Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate RR42_RS16645 RR42_RS16645 n-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__Cup4G11:RR42_RS16645 Length = 309 Score = 305 bits (780), Expect = 1e-87 Identities = 158/308 (51%), Positives = 205/308 (66%), Gaps = 5/308 (1%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 P +FIDG+ GTTGLQI R+ RTDL L ++ AER++ R +N+ DIAILCLPD A Sbjct: 4 PVVFIDGDQGTTGLQIHERLRDRTDLRLFTLAAAERKDPRCRAQAINACDIAILCLPDAA 63 Query: 63 SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 +REAV + N VR+ID S+AHR PDW YGF EM + Q +RI +AR V NPGCYPTGA Sbjct: 64 AREAVDAIV-NPAVRVIDASSAHRTQPDWTYGFPEMTQGQAERIANARRVTNPGCYPTGA 122 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181 I L+RPL QAG++P YPV+++AVSGY+G G+ A +E+ + + AP + +YGL L Sbjct: 123 IGLLRPLLQAGLIPGDYPVSIHAVSGYSGRGR---AGVEEHEGQGAVNAPAYQVYGLALA 179 Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241 HKH PE+++H L + P+F P+ G F QG+++ VPL L L G +H L HYA Sbjct: 180 HKHPPEIQLHAGLAQRPIFVPAYGAFRQGIVLTVPLALRLLPPGVDGAALHACLARHYAD 239 Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301 + V VVPLDES L +D L ++ M L VF HV L A+ DNLGKGASGAAV Sbjct: 240 AAHVRVVPLDESCALQHLDPQALNATNDMHLSVFPNAEHGHVLLSAVFDNLGKGASGAAV 299 Query: 302 QNMDLMLS 309 QN+DLML+ Sbjct: 300 QNLDLMLT 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: 302 Number of extensions: 9 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: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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 RR42_RS16645 RR42_RS16645 (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.27689.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-122 395.1 0.0 1.3e-122 394.9 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS16645 RR42_RS16645 n-acetyl-gamma-glut Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS16645 RR42_RS16645 n-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.9 0.0 1.3e-122 1.3e-122 2 308 .. 4 306 .. 3 308 .. 0.98 Alignments for each domain: == domain 1 score: 394.9 bits; conditional E-value: 1.3e-122 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd 70 p vfidG++GttGlqi+erl +r+dl+l ++++ rkd+ ra+ +na d+ailclpd aareav + lcl|FitnessBrowser__Cup4G11:RR42_RS16645 4 PVVFIDGDQGTTGLQIHERLRDRTDLRLFTLAAAERKDPRCRAQAINACDIAILCLPDAAAREAVDAIV 72 679****************************************************************** PP TIGR01851 71 npntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPv 139 np+++++das+a+rt++dw+yGfpe++ +q e+iana+rv+nPGcy+tgai llrPl++aG++P d+Pv lcl|FitnessBrowser__Cup4G11:RR42_RS16645 73 NPAVRVIDASSAHRTQPDWTYGFPEMTQGQAERIANARRVTNPGCYPTGAIGLLRPLLQAGLIPGDYPV 141 ********************************************************************* PP TIGR01851 140 tinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqG 208 +i+avsGysG G+a ++++e + a ++ a+++yglal hkh pe++ h+gla++Pif+Pa G f qG lcl|FitnessBrowser__Cup4G11:RR42_RS16645 142 SIHAVSGYSGRGRAGVEEHEGQGAVNA--PAYQVYGLALAHKHPPEIQLHAGLAQRPIFVPAYGAFRQG 208 ********************6666655..89************************************** PP TIGR01851 209 llveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgs 277 +++++pl l l v ++++h+ la +y+ ++v+v++ld++ +l + ld+q+ln tn ++l vf++ lcl|FitnessBrowser__Cup4G11:RR42_RS16645 209 IVLTVPLALRLLPPGVDGAALHACLARHYADAAHVRVVPLDESCAL--QHLDPQALNATNDMHLSVFPN 275 **********************************************..89******************* PP TIGR01851 278 ddgerallvarldnlGkGasGaavqnlnial 308 ++ +++ll a +dnlGkGasGaavqnl+++l lcl|FitnessBrowser__Cup4G11:RR42_RS16645 276 AEHGHVLLSAVFDNLGKGASGAAVQNLDLML 306 ******************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (309 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: 7.40 // [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