Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_038201147.1 Q392_RS03145 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000745855.1:WP_038201147.1 Length = 520 Score = 456 bits (1174), Expect = e-133 Identities = 258/521 (49%), Positives = 327/521 (62%), Gaps = 12/521 (2%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L++TL+D GVD CFANPGTSEMHFV+ALD + MR +L LFEGV TGAADGY R Sbjct: 1 MNGAESLVHTLLDAGVDTCFANPGTSEMHFVSALDRIAGMRCVLGLFEGVVTGAADGYYR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +AGRPAA LLHLGPGL NGLANLHNA++AR +V VVG+HAT H DAPL SDI +A Sbjct: 61 MAGRPAATLLHLGPGLANGLANLHNAKKARSGIVNVVGEHATTHLALDAPLTSDIQGLAV 120 Query: 121 TVSGWVRRTEAAADVGADA-EAAIAASRSGSQIATLILPADVCWSDGAHA--AAGVPAQA 177 +S WVR +A + +D EA + AS ++ATL LPAD+ WSD A A A G + Sbjct: 121 PMSHWVRTVRSADAIASDCREAVVQASGRPGRVATLALPADMAWSDTAAAPPALGAVREP 180 Query: 178 AAAPVDVGPVAG----VLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTC 233 A PV+ V + R G ++L+GG A R A RI ATG + E + Sbjct: 181 VALPVEQEAVIAAARILRRHGGSTLLLLGGRAVRARATEWAGRIAAATGCAVMSEFYAER 240 Query: 234 LERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHV 293 +ERGAG V RL Y +GA L H+VL GA PV+FF YP P L G Sbjct: 241 IERGAGRVPVPRLPYAVQGAVDALSRFDHIVLVGAAEPVAFFGYPDKPGRLAAPGTTFAT 300 Query: 294 LA-EPGGAADALAALADEVAPGTVAPVA---GASRPQLPTGDLTSVSAADVVGALLPERA 349 L+ A AL + +E+ V P A+ +L G +T S ++ AL+PE A Sbjct: 301 LSTHAQDPAQALRMVCEELGAMRVNPATCGRAAAHAELEEGPVTPASIGALLAALIPENA 360 Query: 350 IVVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGS 409 IVVDE+ + G T A HDWLT GG+IGYG+P AVGAA+AAP R VL LE DGS Sbjct: 361 IVVDEAISTGRAFDATTRDAAPHDWLTNMGGSIGYGLPVAVGAAIAAPGRRVLALEGDGS 420 Query: 410 AMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMD 469 AMYT+ LW+ ARE+L+VT V++ N +Y ILR E +VGAGS PG +A D+L I RP +D Sbjct: 421 AMYTLQALWTMARESLNVTVVVFANRSYQILRGEYAQVGAGS-PGRRAGDMLGIDRPALD 479 Query: 470 FVKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 +V +A G GVPA RV+T +F DA+R A A GP L+++V+ Sbjct: 480 WVALASGQGVPACRVSTLGQFGDAVRRANATEGPSLVELVL 520 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: 694 Number of extensions: 33 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: 520 Length adjustment: 35 Effective length of query: 480 Effective length of database: 485 Effective search space: 232800 Effective search space used: 232800 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 Jul 25 2024. The underlying query database was built on Jul 25 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