Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate WP_013430561.1 CALKRO_RS08160 N-acetyl-gamma-glutamyl-phosphate reductase
Query= SwissProt::Q07906 (345 letters) >NCBI__GCF_000166775.1:WP_013430561.1 Length = 343 Score = 279 bits (714), Expect = 7e-80 Identities = 149/338 (44%), Positives = 210/338 (62%), Gaps = 2/338 (0%) Query: 1 MMNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDGAVLHKL 60 M+ +IIGA+GY G EL RLL HP V + SSS + + + ++ P V V + Sbjct: 1 MIKASIIGASGYVGVELIRLLLRHPEVEIVSIISSSSNQLSIDKTNPQFKKVSNLVFEEF 60 Query: 61 EIEALAKYDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREAAPS 120 +IEA+ + D VF A P G+S E+ D G VIDLS DFR KD YA+ Y + P Sbjct: 61 KIEAIQEADVVFCALPHGISQEYVKIGYDIGKVVIDLSADFRYKDLQRYAKDYSQHKYPE 120 Query: 121 AYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAKSGV 180 L ++ YGL E NRE ++ A ++ NPGCYPT+ +LG+APL+K LI ++SII+D+KSGV Sbjct: 121 L-LSKSAYGLCEINREEIKNAQIIGNPGCYPTSAILGIAPLLKNKLIDKNSIIIDSKSGV 179 Query: 181 SGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPMTRG 240 SGAG+K+ F E++EN K Y V H+H EIE+ ++F+ HL+P+ RG Sbjct: 180 SGAGKKSDFAYSFCELDENFKAYSVAKHRHTSEIEEKCSLLFGENLNLSFTPHLLPVKRG 239 Query: 241 IMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLAYDE 300 I++TIYA ++I+ DLV++Y Y+ FVRI + P K V G+N+ DIG D+ Sbjct: 240 ILSTIYATFVKNINKGDLVEIYNEFYKDEYFVRIFE-DDLPELKYVRGTNFVDIGFEIDK 298 Query: 301 RTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGL 338 +T RV ++S IDNL+KGAAGQA+QN N+ +E GL Sbjct: 299 KTNRVIIISCIDNLIKGAAGQAIQNMNIRFSLNEKMGL 336 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: 310 Number of extensions: 15 Number of successful extensions: 4 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: 343 Length adjustment: 29 Effective length of query: 316 Effective length of database: 314 Effective search space: 99224 Effective search space used: 99224 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_013430561.1 CALKRO_RS08160 (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.1839701.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-132 425.7 0.0 8.4e-132 425.5 0.0 1.0 1 NCBI__GCF_000166775.1:WP_013430561.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430561.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.5 0.0 8.4e-132 8.4e-132 1 341 [. 2 339 .. 2 342 .. 0.98 Alignments for each domain: == domain 1 score: 425.5 bits; conditional E-value: 8.4e-132 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvfl 73 ik++i+GasGY G+eL+rll +Hpeve+++++ss+++ ++++++p++k++ +l +ee+++e+i +eadvvf+ NCBI__GCF_000166775.1:WP_013430561.1 2 IKASIIGASGYVGVELIRLLLRHPEVEIVSIISSSSNQLSIDKTNPQFKKVSNLVFEEFKIEAI-QEADVVFC 73 5899*********************************************************976.59****** PP TIGR01850 74 AlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklian 146 Alphg+s+e+v+ ++ g +vidlSadfR kd + Y+k Y + h+++ell++ +YGl+E+nreeik+a++i+n NCBI__GCF_000166775.1:WP_013430561.1 74 ALPHGISQEYVKIGYDIGKVVIDLSADFRYKDLQRYAKDYSQ-HKYPELLSKSAYGLCEINREEIKNAQIIGN 145 ****************************************98.99**************************** PP TIGR01850 147 PGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqels 219 PGCy+T+a+L++aPllk+kli+++sii+d+ksGvSgAG+k + +f+e++en+k+Y+v+kHrHt Eie+++s NCBI__GCF_000166775.1:WP_013430561.1 146 PGCYPTSAILGIAPLLKNKLIDKNSIIIDSKSGVSGAGKKSDFAYSFCELDENFKAYSVAKHRHTSEIEEKCS 218 ************************************************************************* PP TIGR01850 220 klaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfv 292 l +++ ++sftphl+p++rGil+tiya++ k++++ +l ++y+e+Y+de fvr+++ ++lP++k v+g+nfv NCBI__GCF_000166775.1:WP_013430561.1 219 LLFGENLNLSFTPHLLPVKRGILSTIYATFVKNINKGDLVEIYNEFYKDEYFVRIFE-DDLPELKYVRGTNFV 290 ********************************************************8.9************** PP TIGR01850 293 digvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLekl 341 dig+++d++t+rv+++s iDNL+KGaagqA+qn+N+++ ++e+ gL ++ NCBI__GCF_000166775.1:WP_013430561.1 291 DIGFEIDKKTNRVIIISCIDNLIKGAAGQAIQNMNIRFSLNEKMGLIMV 339 **********************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (343 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: 26.17 // [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