Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_013840419.1 DESRU_RS01810 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q07906 (345 letters) >NCBI__GCF_000215085.1:WP_013840419.1 Length = 346 Score = 319 bits (817), Expect = 8e-92 Identities = 170/346 (49%), Positives = 219/346 (63%), Gaps = 1/346 (0%) Query: 1 MMNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKL 60 M+ IIGATGY+G EL RLL HP V + S + G + E FPH+ + VL +L Sbjct: 1 MIKAGIIGATGYAGVELVRLLSRHPRVKLAALTSQTYAGKPMGEVFPHLYGLVDHVLEEL 60 Query: 61 EI-EALAKYDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAP 119 + E +A+ D VF A P G + ++ RG ++IDL DFRLKD VY WY E Sbjct: 61 YLPELVARCDVVFTALPHGHAMPVGEEVMRRGKRLIDLGADFRLKDVDVYQSWYKTEHTA 120 Query: 120 SAYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSG 179 S + AVYGL E NRE ++ +V+++NPGCYPT+ +LGLAPL+ + LI S+I+DAKSG Sbjct: 121 SVLVASAVYGLPELNREEIKDSVIVANPGCYPTSAILGLAPLLTDKLIDAKSLIIDAKSG 180 Query: 180 VSGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTR 239 VSGAGR L THFSE N + Y V H+H PEIEQ L A ++F+ HL PMTR Sbjct: 181 VSGAGRGLSLKTHFSETTNNFQAYGVATHRHTPEIEQELSRLAGAPVTVSFTPHLTPMTR 240 Query: 240 GIMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLAYD 299 GI++T+YA + IS +L + Y++ Y G FVRI G PATK+V GSN+CDI + D Sbjct: 241 GILSTLYANLTEKISTQELTERYRSFYAGERFVRILPPGMLPATKNVAGSNHCDISVTVD 300 Query: 300 ERTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGLRSLPIYP 345 RT RV V+S IDNL+KGAAGQAVQN N+M G E GL +YP Sbjct: 301 SRTGRVIVLSAIDNLLKGAAGQAVQNLNVMAGLPEETGLDFAGMYP 346 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: 363 Number of extensions: 17 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: 345 Length of database: 346 Length adjustment: 29 Effective length of query: 316 Effective length of database: 317 Effective search space: 100172 Effective search space used: 100172 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_013840419.1 DESRU_RS01810 (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.15084.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-143 463.6 0.0 2.4e-143 463.4 0.0 1.0 1 lcl|NCBI__GCF_000215085.1:WP_013840419.1 DESRU_RS01810 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000215085.1:WP_013840419.1 DESRU_RS01810 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.4 0.0 2.4e-143 2.4e-143 1 345 [] 2 346 .] 2 346 .] 0.99 Alignments for each domain: == domain 1 score: 463.4 bits; conditional E-value: 2.4e-143 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 ik++i+Ga+GY+G+eL+rll++Hp+v++++l+s++ agk++ ev+phl glvd+ leel e+ +++d lcl|NCBI__GCF_000215085.1:WP_013840419.1 2 IKAGIIGATGYAGVELVRLLSRHPRVKLAALTSQTYAGKPMGEVFPHLYGLVDHVLEELYLPELVARCD 70 689**************************9999999***********************99999***** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 vvf+Alphg+++++ +e++++g ++idl+adfRlkd +vY++wY+++h+++ l+++avYGlpElnreei lcl|NCBI__GCF_000215085.1:WP_013840419.1 71 VVFTALPHGHAMPVGEEVMRRGKRLIDLGADFRLKDVDVYQSWYKTEHTASVLVASAVYGLPELNREEI 139 ********************************************************************* PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 k++ ++anPGCy+T+a+L+laPll++kli+ ks+i+daksGvSgAGr s k++f+e+++n+++Y v++ lcl|NCBI__GCF_000215085.1:WP_013840419.1 140 KDSVIVANPGCYPTSAILGLAPLLTDKLIDAKSLIIDAKSGVSGAGRGLSLKTHFSETTNNFQAYGVAT 208 ********************************************************************* PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276 HrHtpEieqels+la++ v+vsftphl+pmtrGil+t+ya+l+++++++el++ y+++Y++e+fvr+l+ lcl|NCBI__GCF_000215085.1:WP_013840419.1 209 HRHTPEIEQELSRLAGAPVTVSFTPHLTPMTRGILSTLYANLTEKISTQELTERYRSFYAGERFVRILP 277 ********************************************************************* PP TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 g lP+tk+v+gsn++di+v+vd++t+rv+v+saiDNL+KGaagqAvqnlN+m g++e++gL++ +++p lcl|NCBI__GCF_000215085.1:WP_013840419.1 278 PGMLPATKNVAGSNHCDISVTVDSRTGRVIVLSAIDNLLKGAAGQAVQNLNVMAGLPEETGLDFAGMYP 346 ******************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (346 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.17 // [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