Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate PfGW456L13_793 Acetylglutamate kinase (EC 2.7.2.8)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 Length = 301 Score = 538 bits (1385), Expect = e-158 Identities = 274/301 (91%), Positives = 288/301 (95%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 MTL R+ AA AKVLSEALPYIRR+VGKTLVIKYGGNAMESEELK GFARD+VLMKAVGI Sbjct: 1 MTLEREAAANTAKVLSEALPYIRRYVGKTLVIKYGGNAMESEELKTGFARDIVLMKAVGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NPVVVHGGGPQIGDLLKRLSIESHF+DGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG Sbjct: 61 NPVVVHGGGPQIGDLLKRLSIESHFVDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 GSAIGLTGKDAELIRAKKLTVTRQTPEMT PEIIDIGHVGEV G+N LLN+LVKGDFIP Sbjct: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTTPEIIDIGHVGEVVGINTDLLNLLVKGDFIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGVG+NGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDK G VLTGL+T+QV+ Sbjct: 181 VIAPIGVGANGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKSGTVLTGLTTQQVD 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300 +LIADGTIYGGMLPKIRCALEAVQGGV S+ IIDGRVPNA+LLEIFTD+GVGTLISNRKR Sbjct: 241 DLIADGTIYGGMLPKIRCALEAVQGGVGSSLIIDGRVPNAILLEIFTDTGVGTLISNRKR 300 Query: 301 H 301 H Sbjct: 301 H 301 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: 472 Number of extensions: 12 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: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 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 PfGW456L13_793 (Acetylglutamate kinase (EC 2.7.2.8))
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.13019.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-82 260.2 6.9 9.7e-82 260.0 6.9 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 Acetylglutamate kinase (EC 2.7.2 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 Acetylglutamate kinase (EC 2.7.2.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.0 6.9 9.7e-82 9.7e-82 1 231 [] 29 272 .. 29 272 .. 0.98 Alignments for each domain: == domain 1 score: 260.0 bits; conditional E-value: 9.7e-82 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgieve 54 t+ViK+GG+a++ el++ +a+di+ ++++gi++v+vHGGgp+i ll++l ie + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 29 TLVIKYGGNAMEseELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLSIESH 84 68*********9999***************************************** PP TIGR00761 55 fvnglRvTdketlevvemvligkvnkelvallekhgikavGltgkDgqlltaekld 110 fv+g+RvTd++t++vvemvl g+vnk +v+l+++hg +a+GltgkD++l+ a+kl+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 85 FVDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDAELIRAKKLT 140 *****************************************************888 PP TIGR00761 111 ke............dlgyvGeikkvnkelleallkagiipviaslaldeegqllNv 154 + d+g+vGe+ +n++ll+ l+k ++ipvia++++ ++g+ +N+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 141 VTrqtpemttpeiiDIGHVGEVVGINTDLLNLLVKGDFIPVIAPIGVGANGESYNI 196 88889*************************************************** PP TIGR00761 155 naDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgG 210 naD +A+++A+al+AekL+lLt++aG++++ + ++++ l+++++++li + i+gG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 197 NADLVAGKVAEALKAEKLMLLTNIAGLMDK-SGTVLTGLTTQQVDDLIADGTIYGG 251 ******************************.666********************** PP TIGR00761 211 mipKveaalealesgvkkvvi 231 m pK+++alea+++gv ++ i lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793 252 MLPKIRCALEAVQGGVGSSLI 272 ****************98866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (301 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: 9.47 // [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