Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; EC 1.2.1.38; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase (uncharacterized)
to candidate WP_013553969.1 NITSA_RS05180 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A6Q9U8 (335 letters) >NCBI__GCF_000186245.1:WP_013553969.1 Length = 335 Score = 535 bits (1377), Expect = e-157 Identities = 260/335 (77%), Positives = 290/335 (86%) Query: 1 MIKVGVVGASGYTGLELVKMLITHPGFELTYLATTQGDTTIEALHPSLEGVVTLEVEKAD 60 MI VG+VGA GYTGLELVKML+ HP F L YLATT GD +E LHPSL ++T VE+AD Sbjct: 1 MINVGIVGAGGYTGLELVKMLLNHPRFRLNYLATTSGDIMVEELHPSLLDLITFPVEEAD 60 Query: 61 VNAVADACELVFLALPHKASMGFAKGLIEKGVKVVDLSADYRLELDTYEAHYCEHEDKEH 120 +AD CELVFLALPHKASMG AK LI +GVK+VDLSADYRLE +TYEA YC HED EH Sbjct: 61 PELIADKCELVFLALPHKASMGLAKELIVRGVKIVDLSADYRLERETYEAAYCPHEDPEH 120 Query: 121 LDESVYALIEYYREELKEAELAAGPGCYPTATLLGILPFIPYIDTSAPLFVDAKSGVSGA 180 L E+VY LIEYYR+E++ A L AGPGCYPTATLLG+LPFIPYIDTSAP+F+DAKSGVSGA Sbjct: 121 LGEAVYGLIEYYRDEIRVARLVAGPGCYPTATLLGLLPFIPYIDTSAPIFIDAKSGVSGA 180 Query: 181 GKKLSETTHFVTVNDNIFAYNPLKHRHAPEIAEKIEKVHGAKMNVNFVPHLIPATRGELV 240 GKKLSET+HFVT+NDNIFAYNPLKHRHAPEIAEKI K+HGA+++VNFVPHLIPATRGELV Sbjct: 181 GKKLSETSHFVTINDNIFAYNPLKHRHAPEIAEKIAKIHGAEISVNFVPHLIPATRGELV 240 Query: 241 SVYATLKEDIDPLEVLRKHYANDRFIRIREKPVDIKSTAGTHFCDIYAAKNGHALFVSSA 300 SVYATLKE+IDP EVL K Y +RFIR+R KPVDIKS AGTHFCDIYA +NG ALF+SSA Sbjct: 241 SVYATLKEEIDPQEVLEKAYDTERFIRLRHKPVDIKSVAGTHFCDIYAQRNGKALFISSA 300 Query: 301 IDNLLRGASSQALAAANLMCGYDEGMGLPVIPYMP 335 IDNLLRGA+SQALAAANLM G DEG LPVI Y+P Sbjct: 301 IDNLLRGAASQALAAANLMMGLDEGTALPVIAYVP 335 Lambda K H 0.318 0.136 0.396 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: 447 Number of extensions: 11 Number of successful extensions: 1 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: 335 Length of database: 335 Length adjustment: 28 Effective length of query: 307 Effective length of database: 307 Effective search space: 94249 Effective search space used: 94249 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_013553969.1 NITSA_RS05180 (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.10182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-106 340.9 0.0 4.8e-106 340.8 0.0 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553969.1 NITSA_RS05180 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553969.1 NITSA_RS05180 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 340.8 0.0 4.8e-106 4.8e-106 1 345 [] 2 335 .] 2 335 .] 0.95 Alignments for each domain: == domain 1 score: 340.8 bits; conditional E-value: 4.8e-106 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 i+v+ivGa GYtG eL+++l +Hp+++++ + ++++ + ++e+hp+l +l++ +ee + e i+++++ lcl|NCBI__GCF_000186245.1:WP_013553969.1 2 INVGIVGAGGYTGLELVKMLLNHPRFRLN-YLATTSGDIMVEELHPSLLDLITFPVEEADPELIADKCE 69 68**************************9.7777788999***************************** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 +vflAlph++s+ l++el+ +gvk++dlSad+Rl+ +e+Ye+ Y he++e l eavYGl E +r+ei lcl|NCBI__GCF_000186245.1:WP_013553969.1 70 LVFLALPHKASMGLAKELIVRGVKIVDLSADYRLE-RETYEAAYCP-HEDPEHLGEAVYGLIEYYRDEI 136 ***********************************.779*****76.9999****************** PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepks.iivdaksGvSgAGrkasekslfaevnenlkpYkvt 206 + a+l+a PGCy+Ta+lL+l P++ ++++ i++daksGvSgAG+k se+s+f ++n+n+ +Y++ lcl|NCBI__GCF_000186245.1:WP_013553969.1 137 RVARLVAGPGCYPTATLLGLLPFIPYI--DTSApIFIDAKSGVSGAGKKLSETSHFVTINDNIFAYNPL 203 ************************665..55555*********************************** PP TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275 kHrH+pEi++++ k+++++++v+f+phl+p trG l ++ya+lk+e+ + ++++e++Y++e+f+r+ lcl|NCBI__GCF_000186245.1:WP_013553969.1 204 KHRHAPEIAEKIAKIHGAEISVNFVPHLIPATRGELVSVYATLKEEI---DPQEVLEKAYDTERFIRLR 269 *********************************************77...56667889**********9 PP TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344 + + ++k+v+g++f+di + + k + + saiDNL++Gaa+qA+ + Nlm+g+de ++L+ ++++ lcl|NCBI__GCF_000186245.1:WP_013553969.1 270 H--KPVDIKSVAGTHFCDIYAQRNG--KALFISSAIDNLLRGAASQALAAANLMMGLDEGTALPVIAYV 334 8..5559************988777..89***********************************98877 PP TIGR01850 345 p 345 p lcl|NCBI__GCF_000186245.1:WP_013553969.1 335 P 335 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (335 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.72 // [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