Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_038206433.1 Q392_RS10930 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >NCBI__GCF_000745855.1:WP_038206433.1 Length = 307 Score = 276 bits (706), Expect = 4e-79 Identities = 152/312 (48%), Positives = 199/312 (63%), Gaps = 14/312 (4%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 PK+FIDGE GTTGLQIR R+A +EL+SI R++A+ + DL+ D+ ILCL DDA Sbjct: 2 PKVFIDGEAGTTGLQIRERLALMPQIELVSIAPELRKDASAKRDLMAGVDLVILCLHDDA 61 Query: 63 SREAVAMV--AGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPT 120 +RE+VA++ G R RIID STAHRVAP W YGF E+ Q + ++ A VANPGCY T Sbjct: 62 ARESVALIDGLGERRPRIIDASTAHRVAPGWVYGFPELAAGQAEAVQAADRVANPGCYAT 121 Query: 121 GAIALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTL 180 GAIA++RPL AG+LP P+ + +VSGY+GGG+ MI E P P Y L L Sbjct: 122 GAIAIVRPLVDAGLLPADLPIALPSVSGYSGGGRTMIEAYEAGAAP-----PFETYALGL 176 Query: 181 KHKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYA 240 KHKH+PE+ + L PVF PSVG F QGM+V +PL+L+ L +H AL HYA Sbjct: 177 KHKHIPEIMNYTGLATRPVFIPSVGNFRQGMLVNLPLHLDALPGKPQAADLHDALAAHYA 236 Query: 241 GQS----IVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGA 296 + V+V+P E KL D L ++ +++ VF + H ++A LDNLGKGA Sbjct: 237 KSNTPAQYVKVLPPTEDGKL---DPLALNDTNTLEIRVFPNEDHRHAVVIARLDNLGKGA 293 Query: 297 SGAAVQNMDLML 308 SGAAVQN++LML Sbjct: 294 SGAAVQNLELML 305 Lambda K H 0.319 0.136 0.395 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: 301 Number of extensions: 12 Number of successful extensions: 4 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: 310 Length of database: 307 Length adjustment: 27 Effective length of query: 283 Effective length of database: 280 Effective search space: 79240 Effective search space used: 79240 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: 48 (23.1 bits)
Align candidate WP_038206433.1 Q392_RS10930 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01851 (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/TIGR01851.hmm # target sequence database: /tmp/gapView.2119451.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01851 [M=310] Accession: TIGR01851 Description: argC_other: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-126 406.5 0.0 4.4e-126 406.3 0.0 1.0 1 NCBI__GCF_000745855.1:WP_038206433.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038206433.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.3 0.0 4.4e-126 4.4e-126 2 310 .] 2 307 .] 1 307 [] 0.95 Alignments for each domain: == domain 1 score: 406.3 bits; conditional E-value: 4.4e-126 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd...n 71 pkvfidGeaGttGlqirerla +el+si+++ rkda+++ +l+ +d +ilcl+ddaare+v+l+d + NCBI__GCF_000745855.1:WP_038206433.1 2 PKVFIDGEAGTTGLQIRERLALMPQIELVSIAPELRKDASAKRDLMAGVDLVILCLHDDAARESVALIDglgE 74 8*******************************************************************93334 PP TIGR01851 72 pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinav 144 + +i+dasta+r+a++wvyGfpelaa+q e +++a rvanPGcyatgaia++rPlv+aG+lPad+P+++ +v NCBI__GCF_000745855.1:WP_038206433.1 75 RRPRIIDASTAHRVAPGWVYGFPELAAGQAEAVQAADRVANPGCYATGAIAIVRPLVDAGLLPADLPIALPSV 147 6789********************************************************************* PP TIGR01851 145 sGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhl 217 sGysGGG+++i++ye ++ +f +y+l l+hkh+pe+++++gla++P+f+P+vG+f qG+lv++plhl NCBI__GCF_000745855.1:WP_038206433.1 148 SGYSGGGRTMIEAYEAGA-----APPFETYALGLKHKHIPEIMNYTGLATRPVFIPSVGNFRQGMLVNLPLHL 215 ***************332.....2589********************************************** PP TIGR01851 218 aeldskvsaedihkalaeyykGe....kfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallv 286 l +k+ a+d+h+ala +y+ ++vkv + + d+ ld+ +ln+tn+le+ vf+++d ++a+++ NCBI__GCF_000745855.1:WP_038206433.1 216 DALPGKPQAADLHDALAAHYAKSntpaQYVKVLPPTE-----DGKLDPLALNDTNTLEIRVFPNEDHRHAVVI 283 ********************86423338999998665.....4578*************************** PP TIGR01851 287 arldnlGkGasGaavqnlnialGl 310 arldnlGkGasGaavqnl+++lGl NCBI__GCF_000745855.1:WP_038206433.1 284 ARLDNLGKGASGAAVQNLELMLGL 307 ***********************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (307 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: 00:00:00.00 # Mc/sec: 13.18 // [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