Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_068459661.1 APY04_RS03310 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_001541235.1:WP_068459661.1 Length = 305 Score = 291 bits (744), Expect = 2e-83 Identities = 142/288 (49%), Positives = 209/288 (72%), Gaps = 1/288 (0%) Query: 12 AKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQ 71 A++L+EALP++ ++ +T++IK+GG+AM L FA+DVV +K G+NP+VVHGGGPQ Sbjct: 14 ARILAEALPHLIQYDEQTVIIKFGGHAMGDAALADAFAKDVVYLKQSGVNPIVVHGGGPQ 73 Query: 72 IGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDA 131 I +LK+L I+S F+ G+RVTD T++VVEMVL G +NKDIV+ INR GG A+G++GKDA Sbjct: 74 IAAMLKKLEIKSDFVHGLRVTDKPTVEVVEMVLSGLINKDIVSAINRQGGKAVGISGKDA 133 Query: 132 ELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGVGSNG 191 L+ A ++T P+ + +DIG+VG+ VN +++++ K D IPVIAP+ +G Sbjct: 134 NLMIASRIT-EMPDPQSNLMQAVDIGYVGDPVEVNPHIVDVISKSDIIPVIAPVAASRDG 192 Query: 192 ESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGTIYGG 251 E+ NINAD A +A +KA++L+LLT++AG++DK G++++ L+ E+ LI DGTI GG Sbjct: 193 ETLNINADSFASALAARMKAKRLLLLTDVAGVLDKSGELISQLTIEEARGLIKDGTISGG 252 Query: 252 MLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRK 299 M+PKI +E V+ GV + IIDGRVP+ VLLE+FT GVGTL+ + Sbjct: 253 MIPKIEGCIEVVEAGVEAVVIIDGRVPHCVLLELFTAHGVGTLLGRAR 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: 315 Number of extensions: 15 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: 305 Length adjustment: 27 Effective length of query: 274 Effective length of database: 278 Effective search space: 76172 Effective search space used: 76172 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 WP_068459661.1 APY04_RS03310 (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.4865.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-79 251.7 5.6 3.8e-79 251.5 5.6 1.0 1 lcl|NCBI__GCF_001541235.1:WP_068459661.1 APY04_RS03310 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001541235.1:WP_068459661.1 APY04_RS03310 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.5 5.6 3.8e-79 3.8e-79 1 231 [] 31 273 .. 31 273 .. 0.98 Alignments for each domain: == domain 1 score: 251.5 bits; conditional E-value: 3.8e-79 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t++iK GG+a+ l +++akd++ l+++g+++++vHGGgp+i ++l+kl+i+ +fv+glRvTdk t+ lcl|NCBI__GCF_001541235.1:WP_068459661.1 31 TVIIKFGGHAMGdaALADAFAKDVVYLKQSGVNPIVVHGGGPQIAAMLKKLEIKSDFVHGLRVTDKPTV 99 689********977899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke...........dlgyvGeikkvnk 125 evvemvl g +nk +v +++++g kavG++gkD++l++a ++++ d+gyvG+ +vn+ lcl|NCBI__GCF_001541235.1:WP_068459661.1 100 EVVEMVLSGLINKDIVSAINRQGGKAVGISGKDANLMIASRITEMpdpqsnlmqavDIGYVGDPVEVNP 168 ****************************************9998888999999999************* PP TIGR00761 126 elleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisele 194 ++++ + k++iipvia++a++ +g++lN+naD A++lAa ++A++L+lLtdvaG+l++ + +lis+l+ lcl|NCBI__GCF_001541235.1:WP_068459661.1 169 HIVDVISKSDIIPVIAPVAASRDGETLNINADSFASALAARMKAKRLLLLTDVAGVLDK-SGELISQLT 236 ***********************************************************.555****** PP TIGR00761 195 leeieqlikqavikgGmipKveaalealesgvkkvvi 231 +ee++ lik + i gGmipK+e ++e +e gv++vvi lcl|NCBI__GCF_001541235.1:WP_068459661.1 237 IEEARGLIKDGTISGGMIPKIEGCIEVVEAGVEAVVI 273 ***********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (305 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: 7.79 // [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