Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF3375 HP15_3317 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Marino:GFF3375 Length = 298 Score = 436 bits (1121), Expect = e-127 Identities = 217/296 (73%), Positives = 257/296 (86%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 M L R+ A QVA VLS LPYI+RF GKT+VIKYGGNAME+E+LK+ FARDVVLMK VGI Sbjct: 1 MALDRETAMQVASVLSRGLPYIQRFTGKTVVIKYGGNAMENEDLKSSFARDVVLMKLVGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NP+VVHGGGPQIG+LL+RL+I+S F++GMRVTD+ TMDVVEMVLGGQVNK+IV+LIN HG Sbjct: 61 NPIVVHGGGPQIGELLERLNIQSRFVNGMRVTDSETMDVVEMVLGGQVNKEIVSLINSHG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 G A+GLTGKDA LIRA+KL V ++PE+ +PEIIDIGHVGEV VNV ++ ML + + IP Sbjct: 121 GMAVGLTGKDANLIRARKLEVVDRSPELERPEIIDIGHVGEVASVNVDVIEMLTRSNLIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGVG +G SYNINADLVAGKVAEA+KAEKLMLLTN++GL K+ +VLTGL+ +QVN Sbjct: 181 VIAPIGVGPDGASYNINADLVAGKVAEAMKAEKLMLLTNVSGLKSKEDKVLTGLTAKQVN 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 +LI DGTI+GGMLPKIRCAL AV+ GV ++HIIDGRV +A LLEIFTD GVGTLIS Sbjct: 241 DLIEDGTIHGGMLPKIRCALSAVENGVRTSHIIDGRVAHACLLEIFTDEGVGTLIS 296 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: 368 Number of extensions: 9 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: 298 Length adjustment: 27 Effective length of query: 274 Effective length of database: 271 Effective search space: 74254 Effective search space used: 74254 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 GFF3375 HP15_3317 (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.4894.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-81 259.6 6.0 1.5e-81 259.4 6.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3375 HP15_3317 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3375 HP15_3317 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.4 6.0 1.5e-81 1.5e-81 1 231 [] 29 272 .. 29 272 .. 0.98 Alignments for each domain: == domain 1 score: 259.4 bits; conditional E-value: 1.5e-81 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemv 73 t+ViK+GG+a++ +l+ ++a+d++ ++ +gi++++vHGGgp+i elle+l+i+ +fvng+RvTd et++vvemv lcl|FitnessBrowser__Marino:GFF3375 29 TVVIKYGGNAMEneDLKSSFARDVVLMKLVGINPIVVHGGGPQIGELLERLNIQSRFVNGMRVTDSETMDVVEMV 103 69*********9999************************************************************ PP TIGR00761 74 ligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvnkelleallkagi 136 l g+vnke+v l++ hg avGltgkD++l+ a+kl++ d+g+vGe+ +vn +++e l ++ lcl|FitnessBrowser__Marino:GFF3375 104 LGGQVNKEIVSLINSHGGMAVGLTGKDANLIRARKLEVVdrspelerpeiiDIGHVGEVASVNVDVIEMLTRSNL 178 **********************************777666789******************************** PP TIGR00761 137 ipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGm 211 ipvia++++ +g +N+naD +A+++A+a++AekL+lLt+v+G+ ++ ++++++ l+++++++li+ + i+gGm lcl|FitnessBrowser__Marino:GFF3375 179 IPVIAPIGVGPDGASYNINADLVAGKVAEAMKAEKLMLLTNVSGLKSK-EDKVLTGLTAKQVNDLIEDGTIHGGM 252 **********************************************99.888*********************** PP TIGR00761 212 ipKveaalealesgvkkvvi 231 pK+++al+a+e+gv+ ++i lcl|FitnessBrowser__Marino:GFF3375 253 LPKIRCALSAVENGVRTSHI 272 *****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (298 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.45 // [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