Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_041751704.1 BBTA_RS31170 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000015165.1:WP_041751704.1 Length = 515 Score = 462 bits (1188), Expect = e-134 Identities = 270/519 (52%), Positives = 327/519 (63%), Gaps = 17/519 (3%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TLV GGVDVCF NPGTSEMHFVAALD V MR +L LFEGV TGAADGY R Sbjct: 1 MNGAESLVRTLVAGGVDVCFTNPGTSEMHFVAALDRVEGMRCVLGLFEGVVTGAADGYFR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 + G PA+ LLHLGPGL NGLANLHNA++AR +V +VG HATYH ++APL SDI+ +A Sbjct: 61 MKGTPASTLLHLGPGLANGLANLHNAKKARSGIVNIVGQHATYHIGFNAPLTSDIEGLAR 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRSG-SQIATLILPADVCWSDGAHAAAGVPAQAAA 179 +S WVR + +A V AD AAIAA+RS QIATLILPAD W++ A A VPA+ Sbjct: 121 PMSDWVRTSPSAKAVAADGAAAIAAARSAPPQIATLILPADTAWNE-ADGIADVPAETQR 179 Query: 180 APVDVGPV---AGVLRS-GEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLE 235 V A +L + G ++L+ A GL A RI TG R + +T+ + Sbjct: 180 PSYSADAVEKAAKILHAHGPETLVLMTAGALTEQGLAFAQRIAGKTGCRVMGQTYHPRMA 239 Query: 236 RGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLA 295 RGAG +++R+ Y E A L KH+VL A PV+FFAYP PS L G EVH + Sbjct: 240 RGAGRFSIDRIPYVIEQALPILKNYKHIVLVEANDPVAFFAYPNKPSVLKAEGTEVHRMT 299 Query: 296 EPG-GAADALAALADEVAPGTVAPVAGASRPQL-----PTGDLTSVSAADVVGALLPERA 349 G +A AL ALAD + A QL PTG L + A + +PE A Sbjct: 300 AWGENSAAALEALADHLG----AKAQDVKPQQLAELIKPTGALNHTTIAQAIAYAIPENA 355 Query: 350 IVVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGS 409 I+VDES T G TA A HDWL GG+IG+ P A GAAVA PDR V+CL DGS Sbjct: 356 IIVDESITTGRGFFPPTAAAKPHDWLQNMGGSIGFSTPVATGAAVACPDRKVMCLVGDGS 415 Query: 410 AMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMD 469 AMYTI LW+QARENL+V TV++ N Y ILR E VGAG PG +A D+L I RPT+D Sbjct: 416 AMYTIQSLWTQARENLNVVTVVFANRIYQILRGEFDGVGAG-QPGQRAQDMLKIDRPTLD 474 Query: 470 FVKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDV 508 FV +A+GMGVP R VTT +EF AL A AE GP LI+V Sbjct: 475 FVAMAKGMGVPGRAVTTADEFNAALAEANAEFGPRLIEV 513 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: 613 Number of extensions: 22 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: 515 Length of database: 515 Length adjustment: 35 Effective length of query: 480 Effective length of database: 480 Effective search space: 230400 Effective search space used: 230400 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