Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate AO356_28690 AO356_28690 acetolactate synthase
Query= curated2:O53554 (515 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28690 Length = 513 Score = 394 bits (1011), Expect = e-114 Identities = 241/518 (46%), Positives = 306/518 (59%), Gaps = 13/518 (2%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGAQ ++ V G++ CFANPGT+E+ VAA+ + P ++ +L+LFEGV TGAADGY R Sbjct: 1 MNGAQLIVKAAVASGIEYCFANPGTTEIPLVAAMASAPALKPVLSLFEGVCTGAADGYGR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 IAG+PA L HLGPG NG+ANLHNARRA P+V V+GDHA++H YD PL SDI A+AG Sbjct: 61 IAGKPAMTLTHLGPGFANGIANLHNARRANTPIVNVIGDHASWHVNYDPPLASDIQALAG 120 Query: 121 TVSGWVRRTEAAADVGADAEAAI-AASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAA 179 +VS WVR + A+ VG D + A+ AA ++ QIA+LILP D+ + H A QA Sbjct: 121 SVSKWVRTSRTASGVGEDFQEAVRAAWQANGQIASLILPMDLQANTVQHEKAFTALQAPV 180 Query: 180 ---APVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLER 236 A V VA LR G + ++G GL AA R+ Q G R ETFP R Sbjct: 181 RRFAGDRVEAVAQALRDGRRLVFIVGDQGLSVAGLEAAGRLAQLPGVRLFAETFPRLSYR 240 Query: 237 GAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAE 296 G G+P ++RL YF E A LD +V AG P+S+F Y G+ S L + LAE Sbjct: 241 GGGLPDLDRLPYFPEVAIEILDQYDAVVCAGVPEPISYFGYEGIASRLAERE-RLLCLAE 299 Query: 297 PG-GAADALAALADEV-APGTVAPVAGASRPQLPTGD--LTSVSAADVVGALLPERAIVV 352 G A AL ALAD + AP V G +LP G+ LT S V+ A LP+ IV Sbjct: 300 VGDDVAGALTALADALEAPAYVPTPTGI---ELPPGEATLTPQSVGQVLAASLPDDCIVS 356 Query: 353 DESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMY 412 E TCG A+A A H LT TGGAIG GIP GAA+A V CL+SDGSA Y Sbjct: 357 VEGGTCGYPFFTASAHAARHRVLTNTGGAIGQGIPVGFGAAMAERGNKVFCLQSDGSAQY 416 Query: 413 TISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVK 472 TI LWS ARE L V +I N Y IL+ EL+R G ++ GP+AL L + RP +D+ Sbjct: 417 TIQTLWSIAREQLPVVILIAANHRYAILQNELRRFGM-TELGPEALSLTVLDRPRIDWKA 475 Query: 473 IAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 +A+G G+PA V T E AL A A+ GP LI++ + Sbjct: 476 LAKGYGLPASTVHTNGELQRALANAKADGGPCLIEMAL 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: 585 Number of extensions: 31 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: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 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 09 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