Align Acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate CA265_RS15810 CA265_RS15810 acetolactate synthase small subunit
Query= curated2:P37252 (172 letters) >FitnessBrowser__Pedo557:CA265_RS15810 Length = 212 Score = 101 bits (251), Expect = 9e-27 Identities = 58/154 (37%), Positives = 89/154 (57%), Gaps = 2/154 (1%) Query: 5 ITLTVVNRSGVLNRITGLFTKRHYNIESITVGHTETAGVSRITFVVHVEGENDVEQLTKQ 64 IT+ NR G+LNRI +F+KR NIES+ +E G+ R V+H EG V +L +Q Sbjct: 24 ITVYAENRIGLLNRIAIIFSKRKINIESLNTSPSEIDGIHRFNIVIH-EGYEVVRKLARQ 82 Query: 65 LNKQIDVLKVTDITNQSIVQRELALIKV-VSAPSTRTEINGIIEPFRASVVDVSRDSIVV 123 + KQI+VLKV TN+ I+ +ELAL KV + + + ++ + AS V + +D V Sbjct: 83 IEKQIEVLKVYFNTNEEIIWQELALYKVSTDEIAEKVTVERLLRQYGASAVVIRKDYTVF 142 Query: 124 QVTGESNKIEALIELLKPYGIKEIARTGTTAFAR 157 VTG + +AL++ L+PY + E R+ A + Sbjct: 143 AVTGHREETDALVKALEPYELIEFVRSARVAIIK 176 Lambda K H 0.315 0.131 0.340 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: 78 Number of extensions: 4 Number of successful extensions: 3 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: 172 Length of database: 212 Length adjustment: 20 Effective length of query: 152 Effective length of database: 192 Effective search space: 29184 Effective search space used: 29184 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 (21.6 bits) S2: 44 (21.6 bits)
Align candidate CA265_RS15810 CA265_RS15810 (acetolactate synthase small subunit)
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00119.hmm # target sequence database: /tmp/gapView.12494.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00119 [M=158] Accession: TIGR00119 Description: acolac_sm: acetolactate synthase, small subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-31 95.8 3.1 1.6e-31 95.5 3.1 1.1 1 lcl|FitnessBrowser__Pedo557:CA265_RS15810 CA265_RS15810 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15810 CA265_RS15810 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 95.5 3.1 1.6e-31 1.6e-31 3 156 .. 22 176 .. 20 178 .. 0.96 Alignments for each domain: == domain 1 score: 95.5 bits; conditional E-value: 1.6e-31 TIGR00119 3 hvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 +++v en+ G L+r++ +f++r+ niesl + +e +++ r iv++ +vv ++ +q+ek+++v lcl|FitnessBrowser__Pedo557:CA265_RS15810 22 YTITVYAENRIGLLNRIAIIFSKRKINIESLNTSPSEIDGIHRFNIVIHEGYEVVRKLARQIEKQIEV 89 5799999************************************************************* PP TIGR00119 71 lkvldlteseivkrelvlvkvsalg.eerneikelteifrgrvvDvsedslivelsgkedkisaflkl 137 lkv t++ei+ +el+l kvs+ e+ +++l +++++ v + +d ++ ++g+ + +a++k+ lcl|FitnessBrowser__Pedo557:CA265_RS15810 90 LKVYFNTNEEIIWQELALYKVSTDEiAEKVTVERLLRQYGASAVVIRKDYTVFAVTGHREETDALVKA 157 *********************9976257889************************************* PP TIGR00119 138 lkefgikevarsGlvalsr 156 l+++ + e +rs va+ + lcl|FitnessBrowser__Pedo557:CA265_RS15810 158 LEPYELIEFVRSARVAIIK 176 ***************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (212 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.88 // [ok]
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