Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate GFF1988 PGA1_c20220 acetolactate synthase isozyme 3 small subunit
Query= BRENDA::P00894 (163 letters) >FitnessBrowser__Phaeo:GFF1988 Length = 186 Score = 127 bits (320), Expect = 8e-35 Identities = 73/160 (45%), Positives = 104/160 (65%), Gaps = 3/160 (1%) Query: 2 RRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDP-TLSRMTIQTVGDEKVLEQI 60 R +++L+ENE G L+RVIGLFS RGYNI+SLTVA D LSR+TI T G +V+EQI Sbjct: 28 RHTITILVENEPGVLARVIGLFSGRGYNIDSLTVAEVDHTGHLSRITIVTTGTPQVIEQI 87 Query: 61 EKQLHKLVDVLRVSELG-QGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSL 119 + QL ++V V V++L G VERE+ +VK+ G R E R EIFR +++D T + Sbjct: 88 KAQLGRIVSVHEVTDLTVAGPFVERELAIVKVVGEGEKRVEAMRLAEIFRAKVVDTTLNS 147 Query: 120 YTVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGD 159 + +L G K+DAF +R + + ++AR+GV L RG+ Sbjct: 148 FIFELTGAPDKIDAFAEMMRPLG-LTKIARTGVAALLRGN 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: 89 Number of extensions: 4 Number of successful extensions: 3 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: 186 Length adjustment: 19 Effective length of query: 144 Effective length of database: 167 Effective search space: 24048 Effective search space used: 24048 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 GFF1988 PGA1_c20220 (acetolactate synthase isozyme 3 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.1083.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-56 176.4 0.8 2.4e-56 176.2 0.8 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1988 PGA1_c20220 acetolactate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1988 PGA1_c20220 acetolactate synthase isozyme 3 small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 176.2 0.8 2.4e-56 2.4e-56 2 158 .] 28 186 .] 27 186 .] 0.96 Alignments for each domain: == domain 1 score: 176.2 bits; conditional E-value: 2.4e-56 TIGR00119 2 khvlsvlvenepGvLsrvsGlfarrgfniesltvgeteek.dlsrmtivvegddkvveqiekqleklvdvlkvldl 76 +h++++lvenepGvL+rv+Glf+ rg+ni+sltv+e +++ +lsr+tiv++g +v+eqi+ ql ++v v +v+dl lcl|FitnessBrowser__Phaeo:GFF1988 28 RHTITILVENEPGVLARVIGLFSGRGYNIDSLTVAEVDHTgHLSRITIVTTGTPQVIEQIKAQLGRIVSVHEVTDL 103 8***********************************996527********************************** PP TIGR00119 77 tes.eivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefgikevarsGl 151 t + v+rel++vkv ge+r e ++l+eifr++vvD + +s+i el+g +dki+af ++++++g+ +ar+G+ lcl|FitnessBrowser__Phaeo:GFF1988 104 TVAgPFVERELAIVKVVGEGEKRVEAMRLAEIFRAKVVDTTLNSFIFELTGAPDKIDAFAEMMRPLGLTKIARTGV 179 965289********************************************************************** PP TIGR00119 152 valsrge 158 al rg+ lcl|FitnessBrowser__Phaeo:GFF1988 180 AALLRGN 186 ****985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (186 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: 6.76 // [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