Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_086510219.1 BZY95_RS12275 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_002151265.1:WP_086510219.1 Length = 344 Score = 469 bits (1208), Expect = e-137 Identities = 240/347 (69%), Positives = 270/347 (77%), Gaps = 5/347 (1%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYD-LAFSE 102 +IKVGIVGGTGYTGVELLR+LA H +V V ITSRSEAG+ V +MYPNLRGHYD LAFSE Sbjct: 1 MIKVGIVGGTGYTGVELLRLLAQHSQVEVEAITSRSEAGVRVCDMYPNLRGHYDELAFSE 60 Query: 103 PDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162 PD LGACD VFFATPHGVA + EL+ G RV+DLSADFRL+D +VWA WYG H + Sbjct: 61 PDPQRLGACDAVFFATPHGVAHALAGELLERGTRVIDLSADFRLRDAEVWAEWYGQPHGA 120 Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222 PE +AVYGLPE+ R+ IR A+L+A PGCYPTAVQLG LPLLE GL+D LIAD KSG Sbjct: 121 PELLGEAVYGLPEMHRERIRQARLIAVPGCYPTAVQLGLLPLLEAGLIDADHLIADCKSG 180 Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282 +GAGR K+ L E ES KAYGASGHRHLPEI QGL AA G VG+TFVPHL PMIR Sbjct: 181 VTGAGRGAKVPSLLAEASESMKAYGASGHRHLPEISQGLRDAANGPVGLTFVPHLTPMIR 240 Query: 283 GIEATLYAELK-NPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHR 341 GI ATLY L P D LQALFE+RF DEPFVDVMP GSHPETRSV+GAN CR+A+HR Sbjct: 241 GIHATLYGRLTGEPGD---LQALFERRFADEPFVDVMPAGSHPETRSVKGANVCRLAVHR 297 Query: 342 QEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 + V+V SVIDNLVKGA+GQAVQN+N+MFG E GL APAL+P Sbjct: 298 PGNGDTVVVLSVIDNLVKGASGQAVQNLNLMFGFDEHAGLAAPALMP 344 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: 471 Number of extensions: 13 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: 344 Length adjustment: 30 Effective length of query: 358 Effective length of database: 314 Effective search space: 112412 Effective search space used: 112412 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_086510219.1 BZY95_RS12275 (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.25931.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-133 429.4 0.0 6e-133 429.2 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510219.1 BZY95_RS12275 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510219.1 BZY95_RS12275 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.2 0.0 6e-133 6e-133 1 345 [] 2 344 .] 2 344 .] 0.98 Alignments for each domain: == domain 1 score: 429.2 bits; conditional E-value: 6e-133 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeeeileea 68 ikv+ivG++GYtG+eLlrlla+H++vev++++s++eag ++ +++p+l+g++d l ++e + ++ l ++ lcl|NCBI__GCF_002151265.1:WP_086510219.1 2 IKVGIVGGTGYTGVELLRLLAQHSQVEVEAITSRSEAGVRVCDMYPNLRGHYDeLAFSEPDPQR-LGAC 69 69***************************9999999*****************77888777775.67** PP TIGR01850 69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137 d+vf+A+phgv+++l+ elle+g++vidlSadfRl+daev+++wYg++h ++ell eavYGlpE++re+ lcl|NCBI__GCF_002151265.1:WP_086510219.1 70 DAVFFATPHGVAHALAGELLERGTRVIDLSADFRLRDAEVWAEWYGQPHGAPELLGEAVYGLPEMHRER 138 ********************************************************************* PP TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206 i++a+lia+PGCy+Ta++L+l Pll+++li+ +++i d+ksGv+gAGr a+ sl+ae++e++k+Y ++ lcl|NCBI__GCF_002151265.1:WP_086510219.1 139 IRQARLIAVPGCYPTAVQLGLLPLLEAGLIDADHLIADCKSGVTGAGRGAKVPSLLAEASESMKAYGAS 207 ********************************************************************* PP TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275 +HrH pEi+q l+++a+ v ++f+phl+pm+rGi+at+y +l+ + +l++l+e++++depfv+v+ lcl|NCBI__GCF_002151265.1:WP_086510219.1 208 GHRHLPEISQGLRDAANGPVGLTFVPHLTPMIRGIHATLYGRLTG--EPGDLQALFERRFADEPFVDVM 274 *************99999999***********************9..78******************** PP TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344 ++g+ P+t++v g n+++++v+ + ++vvv+s+iDNLvKGa+gqAvqnlNlm+gfde++gL +l+ lcl|NCBI__GCF_002151265.1:WP_086510219.1 275 PAGSHPETRSVKGANVCRLAVHRPGNGDTVVVLSVIDNLVKGASGQAVQNLNLMFGFDEHAGLAAPALM 343 ****************************************************************99988 PP TIGR01850 345 p 345 p lcl|NCBI__GCF_002151265.1:WP_086510219.1 344 P 344 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (344 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: 10.16 // [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