Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_012567460.1 RC1_RS10975 acetylglutamate kinase
Query= BRENDA::Q9HTN2 (301 letters) >NCBI__GCF_000016185.1:WP_012567460.1 Length = 305 Score = 329 bits (843), Expect = 6e-95 Identities = 159/295 (53%), Positives = 221/295 (74%) Query: 4 SRDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPV 63 SR++ A+ LSEALP++RR+ G+T+V+KYGG+AM E L FA D+VLMK +GI+PV Sbjct: 11 SREEWLAKARTLSEALPFMRRYAGRTVVVKYGGHAMGDESLGRRFANDIVLMKQMGISPV 70 Query: 64 VVHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSA 123 VVHGGGPQIG +L+RL I+S F+DG+RVTD T+++ EMVL G +NK IV LIN GG A Sbjct: 71 VVHGGGPQIGQMLERLKIKSEFVDGLRVTDKETVEIAEMVLSGSINKQIVALINDAGGDA 130 Query: 124 IGLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIA 183 +GL+GKD +LI A+K+T +++ P+ ++ID+G VG+ VN GLL+ L + D IPVIA Sbjct: 131 VGLSGKDDDLIEARKVTRSKRDPDSNIEKVIDLGFVGDPFRVNPGLLHKLQQADIIPVIA 190 Query: 184 PIGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELI 243 PIG+G +G++YNINAD AG +A A+ A +L+LLT++AG++DKQ +++ +S E I Sbjct: 191 PIGIGEDGQTYNINADTAAGAIAAAVNATRLLLLTDVAGVLDKQKRLIPEMSVEAAQRAI 250 Query: 244 ADGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNR 298 DGT GGM+PKI L AV GGV +A I+DGRVP+A++LE+FT+ G GTLI + Sbjct: 251 DDGTATGGMIPKIETCLRAVNGGVEAAVILDGRVPHAIVLELFTEGGAGTLIGRK 305 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: 294 Number of extensions: 10 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: 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_012567460.1 RC1_RS10975 (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.2846.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-81 257.1 3.2 8.2e-81 256.9 3.2 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012567460.1 RC1_RS10975 acetylglutamate kina Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012567460.1 RC1_RS10975 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.9 3.2 8.2e-81 8.2e-81 1 231 [] 36 279 .. 36 279 .. 0.98 Alignments for each domain: == domain 1 score: 256.9 bits; conditional E-value: 8.2e-81 TIGR00761 1 tiViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketl 67 t+V+K+GG+a+ l +++a+di+ +++ gi++v+vHGGgp+i ++le+l+i+ efv+glRvTdket+ lcl|NCBI__GCF_000016185.1:WP_012567460.1 36 TVVVKYGGHAMGdeSLGRRFANDIVLMKQMGISPVVVHGGGPQIGQMLERLKIKSEFVDGLRVTDKETV 104 69*********977899**************************************************** PP TIGR00761 68 evvemvligkvnkelvallekhgikavGltgkDgqlltaekldke............dlgyvGeikkvn 124 e++emvl g++nk++val++ +g avGl+gkD +l++a+k++++ dlg+vG+ +vn lcl|NCBI__GCF_000016185.1:WP_012567460.1 105 EIAEMVLSGSINKQIVALINDAGGDAVGLSGKDDDLIEARKVTRSkrdpdsniekviDLGFVGDPFRVN 173 ****************************************998888999******************** PP TIGR00761 125 kelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkkslisel 193 + ll++l +a+iipvia++++ e+gq++N+naDtaA+++Aaa++A +L+lLtdvaG+l++ +k+li e+ lcl|NCBI__GCF_000016185.1:WP_012567460.1 174 PGLLHKLQQADIIPVIAPIGIGEDGQTYNINADTAAGAIAAAVNATRLLLLTDVAGVLDK-QKRLIPEM 241 ************************************************************.666***** PP TIGR00761 194 eleeieqlikqavikgGmipKveaalealesgvkkvvi 231 ++e +++ i + ++gGmipK+e +l+a+++gv+++vi lcl|NCBI__GCF_000016185.1:WP_012567460.1 242 SVEAAQRAIDDGTATGGMIPKIETCLRAVNGGVEAAVI 279 **********************************9997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.32 // [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