Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate Synpcc7942_1433 Synpcc7942_1433 N-acetyl-gamma-glutamyl-phosphate reductase
Query= uniprot:E4PLW0 (388 letters) >FitnessBrowser__SynE:Synpcc7942_1433 Length = 352 Score = 291 bits (744), Expect = 3e-83 Identities = 148/350 (42%), Positives = 214/350 (61%), Gaps = 2/350 (0%) Query: 41 EKMVIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAF 100 E + VGI+G +GY GV+L+R+L HP++ V+ + AG AE+YP+L H +L Sbjct: 3 ESSRLPVGIIGASGYGGVQLVRLLQDHPQLEVAYLGGDRSAGKEFAELYPHLGPHLNLTI 62 Query: 101 SEPDVN-VLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMA 159 DV+ + C VF + P+G+A + P L+ G +V+DLSAD+R DL +A WYG Sbjct: 63 EAIDVDRIAERCAAVFLSLPNGLAYDLAPALLERGCKVLDLSADYRFHDLKTYALWYGGD 122 Query: 160 HESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADA 219 + A A+YGLPE+ R+ I NAQL+ PGCYPTA L P L+QGL+DP ++ DA Sbjct: 123 RQDAAVAHTAIYGLPELYRNRIANAQLIGCPGCYPTASLLALAPALKQGLIDPDTIVIDA 182 Query: 220 KSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIP 279 KSG SGAGRQ K L E G S AYG + HRH PEI Q +G +V + F PHL+P Sbjct: 183 KSGTSGAGRQAKTNALLAEAGNSVGAYGVARHRHTPEIEQICSDLSGHEVLLQFTPHLMP 242 Query: 280 MIRGIEATLYAELKNP-ADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMA 338 M+RGI AT+YA+L++P + +++ + + P V V+ G++P+T+ G N C + Sbjct: 243 MVRGIHATIYAKLRDPNLTTEDCLTVYQAFYRNAPMVKVLTHGTYPQTKWAAGTNLCYLG 302 Query: 339 LHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 L ++ +++ S IDNL+KG AGQA+Q +N+M G +E +GL P Sbjct: 303 LEVDARTGRIVLLSAIDNLIKGQAGQAIQCLNLMQGWEEGLGLPTLCYYP 352 Lambda K H 0.321 0.137 0.412 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: 386 Number of extensions: 13 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: 388 Length of database: 352 Length adjustment: 30 Effective length of query: 358 Effective length of database: 322 Effective search space: 115276 Effective search space used: 115276 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 Synpcc7942_1433 Synpcc7942_1433 (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.3688628.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-135 436.2 0.0 5.2e-135 436.0 0.0 1.0 1 FitnessBrowser__SynE:Synpcc7942_1433 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SynE:Synpcc7942_1433 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.0 0.0 5.2e-135 5.2e-135 3 345 .] 9 352 .] 7 352 .] 0.99 Alignments for each domain: == domain 1 score: 436.0 bits; conditional E-value: 5.2e-135 TIGR01850 3 vaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvdlkleeleeeeileeadvvflAl 75 v+i+GasGY+G++L+rll++Hp++ev++l ++r+agk+++e++phl +++l++e++++++i+e++ +vfl+l FitnessBrowser__SynE:Synpcc7942_1433 9 VGIIGASGYGGVQLVRLLQDHPQLEVAYLGGDRSAGKEFAELYPHLGPHLNLTIEAIDVDRIAERCAAVFLSL 81 99*********************************************************************** PP TIGR01850 76 phgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeavYGlpElnreeikkaklianPG 148 p+g +++l+p+lle+g+kv+dlSad+R++d ++Y+ wYg ++++ +++++a+YGlpEl+r++i++a+li++PG FitnessBrowser__SynE:Synpcc7942_1433 82 PNGLAYDLAPALLERGCKVLDLSADYRFHDLKTYALWYGGDRQDAAVAHTAIYGLPELYRNRIANAQLIGCPG 154 ************************************************************************* PP TIGR01850 149 CyaTaalLalaPllkekliepksiivdaksGvSgAGrkasekslfaevnenlkpYkvtkHrHtpEieqelskl 221 Cy+Ta+lLalaP+lk++li+p++i++daksG+SgAGr+a+++ l+ae+ +++ +Y v++HrHtpEieq +s+l FitnessBrowser__SynE:Synpcc7942_1433 155 CYPTASLLALAPALKQGLIDPDTIVIDAKSGTSGAGRQAKTNALLAEAGNSVGAYGVARHRHTPEIEQICSDL 227 ************************************************************************* PP TIGR01850 222 aekkvkvsftphlvpmtrGilatiyaklkke.lteeelrklyeevYedepfvrvlkegelPstkavlgsnfvd 293 ++++v ++ftphl+pm+rGi+atiyakl+++ lt+e+ ++y+++Y++ p+v+vl++g++P+tk+ +g+n + FitnessBrowser__SynE:Synpcc7942_1433 228 SGHEVLLQFTPHLMPMVRGIHATIYAKLRDPnLTTEDCLTVYQAFYRNAPMVKVLTHGTYPQTKWAAGTNLCY 300 ****************************9977***************************************** PP TIGR01850 294 igvavdeetkrvvvvsaiDNLvKGaagqAvqnlNlmlgfdetegLeklpllp 345 +g++vd +t+r+v++saiDNL+KG+agqA+q+lNlm g++e gL++l ++p FitnessBrowser__SynE:Synpcc7942_1433 301 LGLEVDARTGRIVLLSAIDNLIKGQAGQAIQCLNLMQGWEEGLGLPTLCYYP 352 **********************************************998887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (352 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 20.34 // [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