Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_085949722.1 FRAAL_RS22700 acetylglutamate kinase
Query= BRENDA::Q6R6P5 (317 letters) >NCBI__GCF_000058485.1:WP_085949722.1 Length = 335 Score = 352 bits (902), Expect = e-102 Identities = 167/283 (59%), Positives = 218/283 (77%) Query: 13 RANVLAEALPWLQHFRDKIVVVKYGGNAMVDDDLKAAFAADMVFLRTVGAKPVVVHGGGP 72 + VL EALPWL F+ +V+KYGGNAM + L+AAFAAD+VFLR G + VVVHGGGP Sbjct: 33 KTQVLIEALPWLSRFQGATIVIKYGGNAMTEPALRAAFAADIVFLRYSGLRVVVVHGGGP 92 Query: 73 QISEMLNRVGLQGEFKGGFRVTTPEVMDIVRMVLFGQVGRDLVGLINSHGPYAVGTSGED 132 QI+ L R+G++ F GG RVTTPE MD+VRMVL GQV RD+VGL+N HGP+AVG SGED Sbjct: 93 QITAHLARLGVESTFVGGLRVTTPETMDVVRMVLLGQVNRDVVGLVNDHGPFAVGLSGED 152 Query: 133 AGLFTAQKRMVNIDGVPTDIGLVGDIINVDASSLMDIIEAGRIPVVSTIAPGEDGQIYNI 192 A LFTA++R +DG D+GLVGDI+ V A ++ ++++G++PVV+++A G DG +YN+ Sbjct: 153 ANLFTARRRPAIVDGQEVDVGLVGDIVEVRAETVDALLDSGKVPVVASVARGIDGGVYNV 212 Query: 193 NADTAAGALAAAIGAERLLVLTNVEGLYTDWPDKSSLVSKIKATELEAILPGLDSGMIPK 252 NADTAA LA A+GA +L+VLT+VEGLY DWP ++S++ TELE +LP L +GMIPK Sbjct: 213 NADTAAAELAVALGATKLVVLTDVEGLYADWPTSDEVLSELSITELEQLLPTLAAGMIPK 272 Query: 253 MESCLNAVRGGVSAAHVIDGRIAHSVLLELLTMGGIGTMVLPD 295 ME+C AVRGGV AHV+DGR+ H+VLLE+ T GIGT++ PD Sbjct: 273 MEACRRAVRGGVPQAHVLDGRVPHAVLLEIFTDDGIGTLITPD 315 Lambda K H 0.319 0.139 0.399 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: 350 Number of extensions: 16 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: 317 Length of database: 335 Length adjustment: 28 Effective length of query: 289 Effective length of database: 307 Effective search space: 88723 Effective search space used: 88723 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_085949722.1 FRAAL_RS22700 (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.1839.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-77 246.3 0.3 1.7e-77 246.0 0.3 1.1 1 lcl|NCBI__GCF_000058485.1:WP_085949722.1 FRAAL_RS22700 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_085949722.1 FRAAL_RS22700 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.0 0.3 1.7e-77 1.7e-77 1 231 [] 51 289 .. 51 289 .. 0.97 Alignments for each domain: == domain 1 score: 246.0 bits; conditional E-value: 1.7e-77 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 tiViK+GG+a++ l+ ++a+di++lr +g+++v+vHGGgp+i++ l +lg+e fv+glRvT+ et+ lcl|NCBI__GCF_000058485.1:WP_085949722.1 51 TIVIKYGGNAMTepALRAAFAADIVFLRYSGLRVVVVHGGGPQITAHLARLGVESTFVGGLRVTTPETM 119 69**********98899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltae....kldke..dlgyvGeikkvnkellea 130 +vv+mvl+g+vn+ +v l++ hg avGl+g+D++l+ta+ +d + d+g+vG+i +v +e ++a lcl|NCBI__GCF_000058485.1:WP_085949722.1 120 DVVRMVLLGQVNRDVVGLVNDHGPFAVGLSGEDANLFTARrrpaIVDGQevDVGLVGDIVEVRAETVDA 188 ****************************************887533433779***************** PP TIGR00761 131 llkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGileg..dkksliselelee 197 ll++g +pv+as+a +g ++NvnaDtaAaelA al+A kLv+Ltdv+G++++ +++++sel++ e lcl|NCBI__GCF_000058485.1:WP_085949722.1 189 LLDSGKVPVVASVARGIDGGVYNVNADTAAAELAVALGATKLVVLTDVEGLYADwpTSDEVLSELSITE 257 ******************************************************998999********* PP TIGR00761 198 ieqlikqavikgGmipKveaalealesgvkkvvi 231 +eql+ + +++GmipK+ea+ +a+++gv+++++ lcl|NCBI__GCF_000058485.1:WP_085949722.1 258 LEQLLPT--LAAGMIPKMEACRRAVRGGVPQAHV 289 ******9..7*********************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (335 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: 8.92 // [ok]
This GapMind analysis is from Apr 10 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