Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate CCNA_01442 CCNA_01442 N-acetyl-gamma-glutamyl-phosphate reductase
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__Caulo:CCNA_01442 Length = 317 Score = 367 bits (942), Expect = e-106 Identities = 183/306 (59%), Positives = 230/306 (75%), Gaps = 1/306 (0%) Query: 3 PKIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDA 62 PK+FIDGE GTTGLQIR R+ GRTDL+L+SI +R++A R ++LNSAD ILCLPDDA Sbjct: 5 PKVFIDGEAGTTGLQIRERLVGRTDLQLISIDPDKRKDADARAEMLNSADAVILCLPDDA 64 Query: 63 SREAVAMVAGNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 ++EAV++V+ N V IID STA+R A WAYGFAE+D Q +I ++ ++NPGCYPTGA Sbjct: 65 AKEAVSLVSNPNTV-IIDASTAYRTAEGWAYGFAELDSEQRGKIAASKRISNPGCYPTGA 123 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQNPDHIGAPHFLYGLTLKH 182 IAL RPL AGILP PV+ NAVSGYTGGGK MIAQ ED+ DH AP+F+YGL+L H Sbjct: 124 IALTRPLVSAGILPAELPVSYNAVSGYTGGGKAMIAQFEDESAADHTRAPYFIYGLSLSH 183 Query: 183 KHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAGQ 242 KHVPEM+ HG L P+F+P+VG++AQGMIV++PL+L L +L IH ALV HY G+ Sbjct: 184 KHVPEMQKHGGLLTRPIFTPAVGRYAQGMIVEMPLHLSTLNGAPSLADIHAALVKHYKGE 243 Query: 243 SIVEVVPLDESAKLARIDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGAAVQ 302 + VEV LDE+ L +D L G++ +KLFVFG+ G LVALLDNLGKGASGAAVQ Sbjct: 244 AFVEVASLDEAKALTTLDPEGLNGTNRLKLFVFGSDAGGQARLVALLDNLGKGASGAAVQ 303 Query: 303 NMDLML 308 N+++ L Sbjct: 304 NLNIAL 309 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: 319 Number of extensions: 5 Number of successful extensions: 2 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: 317 Length adjustment: 27 Effective length of query: 283 Effective length of database: 290 Effective search space: 82070 Effective search space used: 82070 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 CCNA_01442 CCNA_01442 (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.16681.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-172 558.3 0.0 2.7e-172 558.1 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01442 CCNA_01442 N-acetyl-gamma-glutam Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01442 CCNA_01442 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 558.1 0.0 2.7e-172 2.7e-172 1 310 [] 4 311 .. 4 311 .. 1.00 Alignments for each domain: == domain 1 score: 558.1 bits; conditional E-value: 2.7e-172 TIGR01851 1 kpkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdnpn 73 +pkvfidGeaGttGlqirerl++r+dl+l+sid+dkrkdad+ra++ln+ad++ilclpddaa+eavslv+npn lcl|FitnessBrowser__Caulo:CCNA_01442 4 APKVFIDGEAGTTGLQIRERLVGRTDLQLISIDPDKRKDADARAEMLNSADAVILCLPDDAAKEAVSLVSNPN 76 69*********************************************************************** PP TIGR01851 74 tkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsG 146 t+i+dastayrtae+w+yGf+el++eqr+kia++kr++nPGcy+tgaial+rPlv+aGilPa++Pv++navsG lcl|FitnessBrowser__Caulo:CCNA_01442 77 TVIIDASTAYRTAEGWAYGFAELDSEQRGKIAASKRISNPGCYPTGAIALTRPLVSAGILPAELPVSYNAVSG 149 ************************************************************************* PP TIGR01851 147 ysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlae 219 y+GGGka+ia++e+esa+d+++a+++iygl+l+hkh+pem+kh+gl+++PiftPavG++aqG++ve+plhl++ lcl|FitnessBrowser__Caulo:CCNA_01442 150 YTGGGKAMIAQFEDESAADHTRAPYFIYGLSLSHKHVPEMQKHGGLLTRPIFTPAVGRYAQGMIVEMPLHLST 222 ************************************************************************* PP TIGR01851 220 ldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnl 292 l++++s +dih+al+++ykGe+fv+va+ld+a++l t+ld++glngtnrl+lfvfgsd+g++a+lva+ldnl lcl|FitnessBrowser__Caulo:CCNA_01442 223 LNGAPSLADIHAALVKHYKGEAFVEVASLDEAKAL--TTLDPEGLNGTNRLKLFVFGSDAGGQARLVALLDNL 293 ***********************************..************************************ PP TIGR01851 293 GkGasGaavqnlnialGl 310 GkGasGaavqnlnialGl lcl|FitnessBrowser__Caulo:CCNA_01442 294 GKGASGAAVQNLNIALGL 311 *****************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (317 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.38 // [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