Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate AO353_09240 AO353_09240 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__pseudo3_N2E3:AO353_09240 Length = 301 Score = 532 bits (1371), Expect = e-156 Identities = 273/300 (91%), Positives = 286/300 (95%) Query: 1 MTLSRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGI 60 MT+ R+ AA AKVLSEALPYIRR+VGKTLVIKYGGNAMESEELK GFARD+VLMKAVGI Sbjct: 1 MTIEREAAANTAKVLSEALPYIRRYVGKTLVIKYGGNAMESEELKTGFARDIVLMKAVGI 60 Query: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHG 120 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDA TMDVVEMVLGGQVNKDIVNLINRHG Sbjct: 61 NPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTDAQTMDVVEMVLGGQVNKDIVNLINRHG 120 Query: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIP 180 GSAIGLTGKDAELIRAKKLTVTRQTPEMT+PEIIDIG VGEV G+N LLN+LVKGDFIP Sbjct: 121 GSAIGLTGKDAELIRAKKLTVTRQTPEMTQPEIIDIGQVGEVVGINTDLLNLLVKGDFIP 180 Query: 181 VIAPIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVN 240 VIAPIGVG+NGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDK G VLTGLST+QV+ Sbjct: 181 VIAPIGVGANGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKSGTVLTGLSTQQVD 240 Query: 241 ELIADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRKR 300 ELIADGTIYGGMLPKIRCALEAVQGGV S+ IIDGRVPNA+LLEIFTD+GVGTLISNRKR Sbjct: 241 ELIADGTIYGGMLPKIRCALEAVQGGVGSSLIIDGRVPNAILLEIFTDTGVGTLISNRKR 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: 468 Number of extensions: 13 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 AO353_09240 AO353_09240 (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.31256.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-81 258.1 6.7 4.4e-81 257.8 6.7 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 AO353_09240 acetylglutamate kina Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 AO353_09240 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.8 6.7 4.4e-81 4.4e-81 1 231 [] 29 272 .. 29 272 .. 0.98 Alignments for each domain: == domain 1 score: 257.8 bits; conditional E-value: 4.4e-81 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTd 63 t+ViK+GG+a++ el++ +a+di+ ++++gi++v+vHGGgp+i ll++l ie +f++g+RvTd lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 29 TLVIKYGGNAMEseELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLSIESHFIDGMRVTD 93 68*********9999************************************************** PP TIGR00761 64 ketlevvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgy 116 ++t++vvemvl g+vnk +v+l+++hg +a+GltgkD++l+ a+kl++ d+g lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 94 AQTMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDAELIRAKKLTVTrqtpemtqpeiiDIGQ 158 ********************************************888888899************ PP TIGR00761 117 vGeikkvnkelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGi 181 vGe+ +n++ll+ l+k ++ipvia++++ ++g+ +N+naD +A+++A+al+AekL+lLt++aG+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 159 VGEVVGINTDLLNLLVKGDFIPVIAPIGVGANGESYNINADLVAGKVAEALKAEKLMLLTNIAGL 223 ***************************************************************** PP TIGR00761 182 legdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231 +++ + ++++ l+++++++li + i+gGm pK+++alea+++gv ++ i lcl|FitnessBrowser__pseudo3_N2E3:AO353_09240 224 MDK-SGTVLTGLSTQQVDELIADGTIYGGMLPKIRCALEAVQGGVGSSLI 272 ***.666**************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.83 // [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