Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_043292569.1 acetolactate synthase
Query= curated2:O53554 (515 letters) >NCBI__GCF_000016205.1:WP_043292569.1 Length = 528 Score = 418 bits (1075), Expect = e-121 Identities = 259/521 (49%), Positives = 326/521 (62%), Gaps = 23/521 (4%) Query: 2 NGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARI 61 +GA ++ T + GVD+CFANPGT+EM FV ALD V +R +L LFEGV TGAADGY R+ Sbjct: 14 DGASIVLETARERGVDICFANPGTTEMPFVVALDRVAGVRPILGLFEGVCTGAADGYGRM 73 Query: 62 AGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGT 121 AG+PA LLHLGPG NG+ANLHNARRAR P++ +VGDHA H KYDAPL SDI+++A Sbjct: 74 AGKPAMTLLHLGPGHANGIANLHNARRARTPILNIVGDHARAHLKYDAPLTSDIESLARP 133 Query: 122 VSGWVRRTEAAADVGADAEAAI-AASRSGSQIATLILPADV--------CWSDGAHAAAG 172 VS W R A D+ D AAI AA+ + S +ATL+LP D+ A AA Sbjct: 134 VSVWYRSVAHADDLARDTAAAIAAATAAASGVATLVLPVDLQSAAVNETASQPRAQAAPA 193 Query: 173 VPAQAAAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPT 232 VPA AA + VA +LR+G PA++L+G A G AAARI ATGA ETFP Sbjct: 194 VPAFDAAR---LARVADLLRTGVPAVLLLGVRALSARGQKAAARIAAATGAACFGETFPA 250 Query: 233 CLERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVH 292 ERG G+P ++RL YF E A A L G K +VLAGA +PV++FAY G+P +L P ++ Sbjct: 251 RAERGGGLPDIDRLPYFPEPARAALAGRK-VVLAGALAPVTYFAYEGIPGELAPPE-DLV 308 Query: 293 VLAEPGGAAD-ALAALADEVAPGTVAPVAG--ASRPQLPTGDLTSVSAADVVGALLPERA 349 LA+PG AAD AL ALA+ V G A V G +R + G LT +A V+ LP+ A Sbjct: 309 TLADPGEAADAALEALAEAV--GATADVDGVRVARWNVEAGPLTPQTAGRVLADALPDDA 366 Query: 350 IVVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGS 409 IV E TCG A+A A H LT TGGAIG G+P A+GAAVA P R V L+SDGS Sbjct: 367 IVSIEGGTCGYPFVTASARARRHTILTNTGGAIGQGLPVALGAAVACPARRVFALQSDGS 426 Query: 410 AMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSD-PGPKALDLLDISRPTM 468 A YTI LW+ ARE L + +I +N Y IL+ EL R G +D P L LLD P + Sbjct: 427 AQYTIQALWTMARERLPIVMLIASNRRYAILQTELARNGQPADTPHASRLTLLD--DPPI 484 Query: 469 DFVKIAEGMGVPARRVTTCEEFADALRAAFAE-PGPHLIDV 508 D++ ++ G GVPA RV+T + + AL A A GP LI++ Sbjct: 485 DWLALSAGYGVPAERVSTTQALSRALDDALAHTDGPRLIEM 525 Lambda K H 0.318 0.134 0.402 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: 665 Number of extensions: 28 Number of successful extensions: 5 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: 515 Length of database: 528 Length adjustment: 35 Effective length of query: 480 Effective length of database: 493 Effective search space: 236640 Effective search space used: 236640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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