Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011305464.1 MBAR_RS02340 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000195895.1:WP_011305464.1 Length = 583 Score = 318 bits (815), Expect = 4e-91 Identities = 198/557 (35%), Positives = 300/557 (53%), Gaps = 25/557 (4%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 A+ +++ LE E VE +FG PG + F DA+ S + ++ RHEQ A+ AD Y R +GK Sbjct: 40 AQLIVQCLENEGVEYIFGLPGEENIRFVDAVKDSTIRFIVVRHEQGASFMADIYGRVTGK 99 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 GVCI T GPGA NL+ G A A +DS+P+VA++ QV I + Q +D L +F PI K Sbjct: 100 AGVCISTLGPGAINLLLGTADAFTDSTPLVAISAQVGLNRIYKETHQVVDLLSMFKPITK 159 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGYN 183 I + IPE+ R AFE A+T RPG V++ +P+DV+ + P+ Y Sbjct: 160 WAGMIVGSAAIPEMVREAFEKAKTERPGAVYLCVPEDVEAISGLTGLRPLSQ-----SYE 214 Query: 184 PTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKGC 243 ++ P QI A ++ +A +PIILAG G + A + L++ E L IPV TT MGKG Sbjct: 215 ADSMPGPSQIAYASHVLQAATKPIILAGHGAVRDHAGDALVRFSERLRIPVATTFMGKGI 274 Query: 244 ISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDID 303 +NHP +LG +G N+ E+DV++ +G + + A + KI+H+ Sbjct: 275 FPDNHPNSLGTMGFMKHDYVNFGFDEADVIVCVGYDLQEFDPVRMNPNA-DKKILHLHRY 333 Query: 304 PAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLKKSS 363 PAEI + V V + G+ + + + +L I+ KE + + +L K Sbjct: 334 PAEIDTHYPVTVSVEGN----ISDALDKLAAIV-------TPKEGLDAADRKIRNLLKEE 382 Query: 364 IPVMDY-DDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRSFL 422 + + D P+KPQ++V ++ A + D + I D G +MWMA + T P + + Sbjct: 383 LEDGAHADAYPVKPQRLVSDIRAAMGD-----SDIALVDTGSLKMWMARLYPTNQPNTCV 437 Query: 423 SSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIFDN 482 S GL TM F P AIGAK+A PD KV+ +TGDG F+MN QEL T +IP V+ I+ + Sbjct: 438 ISNGLSTMAFAVPGAIGAKLAYPDRKVLAVTGDGSFLMNSQELETAIREHIPFVVLIWVD 497 Query: 483 RTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAINCD 542 G++ +L G V+FG PDF+K AES+G K IE+ ++ LK+A+ D Sbjct: 498 GAYGLIKWKMDLELG-HHSFVDFGN-PDFVKYAESFGAKGYFIEAAADLLPTLKKALAED 555 Query: 543 EPYLLDFAIDPSSALSM 559 ++ +D S + + Sbjct: 556 VVSVVVCPVDYSENIKL 572 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: 752 Number of extensions: 33 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