Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_012674812.1 SULAZ_RS00400 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_000021545.1:WP_012674812.1 Length = 188 Score = 161 bits (408), Expect = 5e-45 Identities = 78/155 (50%), Positives = 115/155 (74%) Query: 5 HIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVVK 64 H+I+V V + GVL RI+GLF R YNI S+T G T I+R+TIVV+GD++V+EQ++K Sbjct: 20 HVITVKVQHNFGVLARITGLFAGRGYNIESLTVGRTHEPHIARITIVVEGDERVIEQIIK 79 Query: 65 QLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESLT 124 QL KLIE ++V D+ + +EREL LIKI+ + ++ ++++ NIFR +VD+S ++ T Sbjct: 80 QLRKLIETLRVRDITDIPHIERELALIKIHTENDRTRDEIMRLVNIFRAKVVDVSTDTYT 139 Query: 125 VQITGDKTKISAFIKLVKPMGIKEISRTGLTALMR 159 V+ITGD+ KI AFI L+KP GIKE++RTG A++R Sbjct: 140 VEITGDEDKIEAFISLIKPFGIKEMARTGTLAMVR 174 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: 101 Number of extensions: 1 Number of successful extensions: 1 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: 188 Length adjustment: 19 Effective length of query: 150 Effective length of database: 169 Effective search space: 25350 Effective search space used: 25350 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_012674812.1 SULAZ_RS00400 (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.16124.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-68 214.1 5.0 5.8e-68 213.9 5.0 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012674812.1 SULAZ_RS00400 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674812.1 SULAZ_RS00400 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 213.9 5.0 5.8e-68 5.8e-68 2 157 .. 19 175 .. 18 176 .. 0.98 Alignments for each domain: == domain 1 score: 213.9 bits; conditional E-value: 5.8e-68 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 +hv++v v+++ GvL+r++Glfa rg+niesltvg+t e++++r+tivvegd++v+eqi+kql+kl+++ lcl|NCBI__GCF_000021545.1:WP_012674812.1 19 RHVITVKVQHNFGVLARITGLFAGRGYNIESLTVGRTHEPHIARITIVVEGDERVIEQIIKQLRKLIET 87 8******************************************************************** PP TIGR00119 71 lkvldlteseivkrelvlvkvsalg.eerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 l+v+d+t+ +++rel+l+k+++ +r+ei++l++ifr++vvDvs d+++ve++g+edki+af++l+ lcl|NCBI__GCF_000021545.1:WP_012674812.1 88 LRVRDITDIPHIERELALIKIHTENdRTRDEIMRLVNIFRAKVVDVSTDTYTVEITGDEDKIEAFISLI 156 *********************98762689**************************************** PP TIGR00119 139 kefgikevarsGlvalsrg 157 k+fgike+ar+G++a++r+ lcl|NCBI__GCF_000021545.1:WP_012674812.1 157 KPFGIKEMARTGTLAMVRE 175 ******************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (188 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: 7.69 // [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