Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_019895456.1 A377_RS0106595 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000384235.1:WP_019895456.1 Length = 357 Score = 426 bits (1096), Expect = e-124 Identities = 211/348 (60%), Positives = 256/348 (73%), Gaps = 4/348 (1%) Query: 45 IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEPD 104 IK+GIVGGTG+TGVELLR+L+ H +V V IT+RSEAGMPVAEM+PNLRG DL F EP+ Sbjct: 10 IKIGIVGGTGFTGVELLRMLSTHDQVQVDVITARSEAGMPVAEMFPNLRGVTDLVFREPE 69 Query: 105 VNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESPE 164 + L CDLVFFATPHGVAM M P L+ AGVRV+DL ADFRL+DLDVW+ WYGM H + Sbjct: 70 LESLSQCDLVFFATPHGVAMEMAPALVEAGVRVIDLGADFRLEDLDVWSQWYGMEHSAEI 129 Query: 165 WAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGAS 224 + YGLPE R I A+++ANPGCYPTA+ LG LP L+ GLV ++AD KSG S Sbjct: 130 LMRRVAYGLPEWYRQAISQARVIANPGCYPTAILLGALPFLKAGLVKSDGIVADGKSGVS 189 Query: 225 GAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRGI 284 G GR K+ ML E+ ESFKAYG SGHRHLPEI++ A V VTFVPHL+PM+RG+ Sbjct: 190 GGGRGAKVAMLGAEMSESFKAYGISGHRHLPEIQEKASQVAEKPVSVTFVPHLVPMVRGM 249 Query: 285 EATLYAELKNP----ADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALH 340 E TLY L +P ++ LQ+L E + DEPFVDVMP S PETRSVRG+N CR++L Sbjct: 250 ETTLYLPLTDPDSPQSEVAALQSLLEATYADEPFVDVMPPDSLPETRSVRGSNLCRLSLS 309 Query: 341 RQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 R + N ++V+SVIDNLVKGAAGQA+QNMNI+FG E GL+ L+P Sbjct: 310 RPQNGNTLVVTSVIDNLVKGAAGQAIQNMNILFGWPEDKGLQQIGLMP 357 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: 415 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: 357 Length adjustment: 30 Effective length of query: 358 Effective length of database: 327 Effective search space: 117066 Effective search space used: 117066 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_019895456.1 A377_RS0106595 (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.8566.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-129 417.9 0.0 2e-129 417.7 0.0 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019895456.1 A377_RS0106595 N-acetyl-gamma-gl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895456.1 A377_RS0106595 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.7 0.0 2e-129 2e-129 1 345 [] 10 357 .] 10 357 .] 0.96 Alignments for each domain: == domain 1 score: 417.7 bits; conditional E-value: 2e-129 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 ik++ivG++G+tG+eLlr+l++H +v+v +++++eag +++e++p+l+g++dl ++e e e+ l+++d lcl|NCBI__GCF_000384235.1:WP_019895456.1 10 IKIGIVGGTGFTGVELLRMLSTHDQVQVDVITARSEAGMPVAEMFPNLRGVTDLVFREPELES-LSQCD 77 699**************************8999999*********************999885.57*** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 +vf+A+phgv++e++p+l+e+gv+vidl+adfRl+d +v+++wYg++h++e l+++++YGlpE++r++i lcl|NCBI__GCF_000384235.1:WP_019895456.1 78 LVFFATPHGVAMEMAPALVEAGVRVIDLGADFRLEDLDVWSQWYGMEHSAEILMRRVAYGLPEWYRQAI 146 ********************************************************************* PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 ++a++ianPGCy+Ta+lL+ P+lk++l++++ i+ d+ksGvSg+Gr a+ ++l ae++e++k+Y +++ lcl|NCBI__GCF_000384235.1:WP_019895456.1 147 SQARVIANPGCYPTAILLGALPFLKAGLVKSDGIVADGKSGVSGGGRGAKVAMLGAEMSESFKAYGISG 215 *******************************99************************************ PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkke....lteeelrklyeevYedepfv 272 HrH pEi+++ s++aek v+v+f+phlvpm+rG+ +t+y+ l+++ + + l++l+e++Y+depfv lcl|NCBI__GCF_000384235.1:WP_019895456.1 216 HRHLPEIQEKASQVAEKPVSVTFVPHLVPMVRGMETTLYLPLTDPdspqSEVAALQSLLEATYADEPFV 284 ******************************************98642223445678899********** PP TIGR01850 273 rvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLekl 341 +v++ ++lP+t++v+gsn ++++++ ++ +++vv+s+iDNLvKGaagqA+qn+N+ +g++e++gL+++ lcl|NCBI__GCF_000384235.1:WP_019895456.1 285 DVMPPDSLPETRSVRGSNLCRLSLSRPQNGNTLVVTSVIDNLVKGAAGQAIQNMNILFGWPEDKGLQQI 353 ********************************************************************* PP TIGR01850 342 pllp 345 +l+p lcl|NCBI__GCF_000384235.1:WP_019895456.1 354 GLMP 357 9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (357 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: 7.03 // [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