Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Ac3H11_2950 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2950 Length = 312 Score = 324 bits (831), Expect = 1e-93 Identities = 164/307 (53%), Positives = 216/307 (70%), Gaps = 5/307 (1%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 P +FIDG+ GTTGLQI R+ GRTDL LL++P+AER+NAA R + +N DIAILCLPD A Sbjct: 5 PLVFIDGDQGTTGLQIHERLRGRTDLHLLTLPDAERKNAARRAEAINHCDIAILCLPDGA 64 Query: 63 SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 +REAV + N V++ID S+AHR P W YGF E+D AQP RI A+ V+NPGCYPTGA Sbjct: 65 AREAVTAIT-NPAVQVIDASSAHRTDPQWVYGFPELDAAQPARIASAQRVSNPGCYPTGA 123 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181 +AL+RPL QAG+L + VTV+AVSGY+GGG+ A++E+ + P AP F LYGL L+ Sbjct: 124 VALLRPLVQAGLLGREHAVTVHAVSGYSGGGR---ARVEEHEGPGGAQAPAFQLYGLKLE 180 Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241 HKH PE+ H L + P+F P+ G F QG+++ +PL++ L AGA+ E +H L HYAG Sbjct: 181 HKHTPEIAQHAGLAQRPIFVPAYGAFRQGIVLSIPLFVHQLPAGASGERLHACLQQHYAG 240 Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301 + VEV+PL ++ +D L G++ ++L VF V L A+ DNLGKGASGAAV Sbjct: 241 AAHVEVMPLAQAEAAEHLDPQALNGTNQLRLGVFSNARHGQVLLTAVFDNLGKGASGAAV 300 Query: 302 QNMDLML 308 QN+DLML Sbjct: 301 QNLDLML 307 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: 334 Number of extensions: 11 Number of successful extensions: 3 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: 312 Length adjustment: 27 Effective length of query: 283 Effective length of database: 285 Effective search space: 80655 Effective search space used: 80655 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 Ac3H11_2950 (N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
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.19926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-124 399.4 0.0 6.3e-124 399.2 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 N-acetyl-gamma-glutamyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.2 0.0 6.3e-124 6.3e-124 2 309 .. 5 308 .. 4 309 .. 0.98 Alignments for each domain: == domain 1 score: 399.2 bits; conditional E-value: 6.3e-124 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaar 63 p vfidG++GttGlqi+erl +r+dl+ll++ + rk+a+ ra+ +n d+ailclpd aar lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 5 PLVFIDGDQGTTGLQIHERLRGRTDLHLLTLPDAERKNAARRAEAINHCDIAILCLPDGAAR 66 679*********************************************************** PP TIGR01851 64 eavslvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallr 125 eav+ ++np+++++das+a+rt ++wvyGfpel+a q+ +ia+a+rv+nPGcy+tga+allr lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 67 EAVTAITNPAVQVIDASSAHRTDPQWVYGFPELDAAQPARIASAQRVSNPGCYPTGAVALLR 128 ************************************************************** PP TIGR01851 126 PlveaGilPadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemr 187 Plv+aG+l ++ vt++avsGysGGG+a ++++e + ++ af+ ygl+lehkh pe+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 129 PLVQAGLLGREHAVTVHAVSGYSGGGRARVEEHEG--PGGAQAPAFQLYGLKLEHKHTPEIA 188 *********************************93..33344679***************** PP TIGR01851 188 khsglaskPiftPavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaeld 249 +h+gla++Pif+Pa G f qG+++ ipl +++l + +s+e +h+ l+++y+G ++v+v++l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 189 QHAGLAQRPIFVPAYGAFRQGIVLSIPLFVHQLPAGASGERLHACLQQHYAGAAHVEVMPLA 250 ************************************************************** PP TIGR01851 250 daellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnialG 309 +ae+ + ld+q+lngtn+l l vf+++ +++ll+a +dnlGkGasGaavqnl+++lG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2950 251 QAEAA--EHLDPQALNGTNQLRLGVFSNARHGQVLLTAVFDNLGKGASGAAVQNLDLMLG 308 ***66..99**************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (312 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.47 // [ok]
This GapMind analysis is from Apr 09 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