Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate H281DRAFT_02211 H281DRAFT_02211 N-acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Burk376:H281DRAFT_02211 Length = 299 Score = 332 bits (851), Expect = 6e-96 Identities = 170/285 (59%), Positives = 214/285 (75%), Gaps = 5/285 (1%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L+EALPYIR++ GKT+VIKYGGNAM E LK GFARDV+L+K VGINPV+VHGGGPQ Sbjct: 16 AEILAEALPYIRQYHGKTVVIKYGGNAMTEERLKQGFARDVILLKLVGINPVIVHGGGPQ 75 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I LK++ + FI GMRVTD TM+VVE VLGG+V +DIV LIN GG A+GLTGKD Sbjct: 76 IDQALKKVGKQGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVTLINHFGGHAVGLTGKDG 135 Query: 132 ELIRAKKLTVTRQTPEMTKP-EIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSN 190 LI A+K+ + P+ P + +DIG VGEV +N ++ L FIPVI+PIG G + Sbjct: 136 GLIHARKMLM----PDRDNPGQYVDIGQVGEVEAINPAVVKALQDDAFIPVISPIGFGED 191 Query: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYG 250 G SYNINADLVAGK+A L AEKL+++TNI G+MDK+G +LT LS +++ L ADGTI G Sbjct: 192 GLSYNINADLVAGKLAVVLNAEKLVMMTNIPGVMDKEGNLLTDLSAREIDGLFADGTISG 251 Query: 251 GMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 GMLPKI AL+A + GV S HIIDGR+ ++VLLEI T+ GT+I Sbjct: 252 GMLPKISSALDAAKSGVRSVHIIDGRIEHSVLLEILTEQPFGTMI 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: 324 Number of extensions: 13 Number of successful extensions: 2 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 H281DRAFT_02211 H281DRAFT_02211 (N-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.3229.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-75 240.0 2.4 1.5e-75 239.7 2.4 1.1 1 lcl|FitnessBrowser__Burk376:H281DRAFT_02211 H281DRAFT_02211 N-acetylglutamat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_02211 H281DRAFT_02211 N-acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.7 2.4 1.5e-75 1.5e-75 1 231 [] 33 273 .. 33 273 .. 0.97 Alignments for each domain: == domain 1 score: 239.7 bits; conditional E-value: 1.5e-75 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdk 64 t+ViK+GG+a++ +l++ +a+d++ l+ +gi++vivHGGgp+i+++l+k+g + f++g+RvTd+ lcl|FitnessBrowser__Burk376:H281DRAFT_02211 33 TVVIKYGGNAMTeeRLKQGFARDVILLKLVGINPVIVHGGGPQIDQALKKVGKQGTFIQGMRVTDE 98 69*********998999************************************************* PP TIGR00761 65 etlevvemvligkvnkelvallekhgikavGltgkDgqlltaekldke.........dlgyvGeik 121 et+evve vl g+v++ +v+l+++ g +avGltgkDg l+ a+k+ d+g vGe++ lcl|FitnessBrowser__Burk376:H281DRAFT_02211 99 ETMEVVEWVLGGEVQQDIVTLINHFGGHAVGLTGKDGGLIHARKMLMPdrdnpgqyvDIGQVGEVE 164 *******************************************5544446899************* PP TIGR00761 122 kvnkelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkk 187 ++n+++++al + +ipvi+++++ e+g +N+naD +A++lA +l+AekLv++t+++G++++ + lcl|FitnessBrowser__Burk376:H281DRAFT_02211 165 AINPAVVKALQDDAFIPVISPIGFGEDGLSYNINADLVAGKLAVVLNAEKLVMMTNIPGVMDK-EG 229 ***************************************************************.55 PP TIGR00761 188 sliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +l++ l+++ei+ l + i gGm pK+++al+a++sgv++v+i lcl|FitnessBrowser__Burk376:H281DRAFT_02211 230 NLLTDLSAREIDGLFADGTISGGMLPKISSALDAAKSGVRSVHI 273 5*****************************************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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.19 // [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