Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_026223550.1 A3OW_RS0112385 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000372865.1:WP_026223550.1 Length = 343 Score = 436 bits (1122), Expect = e-127 Identities = 213/345 (61%), Positives = 263/345 (76%), Gaps = 2/345 (0%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103 +I+ GIVGGTGYTGVELLRILA+H EV V+ +TSR++AG V +YP LRG+ + FS P Sbjct: 1 MIRAGIVGGTGYTGVELLRILALHEEVEVAVVTSRADAGSRVDAVYPGLRGYVEATFSAP 60 Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163 DV +L CD+VFFATP+G AM M +L++ GV+++DLSADFR+KD W+ WYGM H P Sbjct: 61 DVAILAECDVVFFATPNGTAMGMAEQLLARGVKIIDLSADFRIKDAGEWSRWYGMEHACP 120 Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223 + +A+YGLPEV R+ I+ A+L+A PGCYPT+VQLGFLPL+E L+D LIAD KSG Sbjct: 121 DLIAEAIYGLPEVNREAIKTARLIACPGCYPTSVQLGFLPLIENDLIDSDHLIADVKSGV 180 Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283 SGAGR+ ++ L E GESFKAY GHRHLPEI QGL AAG VG+TFVPHL PMIRG Sbjct: 181 SGAGRKAELATLMSECGESFKAYAVGGHRHLPEISQGLKAAAGKAVGLTFVPHLTPMIRG 240 Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343 I ATLY +LK D LQ+L+EQR+ DE FVDV+P GSHP+TR+VRG+N C++AL+R + Sbjct: 241 IHATLYGQLK--TSVDDLQSLYEQRYRDELFVDVLPSGSHPDTRNVRGSNNCQIALYRPQ 298 Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 V+V SVIDNLVKGAAGQAVQNMN+MFG E GL+ AL P Sbjct: 299 GGRTVVVLSVIDNLVKGAAGQAVQNMNLMFGFNEETGLKTVALYP 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: 413 Number of extensions: 11 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_026223550.1 A3OW_RS0112385 (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.14916.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-135 435.3 0.0 9.6e-135 435.1 0.0 1.0 1 lcl|NCBI__GCF_000372865.1:WP_026223550.1 A3OW_RS0112385 N-acetyl-gamma-gl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_026223550.1 A3OW_RS0112385 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.1 0.0 9.6e-135 9.6e-135 1 345 [] 2 343 .] 2 343 .] 0.98 Alignments for each domain: == domain 1 score: 435.1 bits; conditional E-value: 9.6e-135 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileea 68 i+++ivG++GYtG+eLlr+la H+evev+ +v+sr+ ag+++++v+p l+g v++++++ +++ il+e+ lcl|NCBI__GCF_000372865.1:WP_026223550.1 2 IRAGIVGGTGYTGVELLRILALHEEVEVA-VVTSRAdAGSRVDAVYPGLRGYVEATFSAPDVA-ILAEC 68 5899*************************.6666666*********************98877.899** PP TIGR01850 69 dvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnree 137 dvvf+A+p+g+++ ++++ll++gvk+idlSadfR+kda ++++wYg++h+ ++l++ea+YGlpE+nre+ lcl|NCBI__GCF_000372865.1:WP_026223550.1 69 DVVFFATPNGTAMGMAEQLLARGVKIIDLSADFRIKDAGEWSRWYGMEHACPDLIAEAIYGLPEVNREA 137 ********************************************************************* PP TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206 ik+a+lia+PGCy+T+++L+ Pl++++li+++++i d+ksGvSgAGrka+ ++l++e+ e++k+Y+v lcl|NCBI__GCF_000372865.1:WP_026223550.1 138 IKTARLIACPGCYPTSVQLGFLPLIENDLIDSDHLIADVKSGVSGAGRKAELATLMSECGESFKAYAVG 206 ********************************************************************* PP TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275 +HrH pEi+q l+++a+k v ++f+phl+pm+rGi+at+y +lk+++ ++l++lye++Y+de fv+vl lcl|NCBI__GCF_000372865.1:WP_026223550.1 207 GHRHLPEISQGLKAAAGKAVGLTFVPHLTPMIRGIHATLYGQLKTSV--DDLQSLYEQRYRDELFVDVL 273 *************99999999************************65..99****************** PP TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344 ++g+ P+t++v+gsn ++i++ + ++vvv+s+iDNLvKGaagqAvqn+Nlm+gf+e++gL++++l+ lcl|NCBI__GCF_000372865.1:WP_026223550.1 274 PSGSHPDTRNVRGSNNCQIALYRPQGGRTVVVLSVIDNLVKGAAGQAVQNMNLMFGFNEETGLKTVALY 342 *******************************************************************99 PP TIGR01850 345 p 345 p lcl|NCBI__GCF_000372865.1:WP_026223550.1 343 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: 9.37 // [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