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_011841120.1 RSPH17029_RS08060 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q93Z70 (401 letters) >NCBI__GCF_000015985.1:WP_011841120.1 Length = 342 Score = 352 bits (904), Expect = e-102 Identities = 177/342 (51%), Positives = 237/342 (69%), Gaps = 5/342 (1%) Query: 61 IGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQSMESVFPHLRAQKLPTLVSVKDA 120 I +LGASGYTGAE+VRL+A HP ++ ++ DRKAG +M VFP LR LP L +++ Sbjct: 5 IAILGASGYTGAELVRLIATHPAMRIVALSGDRKAGMAMSEVFPFLRHLDLPRLQKIEEI 64 Query: 121 DFSTVDAVFCCLPHGTTQEIIKELPTALKIVDLSADFRLRNIAEYEEWYGQPHKAVELQK 180 DFS+VD FC LPH T+Q +I +LP LK+VDLSADFRLR+ A YE WYG+PH A ELQK Sbjct: 65 DFSSVDLAFCALPHATSQAVIADLPRDLKVVDLSADFRLRDPAAYETWYGKPHAAPELQK 124 Query: 181 EVVYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLKANLIKHENIIIDAKSGVSGAG 240 E VYGLTE R++I+ ARLVA GC T Q + PL++A +I ++I+ID K+GVSGAG Sbjct: 125 EAVYGLTEFYRDEIRGARLVAGTGCNAATGQYAIRPLIEAGVIDLDDILIDLKAGVSGAG 184 Query: 241 RGAKEANLYSEIAEGISSYGV-TRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQS 299 R KE L++E++EG +Y RHRH+ E +Q S +A V V FTPHL PM RG+ + Sbjct: 185 RSLKENLLHAELSEGTHAYSAGGRHRHLGEFDQEFSKIAGRPVQVRFTPHLTPMNRGILA 244 Query: 300 TIYVEMAPGVRTEDLHQQLKTSYEDEEFVKVLDEGVVPRTHNVRGSNYCHMSVFPDRIPG 359 +YV+ P + +H+ L Y E F++VL G +P T ++RGSNY H+ V DR+PG Sbjct: 245 NVYVKGDP----QAVHRALAERYLTETFLEVLPFGALPSTRDIRGSNYVHIGVIGDRVPG 300 Query: 360 RAIIISVIDNLVKGASGQALQNLNIMLGYPETTGLLHQPLFP 401 A++++V+DNL KG+SGQA+QN N+MLG E GL P+FP Sbjct: 301 CAMVVAVLDNLCKGSSGQAIQNANLMLGLDEAEGLRLAPVFP 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: 418 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: 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_011841120.1 RSPH17029_RS08060 (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.6576.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-112 362.2 0.0 1.7e-112 362.0 0.0 1.0 1 lcl|NCBI__GCF_000015985.1:WP_011841120.1 RSPH17029_RS08060 N-acetyl-gamma Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_011841120.1 RSPH17029_RS08060 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.0 0.0 1.7e-112 1.7e-112 2 345 .] 4 342 .] 3 342 .] 0.98 Alignments for each domain: == domain 1 score: 362.0 bits; conditional E-value: 1.7e-112 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 ++ai+GasGYtGaeL+rl+a+Hp++++++l ++r+ag +sev+p l++l +l+++ee ++ +++d+ lcl|NCBI__GCF_000015985.1:WP_011841120.1 4 NIAILGASGYTGAELVRLIATHPAMRIVALSGDRKAGMAMSEVFPFLRHLDLPRLQKIEEIDF-SSVDL 71 699**********************************************99999999988655.69*** PP TIGR01850 71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeik 139 f+Alph +s++++++ l +++kv+dlSadfRl+d+++Ye+wYgk+h+++el++eavYGl+E++r+ei+ lcl|NCBI__GCF_000015985.1:WP_011841120.1 72 AFCALPHATSQAVIAD-LPRDLKVVDLSADFRLRDPAAYETWYGKPHAAPELQKEAVYGLTEFYRDEIR 139 **************77.5889************************************************ PP TIGR01850 140 kaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.k 207 +a+l+a GC+a + + a+ Pl+++++i+ ++i++d k+GvSgAGr+ +e+ l+ae++e ++Y++ + lcl|NCBI__GCF_000015985.1:WP_011841120.1 140 GARLVAGTGCNAATGQYAIRPLIEAGVIDLDDILIDLKAGVSGAGRSLKENLLHAELSEGTHAYSAGgR 208 ******************************************************************999 PP TIGR01850 208 HrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlk 276 HrH E qe sk+a++ v+v+ftphl+pm rGila +y+k + + ++++++e+Y +e+f +vl+ lcl|NCBI__GCF_000015985.1:WP_011841120.1 209 HRHLGEFDQEFSKIAGRPVQVRFTPHLTPMNRGILANVYVKGDP----QAVHRALAERYLTETFLEVLP 273 *****************************************998....78******************* PP TIGR01850 277 egelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 g lPst++++gsn+v+igv d+ + ++vv+++DNL KG +gqA+qn Nlmlg+de egL+ p++p lcl|NCBI__GCF_000015985.1:WP_011841120.1 274 FGALPSTRDIRGSNYVHIGVIGDRVPGCAMVVAVLDNLCKGSSGQAIQNANLMLGLDEAEGLRLAPVFP 342 ******************************************************************998 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: 00:00:00.01 # Mc/sec: 10.25 // [ok]
This GapMind analysis is from Apr 10 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