Align Probable acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate 8501909 DvMF_2624 acetolactate synthase, small subunit (RefSeq)
Query= curated2:O28555 (159 letters) >FitnessBrowser__Miya:8501909 Length = 160 Score = 118 bits (296), Expect = 4e-32 Identities = 58/158 (36%), Positives = 99/158 (62%), Gaps = 1/158 (0%) Query: 1 MKHTIAVLVENKPGVLARVAGLFRRRGFNIESLTVGTTERDDLSRMTIVVEGDDKVVEQV 60 MKHT++VLV+N+ G +A +FRRRG + S++ TE D+SR+ + VE + +E + Sbjct: 1 MKHTLSVLVKNRAGAVAEATDVFRRRGISFRSISCAETEDFDVSRLVLTVEDHEAELESI 60 Query: 61 IKQLNKLIETIKVSEITESS-VERELCLIRVHAPPEKRGEIVELTNIFRARIVDVSRDSF 119 ++L V +++ V+REL L++V E +I+++ +FRA ++ + +++ Sbjct: 61 AEELRAQDVVAMVEDLSRRDFVDRELVLVKVDVTRETTTQIMQVCEVFRASVIGMGQETM 120 Query: 120 IIEVTGDEDKVSAFIDLMRQYGIKELARTGKVAMVRGN 157 +E+TGD KV FI ++R +GI+ LARTG VAM RG+ Sbjct: 121 TVEMTGDTQKVDGFIRMLRPFGIRSLARTGVVAMKRGD 158 Lambda K H 0.319 0.137 0.365 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: 81 Number of extensions: 5 Number of successful extensions: 2 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: 159 Length of database: 160 Length adjustment: 17 Effective length of query: 142 Effective length of database: 143 Effective search space: 20306 Effective search space used: 20306 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 43 (21.2 bits)
Align candidate 8501909 DvMF_2624 (acetolactate synthase, small subunit (RefSeq))
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.1176.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-42 130.0 5.5 4.2e-42 129.9 5.5 1.0 1 lcl|FitnessBrowser__Miya:8501909 DvMF_2624 acetolactate synthase, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501909 DvMF_2624 acetolactate synthase, small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 129.9 5.5 4.2e-42 4.2e-42 1 158 [] 1 158 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 129.9 bits; conditional E-value: 4.2e-42 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldlt 77 +kh+lsvlv+n++G+++ + +f+rrg s+ +ete+ d+sr+ ++ve ++ +e i l+ + v v+dl+ lcl|FitnessBrowser__Miya:8501909 1 MKHTLSVLVKNRAGAVAEATDVFRRRGISFRSISCAETEDFDVSRLVLTVEDHEAELESIAEELRAQDVVAMVEDLS 77 79*****************************************************************9999****** PP TIGR00119 78 eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlval 154 ++ v+relvlvkv ++ e+ ++i+++ e+fr++v+ + +++++ve++g+ +k++ f+++l++fgi+ +ar+G+va+ lcl|FitnessBrowser__Miya:8501909 78 RRDFVDRELVLVKVDVTRETTTQIMQVCEVFRASVIGMGQETMTVEMTGDTQKVDGFIRMLRPFGIRSLARTGVVAM 154 ***************************************************************************** PP TIGR00119 155 srge 158 rg+ lcl|FitnessBrowser__Miya:8501909 155 KRGD 158 **85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (160 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: 4.50 // [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