Align N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) (characterized)
to candidate 199470 SO0275 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
Query= BRENDA::P11446 (334 letters) >FitnessBrowser__MR1:199470 Length = 326 Score = 298 bits (762), Expect = 2e-85 Identities = 165/329 (50%), Positives = 208/329 (63%), Gaps = 9/329 (2%) Query: 1 MLNTLIVGASGYAGAELVTYVNRHPHMNITALTVSAQSNDAGKLISDLHPQLKGIVDLPL 60 M N I+GASGY GA+L V+ ++I L VS S D G+ ++DL+P I +L L Sbjct: 1 MKNIAIIGASGYTGAQLTALVHAESELSIQGLYVSENSLDKGRALADLYPVYSHI-ELTL 59 Query: 61 QPMSDISEFS--PGVDVVFLATAHEVSHDLAPQFLEAGCVVFDLSGAFRVNDATFYEKYY 118 P+++ ++ + D V LAT H VS LA F G VFDLSGA+R +D Y K+Y Sbjct: 60 SPLTEEAKANIVAEADAVVLATEHSVSLHLAAWFYSQGLAVFDLSGAYRFSDVAQYPKWY 119 Query: 119 GFTHQYPELLEQAAYGLAEWCGNKLKEANLIAVPGCYPTAAQLALKPLIDADLLDLNQWP 178 GF H+YPE+L +A YGLAEW + +IAVPGCYPTA+ ALKPL + L + +P Sbjct: 120 GFEHEYPEVLAKAVYGLAEWNAKDVAATKMIAVPGCYPTASLTALKPLKN---LLTSAYP 176 Query: 179 VINATSGVSGAGRKAAISNSFCEVSLQPYGVFTHRHQPEIATHLGADVIFTPHLGNFPRG 238 VINA SGV+GAGRKA + SFCEVSL PYGV HRHQPEIAT LG +VIFTPHLGNF RG Sbjct: 177 VINAVSGVTGAGRKAQLHTSFCEVSLTPYGVLGHRHQPEIATQLGQEVIFTPHLGNFKRG 236 Query: 239 ILETITCRLKSGVTQAQVAQVLQQAYAHKPLVRLYDKGVPALKNVVGLPFCDIG--FAVQ 296 IL TIT +LK G T A VA Y PLV + P + +VV P C +G F Sbjct: 237 ILATITVQLKPGTTTADVA-AAYSVYDQAPLVTVKQNQFPKVDDVVLTPNCHLGWKFDES 295 Query: 297 GEHLIIVATEDNLLKGAAAQAVQCANIRF 325 +L++ + DNL+KGAA+QA+QC I F Sbjct: 296 SGYLVVASAIDNLMKGAASQALQCIKIHF 324 Lambda K H 0.321 0.136 0.409 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: 353 Number of extensions: 11 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: 334 Length of database: 326 Length adjustment: 28 Effective length of query: 306 Effective length of database: 298 Effective search space: 91188 Effective search space used: 91188 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate 199470 SO0275 (N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file))
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.13021.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-105 338.4 0.4 3e-105 338.2 0.4 1.0 1 lcl|FitnessBrowser__MR1:199470 SO0275 N-acetyl-gamma-glutamyl-p Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199470 SO0275 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 338.2 0.4 3e-105 3e-105 2 331 .. 3 325 .. 2 326 .] 0.95 Alignments for each domain: == domain 1 score: 338.2 bits; conditional E-value: 3e-105 TIGR01850 2 kvaivGasGYtGaeLlrllakHpevevtklvssre...agkklsevhphlkglvd..lkleeleeeeileeadvvflAl 75 ++ai+GasGYtGa+L l+++ +e++++ l++s++ +g+ l++++p ++++ + l+e+++++i +ead+v+lA+ lcl|FitnessBrowser__MR1:199470 3 NIAIIGASGYTGAQLTALVHAESELSIQGLYVSENsldKGRALADLYPVYSHIELtlSPLTEEAKANIVAEADAVVLAT 81 79***************************99998889***********998865434566666679999********** PP TIGR01850 76 phgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPGCyaTaa 154 h vs +l++ ++++g+ v+dlS+++R++d ++Y kwYg++he++e+l++avYGl+E+n ++++ +k+ia+PGCy+Ta+ lcl|FitnessBrowser__MR1:199470 82 EHSVSLHLAAWFYSQGLAVFDLSGAYRFSDVAQYPKWYGFEHEYPEVLAKAVYGLAEWNAKDVAATKMIAVPGCYPTAS 160 ******************************************************************************* PP TIGR01850 155 lLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftph 233 l al+Pl +l+++ ++++a+sGv+gAGrka+ +++f+ev +l+pY v +HrH+pEi+++l+ +v+ftph lcl|FitnessBrowser__MR1:199470 161 LTALKPLK--NLLTSAYPVINAVSGVTGAGRKAQLHTSFCEV--SLTPYGVLGHRHQPEIATQLG------QEVIFTPH 229 *******8..6677777*************************..*********************......579***** PP TIGR01850 234 lvpmtrGilatiyaklkkelteeelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiD 312 l +++rGilati+++lk ++t+++++++y +vY++ p+v+v + +++P++ +v+ + +++g++ de+++ +vv saiD lcl|FitnessBrowser__MR1:199470 230 LGNFKRGILATITVQLKPGTTTADVAAAY-SVYDQAPLVTVKQ-NQFPKVDDVVLTPNCHLGWKFDESSGYLVVASAID 306 ****************************8.69*********98.9********************************** PP TIGR01850 313 NLvKGaagqAvqnlNlmlg 331 NL+KGaa+qA+q++ ++++ lcl|FitnessBrowser__MR1:199470 307 NLMKGAASQALQCIKIHFN 325 **************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (326 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: 9.39 // [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