Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate 209572 DVU0626 acetolactate synthase, small subunit
Query= metacyc::MONOMER-11901 (169 letters) >MicrobesOnline__882:209572 Length = 159 Score = 118 bits (296), Expect = 4e-32 Identities = 62/160 (38%), Positives = 104/160 (65%), Gaps = 3/160 (1%) Query: 1 MKNTHIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVE 60 MKNT +SVLV N+ GV+ + + +F + N++SI+ T++ D+SR+ + V+G + + + Sbjct: 1 MKNT--LSVLVRNQVGVVAQATEVFRQHNVNLNSISCAETEAFDVSRLMLTVEGQEHLFD 58 Query: 61 QVVKQLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQ 120 V L V++V DL + V+REL L+K+ A T + +QV+Q +FR +V + Q Sbjct: 59 AVKADLASKDFVLEVEDLSARDLVDRELALVKV-AVTRETTTQVMQVCEVFRATVVGMGQ 117 Query: 121 ESLTVQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRG 160 E++T++ITGD K+ FI+L++P GI+ ++RTG AL RG Sbjct: 118 ETMTLEITGDMRKVDGFIRLLRPFGIRSLARTGSVALARG 157 Lambda K H 0.317 0.134 0.362 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: 52 Number of extensions: 6 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: 169 Length of database: 159 Length adjustment: 18 Effective length of query: 151 Effective length of database: 141 Effective search space: 21291 Effective search space used: 21291 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 (21.7 bits) S2: 43 (21.2 bits)
Align candidate 209572 DVU0626 (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.1653.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-41 125.9 4.2 7.8e-41 125.8 4.2 1.0 1 lcl|MicrobesOnline__882:209572 DVU0626 acetolactate synthase, s Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209572 DVU0626 acetolactate synthase, small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 125.8 4.2 7.8e-41 7.8e-41 1 158 [] 1 158 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 125.8 bits; conditional E-value: 7.8e-41 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldltes 79 +k +lsvlv+n+ Gv+++ + +f++ + n++s+ +ete d+sr+ ++veg+++ + ++ l vl+v+dl+ + lcl|MicrobesOnline__882:209572 1 MKNTLSVLVRNQVGVVAQATEVFRQHNVNLNSISCAETEAFDVSRLMLTVEGQEHLFDAVKADLASKDFVLEVEDLSAR 79 6899*************************************************************************** PP TIGR00119 80 eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGlvalsrge 158 + v+rel+lvkv ++ e+ ++++++ e+fr+ vv + ++++++e++g+ k++ f++ll++fgi+ +ar+G val+rg+ lcl|MicrobesOnline__882:209572 80 DLVDRELALVKVAVTRETTTQVMQVCEVFRATVVGMGQETMTLEITGDMRKVDGFIRLLRPFGIRSLARTGSVALARGD 158 *****************************************************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (159 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 4.24 // [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