Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate NP_350234.1 CA_C3652 acetolactate synthase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000008765.1:NP_350234.1 Length = 563 Score = 337 bits (865), Expect = 6e-97 Identities = 204/561 (36%), Positives = 304/561 (54%), Gaps = 30/561 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN AE ++K LE E VE +FG PG L AL S + + TRHEQ AA AD Y R Sbjct: 23 MNTAELVVKCLENENVEYIFGIPGEENLALIKALTKSPIKFITTRHEQGAAFMADVYGRL 82 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNL+TGVA A+ D +P++A+TGQV T + ++ Q +D + +F P Sbjct: 83 TGRPGVCLSTLGPGATNLMTGVADANLDGAPLIAITGQVGTDRMHIESHQHLDLVAMFAP 142 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K N QI + PEI R AF+ A +PG HIDLP+++ ++ P+ K Sbjct: 143 VTKWNKQIVRPDTAPEIVRKAFKTAVDEKPGACHIDLPQNIADM-------PVQGKPLRH 195 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 + I+KA I+ AK P+IL+G G + S A++ +L + E LNIPV T MG Sbjct: 196 TVTDKSFAAYSSIEKAAIAISRAKSPLILSGNGAIRSKASKAVLDMAERLNIPVANTFMG 255 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNA--KII 298 KG I NHPL+L +G+ N ++D++I+IG D + K + + +II Sbjct: 256 KGIIPFNHPLSLWSMGLAQKDYINRIFEKTDLVIAIG---YDIVEYSPKKWNSKGEIRII 312 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358 HI AE+ + +V ++GD ++E+I++ D I E Q ++ Sbjct: 313 HIGEKKAEVNNSYLPEVEVIGDISDSIQEIIRRSDRI-----------ETPKQALKIKED 361 Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 + K+ D P+KPQK++ +L V + ++ I+ +DVG ++MW+A + P Sbjct: 362 MHKNYEEYSDDQSFPMKPQKVLYDLRRV-----MGEDDIVISDVGAHKMWIARNYHCYKP 416 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478 + + S G +MG P A+ AK+ PD KV+ +TGDGGFMMN QEL T P V Sbjct: 417 NTCIISNGFASMGIAIPGALAAKLVNPDKKVVAVTGDGGFMMNSQELETALRIGTPFVTL 476 Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 IF++ G++ Q YG+ +NF PDF AES G+K RI E+ L+EA Sbjct: 477 IFNDSNYGLIKWKQEERYGE-SAYINFTN-PDFKMYAESMGLKGYRITKAEELIPTLEEA 534 Query: 539 INCDEPYLLDFAIDPSSALSM 559 + P ++D A+D S L + Sbjct: 535 FSQKVPSVIDCAVDYSENLKL 555 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: 738 Number of extensions: 27 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: 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 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