Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_022949922.1 H035_RS0115740 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000421465.1:WP_022949922.1 Length = 563 Score = 267 bits (683), Expect = 8e-76 Identities = 177/573 (30%), Positives = 280/573 (48%), Gaps = 46/573 (8%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M ++ ++ALEAE VE LFG PG L D+L S + +LTRHEQAA A Y R Sbjct: 1 MKASDLFVQALEAEGVEYLFGIPGEENLDLLDSLKDSSIRLVLTRHEQAAGFMAATYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNLVT A A + PM+ +TGQ P K AFQ +D + + P Sbjct: 61 TGRTGVCLATLGPGATNLVTAAAYAQLGAMPMLMITGQKPIKASKQGAFQIVDVVDMMQP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K+ Q+ IP R AF A+ RPG VH++LP+D+ D +I Sbjct: 121 LTKYTRQLSSGGHIPSQVREAFRRAEDERPGAVHLELPEDIARETTD---------AAII 171 Query: 181 G----YNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCT 236 G NP R + +A +I SA+ P++L G G L ++ IP + Sbjct: 172 GRSRFENPR--ASERSLAEATAMIQSARCPLLLIGAGANRRHTCRVLRNFIDRTGIPFFS 229 Query: 237 TLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDR---ITGDI----- 288 T MGKG I E HPL LG + + + +D++I++G ++ I GD Sbjct: 230 TQMGKGVIDETHPLFLGTAALSSGDFLHRAIEAADLIINVGHDVVEKPPFIMGDRPPVEP 289 Query: 289 -------KSFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSK 341 + A +A++IH++ A I + ++GD + + I++L + + Sbjct: 290 ADPDIAGAARAGSARVIHVNYVTAAIDPIYHPQQGVIGD----IADSIERLTAAVAFQAH 345 Query: 342 ENNDKENISQWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTD 401 + D+ ++ L+ + D D P+ PQ++V ++ V+ + +IT D Sbjct: 346 WDFDR-----FMTVKARLEAHILEDADDDRFPVYPQRLVADVRKVMPG-----DGVITLD 395 Query: 402 VGQNQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMN 461 G ++W A + P + L L +MG G PSAI AK+ P +V+ I GDGGFMMN Sbjct: 396 NGIYKIWFARNYPACQPNTVLLDNALASMGAGLPSAIAAKIVYPQRRVMAICGDGGFMMN 455 Query: 462 CQELGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIK 521 QEL T + +V+ + + GM+ +W+ G +++G PDF++ A SYG + Sbjct: 456 SQELETAVRLGLDLVVLVLRDNAYGMI-KWKQANMGFADFGLDYGN-PDFVQYARSYGAQ 513 Query: 522 ARRIESPNEINEALKEAINCDEPYLLDFAIDPS 554 R+ + E+ + +L++ +D S Sbjct: 514 GHRLAAAGELIPVVDRCFETPGVHLVEVPVDYS 546 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: 734 Number of extensions: 32 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: 563 Length adjustment: 36 Effective length of query: 563 Effective length of database: 527 Effective search space: 296701 Effective search space used: 296701 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