Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_093393434.1 BM091_RS03290 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_900114975.1:WP_093393434.1 Length = 174 Score = 168 bits (426), Expect = 4e-47 Identities = 85/161 (52%), Positives = 120/161 (74%) Query: 4 KTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQI 63 K HT+ VLVE++PGVL+RVA LFS RGFNIESL V T SR+T+V + ++ +EQI Sbjct: 11 KRHTIGVLVENQPGVLSRVAGLFSGRGFNIESLTVAETNEPGMSRITLVTTGDEHIVEQI 70 Query: 64 TKQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESL 123 KQLNKLINVIK+++ D V RE+ALIKV+AD SR++++ V++FRA V+DVSP S Sbjct: 71 IKQLNKLINVIKVLDFRDTEFVEREMALIKVKADKQSRAEILRIVDIFRAKVVDVSPHSY 130 Query: 124 TVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGI 164 VE TG+ GK++A+L +L +GI E+A++G +++RG + I Sbjct: 131 IVEVTGDEGKIQAILDLLSEYGILELARTGKAAMARGKKDI 171 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: 105 Number of extensions: 2 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_093393434.1 BM091_RS03290 (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.9182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-71 223.9 2.3 5.4e-71 223.8 2.3 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093393434.1 BM091_RS03290 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093393434.1 BM091_RS03290 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 223.8 2.3 5.4e-71 5.4e-71 1 157 [. 11 167 .. 11 168 .. 0.99 Alignments for each domain: == domain 1 score: 223.8 bits; conditional E-value: 5.4e-71 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 k+h++ vlven+pGvLsrv+Glf+ rgfniesltv+et+e+++sr+t+v++gd+++veqi+kql+kl++ lcl|NCBI__GCF_900114975.1:WP_093393434.1 11 KRHTIGVLVENQPGVLSRVAGLFSGRGFNIESLTVAETNEPGMSRITLVTTGDEHIVEQIIKQLNKLIN 79 69******************************************************************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 v+kvld+ ++e v+re++l+kv+a ++r+ei ++++ifr++vvDvs++s+ive++g+e+ki+a+l+ll lcl|NCBI__GCF_900114975.1:WP_093393434.1 80 VIKVLDFRDTEFVEREMALIKVKADKQSRAEILRIVDIFRAKVVDVSPHSYIVEVTGDEGKIQAILDLL 148 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrg 157 e+gi+e+ar+G+ a++rg lcl|NCBI__GCF_900114975.1:WP_093393434.1 149 SEYGILELARTGKAAMARG 167 ******************8 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.87 // [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