Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012591926.1 MSIL_RS14965 benzoylformate decarboxylase
Query= curated2:O53554 (515 letters) >NCBI__GCF_000021745.1:WP_012591926.1 Length = 528 Score = 160 bits (406), Expect = 8e-44 Identities = 167/529 (31%), Positives = 230/529 (43%), Gaps = 58/529 (10%) Query: 15 GVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARIAGRPAAVLLHLGP 74 GV F NPG++E+ F+ D R +L L EG A G ADGYA+ G V LH Sbjct: 16 GVTTIFGNPGSNELLFLE--DFPSDFRYILALHEGAAIGMADGYAQATGHTGFVNLHSAA 73 Query: 75 GLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVA--GTVSGWVRRTEAA 132 G GN + NA A P+VV G + PL ++IDA + W A Sbjct: 74 GTGNAMGGFANAWNAHTPLVVTAGQQVRAMMGIE-PLLTNIDATTLPKPLVKWSCEPARA 132 Query: 133 ADVGADAEAAIAASRSGSQIAT-LILPADVCWSDGAHAAAG---VPAQAAAAPVDVGPVA 188 DV A+ S + L +P D W A + A +AA +D G +A Sbjct: 133 EDVPLAISRALHLSALPAPGPVYLSIPYDD-WDKPAEPESLRLLKRAVSAAGALDAGALA 191 Query: 189 GVL----RSGEPAMMLIGGDATRGPGLTAAARIVQATGAR-WLCETFPTCLERGAGIPAV 243 + RS P ++L G D A R+ + A W+ + P C Sbjct: 192 ALAARLDRSANPVIVL-GPDVDAARANAHAVRLAERLKAPVWVAPSAPRCPFPTTHPNFR 250 Query: 244 ERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCE-VHVLAEPGGAAD 302 L + QL+G +++AGA PV F + P L+P G E + + + AA Sbjct: 251 GLLTASMADISRQLEGHDLVLVAGA--PV-FRYHQYEPGPLLPPGAELIQITCDADEAAR 307 Query: 303 A-------------LAALADEVAPG---------TVAPVAGASRPQLPTGDLTSVSAADV 340 A LAALAD++ T AP A S P L + D+ Sbjct: 308 APMGDAVVGDVGRILAALADKIGEAARPAPQPRETPAPSAPGSVP------LAAERVLDL 361 Query: 341 VGALLPERAIVVDES-NTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDR 399 + L P AI V+ES +T + + P + GG +G+ +PAAVG +A PDR Sbjct: 362 MDELAPSDAIYVNESTSTIEAMWERMRWEHPGSYYFGAAGG-LGFAMPAAVGVQLAEPDR 420 Query: 400 PVLCLESDGSAMYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALD 459 V+ L DGSA Y+++ LW+ A+ ++ V VI NG Y LR + + A P ALD Sbjct: 421 QVIALIGDGSANYSVTALWTAAQHSVPVVFVILRNGTYGALRWFARALKAEHVP---ALD 477 Query: 460 LLDISRPTMDFVKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDV 508 + P +DFV IA G GV A RV T E FA A A P LI+V Sbjct: 478 V-----PDIDFVAIATGYGVEAVRVDTDEAFASAFARALKAGKPSLIEV 521 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: 614 Number of extensions: 27 Number of successful extensions: 4 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