Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012566957.1 RC1_RS08515 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000016185.1:WP_012566957.1 Length = 517 Score = 454 bits (1169), Expect = e-132 Identities = 261/520 (50%), Positives = 320/520 (61%), Gaps = 13/520 (2%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA+AL L G+D FANPGTSEMH V AL AVP MR + LFEGV +GAAD +AR Sbjct: 1 MNGAEALAQGLRSAGLDTVFANPGTSEMHLVGALAAVPGMRLVPGLFEGVLSGAADAHAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 + GRPA +LLHLGPGL N ANLHNA RA P+V +VG+H + +D PL SDI+A+A Sbjct: 61 LTGRPAGLLLHLGPGLANATANLHNASRAGSPVVSIVGEHRSSLLPFDPPLASDIEAIAR 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAAS-RSGSQIATLILPADVCWSDGAHAAAGVPAQAAA 179 +GWVRR E + A AA+AA+ + ++ A LI+PADV W + G A A Sbjct: 121 PYAGWVRRLERPEEAAEAARAAVAAALGTPARHAVLIVPADVAWGEAGRPDTG--GDAPA 178 Query: 180 APVDVGP------VAGVLRS-GEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPT 232 A VD P +A +LR+ G + +L+GG G G A RI ATG R L ETFPT Sbjct: 179 ARVDPVPDARIELMADMLRTGGHASALLLGGGLLDGRGSLLAGRIAAATGCRVLSETFPT 238 Query: 233 CLERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVH 292 RGAG+P +ERL YF LDGV+ LVLAGAR PV+FF YPG P LVP GC V Sbjct: 239 AQRRGAGLPYLERLPYFPADVLQTLDGVRSLVLAGAREPVAFFGYPGRPDRLVPEGCGVD 298 Query: 293 VLAEPG-GAADALAALADEVAPGTVAPV-AGASRPQLPTGDLTSVSAADVVGALLPERAI 350 L PG AL ALA + G+ PV RP P G LT + +G+LLPE AI Sbjct: 299 RLCGPGEDGHAALEALAGLLGAGSSDPVLLPEQRPLRPEGRLTVDAVGQAIGSLLPENAI 358 Query: 351 VVDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSA 410 VVDE+ T G + T AP HDWL+LTGG++G+G+PAA+GAA+AAP R VL L DGSA Sbjct: 359 VVDEAITSGAPCYRFTVQAPTHDWLSLTGGSLGFGLPAALGAAMAAPGRKVLALVGDGSA 418 Query: 411 MYTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDF 470 +YT LWS AR DV V++ N AY IL++E +G GS P P A DL+ + P +DF Sbjct: 419 LYTNQALWSLARTGADVVVVVFANRAYRILQLEYANMGLGS-PAPAAQDLMRLDTPDLDF 477 Query: 471 VKIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 V +A G G+ A R EF L A AEPGP LI+ VV Sbjct: 478 VSLARGFGILAARADEAGEFTRILERALAEPGPFLIETVV 517 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: 762 Number of extensions: 37 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: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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