Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_013076226.1 BTUS_RS11400 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q07906 (345 letters) >NCBI__GCF_000092905.1:WP_013076226.1 Length = 348 Score = 339 bits (870), Expect = 5e-98 Identities = 173/349 (49%), Positives = 228/349 (65%), Gaps = 5/349 (1%) Query: 1 MMNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKL 60 M+ VA++GATGY+G EL RLL HP V S S GI LS +PH+ + L Sbjct: 1 MIRVAVVGATGYAGVELVRLLVRHPEAELAMVTSDSHAGIQLSRVYPHLTGIADFELQAF 60 Query: 61 EIEALAKY-DAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAP 119 + + +A+ + F A P G+S P+L +RGV+VIDL GDFR+ G ++ +WY ++ Sbjct: 61 DPDRVAEEANVAFLALPAGLSSTMVPSLRERGVRVIDLGGDFRIP-GPLFREWYKKDPPS 119 Query: 120 SAYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSG 179 A E AVYGLTEWNRE V GA +SNPGCYPTA LLGL P V+ ++ D +I+DAKSG Sbjct: 120 DAVREEAVYGLTEWNRERVAGASFVSNPGCYPTAALLGLLPAVRNRGVEADGLIIDAKSG 179 Query: 180 VSGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTR 239 V+GAGR LG HF+EV EN K YKV HQH PEIE L + + A ++F+ HL+PM R Sbjct: 180 VTGAGRGVNLGNHFAEVAENFKAYKVAEHQHTPEIEYHLAVFGQGSARVSFTAHLLPMGR 239 Query: 240 GIMATIYAKAK---QSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGL 296 GI+ T Y + + + ++Y+ +Y PFVR++ GQ+P TK+V G+N CDIGL Sbjct: 240 GILVTAYGTLTGEWREWTTERVWEVYQDAYRQEPFVRVQPAGQWPQTKEVRGTNLCDIGL 299 Query: 297 AYDERTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGLRSLPIYP 345 + RT R+ VVSVIDNL+KGAAGQAVQN N+MMGW E GL +P+YP Sbjct: 300 TVERRTGRMIVVSVIDNLVKGAAGQAVQNLNVMMGWPETMGLDLVPMYP 348 Lambda K H 0.318 0.135 0.404 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: 396 Number of extensions: 18 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: 345 Length of database: 348 Length adjustment: 29 Effective length of query: 316 Effective length of database: 319 Effective search space: 100804 Effective search space used: 100804 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: 49 (23.5 bits)
Align candidate WP_013076226.1 BTUS_RS11400 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
# 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/TIGR01850.hmm # target sequence database: /tmp/gapView.20336.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01850 [M=345] Accession: TIGR01850 Description: argC: N-acetyl-gamma-glutamyl-phosphate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-133 428.5 0.0 1.1e-132 428.4 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013076226.1 BTUS_RS11400 N-acetyl-gamma-glut Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013076226.1 BTUS_RS11400 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.4 0.0 1.1e-132 1.1e-132 1 345 [] 2 348 .] 2 348 .] 0.97 Alignments for each domain: == domain 1 score: 428.4 bits; conditional E-value: 1.1e-132 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 i+va+vGa+GY+G+eL+rll +Hpe+e++ ++s+++ag +ls+v+phl+g++d +l++++ ++++eea+ lcl|NCBI__GCF_000092905.1:WP_013076226.1 2 IRVAVVGATGYAGVELVRLLVRHPEAELAMVTSDSHAGIQLSRVYPHLTGIADFELQAFDPDRVAEEAN 70 69***************************8888888********************************* PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 v flAlp+g s+++vp+l e+gv+vidl++dfR+ + ++++wY+k+ +++++ eeavYGl+E+nre++ lcl|NCBI__GCF_000092905.1:WP_013076226.1 71 VAFLALPAGLSSTMVPSLRERGVRVIDLGGDFRIPGP-LFREWYKKDPPSDAVREEAVYGLTEWNRERV 138 ***********************************77.9****************************** PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 ++a++++nPGCy+TaalL+l P+++++ +e + +i+daksGv+gAGr + ++faev+en+k+Ykv++ lcl|NCBI__GCF_000092905.1:WP_013076226.1 139 AGASFVSNPGCYPTAALLGLLPAVRNRGVEADGLIIDAKSGVTGAGRGVNLGNHFAEVAENFKAYKVAE 207 *******************************99************************************ PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkke...lteeelrklyeevYedepfvr 273 H+HtpEie +l + + +++vsft+hl+pm rGil t+y +l+ e +t+e+++++y+++Y++epfvr lcl|NCBI__GCF_000092905.1:WP_013076226.1 208 HQHTPEIEYHLAVFGQGSARVSFTAHLLPMGRGILVTAYGTLTGEwreWTTERVWEVYQDAYRQEPFVR 276 ************88888999********************99976444899****************** PP TIGR01850 274 vlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklp 342 v+++g++P+tk+v+g+n +dig++v+++t+r++vvs+iDNLvKGaagqAvqnlN+m+g++et gL+ +p lcl|NCBI__GCF_000092905.1:WP_013076226.1 277 VQPAGQWPQTKEVRGTNLCDIGLTVERRTGRMIVVSVIDNLVKGAAGQAVQNLNVMMGWPETMGLDLVP 345 ********************************************************************* PP TIGR01850 343 llp 345 ++p lcl|NCBI__GCF_000092905.1:WP_013076226.1 346 MYP 348 *98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (348 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: 00:00:00.01 # Mc/sec: 11.71 // [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