Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_012330228.1 M446_RS01150 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_000019365.1:WP_012330228.1 Length = 180 Score = 121 bits (303), Expect = 7e-33 Identities = 65/158 (41%), Positives = 104/158 (65%), Gaps = 3/158 (1%) Query: 5 HIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTD-ISRMTIVVKGDDKVVEQVV 63 H ++V+V N+PGVL RI+GLF+ R YNI S+T T+ T +SR+TIV G + V++Q+ Sbjct: 20 HTLAVIVDNEPGVLSRIAGLFSGRGYNIESLTVSETEHTQHLSRITIVTTGTNAVIDQIK 79 Query: 64 KQLNKLIEVIKVIDLD-EEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQES 122 QL++L+ V +V+DL + E +ERELCL+K+ E + + ++ A+ F +D + S Sbjct: 80 AQLDRLVPVHRVVDLTLQGESLERELCLVKVVGKGE-HRVEAMRLASSFGARTLDATLNS 138 Query: 123 LTVQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRG 160 ++TG +I FI+L+ +G+ EISRTG+ A+ RG Sbjct: 139 FVFELTGSTDEIERFIRLMSEIGLVEISRTGVAAMSRG 176 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: 62 Number of extensions: 5 Number of successful extensions: 4 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: 180 Length adjustment: 19 Effective length of query: 150 Effective length of database: 161 Effective search space: 24150 Effective search space used: 24150 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: 44 (21.6 bits)
Align candidate WP_012330228.1 M446_RS01150 (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.12093.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-55 173.3 1.3 2.1e-55 173.1 1.3 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012330228.1 M446_RS01150 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012330228.1 M446_RS01150 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 173.1 1.3 2.1e-55 2.1e-55 2 157 .. 19 176 .. 18 177 .. 0.97 Alignments for each domain: == domain 1 score: 173.1 bits; conditional E-value: 2.1e-55 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgetee.kdlsrmtivvegddkvveqiekqleklvd 69 +h+l+v+v+nepGvLsr++Glf+ rg+niesltv+ete+ ++lsr+tiv++g + v++qi+ ql++lv+ lcl|NCBI__GCF_000019365.1:WP_012330228.1 19 RHTLAVIVDNEPGVLSRIAGLFSGRGYNIESLTVSETEHtQHLSRITIVTTGTNAVIDQIKAQLDRLVP 87 8************************************96267*************************** PP TIGR00119 70 vlkvldlt.eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkl 137 v +v+dlt + e+++rel+lvkv +ge+r e ++l++ f++r +D + +s++ el+g+ d i+ f++l lcl|NCBI__GCF_000019365.1:WP_012330228.1 88 VHRVVDLTlQGESLERELCLVKVVGKGEHRVEAMRLASSFGARTLDATLNSFVFELTGSTDEIERFIRL 156 *******95669********************************************************* PP TIGR00119 138 lkefgikevarsGlvalsrg 157 + e+g++e++r+G+ a+srg lcl|NCBI__GCF_000019365.1:WP_012330228.1 157 MSEIGLVEISRTGVAAMSRG 176 *******************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (180 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: 5.56 // [ok]
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