Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 8499377 DvMF_0154 acetolactate synthase 3 regulatory subunit (RefSeq)
Query= BRENDA::P9WKJ3 (168 letters) >FitnessBrowser__Miya:8499377 Length = 163 Score = 157 bits (396), Expect = 1e-43 Identities = 82/154 (53%), Positives = 112/154 (72%) Query: 6 HTLSVLVEDKPGVLARVAALFSRRGFNIESLAVGATECKDRSRMTIVVSAEDTPLEQITK 65 H LSVLVE++PGVL+RVA LFS RGFNIESL V T + S MTI S E+ +EQI K Sbjct: 3 HVLSVLVENEPGVLSRVAGLFSGRGFNIESLNVAPTLEEGVSLMTITTSGEEQIIEQIVK 62 Query: 66 QLNKLINVIKIVEQDDEHSVSRELALIKVQADAGSRSQVIEAVNLFRANVIDVSPESLTV 125 QL KL+ VIK+V+ D +V RE+ ++KVQAD R++V+ ++FR V+DVS LT+ Sbjct: 63 QLRKLVTVIKVVDFIDVSAVEREMVMVKVQADDARRAEVLRIADIFRCKVVDVSLNDLTL 122 Query: 126 EATGNRGKLEALLRVLEPFGIREIAQSGMVSLSR 159 EATG+ GK++A+L +L FGI+EIA++G V++ R Sbjct: 123 EATGDHGKIQAILSLLARFGIKEIARTGTVAMRR 156 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: 95 Number of extensions: 3 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: 163 Length adjustment: 18 Effective length of query: 150 Effective length of database: 145 Effective search space: 21750 Effective search space used: 21750 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 8499377 DvMF_0154 (acetolactate synthase 3 regulatory subunit (RefSeq))
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.27050.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-63 197.2 6.6 8.9e-63 197.1 6.6 1.0 1 lcl|FitnessBrowser__Miya:8499377 DvMF_0154 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499377 DvMF_0154 acetolactate synthase 3 regulatory subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.1 6.6 8.9e-63 8.9e-63 1 157 [. 1 157 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 197.1 bits; conditional E-value: 8.9e-63 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldlt 77 ++hvlsvlvenepGvLsrv+Glf+ rgfniesl v+ t e+++s mti+++g+++++eqi kql+klv v+kv+d+ lcl|FitnessBrowser__Miya:8499377 1 MRHVLSVLVENEPGVLSRVAGLFSGRGFNIESLNVAPTLEEGVSLMTITTSGEEQIIEQIVKQLRKLVTVIKVVDFI 77 69*************************************************************************** PP TIGR00119 78 eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlval 154 + + v+re+v+vkv+a +r+e+ ++++ifr +vvDvs + l++e +g+++ki+a+l+ll+ fgike+ar+G+va+ lcl|FitnessBrowser__Miya:8499377 78 DVSAVEREMVMVKVQADDARRAEVLRIADIFRCKVVDVSLNDLTLEATGDHGKIQAILSLLARFGIKEIARTGTVAM 154 ***************************************************************************** PP TIGR00119 155 srg 157 r+ lcl|FitnessBrowser__Miya:8499377 155 RRS 157 995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (163 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: 7.31 // [ok]
This GapMind analysis is from Apr 09 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