Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_026127525.1 D471_RS0108135 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000341125.1:WP_026127525.1 Length = 174 Score = 202 bits (513), Expect = 3e-57 Identities = 101/160 (63%), Positives = 130/160 (81%) Query: 5 THTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQIT 64 +HTLSVLVED PG+LAR ++LFSRRGFNI+SL+V TE SRMTIVV+ + PLEQ+T Sbjct: 3 SHTLSVLVEDTPGILARASSLFSRRGFNIDSLSVSTTEYAGLSRMTIVVNCDLHPLEQVT 62 Query: 65 KQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLT 124 KQLNKL+NV+KIVE D SV REL L+KV+ADA SR+ V++ LFRA+V+DVSP+ + Sbjct: 63 KQLNKLVNVVKIVEMDTTASVQRELLLVKVKADASSRTHVLQTAELFRAHVVDVSPDVVV 122 Query: 125 VEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 +EATG+ KL+AL++ LEPFGIRE+ +SG+V+L RGPR I Sbjct: 123 IEATGDPEKLDALVKNLEPFGIRELVKSGLVALGRGPRSI 162 Lambda K H 0.315 0.131 0.347 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: 124 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: 168 Length of database: 174 Length adjustment: 18 Effective length of query: 150 Effective length of database: 156 Effective search space: 23400 Effective search space used: 23400 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: 43 (21.2 bits)
Align candidate WP_026127525.1 D471_RS0108135 (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.24556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-62 195.4 0.3 3.4e-62 195.2 0.3 1.0 1 lcl|NCBI__GCF_000341125.1:WP_026127525.1 D471_RS0108135 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_026127525.1 D471_RS0108135 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 195.2 0.3 3.4e-62 3.4e-62 2 158 .] 3 159 .. 2 159 .. 0.99 Alignments for each domain: == domain 1 score: 195.2 bits; conditional E-value: 3.4e-62 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 h+lsvlve+ pG+L+r s lf+rrgfni+sl v++te ++lsrmtivv+ d + +eq++kql+klv+v lcl|NCBI__GCF_000341125.1:WP_026127525.1 3 SHTLSVLVEDTPGILARASSLFSRRGFNIDSLSVSTTEYAGLSRMTIVVNCDLHPLEQVTKQLNKLVNV 71 69******************************************************************* PP TIGR00119 71 lkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllk 139 +k+++++ +++v+rel+lvkv+a +++r+++ +++e fr++vvDvs+d +++e +g+++k++a++k l+ lcl|NCBI__GCF_000341125.1:WP_026127525.1 72 VKIVEMDTTASVQRELLLVKVKADASSRTHVLQTAELFRAHVVDVSPDVVVIEATGDPEKLDALVKNLE 140 ********************************************************************* PP TIGR00119 140 efgikevarsGlvalsrge 158 +fgi+e+++sGlval rg+ lcl|NCBI__GCF_000341125.1:WP_026127525.1 141 PFGIRELVKSGLVALGRGP 159 *****************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (174 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.82 // [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