Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_010936560.1 DET_RS04340 acetolactate synthase small subunit
Query= BRENDA::P9WKJ3 (168 letters) >NCBI__GCF_000011905.1:WP_010936560.1 Length = 178 Score = 165 bits (417), Expect = 4e-46 Identities = 81/167 (48%), Positives = 125/167 (74%), Gaps = 2/167 (1%) Query: 1 MSPKTHTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPL 60 MSP HT+ LVED+PGVL R+A+LF RRGFNI+S+AVG +E SRMTIVV +T + Sbjct: 1 MSPTKHTIVALVEDRPGVLNRMASLFRRRGFNIDSIAVGRSETPGFSRMTIVVDGANTMV 60 Query: 61 EQITKQLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSP 120 EQ+ KQL+K+++V+K+ + + + RELALIKV++ +RS++++ V++FRA ++DV+ Sbjct: 61 EQVRKQLDKVVDVVKVSDITGQDIICRELALIKVKSTPANRSEIMQIVDIFRAKIVDVAS 120 Query: 121 ESLTVEATGNRGKLEALLRVLEPFGIREIAQSGMVSLSRGPRGIGTA 167 +SLTVE TG+ K+ +L +L FGI+EI ++G ++++RG G+ TA Sbjct: 121 DSLTVEVTGDEEKVNSLYNLLRAFGIKEITRTGRIAMTRG--GLATA 165 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: 103 Number of extensions: 4 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: 178 Length adjustment: 18 Effective length of query: 150 Effective length of database: 160 Effective search space: 24000 Effective search space used: 24000 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_010936560.1 DET_RS04340 (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.2134753.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-65 204.1 4.6 6.9e-65 203.9 4.6 1.0 1 NCBI__GCF_000011905.1:WP_010936560.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000011905.1:WP_010936560.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 203.9 4.6 6.9e-65 6.9e-65 2 157 .. 5 160 .. 4 161 .. 0.99 Alignments for each domain: == domain 1 score: 203.9 bits; conditional E-value: 6.9e-65 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvl 74 kh++ +lve++pGvL+r++ lf+rrgfni+s++vg++e+++ srmtivv+g + +veq++kql+k+vdv+kv+ NCBI__GCF_000011905.1:WP_010936560.1 5 KHTIVALVEDRPGVLNRMASLFRRRGFNIDSIAVGRSETPGFSRMTIVVDGANTMVEQVRKQLDKVVDVVKVS 77 8************************************************************************ PP TIGR00119 75 dlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikeva 147 d+t ++i+ rel+l+kv++++ +r+ei+++++ifr+++vDv+ dsl+ve++g+e+k++++ +ll+ fgike++ NCBI__GCF_000011905.1:WP_010936560.1 78 DITGQDIICRELALIKVKSTPANRSEIMQIVDIFRAKIVDVASDSLTVEVTGDEEKVNSLYNLLRAFGIKEIT 150 ************************************************************************* PP TIGR00119 148 rsGlvalsrg 157 r+G +a++rg NCBI__GCF_000011905.1:WP_010936560.1 151 RTGRIAMTRG 160 ********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (178 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: 9.32 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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