Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_068174298.1 HTA01S_RS18950 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_001592305.1:WP_068174298.1 Length = 523 Score = 385 bits (990), Expect = e-111 Identities = 241/521 (46%), Positives = 300/521 (57%), Gaps = 15/521 (2%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 M GA AL+ L D GV VCFANPGT+E+ V +L+ RMR ++ L E V TG ADGY R Sbjct: 7 MTGADALLAALADEGVTVCFANPGTTELDLVRSLEREERMRCVVGLQENVCTGGADGYGR 66 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 + GRPAA LLHLGPG NG+ANLHNARRA P+V ++GDH ++H YD+PL SDI+++A Sbjct: 67 MTGRPAATLLHLGPGFANGIANLHNARRAHTPIVNLIGDHTSWHLPYDSPLTSDIESLAR 126 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPAD-VCWSDGAHAAAGVPAQ-- 176 VSGWV R A A A+ S + G Q ATLI PAD + G A PA Sbjct: 127 PVSGWVHRIAAVEQSDAAGREAVKQSLARGGQGATLIFPADHQAHTGGEQVALQQPAADV 186 Query: 177 AAAAPVDVGPVAGVLR---SGEPAMMLIGGDATRGPGL---TAAARIVQATGARWLCETF 230 A P PVA V R + +L GG G G+ A R+ A GA ETF Sbjct: 187 GAEVPAAFDPVAAVQRLKAANRIVFLLGGGGELSGLGVRAQKAVQRLCAALGATAYAETF 246 Query: 231 PTCLERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCE 290 P+ ERG G+PA +RL YF E A LD +VL GA PV++F Y G PS LVPA Sbjct: 247 PSRSERGQGLPAFDRLPYFPEPAREVLDPADLVVLVGALPPVTYFGYEGHPSLLVPAERL 306 Query: 291 VHVLAEPGGAADALAALADEVAPGTVA-PVAGASRPQLPTGDLTSVSAADVVGALLPERA 349 + + A AA L +AD + VA PVA S P+ G LT A + LPERA Sbjct: 307 LKLAAVGDDAATRLEQVADLLGAVEVAIPVAVLSPPE--EGPLTPARIALALANELPERA 364 Query: 350 IVVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGS 409 IV E TCG +A A H LT TGGAIG G+P A+GAA+A P+R V+ L SDGS Sbjct: 365 IVSVEGGTCGYPFYAVSAAARPHTTLTNTGGAIGQGLPVAMGAAIACPNRQVVALLSDGS 424 Query: 410 AMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMD 469 YTI LWS A E+LDV +I N Y ILR EL+R GA G +A ++ + +P +D Sbjct: 425 TQYTIQTLWSLAHEDLDVVVLIAANHQYAILRNELRRGGAVL--GNRAAEITSLDKPRID 482 Query: 470 FVKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 +V +A+ GVP R TT E LR AFA+ GP LI++ + Sbjct: 483 WVTLAQSYGVPGGRATTSSELTALLRQAFAKRGPMLIEMAL 523 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: 615 Number of extensions: 24 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: 523 Length adjustment: 35 Effective length of query: 480 Effective length of database: 488 Effective search space: 234240 Effective search space used: 234240 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