Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate WP_013644555.1 METBO_RS04830 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >NCBI__GCF_000191585.1:WP_013644555.1 Length = 336 Score = 285 bits (728), Expect = 2e-81 Identities = 152/345 (44%), Positives = 217/345 (62%), Gaps = 9/345 (2%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFSEP 103 +I+VGI+G +GYTG EL+R L HP+V + TSR PV +++PNLR +L F Sbjct: 1 MIEVGIIGASGYTGGELIRFLMKHPDVDIVAATSRKFDDEPVYKVHPNLRD-CELKFKNI 59 Query: 104 DVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHESP 163 + + L A DLVF ATPHG +M++VPEL+ +RVVDLS D+R + +++ WYG H +P Sbjct: 60 EPSKLEA-DLVFTATPHGASMKIVPELIDKNIRVVDLSGDYRFESTEIYEKWYGFKHSNP 118 Query: 164 EWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSGA 223 AVYGLPE+ R EI++A LVANPGCYPT L LP++ + L D ++ D+KSG Sbjct: 119 L---NAVYGLPEINRKEIKHADLVANPGCYPTGAILACLPIVSENLAD--NIVVDSKSGV 173 Query: 224 SGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIRG 283 SGAG + +S Y + HRH PEI++ L + G+ V+F PHL+P+IRG Sbjct: 174 SGAGVNPTDTTHYPNCSDSVSPYAVTTHRHGPEIQEKL--SKYGNSKVSFTPHLVPVIRG 231 Query: 284 IEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQE 343 I T++ L + + + L+++ +D EPFV V+ G P SVRG+N C + + Sbjct: 232 IMTTVHGFLTSDVSPEYIHELYKEFYDGEPFVRVLEKGESPRMSSVRGSNNCHIGCFEID 291 Query: 344 QSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 ++ ++V+S IDNLVKGA+GQAV NMN+MFG KET ++ L P Sbjct: 292 ENGRLVVASSIDNLVKGASGQAVHNMNLMFGFKETESIDNIGLHP 336 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: 419 Number of extensions: 24 Number of successful extensions: 6 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: 336 Length adjustment: 29 Effective length of query: 359 Effective length of database: 307 Effective search space: 110213 Effective search space used: 110213 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_013644555.1 METBO_RS04830 (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.4029722.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-134 433.4 0.0 3.6e-134 433.3 0.0 1.0 1 NCBI__GCF_000191585.1:WP_013644555.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000191585.1:WP_013644555.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.3 0.0 3.6e-134 3.6e-134 1 345 [] 2 336 .] 2 336 .] 0.96 Alignments for each domain: == domain 1 score: 433.3 bits; conditional E-value: 3.6e-134 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvdlkleeleeeeileeadvvf 72 i+v+i+GasGYtG+eL+r+l kHp+v+++ +++sr+ ++++ +vhp+l++ +lk++++e +++ ead+vf NCBI__GCF_000191585.1:WP_013644555.1 2 IEVGIIGASGYTGGELIRFLMKHPDVDIV-AATSRKfDDEPVYKVHPNLRDC-ELKFKNIEPSKL--EADLVF 70 589**************************.6777777************985.699999998865..7***** PP TIGR01850 73 lAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklia 145 +A+phg+s+++vpel++k+++v+dlS+d+R++++e+YekwYg+kh+++ +avYGlpE+nr+eik+a+l+a NCBI__GCF_000191585.1:WP_013644555.1 71 TATPHGASMKIVPELIDKNIRVVDLSGDYRFESTEIYEKWYGFKHSNP---LNAVYGLPEINRKEIKHADLVA 140 ***********************************************7...79******************** PP TIGR01850 146 nPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqel 218 nPGCy+T+a+La+ P+++e+l ++ i+vd+ksGvSgAG ++++++++++++++++pY+vt+HrH pEi+++l NCBI__GCF_000191585.1:WP_013644555.1 141 NPGCYPTGAILACLPIVSENLADN--IVVDSKSGVSGAGVNPTDTTHYPNCSDSVSPYAVTTHRHGPEIQEKL 211 ********************9885..9********************************************** PP TIGR01850 219 sklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnf 291 sk + kvsftphlvp++rGi++t++ l+++++ e +++ly+e+Y++epfvrvl++ge P++++v+gsn NCBI__GCF_000191585.1:WP_013644555.1 212 SKYG--NSKVSFTPHLVPVIRGIMTTVHGFLTSDVSPEYIHELYKEFYDGEPFVRVLEKGESPRMSSVRGSNN 282 *554..7789*************************************************************** PP TIGR01850 292 vdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 ++ig+ +e++r+vv s iDNLvKGa+gqAv n+Nlm+gf+ete++++++l+p NCBI__GCF_000191585.1:WP_013644555.1 283 CHIGCFEIDENGRLVVASSIDNLVKGASGQAVHNMNLMFGFKETESIDNIGLHP 336 ****6666669**************************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (336 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.69 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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