Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_010960038.1 MCA_RS03455 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000008325.1:WP_010960038.1 Length = 348 Score = 441 bits (1135), Expect = e-128 Identities = 217/345 (62%), Positives = 266/345 (77%), Gaps = 4/345 (1%) Query: 45 IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPD 104 I+VGIVGGTGYTGVELLR+LA+HP V + +TSR++AG VA++YPNLRGH D+ F+ P+ Sbjct: 7 IEVGIVGGTGYTGVELLRLLALHPGVRIRAVTSRADAGKAVADLYPNLRGHVDVVFTGPE 66 Query: 105 VNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPE 164 V LG CD+VFFATPHG+AM+ P L+ G+ V+DLSADFRLKD D WA+WYG H P Sbjct: 67 VENLGGCDVVFFATPHGIAMQSAPALLEQGIVVIDLSADFRLKDADEWAHWYGQEHACPG 126 Query: 165 WAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGAS 224 +AVYGLPEV R+ +R+A+L+ANPGCYPTAVQLG LPLLE LV RLIAD KSG S Sbjct: 127 LLSEAVYGLPEVRREAVRSARLIANPGCYPTAVQLGLLPLLENRLVAADRLIADVKSGVS 186 Query: 225 GAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGI 284 GAGR+ ++ +L E GESFKAY +GHRH PEI QGL AG VG+TFVPHL+PMIRGI Sbjct: 187 GAGRKAEVPLLMSETGESFKAYAVAGHRHWPEIVQGLVELAGEPVGLTFVPHLLPMIRGI 246 Query: 285 EATLYA-ELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343 ATLYA + P D +Q L+E+R+ DEPFVDV+P GSHP+TR VRG+N+C++A+ Sbjct: 247 HATLYAVPVGEPGD---IQRLYEERYCDEPFVDVLPPGSHPDTRDVRGSNRCQIAVFELR 303 Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 +S ++V SVIDNLVKGAAGQAVQNMN+ FG ET GL+A L P Sbjct: 304 RSGQIVVLSVIDNLVKGAAGQAVQNMNLRFGFAETTGLQAIGLYP 348 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: 449 Number of extensions: 14 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: 388 Length of database: 348 Length adjustment: 30 Effective length of query: 358 Effective length of database: 318 Effective search space: 113844 Effective search space used: 113844 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_010960038.1 MCA_RS03455 (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.3949276.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-134 432.0 0.0 9.8e-134 431.8 0.0 1.0 1 NCBI__GCF_000008325.1:WP_010960038.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000008325.1:WP_010960038.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.8 0.0 9.8e-134 9.8e-134 1 345 [] 7 348 .] 7 348 .] 0.97 Alignments for each domain: == domain 1 score: 431.8 bits; conditional E-value: 9.8e-134 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 i+v+ivG++GYtG+eLlrlla Hp v++ +++s+ agk +++++p+l+g+vd+ ++ e+e++ +dvvf+ NCBI__GCF_000008325.1:WP_010960038.1 7 IEVGIVGGTGYTGVELLRLLALHPGVRIRAVTSRADAGKAVADLYPNLRGHVDVVFTGPEVENL-GGCDVVFF 78 589**************************6555555*********************9999865.6******* PP TIGR01850 74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146 A+phg++++ +p+lle+g++vidlSadfRlkda+++++wYg++h+ + ll+eavYGlpE++re++++a+lian NCBI__GCF_000008325.1:WP_010960038.1 79 ATPHGIAMQSAPALLEQGIVVIDLSADFRLKDADEWAHWYGQEHACPGLLSEAVYGLPEVRREAVRSARLIAN 151 ************************************************************************* PP TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219 PGCy+Ta++L+l Pll+++l+ +++i d+ksGvSgAGrka+ l++e+ e++k+Y+v++HrH pEi+q l NCBI__GCF_000008325.1:WP_010960038.1 152 PGCYPTAVQLGLLPLLENRLVAADRLIADVKSGVSGAGRKAEVPLLMSETGESFKAYAVAGHRHWPEIVQGLV 224 ************************************************************************* PP TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292 +la++ v ++f+phl+pm+rGi+at+ya + ++++lyee+Y depfv+vl+ g+ P+t++v+gsn + NCBI__GCF_000008325.1:WP_010960038.1 225 ELAGEPVGLTFVPHLLPMIRGIHATLYAVPVG--EPGDIQRLYEERYCDEPFVDVLPPGSHPDTRDVRGSNRC 295 ***************************99888..78************************************* PP TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +i+v ++++++vv+s+iDNLvKGaagqAvqn+Nl++gf+et+gL+ ++l+p NCBI__GCF_000008325.1:WP_010960038.1 296 QIAVFELRRSGQIVVLSVIDNLVKGAAGQAVQNMNLRFGFAETTGLQAIGLYP 348 ***999999*****************************************998 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 12.39 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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