Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_019867255.1 METMI_RS0115735 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000384075.1:WP_019867255.1 Length = 299 Score = 394 bits (1011), Expect = e-114 Identities = 193/290 (66%), Positives = 238/290 (82%) Query: 11 VAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGP 70 +A+VL EALPYI+RF GKT+V+K+GGNAM E LK FARD+VLMK VG NP+VVHGGGP Sbjct: 10 IAEVLIEALPYIQRFKGKTVVVKFGGNAMVDESLKNSFARDIVLMKLVGFNPIVVHGGGP 69 Query: 71 QIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKD 130 QIG LL++L + F+DGMR+TD+ TMDVVEMVLGG VNK+IVNLIN +GG A+GLTGKD Sbjct: 70 QIGQLLEKLGKTTGFVDGMRITDSETMDVVEMVLGGLVNKEIVNLINMNGGKAVGLTGKD 129 Query: 131 AELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 + IRAKK+ + R + + EIID+GHVGEV+ ++ ++ ML + DFIPVIAPIGVG++ Sbjct: 130 GDFIRAKKINLKRSSLDAEASEIIDLGHVGEVSSIDPSVVEMLGRSDFIPVIAPIGVGAD 189 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 G SYNINADLVAGK+AE LKAEKL+LLTN AG++DKQG +LTGLS ++ LIADGTI G Sbjct: 190 GHSYNINADLVAGKIAEVLKAEKLILLTNTAGILDKQGSLLTGLSVTDIDSLIADGTISG 249 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300 GM+PK RCA +A+ GGV S HIIDGRV +AVLLE+FTD GVGTL+ +R R Sbjct: 250 GMIPKTRCATDALNGGVHSVHIIDGRVAHAVLLELFTDQGVGTLLLSRPR 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: 343 Number of extensions: 7 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: 299 Length adjustment: 27 Effective length of query: 274 Effective length of database: 272 Effective search space: 74528 Effective search space used: 74528 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_019867255.1 METMI_RS0115735 (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.3021.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-76 242.5 4.8 2.5e-76 242.2 4.8 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019867255.1 METMI_RS0115735 acetylglutamate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019867255.1 METMI_RS0115735 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 242.2 4.8 2.5e-76 2.5e-76 1 231 [] 28 271 .. 28 271 .. 0.97 Alignments for each domain: == domain 1 score: 242.2 bits; conditional E-value: 2.5e-76 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+V+K GG+a+ l++++a+di+ ++ +g ++++vHGGgp+i +lleklg + fv+g+R+Td et+ lcl|NCBI__GCF_000384075.1:WP_019867255.1 28 TVVVKFGGNAMVdeSLKNSFARDIVLMKLVGFNPIVVHGGGPQIGQLLEKLGKTTGFVDGMRITDSETM 96 69*********988899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 +vvemvl g vnke+v+l++ +g kavGltgkDg+ + a+k++ + dlg+vGe+++++ lcl|NCBI__GCF_000384075.1:WP_019867255.1 97 DVVEMVLGGLVNKEIVNLINMNGGKAVGLTGKDGDFIRAKKINLKrssldaeaseiiDLGHVGEVSSID 165 ****************************************777666788899***************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 ++++e l +++ipvia++++ ++g+ +N+naD +A+++A++l+AekL+lLt++aGil++ + sl++ l lcl|NCBI__GCF_000384075.1:WP_019867255.1 166 PSVVEMLGRSDFIPVIAPIGVGADGHSYNINADLVAGKIAEVLKAEKLILLTNTAGILDK-QGSLLTGL 233 ************************************************************.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++ +i+ li + i gGmipK ++a +al++gv++v+i lcl|NCBI__GCF_000384075.1:WP_019867255.1 234 SVTDIDSLIADGTISGGMIPKTRCATDALNGGVHSVHI 271 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (299 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: 11.80 // [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