Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate WP_037570918.1 BS73_RS08940 N-acetyl-gamma-glutamyl-phosphate reductase
Query= BRENDA::P9WPZ9 (352 letters) >NCBI__GCF_000744815.1:WP_037570918.1 Length = 342 Score = 426 bits (1095), Expect = e-124 Identities = 216/346 (62%), Positives = 253/346 (73%), Gaps = 7/346 (2%) Query: 9 ATKVAVAGASGYAGGEILRLLLGHPAYADGRLRIGALTAATSAGSTLGEHHPHLTPLAHR 68 A + AVAGASGYAGGE+LRLLL HP + IGA+TA ++AGS LG PHL PLA R Sbjct: 2 AYRAAVAGASGYAGGEVLRLLLQHP-----EIEIGAVTAGSNAGSRLGALQPHLAPLADR 56 Query: 69 VVEPTEAAVLGGHDAVFLALPHGHSAVLAQQLSPETLIIDCGADFRLTDAAVWERFYGSS 128 ++ T A L GHD VFLALPHG SA +A+QL P+ L++DCGADFRL D A WERFYGS+ Sbjct: 57 ILGETTAETLAGHDVVFLALPHGQSAAVAEQLGPDVLVVDCGADFRLEDPAAWERFYGSA 116 Query: 129 HAGSWPYGLPELPGARDQLRGTRRIAVPGCYPTAALLALFPALAADLIEPAVTVVAVSGT 188 HAG+WPYGLPELPGAR++L G+RRIAVPGCYPTA LALFPA AA L EP VVA SGT Sbjct: 117 HAGTWPYGLPELPGARERLAGSRRIAVPGCYPTAVSLALFPAYAAGLAEPQAVVVAASGT 176 Query: 189 SGAGRAATTDLLGAEVIGSARAYNIAGVHRHTPEIAQGLRAVTDRDVSVSFTPVLIPASR 248 SGAG++A LLG+EV+GS Y + GVHRHTPE+ Q L AV V+VSFTP L P R Sbjct: 177 SGAGKSAKPHLLGSEVMGSMSPYGVGGVHRHTPEMQQNLSAVAGEPVAVSFTPTLAPMPR 236 Query: 249 GILATCTARTR--SPLSQLRAAYEKAYHAEPFIYLMPEGQLPRTGAVIGSNAAHIAVAVD 306 GILATC+A+ R + LRAAY+K Y E F+ L+PEGQ P T AV G+N + VA+D Sbjct: 237 GILATCSAQARPGTTAESLRAAYQKVYGDEEFVSLLPEGQWPATAAVYGANTVQVQVALD 296 Query: 307 EDAQTFVAIAAIDNLVKGTAGAAVQSMNLALGWPETDGLSVVGVAP 352 E + I+AIDNL KGTAG AVQSMNLALG PE GL +GVAP Sbjct: 297 ESVGRIIVISAIDNLTKGTAGGAVQSMNLALGLPEGLGLPKIGVAP 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: 467 Number of extensions: 24 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: 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_037570918.1 BS73_RS08940 (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.231477.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-120 388.3 0.0 1.9e-120 388.1 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037570918.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037570918.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.1 0.0 1.9e-120 1.9e-120 2 345 .] 4 342 .] 3 342 .] 0.97 Alignments for each domain: == domain 1 score: 388.1 bits; conditional E-value: 1.9e-120 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflA 74 ++a+ GasGY+G+e+lrll +Hpe+e+ ++++ ++ag++l ++ phl l+d l e+++e +l+ +dvvflA NCBI__GCF_000744815.1:WP_037570918.1 4 RAAVAGASGYAGGEVLRLLLQHPEIEIGAVTAGSNAGSRLGALQPHLAPLADRILGETTAE-TLAGHDVVFLA 75 689*************************9999999*****************888887776.567******** PP TIGR01850 75 lphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpEln..reeikkaklia 145 lphg+sa+++ e l +v v+d++adfRl+d++++e++Yg+ h+ ++ YGlpEl re+++++++ia NCBI__GCF_000744815.1:WP_037570918.1 76 LPHGQSAAVA-EQLGPDVLVVDCGADFRLEDPAAWERFYGSAHAG-----TWPYGLPELPgaRERLAGSRRIA 142 *******999.667999**************************99.....8********999*********** PP TIGR01850 146 nPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvt.kHrHtpEieqe 217 +PGCy+Ta+ Lal+P+++++l ep+ ++v a sG+SgAG++a+++ l +ev+++++pY v HrHtpE++q+ NCBI__GCF_000744815.1:WP_037570918.1 143 VPGCYPTAVSLALFPAYAAGLAEPQ-AVVVAASGTSGAGKSAKPHLLGSEVMGSMSPYGVGgVHRHTPEMQQN 214 ***********************96.9999******************************989********** PP TIGR01850 218 lsklaekkvkvsftphlvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsn 290 ls++a++ v vsftp+l+pm rGilat++a+++ ++t+e+lr++y++vY de+fv++l+eg++P+t av+g n NCBI__GCF_000744815.1:WP_037570918.1 215 LSAVAGEPVAVSFTPTLAPMPRGILATCSAQARPGTTAESLRAAYQKVYGDEEFVSLLPEGQWPATAAVYGAN 287 ************************************************************************* PP TIGR01850 291 fvdigvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +v+++va+de+ +r++v+saiDNL+KG+ag Avq++Nl+lg++e gL+k++++p NCBI__GCF_000744815.1:WP_037570918.1 288 TVQVQVALDESVGRIIVISAIDNLTKGTAGGAVQSMNLALGLPEGLGLPKIGVAP 342 ***************************************************9988 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: 00:00:00.00 # Mc/sec: 15.01 // [ok]
This GapMind analysis is from Jul 25 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