Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_057507191.1 ABB28_RS02940 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_001431535.1:WP_057507191.1 Length = 551 Score = 275 bits (702), Expect = 5e-78 Identities = 175/554 (31%), Positives = 281/554 (50%), Gaps = 28/554 (5%) Query: 3 GAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASG 62 G++ ++KALE E V+ +FG PG L F ++L +S + +LTRHEQAAA A + R +G Sbjct: 4 GSDLLVKALENEGVDRIFGVPGEENLDFLESLRNSKIELVLTRHEQAAAFMAATHGRLTG 63 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 + GVC+ T GPGA N TG A AH + PM+ +TGQ FQ +D + P+ Sbjct: 64 RPGVCLATLGPGALNFSTGAAYAHLGAWPMILITGQKAVMSAKQARFQIVDIVASMKPLT 123 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDV--QELELDIDKHPIPSKVKLI 180 K QI IP + R AF +A RPGPVH++LP+D+ +E+E D+ PI + + Sbjct: 124 KMTRQIVSPASIPAMVRDAFRVAMEERPGPVHLELPEDIAGEEVE-DVPVIPIHALER-- 180 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 I P + +A I +AKRP+++ G E L V +P T MG Sbjct: 181 -----PIAAPAALDRAEAAILAAKRPLVMIGAAGSRPWLTEALSAFVARTRLPFFNTQMG 235 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG ++ L +G + + ++ +D++I+IG ++ +KS + K+IHI Sbjct: 236 KGAVTGGSNLYMGTAALSEGDYVHEAVARADLIIAIGHDTIEKPPFLMKS-SGGPKVIHI 294 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360 A + + + D+ ++GD ++ + ++L+ + D ++ I + +N Sbjct: 295 SFQSATVEQVYHPDIEVLGDIGASVEALAERLEGRLPADEGMTELRQKI---LARLNDR- 350 Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420 D D PI PQ+IV ++ + D + I+ D G ++W A ++T + Sbjct: 351 ------ADEDRFPITPQRIVHDVRQAVPD-----DGIVCLDNGMYKIWFARNYRTHVANT 399 Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480 L L TMG G PSA+ A + P +V+ + GDGGFMMN QEL T + +V+ I Sbjct: 400 LLLDNALATMGAGLPSAMMAAMLYPQRRVLAVCGDGGFMMNSQELETAVRLGLNLVVVIL 459 Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540 ++ GM+ +W+ G + FG PDF+K AE+YG K R+ + E+ ++ A Sbjct: 460 NDSAYGMI-RWKQAVDGFEDFGMRFGN-PDFVKYAEAYGAKGSRVSAVEELVPMIEAAFA 517 Query: 541 CDEPYLLDFAIDPS 554 ++LD ID S Sbjct: 518 GGGVHVLDVPIDYS 531 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: 742 Number of extensions: 38 Number of successful extensions: 7 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: 551 Length adjustment: 36 Effective length of query: 563 Effective length of database: 515 Effective search space: 289945 Effective search space used: 289945 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