 438 ISNGLATMAFAVPGAIGAKLAYPDRKVLAVTGDGSFLMNSQELETAIRERIPFVVLVWVD 497 Query: 483 RTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCD 542 G++ +L G R V+FG PD +K AES+G + RIE ++ LK+A+ D Sbjct: 498 DAYGLIKWKMDLELG-RHSFVDFGN-PDLVKYAESFGARGYRIEVAADLLPTLKKALAED 555 Query: 543 EPYLLDFAIDPSSALSMVPPGAKLTNII 570 ++ +D S + + +LT I Sbjct: 556 VVSVVVCPVDYSENIRLTDKLGQLTQPI 583 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: 769 Number of extensions: 29 Number of successful extensions: 6 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: 583 Length adjustment: 37 Effective length of query: 562 Effective length of database: 546 Effective search space: 306852 Effective search space used: 306852 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