Align Probable N-acetyl-gamma-glutamyl-phosphate reductase, chloroplastic; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_085637320.1 MGEO_RS11185 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q93Z70 (401 letters) >NCBI__GCF_002115805.1:WP_085637320.1 Length = 342 Score = 354 bits (908), Expect = e-102 Identities = 181/344 (52%), Positives = 240/344 (69%), Gaps = 5/344 (1%) Query: 59 IRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVK 118 + I ++GASGYTGAE++RL+A HP ++ + A+ KAGQ++ VFP LR LP LV+ + Sbjct: 3 LSIAIIGASGYTGAELLRLIATHPDMEIAALAANSKAGQTIAQVFPFLRHLDLPQLVTWE 62 Query: 119 DADFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVEL 178 + DFS++D FC LPH T+QE+I +LPT LKIVDLSADFRLR+ A YE WYG PH AVE+ Sbjct: 63 EIDFSSIDLCFCALPHKTSQEVISKLPTDLKIVDLSADFRLRDPAAYETWYGNPHAAVEM 122 Query: 179 QKEVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSG 238 QKE VYGLTE R+ I+ ARLVA GC T Q L PL+ +I ++II+D K VSG Sbjct: 123 QKEAVYGLTEFYRDAIRDARLVAGTGCNAATGQYILRPLIAEKVIGLKDIILDLKCAVSG 182 Query: 239 AGRGAKEANLYSEIAEGISSYGV-TRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGM 297 AGR KE+ L++E++EG ++Y V HRH+ E +Q S +A +V V FTPHL+P RG+ Sbjct: 183 AGRSLKESLLHAELSEGYNAYSVGGTHRHLGEFDQEFSALAGEEVRVQFTPHLIPANRGI 242 Query: 298 QSTIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRI 357 +T YV + ++ L ++Y DE F++VL G P TH+VRGSN+CH+ V DRI Sbjct: 243 LATCYV----SGDAQAVYGALASAYADEPFIEVLPFGETPSTHHVRGSNFCHIGVTGDRI 298 Query: 358 PGRAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401 GRAII++ +DNL KG+SGQALQN N+MLG ET GL+ P FP Sbjct: 299 EGRAIIVAALDNLTKGSSGQALQNANLMLGLEETAGLMLAPCFP 342 Lambda K H 0.318 0.134 0.386 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: 401 Number of extensions: 8 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: 401 Length of database: 342 Length adjustment: 30 Effective length of query: 371 Effective length of database: 312 Effective search space: 115752 Effective search space used: 115752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_085637320.1 MGEO_RS11185 (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.171229.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-115 372.4 0.0 1.3e-115 372.2 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085637320.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085637320.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.2 0.0 1.3e-115 1.3e-115 2 345 .] 4 342 .] 3 342 .] 0.97 Alignments for each domain: == domain 1 score: 372.2 bits; conditional E-value: 1.3e-115 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 +ai+GasGYtGaeLlrl+a+Hp++e+++l+++++ag+++++v+p l++l +l + ee + +++d+ f+A NCBI__GCF_002115805.1:WP_085637320.1 4 SIAIIGASGYTGAELLRLIATHPDMEIAALAANSKAGQTIAQVFPFLRHLDLPQLVTWEEID-FSSIDLCFCA 75 689**********************************************9886666666644.579******* PP TIGR01850 75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianP 147 lph++s+e++++ l +++k++dlSadfRl+d+++Ye+wYg++h++ e+++eavYGl+E++r++i++a+l+a NCBI__GCF_002115805.1:WP_085637320.1 76 LPHKTSQEVISK-LPTDLKIVDLSADFRLRDPAAYETWYGNPHAAVEMQKEAVYGLTEFYRDAIRDARLVAGT 147 **********77.5888******************************************************** PP TIGR01850 148 GCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieqels 219 GC+a + + l Pl++ek+i k+ii d k +vSgAGr+ +e+ l+ae++e ++Y+v +HrH E qe s NCBI__GCF_002115805.1:WP_085637320.1 148 GCNAATGQYILRPLIAEKVIGLKDIILDLKCAVSGAGRSLKESLLHAELSEGYNAYSVGgTHRHLGEFDQEFS 220 **********************************************************99************* PP TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292 +la+++v+v+ftphl+p rGilat+y+ ++ + ++ +++++Y+depf++vl+ ge+Pst++v+gsnf+ NCBI__GCF_002115805.1:WP_085637320.1 221 ALAGEEVRVQFTPHLIPANRGILATCYVSGDA----QAVYGALASAYADEPFIEVLPFGETPSTHHVRGSNFC 289 ****************************9988....88*********************************** PP TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +igv+ d+ ++r+++v+a+DNL+KG +gqA+qn Nlmlg++et+gL p++p NCBI__GCF_002115805.1:WP_085637320.1 290 HIGVTGDRIEGRAIIVAALDNLTKGSSGQALQNANLMLGLEETAGLMLAPCFP 342 ***********************************************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (342 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: 00:00:00.00 # Mc/sec: 26.91 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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