Align Acetolactate synthase small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase small subunit; AHAS; ALS (uncharacterized)
to candidate Echvi_2057 Echvi_2057 acetolactate synthase, small subunit
Query= curated2:A0QUX7 (170 letters) >FitnessBrowser__Cola:Echvi_2057 Length = 167 Score = 95.9 bits (237), Expect = 3e-25 Identities = 52/154 (33%), Positives = 93/154 (60%), Gaps = 1/154 (0%) Query: 8 HTLSVLVEDKPGVLARVSSLFSRRGFNIQSLAVGATEQKDMSRMTIVVSVEDSPLEQITK 67 +T+S+ E+ G+L RV+ +F+RRG NI +L +++ + R+TI V+ + + QI K Sbjct: 4 YTVSLFTENFIGILNRVTLIFTRRGVNIDALTASESKEDGVHRITIEVTTTEDQVIQIVK 63 Query: 68 QLNKLINVIKIVEQEEDNSVSRELALIKVRADATTRGQIIEAVNLFRAKVVDVSTESLTI 127 Q K+I+VIK ++D V +E+AL K+ + G + + + + A+++ E + I Sbjct: 64 QTEKIIDVIKSFYYKDDEVVYQEIALYKIPISSLDPG-LEKVIRQYNARIISAEKEFVVI 122 Query: 128 EATGTPEKLEALLRVLEPYGIREIAQSGVVSVSR 161 E TG E +ALL +L+ + I E A+SG V+V++ Sbjct: 123 EMTGHKEDTKALLEILKDFNILEFARSGRVAVAK 156 Lambda K H 0.313 0.130 0.334 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: 73 Number of extensions: 4 Number of successful extensions: 2 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: 170 Length of database: 167 Length adjustment: 18 Effective length of query: 152 Effective length of database: 149 Effective search space: 22648 Effective search space used: 22648 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 43 (21.2 bits)
Align candidate Echvi_2057 Echvi_2057 (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.723.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-36 110.8 2.6 3.7e-36 110.5 2.6 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2057 Echvi_2057 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2057 Echvi_2057 acetolactate synthase, small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 110.5 2.6 3.7e-36 3.7e-36 2 156 .. 3 156 .. 2 158 .. 0.95 Alignments for each domain: == domain 1 score: 110.5 bits; conditional E-value: 3.7e-36 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvld 75 + ++s+ en G+L+rv+ +f+rrg ni++lt +e+ e+++ r+ti+v++ ++ v qi kq ek++dv+k lcl|FitnessBrowser__Cola:Echvi_2057 3 RYTVSLFTENFIGILNRVTLIFTRRGVNIDALTASESKEDGVHRITIEVTTTEDQVIQIVKQTEKIIDVIKSFY 76 567899999***************************************************************** PP TIGR00119 76 lteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevars 149 ++++e+v +e++l k+ ++ + +++++ ++ +r++ ++ +++e++g+++ +a+l++lk+f i+e ars lcl|FitnessBrowser__Cola:Echvi_2057 77 YKDDEVVYQEIALYKIPISSLD-PGLEKVIRQYNARIISAEKEFVVIEMTGHKEDTKALLEILKDFNILEFARS 149 ****************987654.57899999******************************************* PP TIGR00119 150 Glvalsr 156 G va+++ lcl|FitnessBrowser__Cola:Echvi_2057 150 GRVAVAK 156 ****986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (167 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: 4.83 // [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