Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_041778980.1 BIND_RS16900 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000019845.1:WP_041778980.1 Length = 284 Score = 275 bits (702), Expect = 1e-78 Identities = 135/289 (46%), Positives = 201/289 (69%), Gaps = 8/289 (2%) Query: 8 AAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHG 67 A + A++L +ALP++ R+ +V+KYGG+AM+ EE FA+D+VL++ G+NPVVVHG Sbjct: 3 AQEQAEILMQALPHMLRYDDAIVVVKYGGHAMDDEESARNFAKDMVLLEQSGVNPVVVHG 62 Query: 68 GGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLT 127 GGPQIG +L +L I+S F G+R+TD AT+++VEMVL G +NK IV IN GG AIGL Sbjct: 63 GGPQIGAMLAKLGIKSVFSQGLRITDRATIEIVEMVLAGSINKQIVGFINAEGGRAIGLC 122 Query: 128 GKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGV 187 GKD ++ A KL + +D+G VGE V+ +L+ ++ + IPV+AP+ Sbjct: 123 GKDGNMVTAHKLG--------QPGDAVDLGFVGEPAKVDTTVLDQVLGRELIPVLAPVAQ 174 Query: 188 GSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIADGT 247 G +GE+YNINAD AG +A AL+A++L+ LT++ G++D+Q +++ L E++ LIADGT Sbjct: 175 GVDGETYNINADTFAGAIAGALQAKRLLFLTDVPGVLDRQKRLIKQLRVEEIRTLIADGT 234 Query: 248 IYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLIS 296 I GGM+PK+ + A++ GV I+DG+ P+AVL+E+ TD G GTLI+ Sbjct: 235 ITGGMIPKVETCIYALEQGVEGVVILDGKTPHAVLVELLTDHGAGTLIT 283 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: 271 Number of extensions: 7 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: 284 Length adjustment: 26 Effective length of query: 275 Effective length of database: 258 Effective search space: 70950 Effective search space used: 70950 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_041778980.1 BIND_RS16900 (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.24454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-82 261.0 3.0 5.5e-82 260.8 3.0 1.1 1 lcl|NCBI__GCF_000019845.1:WP_041778980.1 BIND_RS16900 acetylglutamate kin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_041778980.1 BIND_RS16900 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.8 3.0 5.5e-82 5.5e-82 2 231 .] 25 259 .. 24 259 .. 0.98 Alignments for each domain: == domain 1 score: 260.8 bits; conditional E-value: 5.5e-82 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketle 68 +V+K+GG+a++ e +++akd++ l+++g+++v+vHGGgp+i ++l klgi+ f++glR+Td++t+e lcl|NCBI__GCF_000019845.1:WP_041778980.1 25 VVVKYGGHAMDdeESARNFAKDMVLLEQSGVNPVVVHGGGPQIGAMLAKLGIKSVFSQGLRITDRATIE 93 8**********888999**************************************************** PP TIGR00761 69 vvemvligkvnkelvallekhgikavGltgkDgqlltaekldke....dlgyvGeikkvnkelleallk 133 +vemvl+g++nk++v +++ +g +a+Gl+gkDg+++ta+kl + dlg+vGe kv++ +l+++l lcl|NCBI__GCF_000019845.1:WP_041778980.1 94 IVEMVLAGSINKQIVGFINAEGGRAIGLCGKDGNMVTAHKLGQPgdavDLGFVGEPAKVDTTVLDQVLG 162 ***************************************998888899********************* PP TIGR00761 134 agiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqli 202 + ipv+a++a +g+++N+naDt A+++A al+A++L++Ltdv+G+l++ +k+li++l++eei+ li lcl|NCBI__GCF_000019845.1:WP_041778980.1 163 RELIPVLAPVAQGVDGETYNINADTFAGAIAGALQAKRLLFLTDVPGVLDR-QKRLIKQLRVEEIRTLI 230 ***************************************************.666************** PP TIGR00761 203 kqavikgGmipKveaalealesgvkkvvi 231 + i+gGmipKve ++ ale+gv+ vvi lcl|NCBI__GCF_000019845.1:WP_041778980.1 231 ADGTITGGMIPKVETCIYALEQGVEGVVI 259 *************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (284 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.80 // [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