Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_010530240.1 ON01_RS06665 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q07906 (345 letters) >NCBI__GCF_000224785.1:WP_010530240.1 Length = 345 Score = 388 bits (996), Expect = e-112 Identities = 194/345 (56%), Positives = 239/345 (69%), Gaps = 1/345 (0%) Query: 2 MNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKLE 61 M AI+GATGY GAEL R+L HP V+ SSS G ++E +PH AV L ++ Sbjct: 1 MKAAIVGATGYGGAELIRILQQHPDVTLQSYHSSSHQGESMAEKYPHFKAVSEMDLEGID 60 Query: 62 IEALAK-YDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAPS 120 E +A+ D VF ATP GVS E P + G +VIDLSGDFRLKD Y +WY ++A Sbjct: 61 PEYIAQDADVVFVATPSGVSAELVPEFIKAGARVIDLSGDFRLKDTLQYEKWYKKKAPDE 120 Query: 121 AYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSGV 180 LE AVYGLTEW L++NPGCYPTA LLGLAPLVK LI +SII+DAK+GV Sbjct: 121 TILENAVYGLTEWLDTEATETQLMTNPGCYPTAALLGLAPLVKNQLIHPNSIIIDAKTGV 180 Query: 181 SGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTRG 240 SGAG+ THF+E+N+N+K+YKV HQH PEIEQ L WN P+TF THL+PMTRG Sbjct: 181 SGAGKNPTAVTHFTEMNDNLKVYKVLEHQHTPEIEQVLAGWNPNTGPVTFGTHLVPMTRG 240 Query: 241 IMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLAYDE 300 IM TIYA A + ++ L DLYK +Y+ S FVRIR+ G +P+TK+VYGSN+CD+ +AYDE Sbjct: 241 IMTTIYADAAEDMTAAKLSDLYKETYKDSYFVRIREQGTYPSTKEVYGSNFCDVSVAYDE 300 Query: 301 RTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGLRSLPIYP 345 RT R+ +VSVIDNL+KGA+GQAVQN N M G DE GL P+YP Sbjct: 301 RTNRIMIVSVIDNLVKGASGQAVQNMNRMFGIDEKAGLAFAPVYP 345 Lambda K H 0.318 0.135 0.404 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: 371 Number of extensions: 11 Number of successful extensions: 2 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: 345 Length of database: 345 Length adjustment: 29 Effective length of query: 316 Effective length of database: 316 Effective search space: 99856 Effective search space used: 99856 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_010530240.1 ON01_RS06665 (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.3706868.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-142 459.2 0.1 5.1e-142 459.1 0.1 1.0 1 NCBI__GCF_000224785.1:WP_010530240.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530240.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.1 0.1 5.1e-142 5.1e-142 1 345 [] 1 345 [] 1 345 [] 0.99 Alignments for each domain: == domain 1 score: 459.1 bits; conditional E-value: 5.1e-142 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 +k+aivGa+GY+GaeL+r+l++Hp+v++++++ss+++g++++e +ph+k + ++ le ++ e i+++advvf+ NCBI__GCF_000224785.1:WP_010530240.1 1 MKAAIVGATGYGGAELIRILQQHPDVTLQSYHSSSHQGESMAEKYPHFKAVSEMDLEGIDPEYIAQDADVVFV 73 689********************************************************************** PP TIGR01850 74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146 A+p+gvsaelvpe++++g++vidlS+dfRlkd+ +YekwY+kk+++e++le+avYGl+E+ e ++++l+ n NCBI__GCF_000224785.1:WP_010530240.1 74 ATPSGVSAELVPEFIKAGARVIDLSGDFRLKDTLQYEKWYKKKAPDETILENAVYGLTEWLDTEATETQLMTN 146 ************************************************************************* PP TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219 PGCy+TaalL+laPl+k++li+p+sii+dak+GvSgAG+++++ ++f+e+n+nlk+Ykv +H+HtpEieq l NCBI__GCF_000224785.1:WP_010530240.1 147 PGCYPTAALLGLAPLVKNQLIHPNSIIIDAKTGVSGAGKNPTAVTHFTEMNDNLKVYKVLEHQHTPEIEQVLA 219 ************************************************************************* PP TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292 ++ ++ v+f +hlvpmtrGi++tiya +++++t+++l +ly+e+Y+d+ fvr+ ++g++Pstk+v+gsnf+ NCBI__GCF_000224785.1:WP_010530240.1 220 GWNPNTGPVTFGTHLVPMTRGIMTTIYADAAEDMTAAKLSDLYKETYKDSYFVRIREQGTYPSTKEVYGSNFC 292 ***99999***************************************************************** PP TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 d++va+de+t+r+++vs+iDNLvKGa+gqAvqn+N m+g de++gL + p++p NCBI__GCF_000224785.1:WP_010530240.1 293 DVSVAYDERTNRIMIVSVIDNLVKGASGQAVQNMNRMFGIDEKAGLAFAPVYP 345 ***************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (345 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: 26.80 // [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