Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 17998 b3959 acetylglutamate kinase (RefSeq)
Query= BRENDA::A0A140NEG9 (258 letters) >FitnessBrowser__Keio:17998 Length = 258 Score = 499 bits (1285), Expect = e-146 Identities = 258/258 (100%), Positives = 258/258 (100%) Query: 1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK 60 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK Sbjct: 1 MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVK 60 Query: 61 KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG 120 KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG Sbjct: 61 KKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELG 120 Query: 121 HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS 180 HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS Sbjct: 121 HVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLS 180 Query: 181 DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA 240 DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA Sbjct: 181 DVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHA 240 Query: 241 EQLPALFNGMPMGTRILA 258 EQLPALFNGMPMGTRILA Sbjct: 241 EQLPALFNGMPMGTRILA 258 Lambda K H 0.317 0.136 0.381 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: 375 Number of extensions: 5 Number of successful extensions: 1 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate 17998 b3959 (acetylglutamate kinase (RefSeq))
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))
# 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/TIGR00761.hmm # target sequence database: /tmp/gapView.24063.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00761 [M=231] Accession: TIGR00761 Description: argB: acetylglutamate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-82 261.5 2.0 3.7e-82 261.3 2.0 1.0 1 lcl|FitnessBrowser__Keio:17998 b3959 acetylglutamate kinase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17998 b3959 acetylglutamate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.3 2.0 3.7e-82 3.7e-82 2 231 .] 5 234 .. 4 234 .. 0.98 Alignments for each domain: == domain 1 score: 261.3 bits; conditional E-value: 3.7e-82 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegik.lvivHGGgpeinelleklgievefvnglRvTdketlevvemvligk 77 ++iK+GG++++ e+le+l+++++++r+++++ lvivHGGg+ ++el++ l+++v+++nglRvT ++++++++ +l+g+ lcl|FitnessBrowser__Keio:17998 5 LIIKLGGVLLDseEALERLFSALVNYRESHQRpLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGT 83 69********9999******************889******************************************** PP TIGR00761 78 vnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllNvna 156 +nk+l+a+ +kh+i+avGl+ +Dg+ +++++ld+e lg+vG ++ +++l+++ll++g++pv++s+++++egql+Nvna lcl|FitnessBrowser__Keio:17998 84 ANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEE-LGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNA 161 **********************************9.******************************************* PP TIGR00761 157 DtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231 D+aA++lAa+l+A+ L+lL+dv+Gil+g+++ +i+e++++++eqli+q++i++Gmi Kv+aal+a++++ + v i lcl|FitnessBrowser__Keio:17998 162 DQAATALAATLGAD-LILLSDVSGILDGKGQ-RIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDI 234 **************.*************555.*************************************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (258 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: 10.55 // [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