Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_023625258.1 PN53_RS01915 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_000816635.1:WP_023625258.1 Length = 163 Score = 167 bits (423), Expect = 8e-47 Identities = 85/159 (53%), Positives = 122/159 (76%), Gaps = 1/159 (0%) Query: 5 HIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVVK 64 +++SVLV N PGVL +I+GLF+RR YNI S+T G T+ +ISRMTIV GDD + EQ+ K Sbjct: 4 YVLSVLVENHPGVLSKIAGLFSRRGYNIHSLTVGITEDPEISRMTIVSVGDDYMFEQINK 63 Query: 65 QLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESLT 124 QLNKLIEVIKVIDL + + V REL L+K+ A + ++K +++ A+ FR ++D+ ++S+ Sbjct: 64 QLNKLIEVIKVIDLSDHKAVARELSLVKVSADS-NNKVLIMEIAHTFRAKVLDMDEKSMI 122 Query: 125 VQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRGPKI 163 ++ITG + KIS+FI+L++P GIKE RTGLT+L RG K+ Sbjct: 123 IEITGSERKISSFIELMRPYGIKESIRTGLTSLQRGNKL 161 Lambda K H 0.317 0.134 0.362 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: 105 Number of extensions: 3 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: 169 Length of database: 163 Length adjustment: 18 Effective length of query: 151 Effective length of database: 145 Effective search space: 21895 Effective search space used: 21895 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: 43 (21.2 bits)
Align candidate WP_023625258.1 PN53_RS01915 (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.3272818.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-65 205.6 1.5 2.5e-65 205.4 1.5 1.0 1 NCBI__GCF_000816635.1:WP_023625258.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000816635.1:WP_023625258.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 205.4 1.5 2.5e-65 2.5e-65 2 158 .] 3 159 .. 2 159 .. 0.99 Alignments for each domain: == domain 1 score: 205.4 bits; conditional E-value: 2.5e-65 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvl 74 k vlsvlven+pGvLs+++Glf+rrg+ni+sltvg te++++srmtiv gdd + eqi+kql+kl++v+kv NCBI__GCF_000816635.1:WP_023625258.1 3 KYVLSVLVENHPGVLSKIAGLFSRRGYNIHSLTVGITEDPEISRMTIVSVGDDYMFEQINKQLNKLIEVIKVI 75 78*********************************************************************** PP TIGR00119 75 dlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikeva 147 dl++++ v rel lvkvsa ++++ i+e++++fr++v+D+ e+s+i+e++g+e kis+f++l++++gike NCBI__GCF_000816635.1:WP_023625258.1 76 DLSDHKAVARELSLVKVSADSNNKVLIMEIAHTFRAKVLDMDEKSMIIEITGSERKISSFIELMRPYGIKESI 148 ************************************************************************* PP TIGR00119 148 rsGlvalsrge 158 r+Gl++l rg+ NCBI__GCF_000816635.1:WP_023625258.1 149 RTGLTSLQRGN 159 *********85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (163 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.13 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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