Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate HSERO_RS14025 HSERO_RS14025 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__HerbieS:HSERO_RS14025 Length = 309 Score = 310 bits (793), Expect = 4e-89 Identities = 160/307 (52%), Positives = 208/307 (67%), Gaps = 3/307 (0%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 P IFIDG+ GTTGLQI R+ R DL +L++P AER++A R + +NSADIA+LCLPD A Sbjct: 5 PLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPDAA 64 Query: 63 SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 +REAVAM++ N RVR+ID S+AHR +PDW YGF EM Q + I A V+NPGCYPTGA Sbjct: 65 AREAVAMIS-NPRVRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTGA 123 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTLKH 182 IAL+RPL QAG++P YP+ ++AVSGY+GGG+ + Q E + AP YGL L+H Sbjct: 124 IALLRPLVQAGLVPADYPLNIHAVSGYSGGGRAQVEQYEGAEAAH--AAPFVTYGLGLQH 181 Query: 183 KHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAGQ 242 KH PEM++H L + P+F PS G F QG+++ + L L A A+LE + L HY G Sbjct: 182 KHPPEMQLHAGLSQRPLFVPSYGAFRQGIVLTIALQSRLLPAQASLERLRATLQAHYDGA 241 Query: 243 SIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAVQ 302 V V+ +S ++D T S+ M L VFG G H+ L A+ DNLGKGASGAAVQ Sbjct: 242 HYVTVLDAAQSESTTQLDPTRHNHSNQMSLGVFGHAGHGHILLCAVFDNLGKGASGAAVQ 301 Query: 303 NMDLMLS 309 N+DLML+ Sbjct: 302 NLDLMLT 308 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: 316 Number of extensions: 15 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 HSERO_RS14025 HSERO_RS14025 (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.31039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-123 397.2 0.0 3e-123 397.0 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS14025 HSERO_RS14025 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS14025 HSERO_RS14025 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.0 0.0 3e-123 3e-123 2 308 .. 5 307 .. 4 309 .] 0.98 Alignments for each domain: == domain 1 score: 397.0 bits; conditional E-value: 3e-123 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslv 69 p +fidG++GttGlqi+erl r+dl++l++ + rkda+ ra+ +n+ad+a+lclpd aareav+++ lcl|FitnessBrowser__HerbieS:HSERO_RS14025 5 PLIFIDGDQGTTGLQIHERLRARQDLRVLTLPAAERKDAQRRAEAINSADIALLCLPDAAAREAVAMI 72 569***************************************************************** PP TIGR01851 70 dnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadf 137 +np+++++das+a+rt++dwvyGfpe+aa+q e ia a rv+nPGcy+tgaiallrPlv+aG++Pad+ lcl|FitnessBrowser__HerbieS:HSERO_RS14025 73 SNPRVRVIDASSAHRTSPDWVYGFPEMAAGQAEAIATALRVSNPGCYPTGAIALLRPLVQAGLVPADY 140 ******************************************************************** PP TIGR01851 138 PvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdf 205 P++i+avsGysGGG+a +++ye a++++ a+f++ygl l+hkh pem+ h+gl ++P+f+P+ G f lcl|FitnessBrowser__HerbieS:HSERO_RS14025 141 PLNIHAVSGYSGGGRAQVEQYE--GAEAAHAAPFVTYGLGLQHKHPPEMQLHAGLSQRPLFVPSYGAF 206 **********************..45555579************************************ PP TIGR01851 206 aqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelf 273 qG++++i+l+ l +++s e + ++l+ +y+G ++v v +++++e + t ld++ n +n+++l lcl|FitnessBrowser__HerbieS:HSERO_RS14025 207 RQGIVLTIALQSRLLPAQASLERLRATLQAHYDGAHYVTVLDAAQSE--STTQLDPTRHNHSNQMSLG 272 *******************************************9999..459**************** PP TIGR01851 274 vfgsddgerallvarldnlGkGasGaavqnlnial 308 vfg + +++ll+a +dnlGkGasGaavqnl+++l lcl|FitnessBrowser__HerbieS:HSERO_RS14025 273 VFGHAGHGHILLCAVFDNLGKGASGAAVQNLDLML 307 **********************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.50 // [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