Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate WP_012475113.1 CPHAMN1_RS08565 acetolactate synthase small subunit
Query= metacyc::MONOMER-11901 (169 letters) >NCBI__GCF_000020545.1:WP_012475113.1 Length = 159 Score = 141 bits (356), Expect = 5e-39 Identities = 64/156 (41%), Positives = 110/156 (70%), Gaps = 1/156 (0%) Query: 5 HIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTDSTDISRMTIVVKGDDKVVEQVVK 64 HIISVLV NK G L R++ +F+ R +N+ SI+ G T+ +ISRMTIV +GDD ++ Q++K Sbjct: 3 HIISVLVENKFGTLNRVAAMFSARGFNLESISIGETEDNEISRMTIVTRGDDSIISQILK 62 Query: 65 QLNKLIEVIKVIDLDEEECVERELCLIKIYAPTESSKSQVIQYANIFRGNIVDLSQESLT 124 QLN+LI+ +KV+D+ + + RE+ L+ + + S+ ++ ++F+ +VD+ Q+S+T Sbjct: 63 QLNRLIDTLKVVDVTNKPHISREVLLMTLNR-GKQSQQEIFNLIDVFKAKVVDIKQKSIT 121 Query: 125 VQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRG 160 +++ G KI+ I++ +P+GIKEI+R+G A+ RG Sbjct: 122 IEVVGSPDKINTTIEMFRPLGIKEIARSGTVAMTRG 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: 81 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: 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 WP_012475113.1 CPHAMN1_RS08565 (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.2449.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-61 191.5 5.6 5e-61 191.4 5.6 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012475113.1 CPHAMN1_RS08565 acetolactate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012475113.1 CPHAMN1_RS08565 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 191.4 5.6 5e-61 5e-61 1 158 [] 1 158 [. 1 158 [. 0.99 Alignments for each domain: == domain 1 score: 191.4 bits; conditional E-value: 5e-61 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvd 69 +kh++svlven+ G L+rv+ +f++rgfn+es+ +gete++++srmtiv++gdd ++ qi kql++l+d lcl|NCBI__GCF_000020545.1:WP_012475113.1 1 MKHIISVLVENKFGTLNRVAAMFSARGFNLESISIGETEDNEISRMTIVTRGDDSIISQILKQLNRLID 69 79******************************************************************* PP TIGR00119 70 vlkvldlteseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkll 138 +lkv+d+t++ ++ re++l+ ++ ++++ei +l+++f+++vvD+ ++s+++e++g++dki+ +++ lcl|NCBI__GCF_000020545.1:WP_012475113.1 70 TLKVVDVTNKPHISREVLLMTLNRGKQSQQEIFNLIDVFKAKVVDIKQKSITIEVVGSPDKINTTIEMF 138 ********************************************************************* PP TIGR00119 139 kefgikevarsGlvalsrge 158 +++gike+arsG+va++rge lcl|NCBI__GCF_000020545.1:WP_012475113.1 139 RPLGIKEIARSGTVAMTRGE 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 5.35 // [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