Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_084056108.1 B9A12_RS02885 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_900176285.1:WP_084056108.1 Length = 345 Score = 324 bits (831), Expect = 2e-93 Identities = 167/346 (48%), Positives = 226/346 (65%), Gaps = 2/346 (0%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103 +++V I G +GYTG ELLRIL+ HP+V+V+ +TSR+ G VA++YP LRGH L F Sbjct: 1 MVRVAIAGASGYTGFELLRILSRHPQVTVTTVTSRAHTGQAVADVYPALRGHCPLIFQNT 60 Query: 104 DVNVLGA-CDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162 VL A DLVF A PH AM +VP+L+S GV+VVDLSADFR +D V+ WY H + Sbjct: 61 TAEVLTAEADLVFTALPHQAAMGIVPDLLSRGVKVVDLSADFRFRDPRVYEAWY-QEHTA 119 Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222 P+ + VYGLPE+ RD I A+LV NPGCYPT++ L PL+++ LVDP+ +IAD+KSG Sbjct: 120 PDLLSETVYGLPELYRDAIARARLVGNPGCYPTSILLAAAPLVKRRLVDPRTIIADSKSG 179 Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282 SGAGR + E+ + FKAY + HRH PEI Q L AG + ++F PHL+PM R Sbjct: 180 VSGAGRGLSLATHFCEVHDGFKAYKVAEHRHTPEIEQELSALAGEQLHISFTPHLVPMTR 239 Query: 283 GIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQ 342 GI +T+YA+L+ + + A + + E F+ + P G P T VRG N C +A Sbjct: 240 GILSTVYAQLRPGVTGEEVDAAYRDLYGTERFLRLCPPGRFPSTLQVRGTNYCDLAWKVD 299 Query: 343 EQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 +++ ++V SVIDNL +GA+GQAV NMN+M GL E GLEA +P Sbjct: 300 PRTDRIVVVSVIDNLTRGASGQAVCNMNLMMGLDEACGLEAAPWMP 345 Lambda K H 0.321 0.137 0.412 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: 343 Number of extensions: 11 Number of successful extensions: 3 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: 388 Length of database: 345 Length adjustment: 30 Effective length of query: 358 Effective length of database: 315 Effective search space: 112770 Effective search space used: 112770 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_084056108.1 B9A12_RS02885 (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.15432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-138 446.9 0.0 2.9e-138 446.7 0.0 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084056108.1 B9A12_RS02885 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084056108.1 B9A12_RS02885 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.7 0.0 2.9e-138 2.9e-138 1 345 [] 2 345 .] 2 345 .] 0.98 Alignments for each domain: == domain 1 score: 446.7 bits; conditional E-value: 2.9e-138 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 ++vai GasGYtG eLlr+l++Hp+v+vt+++s+ + g+ +++v+p l+g+ l ++++++e +++ead lcl|NCBI__GCF_900176285.1:WP_084056108.1 2 VRVAIAGASGYTGFELLRILSRHPQVTVTTVTSRAHTGQAVADVYPALRGHCPLIFQNTTAEVLTAEAD 70 58***************************7777777*************************99****** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 +vf+Alph++++ +vp+ll++gvkv+dlSadfR++d++vYe+wY++ h++++ll+e+vYGlpEl+r++i lcl|NCBI__GCF_900176285.1:WP_084056108.1 71 LVFTALPHQAAMGIVPDLLSRGVKVVDLSADFRFRDPRVYEAWYQE-HTAPDLLSETVYGLPELYRDAI 138 ********************************************98.8999****************** PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 ++a+l++nPGCy+T++lLa aPl+k++l++p++ii d+ksGvSgAGr s +++f+ev++ +k+Ykv++ lcl|NCBI__GCF_900176285.1:WP_084056108.1 139 ARARLVGNPGCYPTSILLAAAPLVKRRLVDPRTIIADSKSGVSGAGRGLSLATHFCEVHDGFKAYKVAE 207 ********************************************************************* PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276 HrHtpEieqels+la+++ ++sftphlvpmtrGil+t+ya+l+ ++t ee+ ++y+++Y +e+f r+++ lcl|NCBI__GCF_900176285.1:WP_084056108.1 208 HRHTPEIEQELSALAGEQLHISFTPHLVPMTRGILSTVYAQLRPGVTGEEVDAAYRDLYGTERFLRLCP 276 ********************************************************************* PP TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 g++Pst +v+g+n++d++++vd +t+r+vvvs+iDNL++Ga+gqAv n+Nlm+g+de gLe p +p lcl|NCBI__GCF_900176285.1:WP_084056108.1 277 PGRFPSTLQVRGTNYCDLAWKVDPRTDRIVVVSVIDNLTRGASGQAVCNMNLMMGLDEACGLEAAPWMP 345 ***************************************************************999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (345 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: 7.42 // [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