Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 8499536 DvMF_0306 acetylglutamate kinase (RefSeq)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Miya:8499536 Length = 320 Score = 330 bits (845), Expect = 3e-95 Identities = 165/284 (58%), Positives = 219/284 (77%), Gaps = 1/284 (0%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 +KVL E LPY+R+F G+T+VIKYGG+AM+ E LK FA ++ L+K VGINPVVVHGGGPQ Sbjct: 22 SKVLIECLPYMRQFHGQTVVIKYGGHAMKDEALKKAFALNIALLKQVGINPVVVHGGGPQ 81 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 IG +L++L I+S F +G+RVTD ATMDVVEMVL G+VNK+IVNL+N G A+GL+GKD Sbjct: 82 IGRMLEQLHIQSQFREGLRVTDDATMDVVEMVLVGKVNKEIVNLLNLSGVKAVGLSGKDG 141 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 +LIRA+K+ + PEIID+G VGEV V LL L + +F+PVIAP+GV NG Sbjct: 142 QLIRARKMEMIVNGGNHA-PEIIDLGKVGEVMRVETTLLRSLERDNFVPVIAPVGVDENG 200 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+YNINAD VAG VA AL+A++L+LLT++AG++DKQ +++ L+T + EL DGT+ GG Sbjct: 201 ETYNINADAVAGAVAAALRAKRLLLLTDVAGILDKQKELIRSLTTREAVELFTDGTLTGG 260 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 M+PK++C LEA++ GV A I+DGRV N +LLE+FTD G+ T I Sbjct: 261 MIPKVKCCLEALEEGVEKAMIVDGRVENCILLELFTDKGISTEI 304 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: 321 Number of extensions: 14 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: 320 Length adjustment: 27 Effective length of query: 274 Effective length of database: 293 Effective search space: 80282 Effective search space used: 80282 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 8499536 DvMF_0306 (acetylglutamate kinase (RefSeq))
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.17776.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-83 263.7 6.8 8.1e-83 263.5 6.8 1.1 1 lcl|FitnessBrowser__Miya:8499536 DvMF_0306 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499536 DvMF_0306 acetylglutamate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.5 6.8 8.1e-83 8.1e-83 1 231 [] 39 281 .. 39 281 .. 0.97 Alignments for each domain: == domain 1 score: 263.5 bits; conditional E-value: 8.1e-83 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvli 75 t+ViK+GG+a++ l++++a +ia l+++gi++v+vHGGgp+i ++le+l i+ +f +glRvTd +t++vvemvl+ lcl|FitnessBrowser__Miya:8499536 39 TVVIKYGGHAMKdeALKKAFALNIALLKQVGINPVVVHGGGPQIGRMLEQLHIQSQFREGLRVTDDATMDVVEMVLV 115 69**********9789999********************************************************** PP TIGR00761 76 gkvnkelvallekhgikavGltgkDgqlltaekldke...........dlgyvGeikkvnkelleallkagiipvia 141 gkvnke+v+ll+ g+kavGl+gkDgql+ a+k++ dlg vGe+ +v++ ll++l +++pvia lcl|FitnessBrowser__Miya:8499536 116 GKVNKEIVNLLNLSGVKAVGLSGKDGQLIRARKMEMIvnggnhapeiiDLGKVGEVMRVETTLLRSLERDNFVPVIA 192 ********************************776666699************************************ PP TIGR00761 142 slaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaa 218 ++++de+g+++N+naD +A+++Aaal A++L+lLtdvaGil++ +k+li++l+++e+ +l + + ++gGmipKv+++ lcl|FitnessBrowser__Miya:8499536 193 PVGVDENGETYNINADAVAGAVAAALRAKRLLLLTDVAGILDK-QKELIRSLTTREAVELFTDGTLTGGMIPKVKCC 268 *******************************************.667****************************** PP TIGR00761 219 lealesgvkkvvi 231 leale+gv+k++i lcl|FitnessBrowser__Miya:8499536 269 LEALEEGVEKAMI 281 ***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (320 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 11.60 // [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