Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Korea:Ga0059261_2530 Length = 299 Score = 300 bits (769), Expect = 2e-86 Identities = 150/284 (52%), Positives = 203/284 (71%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A+ L++ALPY++R+ GKT V+KYGG+AM EL FA DVVL+KAVGINPVVVHGGGPQ Sbjct: 14 AETLTDALPYMQRYAGKTFVVKYGGHAMGDPELARDFAEDVVLLKAVGINPVVVHGGGPQ 73 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 IG +LKRL +ES F+ G+RVTDA T + EMVL G +NK+IV+ I+ GG AIG++GKD+ Sbjct: 74 IGQMLKRLGVESEFVGGLRVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDS 133 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 L+ A+K+T + P +D+G VGE V+ +L L FIPVIAPI +G++G Sbjct: 134 GLVTARKVTRSEADPLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADG 193 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 +YNINAD +AG +A AL A + LLT++ G++ K Q+L+ L ++ L ADGTI GG Sbjct: 194 HTYNINADTMAGAIAGALGASRFFLLTDVPGVLSKDKQLLSDLDPGRIAALKADGTISGG 253 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 M+PK+ + AV GV +A I+DGRVP+++LLEIFT G GTL+ Sbjct: 254 MIPKVETCVAAVDAGVDAAVILDGRVPHSMLLEIFTPQGAGTLV 297 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: 285 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: 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 Ga0059261_2530 Ga0059261_2530 (N-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.29000.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-79 253.3 0.4 1.2e-79 253.1 0.4 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2530 Ga0059261_2530 N-acetylglutamate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 253.1 0.4 1.2e-79 1.2e-79 1 231 [] 31 274 .. 31 274 .. 0.99 Alignments for each domain: == domain 1 score: 253.1 bits; conditional E-value: 1.2e-79 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t V+K+GG+a+ el +++a+d++ l+++gi++v+vHGGgp+i ++l++lg+e efv+glRvTd+et lcl|FitnessBrowser__Korea:Ga0059261_2530 31 TFVVKYGGHAMGdpELARDFAEDVVLLKAVGINPVVVHGGGPQIGQMLKRLGVESEFVGGLRVTDAETA 99 57*********9999****************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 ++emvl+g++nke+v +++ +g ka+G++gkD l+ta+k++++ dlg+vGe +v+ lcl|FitnessBrowser__Korea:Ga0059261_2530 100 RIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLVTARKVTRSeadplqgierhvDLGFVGEPVAVD 168 ****************************************9999889********************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 +++l +l ++g+ipvia++al ++g+++N+naDt+A+++A al+A + lLtdv+G+l++dk+ l+s l lcl|FitnessBrowser__Korea:Ga0059261_2530 169 ASVLTTLSAQGFIPVIAPIALGADGHTYNINADTMAGAIAGALGASRFFLLTDVPGVLSKDKQ-LLSDL 236 ************************************************************888.***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++ +i+ l + i gGmipKve +++a++ gv ++vi lcl|FitnessBrowser__Korea:Ga0059261_2530 237 DPGRIAALKADGTISGGMIPKVETCVAAVDAGVDAAVI 274 **********************************9987 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: 10.05 // [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