Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_019867433.1 METMI_RS0116640 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000384075.1:WP_019867433.1 Length = 343 Score = 438 bits (1127), Expect = e-127 Identities = 219/345 (63%), Positives = 269/345 (77%), Gaps = 2/345 (0%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103 +IK GIVGGTGYTGVELLRILA HP+V V+ +TSR++AG+ V +YP+LR D+ F++P Sbjct: 1 MIKAGIVGGTGYTGVELLRILARHPDVEVAIVTSRADAGVRVDAVYPSLRKLLDVTFTQP 60 Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163 ++ L CD+VFFATP+G AM M L+ GV+V+DLSADFRL+++D W +WYGMAH P Sbjct: 61 EIETLAHCDVVFFATPNGTAMHMAEALLERGVKVIDLSADFRLQNVDEWQHWYGMAHACP 120 Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223 E + AVYGLPE R I+ A LVA PGCYPTAVQLGFLPL+E LVD LIAD KSGA Sbjct: 121 ELVKHAVYGLPETNRAAIQQANLVACPGCYPTAVQLGFLPLIENQLVDLGHLIADVKSGA 180 Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283 SGAGR+ ++ L E GESFKAY GHRHLPEIRQGL AAG V +TFVPHLIPMIRG Sbjct: 181 SGAGRKAELATLMSETGESFKAYAVGGHRHLPEIRQGLGTAAGQAVQLTFVPHLIPMIRG 240 Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343 I ATLYA+LK A +QAL+EQR+ +E FVDV+P G+HP+TR+VRG+N C++ALH+ + Sbjct: 241 IHATLYAQLKVGA--KDIQALYEQRYQNEAFVDVLPPGAHPDTRNVRGSNNCQIALHQPQ 298 Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 N ++V SVIDNLVKGA+GQAVQNMN+MFGL+ET+GL AL P Sbjct: 299 GGNTLVVLSVIDNLVKGASGQAVQNMNLMFGLEETLGLATVALYP 343 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: 448 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: 388 Length of database: 343 Length adjustment: 30 Effective length of query: 358 Effective length of database: 313 Effective search space: 112054 Effective search space used: 112054 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_019867433.1 METMI_RS0116640 (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.30332.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-136 438.8 0.0 8.7e-136 438.6 0.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019867433.1 METMI_RS0116640 N-acetyl-gamma-g Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019867433.1 METMI_RS0116640 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.6 0.0 8.7e-136 8.7e-136 1 345 [] 2 343 .] 2 343 .] 0.98 Alignments for each domain: == domain 1 score: 438.6 bits; conditional E-value: 8.7e-136 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileea 68 ik++ivG++GYtG+eLlr+la+Hp+vev+ +v+sr+ ag ++++v+p+l++l+d+++++ e+e+ l+++ lcl|NCBI__GCF_000384075.1:WP_019867433.1 2 IKAGIVGGTGYTGVELLRILARHPDVEVA-IVTSRAdAGVRVDAVYPSLRKLLDVTFTQPEIET-LAHC 68 689**************************.7777777*********************999985.579* PP TIGR01850 69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137 dvvf+A+p+g++++++++lle+gvkvidlSadfRl++ +++++wYg+ h+ +el+++avYGlpE nr + lcl|NCBI__GCF_000384075.1:WP_019867433.1 69 DVVFFATPNGTAMHMAEALLERGVKVIDLSADFRLQNVDEWQHWYGMAHACPELVKHAVYGLPETNRAA 137 ********************************************************************* PP TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206 i++a+l+a+PGCy+Ta++L+ Pl++++l++ ++i d+ksG SgAGrka+ ++l++e+ e++k+Y+v lcl|NCBI__GCF_000384075.1:WP_019867433.1 138 IQQANLVACPGCYPTAVQLGFLPLIENQLVDLGHLIADVKSGASGAGRKAELATLMSETGESFKAYAVG 206 ********************************************************************* PP TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275 +HrH pEi+q l+++a++ v+++f+phl+pm+rGi+at+ya+lk ++++++lye++Y++e fv+vl lcl|NCBI__GCF_000384075.1:WP_019867433.1 207 GHRHLPEIRQGLGTAAGQAVQLTFVPHLIPMIRGIHATLYAQLKV--GAKDIQALYEQRYQNEAFVDVL 273 *******************************************98..679******************* PP TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344 + g P+t++v+gsn ++i+++ + +++vv+s+iDNLvKGa+gqAvqn+Nlm+g++et gL +++l+ lcl|NCBI__GCF_000384075.1:WP_019867433.1 274 PPGAHPDTRNVRGSNNCQIALHQPQGGNTLVVLSVIDNLVKGASGQAVQNMNLMFGLEETLGLATVALY 342 *******************************************************************99 PP TIGR01850 345 p 345 p lcl|NCBI__GCF_000384075.1:WP_019867433.1 343 P 343 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (343 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: 6.68 // [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