Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_041939657.1 FRAAL_RS22710 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::P9WPZ9 (352 letters) >NCBI__GCF_000058485.1:WP_041939657.1 Length = 342 Score = 332 bits (850), Expect = 1e-95 Identities = 178/344 (51%), Positives = 220/344 (63%), Gaps = 11/344 (3%) Query: 13 AVAGASGYAGGEILRLLLGHPAYADGRLRIGALTAATSAGSTLGEHHPHLTPLAHRVVEP 72 AVAGASGY GGE+LRLLL HP + IGAL A TS G + + HP+L L RV Sbjct: 6 AVAGASGYGGGELLRLLLAHP-----EIEIGALAANTSVGLPVTDVHPNLPDLEGRVFTD 60 Query: 73 TEAAVLGGHDAVFLALPHGHSAVLAQQLSPETLIIDCGADFRLTDAAVWERFYGSSHAGS 132 E D VFLALPHG SA +A L ++D GAD RL D+ W R YG HAG+ Sbjct: 61 AETLAAAEADVVFLALPHGQSAAVAATLPSTVRVVDLGADHRLADSEAWRRAYGGEHAGT 120 Query: 133 WPYGLPELPGARDQLRGTRRIAVPGCYPTAALLALFPALAADLIEPA-VTVVAVSGTSGA 191 W YG+PELPGAR ++ +RR+A PGCYPTA+ LAL P LAA L+EP ++VVA SGTSGA Sbjct: 121 WTYGMPELPGARARIAASRRVAAPGCYPTASSLALAPLLAAGLVEPQDLSVVAASGTSGA 180 Query: 192 GRAATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAVTDRDVSVSFTPVLIPASRGIL 251 GR+A +LLG+EV+G AY + G H+H PEI Q L V VS+SFTPVL P RGIL Sbjct: 181 GRSAKVNLLGSEVMGDLTAYKV-GTHQHRPEIVQALSGVAGTAVSLSFTPVLAPLPRGIL 239 Query: 252 ATCTARTRSPLSQLRAAYE---KAYHAEPFIYLMPEGQLPRTGAVIGSNAAHIAVAVDED 308 ATC+ R +P + A YE AY EPF+ ++P G+ P A +G NA HI D + Sbjct: 240 ATCSGRA-TPGTDADAVYEALRSAYAGEPFVRVLPPGRWPHAAATLGGNAVHIQGTFDAE 298 Query: 309 AQTFVAIAAIDNLVKGTAGAAVQSMNLALGWPETDGLSVVGVAP 352 + + ++AIDNL KG AG A+Q NL LG PET GL+ G+AP Sbjct: 299 SGRAIVVSAIDNLGKGAAGQALQCANLMLGLPETAGLTAQGIAP 342 Lambda K H 0.318 0.133 0.393 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: 406 Number of extensions: 23 Number of successful extensions: 5 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: 352 Length of database: 342 Length adjustment: 29 Effective length of query: 323 Effective length of database: 313 Effective search space: 101099 Effective search space used: 101099 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_041939657.1 FRAAL_RS22710 (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.7786.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-114 368.3 0.0 2.4e-114 368.1 0.0 1.0 1 lcl|NCBI__GCF_000058485.1:WP_041939657.1 FRAAL_RS22710 N-acetyl-gamma-glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_041939657.1 FRAAL_RS22710 N-acetyl-gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.1 0.0 2.4e-114 2.4e-114 2 345 .] 4 342 .] 3 342 .] 0.97 Alignments for each domain: == domain 1 score: 368.1 bits; conditional E-value: 2.4e-114 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadv 70 ++a+ GasGY+G+eLlrll +Hpe+e+ +l+++++ g ++++vhp+l +l +++ e+ +++eadv lcl|NCBI__GCF_000058485.1:WP_041939657.1 4 TAAVAGASGYGGGELLRLLLAHPEIEIGALAANTSVGLPVTDVHPNLPDLEGRVFTDAETL-AAAEADV 71 689**********************************************999888876654.5789*** PP TIGR01850 71 vflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpEln..ree 137 vflAlphg+sa+++ + l + v+v+dl+ad+Rl d+e++++ Yg +h+ +++YG+pEl r + lcl|NCBI__GCF_000058485.1:WP_041939657.1 72 VFLALPHGQSAAVA-ATLPSTVRVVDLGADHRLADSEAWRRAYGGEHAG-----TWTYGMPELPgaRAR 134 ***********999.567889**************************99.....8********9999** PP TIGR01850 138 ikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt 206 i+ ++++a PGCy+Ta+ LalaPll+++l+ep+++ v a sG+SgAGr+a+ + l +ev++ l++Ykv lcl|NCBI__GCF_000058485.1:WP_041939657.1 135 IAASRRVAAPGCYPTASSLALAPLLAAGLVEPQDLSVVAASGTSGAGRSAKVNLLGSEVMGDLTAYKVG 203 ********************************************************************* PP TIGR01850 207 kHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvl 275 +H+H pEi+q ls +a++ v++sftp l+p+ rGilat++ +++ +++++ ++++++++Y++epfvrvl lcl|NCBI__GCF_000058485.1:WP_041939657.1 204 THQHRPEIVQALSGVAGTAVSLSFTPVLAPLPRGILATCSGRATPGTDADAVYEALRSAYAGEPFVRVL 272 ********************************************************************* PP TIGR01850 276 kegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpll 344 + g++P+ a+lg n+v+i+ + d e++r++vvsaiDNL KGaagqA+q+ Nlmlg++et+gL+ ++++ lcl|NCBI__GCF_000058485.1:WP_041939657.1 273 PPGRWPHAAATLGGNAVHIQGTFDAESGRAIVVSAIDNLGKGAAGQALQCANLMLGLPETAGLTAQGIA 341 *****************************************************************9998 PP TIGR01850 345 p 345 p lcl|NCBI__GCF_000058485.1:WP_041939657.1 342 P 342 7 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.24 // [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