Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_036264249.1 DL86_RS17400 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000746085.1:WP_036264249.1 Length = 183 Score = 130 bits (328), Expect = 9e-36 Identities = 72/163 (44%), Positives = 102/163 (62%), Gaps = 2/163 (1%) Query: 4 KTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVG-ATECKDRSRMTIVVSAEDTPLEQ 62 + HTLSVLV+++PGVLARV LFS RG+NIESL V + SR+TIV S +EQ Sbjct: 21 EVHTLSVLVDNEPGVLARVVGLFSGRGYNIESLTVAEVAHAEHLSRITIVTSGTPEAIEQ 80 Query: 63 ITKQLNKLINVIKIVEQDDEH-SVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPE 121 I QL +L+ + K+ + +V RELA+IKV R + + + FRA VID S E Sbjct: 81 IGHQLERLVPIHKVTDLTLRGGAVERELAMIKVAGKGACRDEALRLADAFRARVIDASIE 140 Query: 122 SLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 S E TGN GK++ + ++ P G+ E+A++G+ ++SRGP I Sbjct: 141 SFVFELTGNVGKIDQFIDLMRPIGLVEVARTGVAAISRGPNPI 183 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: 81 Number of extensions: 3 Number of successful extensions: 3 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: 183 Length adjustment: 19 Effective length of query: 149 Effective length of database: 164 Effective search space: 24436 Effective search space used: 24436 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: 44 (21.6 bits)
Align candidate WP_036264249.1 DL86_RS17400 (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.30998.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-57 178.0 0.2 7.7e-57 177.8 0.2 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036264249.1 DL86_RS17400 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036264249.1 DL86_RS17400 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 177.8 0.2 7.7e-57 7.7e-57 3 158 .] 23 180 .. 21 180 .. 0.96 Alignments for each domain: == domain 1 score: 177.8 bits; conditional E-value: 7.7e-57 TIGR00119 3 hvlsvlvenepGvLsrvsGlfarrgfniesltvge.teekdlsrmtivvegddkvveqiekqleklvdv 70 h+lsvlv+nepGvL+rv+Glf+ rg+niesltv+e + ++lsr+tiv++g +++eqi +qle+lv++ lcl|NCBI__GCF_000746085.1:WP_036264249.1 23 HTLSVLVDNEPGVLARVVGLFSGRGYNIESLTVAEvAHAEHLSRITIVTSGTPEAIEQIGHQLERLVPI 91 99********************************8346789**************************** PP TIGR00119 71 lkvldlt.eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 kv+dlt v+rel+++kv +g r+e +l++ fr+rv+D s +s++ el+g+ +ki+ f++l+ lcl|NCBI__GCF_000746085.1:WP_036264249.1 92 HKVTDLTlRGGAVERELAMIKVAGKGACRDEALRLADAFRARVIDASIESFVFELTGNVGKIDQFIDLM 160 ******944579********************************************************* PP TIGR00119 139 kefgikevarsGlvalsrge 158 +++g++evar+G+ a+srg+ lcl|NCBI__GCF_000746085.1:WP_036264249.1 161 RPIGLVEVARTGVAAISRGP 180 ******************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (183 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: 6.70 // [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