Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_013135582.1 ARNIT_RS08880 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_000092245.1:WP_013135582.1 Length = 165 Score = 114 bits (284), Expect = 1e-30 Identities = 62/154 (40%), Positives = 101/154 (65%), Gaps = 4/154 (2%) Query: 6 IISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVVKQ 65 +ISV+VLN+ VL RI+GLF+ R YNI S+T ++ SRMTIV GD +V++Q+VKQ Sbjct: 16 VISVIVLNENNVLSRIAGLFSARGYNIDSLTVAPISDSEYSRMTIVTTGDRRVIDQIVKQ 75 Query: 66 LNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESLTV 125 LNKLI V++V + + VE+E L+KI P + + S V A + G+I +++Q+ + + Sbjct: 76 LNKLIPVLRV--NEHFDVVEKETVLVKI--PVDQNLSDVDVLARAYNGSIQNVTQDCIII 131 Query: 126 QITGDKTKISAFIKLVKPMGIKEISRTGLTALMR 159 T + ++I+ F+K++K EI ++G+ A+ R Sbjct: 132 SATDEPSRIANFVKVIKNYNPIEIVKSGVVAMER 165 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: 79 Number of extensions: 3 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: 165 Length adjustment: 18 Effective length of query: 151 Effective length of database: 147 Effective search space: 22197 Effective search space used: 22197 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 WP_013135582.1 ARNIT_RS08880 (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.30939.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-45 140.3 5.1 3e-45 140.1 5.1 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013135582.1 ARNIT_RS08880 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013135582.1 ARNIT_RS08880 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 140.1 5.1 3e-45 3e-45 2 156 .. 14 165 .] 13 165 .] 0.97 Alignments for each domain: == domain 1 score: 140.1 bits; conditional E-value: 3e-45 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdv 70 ++v+sv+v ne vLsr++Glf++rg+ni+sltv+ +++ srmtiv++gd +v++qi kql+kl++v lcl|NCBI__GCF_000092245.1:WP_013135582.1 14 RKVISVIVLNENNVLSRIAGLFSARGYNIDSLTVAPISDSEYSRMTIVTTGDRRVIDQIVKQLNKLIPV 82 89******************************************************************* PP TIGR00119 71 lkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllk 139 l+v++ ++v++e vlvk+ + ++++++ l+ + g++ +v++d +i+ + ++ +i f+k++k lcl|NCBI__GCF_000092245.1:WP_013135582.1 83 LRVNEHF--DVVEKETVLVKIPV-DQNLSDVDVLARAYNGSIQNVTQDCIIISATDEPSRIANFVKVIK 148 ***9876..57**********86.5789***************************************** PP TIGR00119 140 efgikevarsGlvalsr 156 ++ e+++sG+va+ r lcl|NCBI__GCF_000092245.1:WP_013135582.1 149 NYNPIEIVKSGVVAMER 165 ***************88 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (165 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: 4.97 // [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