Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Dsui_0782 Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form
Query= reanno::Smeli:SMc01801 (310 letters) >FitnessBrowser__PS:Dsui_0782 Length = 319 Score = 273 bits (699), Expect = 3e-78 Identities = 145/309 (46%), Positives = 206/309 (66%), Gaps = 7/309 (2%) Query: 4 KIFIDGEHGTTGLQIRVRMAGRTDLELLSIPEAERRNAAMREDLLNSADIAILCLPDDAS 63 K+FIDG HGTTGL+I R++ R ++E+L+IPE +R++ A++ + +NSAD+ LCLPD AS Sbjct: 4 KVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPDAAS 63 Query: 64 REAVAMVA-GNNRVRIIDTSTAHRVAPDWAYGFAEMDKAQPQRIRDARHVANPGCYPTGA 122 RE+VA++A GN R R +D STAHR PDW YG E++ Q +R+ A+ VA PGC+ +G Sbjct: 64 RESVALLAPGNTRTRFLDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHASGF 123 Query: 123 IALIRPLRQAGILPDGYPVTVNAVSGYTGGGKQMIAQMEDDQN-PDHIGAPHFLYGLTLK 181 I L+ PL GI+P YPV+ +++GY+GGGK+MIA E+ + PD + +P F Y L L Sbjct: 124 IMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKEMIASYEEPASLPDAMKSPRF-YALGLT 182 Query: 182 HKHVPEMKMHGLLERAPVFSPSVGKFAQGMIVQVPLYLEDLAAGATLETIHRALVDHYAG 241 HKH+PEM+M L P+F+P VG FAQGM+V VPL L T + ++YAG Sbjct: 183 HKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQAFYSEYYAG 242 Query: 242 QSIVEVVPLDESAKLAR--IDATELAGSDAMKLFVFGTKGGAHVNLVALLDNLGKGASGA 299 + V+V+PLD + L + AT ++ ++FVFG G + + + DNLGKGASGA Sbjct: 243 EVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFG--HGEQILVASRFDNLGKGASGA 300 Query: 300 AVQNMDLML 308 A+Q M+LML Sbjct: 301 AIQCMNLML 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: 310 Number of extensions: 19 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: 319 Length adjustment: 27 Effective length of query: 283 Effective length of database: 292 Effective search space: 82636 Effective search space used: 82636 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 Dsui_0782 Dsui_0782 (N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form)
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.29055.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-134 431.5 0.0 1.1e-133 431.3 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0782 Dsui_0782 N-acetyl-gamma-glutamy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0782 Dsui_0782 N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.3 0.0 1.1e-133 1.1e-133 2 310 .] 3 311 .. 2 311 .. 0.98 Alignments for each domain: == domain 1 score: 431.3 bits; conditional E-value: 1.1e-133 TIGR01851 2 pkvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvd..npntki 76 +kvfidG+ GttGl+i erl+ r ++e+l+i edkrkd++ +a+ +n+adv++lclpd a+re+v+l n++t+ lcl|FitnessBrowser__PS:Dsui_0782 3 FKVFIDGRHGTTGLKIDERLSIRPEIEILTIPEDKRKDPAVKAEYINSADVVFLCLPDAASRESVALLApgNTRTRF 79 8******************************************************************974477789* PP TIGR01851 77 ldastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvtinavsGysGGGka 153 ldasta+rt++dwvyG+pel+ +qre++a+a++va+PGc+a+g+i+l++Plv+ Gi+P d+Pv++ +++GysGGGk+ lcl|FitnessBrowser__PS:Dsui_0782 80 LDASTAHRTNPDWVYGLPELNGGQRERVAKAQKVAVPGCHASGFIMLMAPLVAGGIVPKDYPVSTYSITGYSGGGKE 156 ***************************************************************************** PP TIGR01851 154 liakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGllveiplhlaeldskvsaedih 230 +ia+yee ++ + + ++++ y+l l+hkhlpem+ ++gla++P+ftP vG+faqG++v +pl + l++kv+++d++ lcl|FitnessBrowser__PS:Dsui_0782 157 MIASYEEPASLPDAMKSPRFYALGLTHKHLPEMQMQTGLAHQPLFTPIVGNFAQGMVVAVPLLPRMLGKKVTPADLQ 233 ***************************************************************************** PP TIGR01851 231 kalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsddgerallvarldnlGkGasGaavqnlnia 307 + eyy+Ge fvkv++ld a++ld+++l a++ n+tnr+e+fvfg e++l+++r+dnlGkGasGaa+q++n++ lcl|FitnessBrowser__PS:Dsui_0782 234 AFYSEYYAGEVFVKVMPLDAAPVLDNGFLPATACNDTNRAEIFVFGHG--EQILVASRFDNLGKGASGAAIQCMNLM 308 **********************************************76..*************************** PP TIGR01851 308 lGl 310 lG+ lcl|FitnessBrowser__PS:Dsui_0782 309 LGV 311 **7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (319 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: 00:00:00.00 # Mc/sec: 10.41 // [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