Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_029133237.1 A3GO_RS0109765 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000428045.1:WP_029133237.1 Length = 342 Score = 473 bits (1218), Expect = e-138 Identities = 229/345 (66%), Positives = 275/345 (79%), Gaps = 3/345 (0%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103 ++KVGIVGGTGYTGVELLR+LA HPEV V+ ITSR+EAG V+++YPNLRGH+D+ F+EP Sbjct: 1 MVKVGIVGGTGYTGVELLRLLAGHPEVEVAVITSRAEAGRLVSDIYPNLRGHFDIPFTEP 60 Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163 D+ L CDLVFFATP+G AM++VPEL+ G RVVDL+ADFR++D+ +W WYGM H P Sbjct: 61 DLTALSDCDLVFFATPNGTAMKLVPELLEKGCRVVDLAADFRIRDIALWEQWYGMTHSCP 120 Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223 E +AVYGLPE+ R+ IR A LVANPGCYPTA LGFLPL+E GLV L+AD KSG Sbjct: 121 ELVAEAVYGLPEINREAIRTASLVANPGCYPTATTLGFLPLIESGLVRLTGLVADCKSGV 180 Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283 SGAGR +GML GE+GESFKAYG GHRH+PEIRQ L A +V +TFV HL+PMIRG Sbjct: 181 SGAGRGASVGMLMGEVGESFKAYGVPGHRHMPEIRQNLSAVANSNVELTFVAHLLPMIRG 240 Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343 I +TLYA L + D LQAL+E RF +EPFVDV+P GSHPETRSVRG N CR+A+HR + Sbjct: 241 IHSTLYATLTDEVD---LQALYESRFREEPFVDVLPAGSHPETRSVRGINHCRIAVHRPQ 297 Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 + V+V SVIDNLVKGAAGQA+QNMNIM GL+ET+GL+A ALLP Sbjct: 298 GGDTVVVLSVIDNLVKGAAGQAIQNMNIMLGLEETLGLQAVALLP 342 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: 457 Number of extensions: 13 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: 342 Length adjustment: 29 Effective length of query: 359 Effective length of database: 313 Effective search space: 112367 Effective search space used: 112367 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_029133237.1 A3GO_RS0109765 (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.18242.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-133 430.9 0.0 2.1e-133 430.7 0.0 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029133237.1 A3GO_RS0109765 N-acetyl-gamma-gl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029133237.1 A3GO_RS0109765 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.7 0.0 2.1e-133 2.1e-133 1 345 [] 2 342 .] 2 342 .] 0.98 Alignments for each domain: == domain 1 score: 430.7 bits; conditional E-value: 2.1e-133 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileead 69 +kv+ivG++GYtG+eLlrlla Hpevev+ ++s+ eag+ +s+++p+l+g++d ++e + ++ l+++d lcl|NCBI__GCF_000428045.1:WP_029133237.1 2 VKVGIVGGTGYTGVELLRLLAGHPEVEVAVITSRAEAGRLVSDIYPNLRGHFDIPFTEPDLTA-LSDCD 69 69***************************7777777*********************999985.67*** PP TIGR01850 70 vvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreei 138 +vf+A+p+g++++lvpellekg++v+dl+adfR++d +++e+wYg++h+ +el++eavYGlpE+nre+i lcl|NCBI__GCF_000428045.1:WP_029133237.1 70 LVFFATPNGTAMKLVPELLEKGCRVVDLAADFRIRDIALWEQWYGMTHSCPELVAEAVYGLPEINREAI 138 ********************************************************************* PP TIGR01850 139 kkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtk 207 ++a+l+anPGCy+Ta++L+ Pl++++l++ + ++ d+ksGvSgAGr as +l+ ev e++k+Y v + lcl|NCBI__GCF_000428045.1:WP_029133237.1 139 RTASLVANPGCYPTATTLGFLPLIESGLVRLTGLVADCKSGVSGAGRGASVGMLMGEVGESFKAYGVPG 207 ********************************************************************* PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276 HrH pEi+q+ls++a+++v+++f++hl+pm+rGi++t+ya+l++e+ +l++lye+++++epfv+vl+ lcl|NCBI__GCF_000428045.1:WP_029133237.1 208 HRHMPEIRQNLSAVANSNVELTFVAHLLPMIRGIHSTLYATLTDEV---DLQALYESRFREEPFVDVLP 273 ********************************************65...9******************* PP TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +g+ P+t++v+g n+++i+v+ + ++vvv+s+iDNLvKGaagqA+qn+N+mlg++et gL+ ++llp lcl|NCBI__GCF_000428045.1:WP_029133237.1 274 AGSHPETRSVRGINHCRIAVHRPQGGDTVVVLSVIDNLVKGAAGQAIQNMNIMLGLEETLGLQAVALLP 342 ***************************************************************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (342 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: 7.25 // [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