Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_012045963.1 BBTA_RS28460 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000015165.1:WP_012045963.1 Length = 180 Score = 135 bits (339), Expect = 5e-37 Identities = 70/163 (42%), Positives = 107/163 (65%), Gaps = 2/163 (1%) Query: 4 KTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATEC-KDRSRMTIVVSAEDTPLEQ 62 +THTLSVLV+++PGVLARV LFS RG+NIESL V TE K SR+TIV + ++Q Sbjct: 18 ETHTLSVLVQNEPGVLARVIGLFSGRGYNIESLTVSETESQKHLSRITIVTTGTPMVIQQ 77 Query: 63 ITKQLNKLINVIKIVEQD-DEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPE 121 I QL++++ V ++V+ + ++ RELA+IKV+ R + + + FRA VID + E Sbjct: 78 IKHQLDRMVPVYRVVDMTLTKRAIERELAMIKVRGTGEPRVEALRLADAFRARVIDATTE 137 Query: 122 SLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 S E TGN K+ + ++ P G+ E+A++G+ ++ RGP G+ Sbjct: 138 SFVFEITGNTDKISQFIDLMRPLGLVEVARTGIAAIGRGPEGM 180 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: 86 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: 180 Length adjustment: 19 Effective length of query: 149 Effective length of database: 161 Effective search space: 23989 Effective search space used: 23989 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_012045963.1 BBTA_RS28460 (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.1742.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-59 185.1 0.8 5e-59 184.9 0.8 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012045963.1 BBTA_RS28460 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012045963.1 BBTA_RS28460 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 184.9 0.8 5e-59 5e-59 2 158 .] 19 177 .. 18 177 .. 0.96 Alignments for each domain: == domain 1 score: 184.9 bits; conditional E-value: 5e-59 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgete.ekdlsrmtivvegddkvveqiekqleklvd 69 +h+lsvlv+nepGvL+rv+Glf+ rg+niesltv+ete +k+lsr+tiv++g v+ qi++ql+++v+ lcl|NCBI__GCF_000015165.1:WP_012045963.1 19 THTLSVLVQNEPGVLARVIGLFSGRGYNIESLTVSETEsQKHLSRITIVTTGTPMVIQQIKHQLDRMVP 87 79***********************************94578*************************** PP TIGR00119 70 vlkvldlt.eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkl 137 v++v+d+t ++ ++rel+++kv+ +ge r e +l++ fr+rv+D + +s++ e++g+ dkis f++l lcl|NCBI__GCF_000015165.1:WP_012045963.1 88 VYRVVDMTlTKRAIERELAMIKVRGTGEPRVEALRLADAFRARVIDATTESFVFEITGNTDKISQFIDL 156 *******944679******************************************************** PP TIGR00119 138 lkefgikevarsGlvalsrge 158 ++++g++evar+G+ a+ rg+ lcl|NCBI__GCF_000015165.1:WP_012045963.1 157 MRPLGLVEVARTGIAAIGRGP 177 *****************9985 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: 7.23 // [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