Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate WP_011652743.1 RL_RS16710 acetolactate synthase small subunit
Query= BRENDA::P00894 (163 letters) >NCBI__GCF_000009265.1:WP_011652743.1 Length = 190 Score = 126 bits (317), Expect = 2e-34 Identities = 70/162 (43%), Positives = 105/162 (64%), Gaps = 9/162 (5%) Query: 5 LSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPT-LSRMTIQTVGDEKVLEQIEKQ 63 LSVL++NE G L+RVIGLFS RGYNIESLTV+ T+ LSR+T+ T G +VLEQI+ Q Sbjct: 26 LSVLVDNEPGVLARVIGLFSGRGYNIESLTVSETEHQAHLSRITVVTRGTPQVLEQIKAQ 85 Query: 64 LHKLVDV-------LRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVT 116 L ++V V +R ELGQ +ERE+ L+K+ G R E R + F +++D T Sbjct: 86 LERIVPVHRVVDLTVRARELGQDRPIEREVALIKVIGEGEMRAETLRLADAFHAKVVDAT 145 Query: 117 PSLYTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 + +++ G S K+D F+A ++ + ++EV R+G+ ++RG Sbjct: 146 IGHFILEITGKSSKIDQFVAIMKPLG-LIEVCRTGIAAMNRG 186 Lambda K H 0.318 0.136 0.360 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: 105 Number of extensions: 10 Number of successful extensions: 4 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: 163 Length of database: 190 Length adjustment: 19 Effective length of query: 144 Effective length of database: 171 Effective search space: 24624 Effective search space used: 24624 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: 44 (21.6 bits)
Align candidate WP_011652743.1 RL_RS16710 (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.932.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-53 165.1 1.7 8.3e-53 164.7 1.7 1.2 1 lcl|NCBI__GCF_000009265.1:WP_011652743.1 RL_RS16710 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011652743.1 RL_RS16710 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 164.7 1.7 8.3e-53 8.3e-53 2 157 .. 23 186 .. 22 187 .. 0.94 Alignments for each domain: == domain 1 score: 164.7 bits; conditional E-value: 8.3e-53 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgetee.kdlsrmtivvegddkvveqiekqleklvd 69 h+lsvlv+nepGvL+rv+Glf+ rg+niesltv+ete+ ++lsr+t+v++g +v+eqi+ qle++v+ lcl|NCBI__GCF_000009265.1:WP_011652743.1 23 SHTLSVLVDNEPGVLARVIGLFSGRGYNIESLTVSETEHqAHLSRITVVTRGTPQVLEQIKAQLERIVP 91 69***********************************96258*************************** PP TIGR00119 70 vlkvldlt.......eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedki 131 v +v+dlt +++ ++re++l+kv ge r+e +l++ f ++vvD + +i+e++gk+ ki lcl|NCBI__GCF_000009265.1:WP_011652743.1 92 VHRVVDLTvrarelgQDRPIEREVALIKVIGEGEMRAETLRLADAFHAKVVDATIGHFILEITGKSSKI 160 ****998733333335678************************************************** PP TIGR00119 132 saflkllkefgikevarsGlvalsrg 157 + f++++k++g+ ev r+G+ a+ rg lcl|NCBI__GCF_000009265.1:WP_011652743.1 161 DQFVAIMKPLGLIEVCRTGIAAMNRG 186 ************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (190 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 4.94 // [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