Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Pf6N2E2_1484 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 Length = 309 Score = 286 bits (733), Expect = 3e-82 Identities = 146/308 (47%), Positives = 203/308 (65%), Gaps = 5/308 (1%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 P +FIDG+ GTTGLQI R+ R DL L ++ R++ R + +N DIA+LCLPD A Sbjct: 4 PLVFIDGDQGTTGLQIHQRLRERNDLRLFTLSPEHRKDPQRRAEAINHCDIAVLCLPDQA 63 Query: 63 SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 +R+AVA + N+ VR+ID S+AHR PDWAYGFAEM+ Q QRI AR V+NPGCYPTGA Sbjct: 64 ARDAVATIE-NSAVRVIDASSAHRTQPDWAYGFAEMNPQQAQRIAAARRVSNPGCYPTGA 122 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHF-LYGLTLK 181 I L+RPL +AG+LP YP+ ++AVSGY+G G+ +++ + A F +YGL L Sbjct: 123 IGLLRPLLEAGLLPRDYPLNIHAVSGYSGKGR---VGVQEHEGAGAAQASAFQVYGLGLA 179 Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241 HKHVPE++ L + P+F P+ G F QG+++ +PL+ LA G + +H L+ HYA Sbjct: 180 HKHVPEIQQQSGLTQCPMFVPAYGAFRQGIVLTIPLHTRLLAPGVSAVQLHGCLMQHYAD 239 Query: 242 QSIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAV 301 V+V+ + E+ L +D L G+D ++L VF V L A+ DNLGKGA+GAAV Sbjct: 240 ARHVQVMSMQEAKALTSLDPQALNGTDDLRLSVFDNDEAGQVLLAAVFDNLGKGAAGAAV 299 Query: 302 QNMDLMLS 309 QN++LML+ Sbjct: 300 QNLNLMLA 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: 306 Number of extensions: 10 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 Pf6N2E2_1484 (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.31927.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-125 403.0 0.0 5.1e-125 402.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 N-acetyl-gamma-glutamyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 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 ! 402.8 0.0 5.1e-125 5.1e-125 2 308 .. 4 306 .. 3 308 .. 0.98 Alignments for each domain: == domain 1 score: 402.8 bits; conditional E-value: 5.1e-125 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaarea 65 p vfidG++GttGlqi++rl er+dl+l ++++++rkd++ ra+ +n d+a+lclpd+aar+a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 4 PLVFIDGDQGTTGLQIHQRLRERNDLRLFTLSPEHRKDPQRRAEAINHCDIAVLCLPDQAARDA 67 679************************************************************* PP TIGR01851 66 vslvdnpntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlve 129 v+ ++n++++++das+a+rt++dw+yGf+e++++q ++ia+a+rv+nPGcy+tgai llrPl+e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 68 VATIENSAVRVIDASSAHRTQPDWAYGFAEMNPQQAQRIAAARRVSNPGCYPTGAIGLLRPLLE 131 **************************************************************** PP TIGR01851 130 aGilPadfPvtinavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsgla 193 aG+lP d+P++i+avsGysG G+ ++++e a++++ +af++ygl l hkh+pe++++sgl+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 132 AGLLPRDYPLNIHAVSGYSGKGRVGVQEHE--GAGAAQASAFQVYGLGLAHKHVPEIQQQSGLT 193 *****************************9..56666679************************ PP TIGR01851 194 skPiftPavGdfaqGllveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddt 257 + P+f+Pa G f qG++++iplh l+ vsa ++h l+++y+ ++v+v+++++a++l t lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 194 QCPMFVPAYGAFRQGIVLTIPLHTRLLAPGVSAVQLHGCLMQHYADARHVQVMSMQEAKAL--T 255 *************************************************************..9 PP TIGR01851 258 ildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnial 308 ld+q+lngt+ l l vf +d+++++ll+a +dnlGkGa+Gaavqnln++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1484 256 SLDPQALNGTDDLRLSVFDNDEAGQVLLAAVFDNLGKGAAGAAVQNLNLML 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.90 // [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