Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_084276093.1 B8779_RS08125 acetylglutamate kinase
Query= BRENDA::Q9X2A4 (282 letters) >NCBI__GCF_900176045.1:WP_084276093.1 Length = 284 Score = 268 bits (686), Expect = 8e-77 Identities = 141/279 (50%), Positives = 195/279 (69%), Gaps = 4/279 (1%) Query: 2 RIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHG 61 +I TV LL++LP+IK+F + FVIK+GGSA + K+ F QDI+LL GIKP++VHG Sbjct: 4 KIQTVQTLLDSLPFIKKFREEIFVIKYGGSAQTDQKLKEKFAQDILLLYTVGIKPVVVHG 63 Query: 62 GGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGKINKEIVMNLNLHGGRAVGIC 121 GG I++++ L I+ F +G RVT E+ MEIVEMVL G INKEIV LN HG +A+GI Sbjct: 64 GGKRITEILTRLQIDTEFIDGQRVTTEEVMEIVEMVLSGDINKEIVSLLNNHGAKALGIS 123 Query: 122 GKDSKLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGED-GH-SYNI 179 GKD+ I A + GY G + +++P +++ L+E +IPVIAP+ GH YNI Sbjct: 124 GKDAHFITA-RPKDFEKFGYTGVIDRIDPAVVYNLLEEQFIPVIAPIAASNKVGHPGYNI 182 Query: 180 NADTAAAEIAKSLMAEKLILLTDVDGVL-KDGKLISTLTPDEAEELIRDGTVTGGMIPKV 238 NAD A+++A SL A+K+I LTD GVL K+GKLISTLT ++ L +DGT++GGMIPKV Sbjct: 183 NADLCASKVAGSLKAKKIIFLTDTPGVLDKEGKLISTLTEEKIGLLKQDGTISGGMIPKV 242 Query: 239 ECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277 + + A+ GV HII+G +EH++LLEIF+ +GIGT + Sbjct: 243 DACLEAIHSGVEKAHIIDGRIEHSLLLEIFTSEGIGTQV 281 Lambda K H 0.318 0.140 0.393 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: 270 Number of extensions: 13 Number of successful extensions: 4 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: 282 Length of database: 284 Length adjustment: 26 Effective length of query: 256 Effective length of database: 258 Effective search space: 66048 Effective search space used: 66048 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_084276093.1 B8779_RS08125 (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.10459.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-81 259.5 1.2 1.6e-81 259.3 1.2 1.1 1 lcl|NCBI__GCF_900176045.1:WP_084276093.1 B8779_RS08125 acetylglutamate ki Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084276093.1 B8779_RS08125 acetylglutamate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.3 1.2 1.6e-81 1.6e-81 2 231 .] 26 258 .. 25 258 .. 0.97 Alignments for each domain: == domain 1 score: 259.3 bits; conditional E-value: 1.6e-81 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketle 68 ViK+GG+a + +l+e++a+di l+ +gik+v+vHGGg+ i+e+l++l+i++ef++g+RvT++e++e lcl|NCBI__GCF_900176045.1:WP_084276093.1 26 FVIKYGGSAQTdqKLKEKFAQDILLLYTVGIKPVVVHGGGKRITEILTRLQIDTEFIDGQRVTTEEVME 94 69*******998899****************************************************** PP TIGR00761 69 vvemvligkvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagii 137 +vemvl g++nke+v ll++hg+ka+G++gkD++ +ta+ d e+ gy+G+i++++++++ +ll++++i lcl|NCBI__GCF_900176045.1:WP_084276093.1 95 IVEMVLSGDINKEIVSLLNNHGAKALGISGKDAHFITARPKDFEKFGYTGVIDRIDPAVVYNLLEEQFI 163 ********************************************************************* PP TIGR00761 138 pviaslald..eegqllNvnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikq 204 pvia++a++ + +N+naD +A+++A +l+A+k+++Ltd++G+l++ + +lis l+ e+i l + lcl|NCBI__GCF_900176045.1:WP_084276093.1 164 PVIAPIAASnkVGHPGYNINADLCASKVAGSLKAKKIIFLTDTPGVLDK-EGKLISTLTEEKIGLLKQD 231 *******995233556*********************************.666**************** PP TIGR00761 205 avikgGmipKveaalealesgvkkvvi 231 + i gGmipKv+a+lea++sgv+k++i lcl|NCBI__GCF_900176045.1:WP_084276093.1 232 GTISGGMIPKVDACLEAIHSGVEKAHI 258 *************************98 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.66 // [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