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_043743989.1 AMB_RS09075 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q6AV34 (415 letters) >NCBI__GCF_000009985.1:WP_043743989.1 Length = 346 Score = 481 bits (1237), Expect = e-140 Identities = 231/345 (66%), Positives = 278/345 (80%) Query: 71 EEVRIAVLGASGYTGAEIVRLLANHPQFRIKVMTADRKAGEQFGSVFPHLITQDLPNLVA 130 ++V IA+LGASGYTGAE+VRLLA HP F+IKVMT DRKAG+ SVFPHL +LP LVA Sbjct: 2 KDVSIAILGASGYTGAELVRLLALHPTFKIKVMTGDRKAGQSMESVFPHLGGLELPTLVA 61 Query: 131 VKDADFSNVDAVFCCLPHGTTQEIIKGLPQELKIVDLSADFRLRDINEYAEWYGHSHRAP 190 + DF+ VDAVFCCLPHGTTQE+I LP +K+VDLSADFRL D++ YA+WYGH HRAP Sbjct: 62 IDQVDFTTVDAVFCCLPHGTTQEVIAALPASVKVVDLSADFRLFDVDTYAQWYGHEHRAP 121 Query: 191 ELQQEAVYGLTEVLRNEIRNARLVANPGCYPTSIQLPLVPLIKAKLIKVSNIIIDAKSGV 250 ELQ++AVYGLTE+ R+ + ARLVANPGCYPTS+QLPL+PL+KA LI+ ++I+IDAKSGV Sbjct: 122 ELQKQAVYGLTELARDAVAKARLVANPGCYPTSVQLPLIPLLKAGLIEAADIVIDAKSGV 181 Query: 251 SGAGRGAKEANLYTEIAEGIHAYGIKGHRHVPEIEQGLSEAAESKVTISFTPNLICMKRG 310 SGAGR AKEANLYTE+ EG+HAYG+ HRH PEIEQGLS AA V +SFTP+LI M RG Sbjct: 182 SGAGRAAKEANLYTEVTEGMHAYGVASHRHAPEIEQGLSAAAGVPVLVSFTPHLIPMSRG 241 Query: 311 MQSTMFVEMAPGVTANDLYQHLKSTYEGEEFVKLLNGSSVPHTRHVVGSNYCFMNVFEDR 370 M ST++V+ G A DL L T+ GE FV+++ VPHTRHV GSN+C +NVF+DR Sbjct: 242 MLSTIYVKTKGGAKAADLRAQLSKTFGGEPFVRVVPEGVVPHTRHVRGSNHCLINVFDDR 301 Query: 371 IPGRAIIISVIDNLVKGASGQAVQNLNLMMGLPENTGLQYQPLFP 415 +PG+ II SVIDNLVKGASGQA+QN+NLM GLPE T L QP+FP Sbjct: 302 VPGKVIITSVIDNLVKGASGQALQNMNLMFGLPETTALAQQPMFP 346 Lambda K H 0.317 0.135 0.391 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: 502 Number of extensions: 10 Number of successful extensions: 1 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: 415 Length of database: 346 Length adjustment: 30 Effective length of query: 385 Effective length of database: 316 Effective search space: 121660 Effective search space used: 121660 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: 50 (23.9 bits)
Align candidate WP_043743989.1 AMB_RS09075 (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.6342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-134 434.0 0.0 2.5e-134 433.8 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043743989.1 AMB_RS09075 N-acetyl-gamma-gluta Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043743989.1 AMB_RS09075 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.8 0.0 2.5e-134 2.5e-134 2 345 .] 5 346 .] 4 346 .] 0.98 Alignments for each domain: == domain 1 score: 433.8 bits; conditional E-value: 2.5e-134 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 +ai+GasGYtGaeL+rlla Hp ++++ ++++r+ag+++++v+phl gl +l ++++ ++ +++d+ lcl|NCBI__GCF_000009985.1:WP_043743989.1 5 SIAILGASGYTGAELVRLLALHPTFKIKVMTGDRKAGQSMESVFPHLGGLELPTLVAIDQVDF-TTVDA 72 699**********************************************99989998988765.69*** PP TIGR01850 71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeik 139 vf++lphg+++e++ ++l ++vkv+dlSadfRl d ++Y++wYg++h+++el+++avYGl+El r++++ lcl|NCBI__GCF_000009985.1:WP_043743989.1 73 VFCCLPHGTTQEVI-AALPASVKVVDLSADFRLFDVDTYAQWYGHEHRAPELQKQAVYGLTELARDAVA 140 **************.567888************************************************ PP TIGR01850 140 kaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkH 208 ka+l+anPGCy+T+++L l+Pllk++lie +i++daksGvSgAGr+a+e++l++ev+e +++Y v++H lcl|NCBI__GCF_000009985.1:WP_043743989.1 141 KARLVANPGCYPTSVQLPLIPLLKAGLIEAADIVIDAKSGVSGAGRAAKEANLYTEVTEGMHAYGVASH 209 ********************************************************************* PP TIGR01850 209 rHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlke 277 rH+pEieq ls++a+ v vsftphl+pm+rG+l+tiy+k+k + ++++lr+++++++ +epfvrv++e lcl|NCBI__GCF_000009985.1:WP_043743989.1 210 RHAPEIEQGLSAAAGVPVLVSFTPHLIPMSRGMLSTIYVKTKGGAKAADLRAQLSKTFGGEPFVRVVPE 278 ***********88888999************************************************** PP TIGR01850 278 gelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 g +P+t++v+gsn++ i+v d+ ++v+++s+iDNLvKGa+gqA+qn+Nlm+g++et++L ++p++p lcl|NCBI__GCF_000009985.1:WP_043743989.1 279 GVVPHTRHVRGSNHCLINVFDDRVPGKVIITSVIDNLVKGASGQALQNMNLMFGLPETTALAQQPMFP 346 *****************************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (346 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: 00:00:00.01 # Mc/sec: 9.09 // [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