Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate 209429 DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >MicrobesOnline__882:209429 Length = 354 Score = 290 bits (741), Expect = 6e-83 Identities = 160/351 (45%), Positives = 214/351 (60%), Gaps = 7/351 (1%) Query: 45 IKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRG--HYDLAFSE 102 I+ G+VG TGYTG+EL R+LA HP + + TSR+EAG + ++YP L G D+ Sbjct: 4 IRAGLVGVTGYTGMELARLLAGHPAMRLVLATSRAEAGRRLDDIYPFLIGLPGGDITIVA 63 Query: 103 PDVNVLGA-CDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHE 161 PD +V+ A CD+ F A PHG AM M L G+RVVDLSADFRL+D+ V+ +WY H Sbjct: 64 PDPDVIAASCDIAFLAVPHGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTDHT 123 Query: 162 SPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKS 221 +AVYGLPE+ ++ A LVANPGCYPT+V LG L+ +V ++ DAKS Sbjct: 124 RKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVILGLAAALDTDIVHRDDIVIDAKS 183 Query: 222 GASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMI 281 GASGAGR+ +G L E+ +SFKAY HRH PEI Q L AG + V+F HL+P+ Sbjct: 184 GASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHLLPID 243 Query: 282 RGIEATLYAELKNPADFDRLQALFEQRFDDEP----FVDVMPFGSHPETRSVRGANQCRM 337 RGI +T+Y +K P D D + A++ + +V ++P G PETR V+G C + Sbjct: 244 RGILSTMYLRMKKPLDLDTVHAMYADYWAAHQTRGGWVRLLPKGRLPETRHVKGTMFCDI 303 Query: 338 ALHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 L ++ +IV S IDNL +GA+GQAV N NIM GL GL L+P Sbjct: 304 GLVVDPRTGRLIVVSAIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354 Lambda K H 0.321 0.137 0.412 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: 425 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: 388 Length of database: 354 Length adjustment: 30 Effective length of query: 358 Effective length of database: 324 Effective search space: 115992 Effective search space used: 115992 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: 49 (23.5 bits)
Align candidate 209429 DVU0492 (N-acetyl-gamma-glutamyl-phosphate reductase)
to HMM TIGR01850 (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/TIGR01850.hmm # target sequence database: /tmp/gapView.980.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01850 [M=345] Accession: TIGR01850 Description: argC: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-121 390.9 0.0 3e-121 390.8 0.0 1.0 1 lcl|MicrobesOnline__882:209429 DVU0492 N-acetyl-gamma-glutamyl- Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209429 DVU0492 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 390.8 0.0 3e-121 3e-121 1 345 [] 4 354 .] 4 354 .] 0.96 Alignments for each domain: == domain 1 score: 390.8 bits; conditional E-value: 3e-121 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssre.agkklsevhphlkglvd..lkleeleeeeileeadvvflAlp 76 i++++vG +GYtG+eL rlla Hp+++++ l++sr+ ag++l++++p l gl ++ + + + i++++d+ flA+p lcl|MicrobesOnline__882:209429 4 IRAGLVGVTGYTGMELARLLAGHPAMRLV-LATSRAeAGRRLDDIYPFLIGLPGgdITIVAPDPDVIAASCDIAFLAVP 81 5789*************************.5555555*************9987446666777799************* PP TIGR01850 77 hgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaal 155 hg+++e++++l e+g++v+dlSadfRl+d +vYe+wY+++h+++ ll eavYGlpEl+ +++++a l+anPGCy+T+++ lcl|MicrobesOnline__882:209429 82 HGAAMEMAASLRERGLRVVDLSADFRLRDVTVYESWYRTDHTRKGLLPEAVYGLPELYGKDVAQAGLVANPGCYPTSVI 160 ******************************************************************************* PP TIGR01850 156 LalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphl 234 L+la +l+++++++++i++daksG SgAGrka slf+ev++++k+Y++ kHrHtpEieqels +a++ +vsf +hl lcl|MicrobesOnline__882:209429 161 LGLAAALDTDIVHRDDIVIDAKSGASGAGRKAAVGSLFCEVHDSFKAYNLGKHRHTPEIEQELSVIAGEALTVSFNTHL 239 *******************************************************************99********** PP TIGR01850 235 vpmtrGilatiyaklkkelteeelrklyeevYedep....fvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvs 309 +p+ rGil+t+y+++kk+l+ ++++++y+++++ ++ +vr+l++g+lP+t++v g+ f+dig+ vd +t+r++vvs lcl|MicrobesOnline__882:209429 240 LPIDRGILSTMYLRMKKPLDLDTVHAMYADYWAAHQtrggWVRLLPKGRLPETRHVKGTMFCDIGLVVDPRTGRLIVVS 318 *******************************9977545559************************************** PP TIGR01850 310 aiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 aiDNL +Ga+gqAv n N+mlg++ ++gL+ pl+p lcl|MicrobesOnline__882:209429 319 AIDNLCRGASGQAVANANIMLGLPVDAGLRLAPLMP 354 ********************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (354 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: 11.75 // [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