Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF3738 Psest_3807 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__psRCH2:GFF3738 Length = 300 Score = 523 bits (1347), Expect = e-153 Identities = 271/300 (90%), Positives = 281/300 (93%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 MTLSR+ A Q AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELK GFARD+VLMKAVGI Sbjct: 1 MTLSREAATQFAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKTGFARDIVLMKAVGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NPVVVHGGGPQIGDLLKRL+IESHFIDGMRVTD+ TMDVVEMVLGGQVNK IV+LIN+HG Sbjct: 61 NPVVVHGGGPQIGDLLKRLNIESHFIDGMRVTDSQTMDVVEMVLGGQVNKSIVSLINQHG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 GSAIGLTGKDA LIRAKKL TRQTPEMTKPEIIDIGHVGEVTGVN LL MLVKG+FIP Sbjct: 121 GSAIGLTGKDAGLIRAKKLKATRQTPEMTKPEIIDIGHVGEVTGVNAELLEMLVKGNFIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGVG NGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQG VLTGLST QV+ Sbjct: 181 VIAPIGVGENGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGSVLTGLSTAQVD 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300 LIADGTIYGGMLPKIRCALEAVQGGV SAHIIDGRVPNAVLLEIFTD GVGTLI+N +R Sbjct: 241 ALIADGTIYGGMLPKIRCALEAVQGGVNSAHIIDGRVPNAVLLEIFTDVGVGTLITNGQR 300 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: 449 Number of extensions: 11 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 GFF3738 Psest_3807 (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.24961.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-83 265.8 7.4 1.9e-83 265.6 7.4 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3738 Psest_3807 acetylglutamate kinas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3738 Psest_3807 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.6 7.4 1.9e-83 1.9e-83 1 231 [] 29 272 .. 29 272 .. 0.98 Alignments for each domain: == domain 1 score: 265.6 bits; conditional E-value: 1.9e-83 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemv 73 t+ViK+GG+a++ el++ +a+di+ ++++gi++v+vHGGgp+i ll++l+ie +f++g+RvTd +t++vvemv lcl|FitnessBrowser__psRCH2:GFF3738 29 TLVIKYGGNAMEseELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLNIESHFIDGMRVTDSQTMDVVEMV 103 68*********9999************************************************************ PP TIGR00761 74 ligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvnkelleallkagi 136 l g+vnk +v l+++hg +a+GltgkD+ l+ a+kl+ d+g+vGe++ vn+elle l+k ++ lcl|FitnessBrowser__psRCH2:GFF3738 104 LGGQVNKSIVSLINQHGGSAIGLTGKDAGLIRAKKLKATrqtpemtkpeiiDIGHVGEVTGVNAELLEMLVKGNF 178 **********************************8888888999******************************* PP TIGR00761 137 ipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGm 211 ipvia++++ e+g+ +N+naD +A+++A+al+AekL+lLt++aG++++ + s+++ l++++++ li + i+gGm lcl|FitnessBrowser__psRCH2:GFF3738 179 IPVIAPIGVGENGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDK-QGSVLTGLSTAQVDALIADGTIYGGM 252 ************************************************.666*********************** PP TIGR00761 212 ipKveaalealesgvkkvvi 231 pK+++alea+++gv++++i lcl|FitnessBrowser__psRCH2:GFF3738 253 LPKIRCALEAVQGGVNSAHI 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.55 // [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