Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate YP_425560.1 Rru_A0468 acetolactate synthase small subunit
Query= BRENDA::P00894 (163 letters) >NCBI__GCF_000013085.1:YP_425560.1 Length = 175 Score = 129 bits (324), Expect = 3e-35 Identities = 70/156 (44%), Positives = 108/156 (69%), Gaps = 3/156 (1%) Query: 5 LSVLLENESGALSRVIGLFSQRGYNIESLTVAPTD-DPTLSRMTIQTVGDEKVLEQIEKQ 63 ++VL++NESG L+RVIGLFS RGYNIESLTVA D D LSR+T+ T G ++EQI+ Q Sbjct: 17 IAVLVDNESGVLARVIGLFSGRGYNIESLTVAEVDVDEQLSRITLVTSGTPMIIEQIKAQ 76 Query: 64 LHKLVDVLRVSELG-QGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLYTV 122 L +LV V +VS+L +G HV RE+ L+K+ +G R E R +IFR +++D + + Sbjct: 77 LGRLVPVHKVSDLTVEGPHVSRELALIKVAGTGEKRVESLRIADIFRARVVDSSNESFVF 136 Query: 123 QLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRG 158 ++ G + K++AF+ + + +++VAR+GV ++RG Sbjct: 137 EIVGKTEKINAFIGLMEPLG-LIDVARTGVAAIARG 171 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: 103 Number of extensions: 6 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: 175 Length adjustment: 18 Effective length of query: 145 Effective length of database: 157 Effective search space: 22765 Effective search space used: 22765 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 YP_425560.1 Rru_A0468 (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.24810.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-57 178.1 1.4 7.2e-57 177.9 1.4 1.0 1 lcl|NCBI__GCF_000013085.1:YP_425560.1 Rru_A0468 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_425560.1 Rru_A0468 acetolactate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 177.9 1.4 7.2e-57 7.2e-57 2 157 .. 14 171 .. 13 172 .. 0.97 Alignments for each domain: == domain 1 score: 177.9 bits; conditional E-value: 7.2e-57 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgetee.kdlsrmtivvegddkvveqiekqleklvdvlk 72 +h+++vlv+ne+GvL+rv+Glf+ rg+niesltv+e ++ ++lsr+t+v++g ++eqi+ ql +lv+v k lcl|NCBI__GCF_000013085.1:YP_425560.1 14 THTIAVLVDNESGVLARVIGLFSGRGYNIESLTVAEVDVdEQLSRITLVTSGTPMIIEQIKAQLGRLVPVHK 85 69***********************************96268****************************** PP TIGR00119 73 vldlt.eseivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgi 143 v+dlt e +v rel+l+kv +ge+r e ++++ifr+rvvD s++s++ e++gk +ki+af+ l++++g+ lcl|NCBI__GCF_000013085.1:YP_425560.1 86 VSDLTvEGPHVSRELALIKVAGTGEKRVESLRIADIFRARVVDSSNESFVFEIVGKTEKINAFIGLMEPLGL 157 ****95679*************************************************************** PP TIGR00119 144 kevarsGlvalsrg 157 +var+G+ a++rg lcl|NCBI__GCF_000013085.1:YP_425560.1 158 IDVARTGVAAIARG 171 ************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (175 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: 5.65 // [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