Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_046010620.1 OLEAN_RS19500 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000967895.1:WP_046010620.1 Length = 300 Score = 443 bits (1139), Expect = e-129 Identities = 219/299 (73%), Positives = 262/299 (87%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 M L+R +A KVLSEALPY+++F GKT+VIKYGGNAM E LK FARD+V++K +GI Sbjct: 1 MPLTRKEAVITTKVLSEALPYLQKFSGKTIVIKYGGNAMTDETLKNSFARDMVMLKLIGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NP+VVHGGGPQIG++L +L+I+S F+DGMRVT + TMDVVEMVLGG VNKDIVNLIN++G Sbjct: 61 NPIVVHGGGPQIGEVLAKLNIKSEFVDGMRVTTSETMDVVEMVLGGLVNKDIVNLINQNG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 G AIGLTGKD +L+ AKKL VT+Q+P+M +PEIIDIGHVGEVT VN +L+ML + DFIP Sbjct: 121 GKAIGLTGKDGQLLHAKKLQVTKQSPDMQQPEIIDIGHVGEVTRVNTQVLDMLSQSDFIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGV ++G SYNINADLVAGKVAE L+AEKL+LLTNI+GL DK G+VLTGL+T++V+ Sbjct: 181 VIAPIGVDADGASYNINADLVAGKVAEVLRAEKLILLTNISGLQDKNGEVLTGLTTQEVD 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRK 299 ELIADGTIYGGMLPKI+CAL+AV GVTSAHIIDGRVPNA LLE+FTD GVGTLI+NRK Sbjct: 241 ELIADGTIYGGMLPKIQCALDAVHAGVTSAHIIDGRVPNATLLELFTDEGVGTLITNRK 299 Lambda K H 0.318 0.138 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: 378 Number of extensions: 10 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: 301 Length of database: 300 Length adjustment: 27 Effective length of query: 274 Effective length of database: 273 Effective search space: 74802 Effective search space used: 74802 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: 48 (23.1 bits)
Align candidate WP_046010620.1 OLEAN_RS19500 (acetylglutamate kinase)
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.14785.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-82 261.8 9.0 3.2e-82 261.5 9.0 1.1 1 lcl|NCBI__GCF_000967895.1:WP_046010620.1 OLEAN_RS19500 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046010620.1 OLEAN_RS19500 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.5 9.0 3.2e-82 3.2e-82 1 231 [] 29 272 .. 29 272 .. 0.97 Alignments for each domain: == domain 1 score: 261.5 bits; conditional E-value: 3.2e-82 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a++ +l++++a+d++ l+ gi++++vHGGgp+i e+l kl+i+ efv+g+RvT+ et+ lcl|NCBI__GCF_000967895.1:WP_046010620.1 29 TIVIKYGGNAMTdeTLKNSFARDMVMLKLIGINPIVVHGGGPQIGEVLAKLNIKSEFVDGMRVTTSETM 97 69*********998899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 +vvemvl g vnk +v+l++++g ka+GltgkDgqll a+kl++ d+g+vGe+++vn lcl|NCBI__GCF_000967895.1:WP_046010620.1 98 DVVEMVLGGLVNKDIVNLINQNGGKAIGLTGKDGQLLHAKKLQVTkqspdmqqpeiiDIGHVGEVTRVN 166 ****************************************66555559********************* PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 +++l+ l ++++ipvia++++d++g +N+naD +A+++A++l AekL+lLt+++G+ ++ + ++++ l lcl|NCBI__GCF_000967895.1:WP_046010620.1 167 TQVLDMLSQSDFIPVIAPIGVDADGASYNINADLVAGKVAEVLRAEKLILLTNISGLQDK-NGEVLTGL 234 **********************************************************99.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++e+++li + i+gGm pK+++al+a++ gv +++i lcl|NCBI__GCF_000967895.1:WP_046010620.1 235 TTQEVDELIADGTIYGGMLPKIQCALDAVHAGVTSAHI 272 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (300 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: 7.58 // [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