Align acetohydroxy-acid synthase small subunit (EC 2.2.1.6) (characterized)
to candidate SMc01430 SMc01430 acetolactate synthase 3 regulatory subunit
Query= metacyc::MONOMER-11901 (169 letters) >FitnessBrowser__Smeli:SMc01430 Length = 190 Score = 129 bits (323), Expect = 4e-35 Identities = 68/170 (40%), Positives = 108/170 (63%), Gaps = 9/170 (5%) Query: 1 MKNTHIISVLVLNKPGVLQRISGLFTRRWYNISSITGGSTD-STDISRMTIVVKGDDKVV 59 + TH +SVLV N+PGVL R+ GLF+ R YNI S+T T+ +SR+TIV +G V+ Sbjct: 20 LAETHTLSVLVDNEPGVLARVIGLFSGRGYNIESLTVSETEHEAHLSRITIVTRGTPHVL 79 Query: 60 EQVVKQLNKLIEVIKVIDLD-------EEECVERELCLIKIYAPTESSKSQVIQYANIFR 112 EQ+ QL +L+ V +V+DL E +EREL L+K++ E + + ++ A+ FR Sbjct: 80 EQIKNQLERLVPVHRVVDLTVRAAGLGHERPIERELALVKVHGSGEH-RVEALRLADAFR 138 Query: 113 GNIVDLSQESLTVQITGDKTKISAFIKLVKPMGIKEISRTGLTALMRGPK 162 +++D + + +ITG +KI FI ++KP+G+ E+ RTG+ A+ RGP+ Sbjct: 139 ASVIDANIDHFVFEITGKPSKIEQFIAIMKPLGLIEVCRTGIAAMNRGPQ 188 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: 75 Number of extensions: 5 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: 169 Length of database: 190 Length adjustment: 19 Effective length of query: 150 Effective length of database: 171 Effective search space: 25650 Effective search space used: 25650 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 SMc01430 SMc01430 (acetolactate synthase 3 regulatory 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.26225.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-56 174.9 0.1 7.4e-56 174.6 0.1 1.1 1 lcl|FitnessBrowser__Smeli:SMc01430 SMc01430 acetolactate synthase 3 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01430 SMc01430 acetolactate synthase 3 regulatory subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 174.6 0.1 7.4e-56 7.4e-56 2 158 .] 23 187 .. 22 187 .. 0.93 Alignments for each domain: == domain 1 score: 174.6 bits; conditional E-value: 7.4e-56 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteek.dlsrmtivvegddkvveqiekqleklvdvlkvld 75 +h+lsvlv+nepGvL+rv+Glf+ rg+niesltv+ete++ +lsr+tiv++g +v+eqi+ qle+lv+v +v+d lcl|FitnessBrowser__Smeli:SMc01430 23 THTLSVLVDNEPGVLARVIGLFSGRGYNIESLTVSETEHEaHLSRITIVTRGTPHVLEQIKNQLERLVPVHRVVD 97 79***********************************97538********************************* PP TIGR00119 76 lt.......eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgi 143 lt +++ ++rel+lvkv+ +ge+r e +l++ fr++v+D d ++ e++gk+ ki+ f++++k++g+ lcl|FitnessBrowser__Smeli:SMc01430 98 LTvraaglgHERPIERELALVKVHGSGEHRVEALRLADAFRASVIDANIDHFVFEITGKPSKIEQFIAIMKPLGL 172 9833333324567************************************************************** PP TIGR00119 144 kevarsGlvalsrge 158 ev r+G+ a+ rg+ lcl|FitnessBrowser__Smeli:SMc01430 173 IEVCRTGIAAMNRGP 187 *************85 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 4.66 // [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