Align N-acetyl-gamma-glutamyl-phosphate reductase; Short=AGPR; EC 1.2.1.38 (characterized, see rationale)
to candidate Pf1N1B4_2559 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
Query= uniprot:E4PLW0 (388 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 Length = 344 Score = 474 bits (1219), Expect = e-138 Identities = 235/346 (67%), Positives = 277/346 (80%), Gaps = 3/346 (0%) Query: 44 VIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYD-LAFSE 102 ++KVGIVGGTGYTGVELLR+LA HP+ V ITSRSEAG+ VA+MYPNLRGHYD LAFS Sbjct: 1 MVKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDGLAFSV 60 Query: 103 PDVNVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANWYGMAHES 162 PD+ LGACD+VFFATPHGVA + EL++AG +V+DLSADFRL+D D WA WYG H + Sbjct: 61 PDIKTLGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGA 120 Query: 163 PEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRLIADAKSG 222 PE E+AVYGLPEV R++I+ A+L+A PGCYPTA QLGFLPLLE GL D RLIAD KSG Sbjct: 121 PELLEEAVYGLPEVNREQIKQARLIAVPGCYPTATQLGFLPLLEAGLADTTRLIADCKSG 180 Query: 223 ASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVPHLIPMIR 282 SGAGR +G L+ E ES KAY GHRHLPEIRQGL AAG DVG+TFVPHL PMIR Sbjct: 181 VSGAGRGASVGSLYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIR 240 Query: 283 GIEATLYAELKNPADFDRLQALFEQRFDDEPFVDVMPFGSHPETRSVRGANQCRMALHRQ 342 GI +TLYA + + + LQALFE+R+ +EPFVDVMP GSHPETRSVRGAN CR+A+HR Sbjct: 241 GIHSTLYATVVDRS--VDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRP 298 Query: 343 EQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLEAPALLP 388 + ++V+V SVIDNLVKGA+GQAVQN+NI+FGL E +GL +LP Sbjct: 299 QDGDLVVVLSVIDNLVKGASGQAVQNLNILFGLDERLGLSHAGMLP 344 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: 462 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: 388 Length of database: 344 Length adjustment: 30 Effective length of query: 358 Effective length of database: 314 Effective search space: 112412 Effective search space used: 112412 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 Pf1N1B4_2559 (N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
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.20496.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-136 441.0 0.0 1.8e-136 440.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 N-acetyl-gamma-glutamyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.8 0.0 1.8e-136 1.8e-136 1 345 [] 2 344 .] 2 344 .] 0.98 Alignments for each domain: == domain 1 score: 440.8 bits; conditional E-value: 1.8e-136 TIGR01850 1 ikvaivGasGYtGaeLlrllakHpevevtklvssreagkklsevhphlkglvd.lkleeleeee 63 +kv+ivG++GYtG+eLlrlla+Hp++ev+ ++s++eag +++++p+l+g++d l ++ +++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 2 VKVGIVGGTGYTGVELLRLLAQHPQAEVVVITSRSEAGLAVADMYPNLRGHYDgLAFSVPDIK- 64 69***************************8888888*****************8888887777. PP TIGR01850 64 ileeadvvflAlphgvsaelvpellekgvkvidlSadfRlkdaevYekwYgkkhekeelleeav 127 +l ++dvvf+A+phgv+++l+ ell++g+kvidlSadfRl+da++++kwYg++h ++elleeav lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 65 TLGACDVVFFATPHGVAHALAGELLAAGTKVIDLSADFRLQDADEWAKWYGQPHGAPELLEEAV 128 567************************************************************* PP TIGR01850 128 YGlpElnreeikkaklianPGCyaTaalLalaPllkekliepksiivdaksGvSgAGrkaseks 191 YGlpE+nre+ik+a+lia+PGCy+Ta++L+ Pll+++l +++++i d+ksGvSgAGr as s lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 129 YGLPEVNREQIKQARLIAVPGCYPTATQLGFLPLLEAGLADTTRLIADCKSGVSGAGRGASVGS 192 **************************************************************** PP TIGR01850 192 lfaevnenlkpYkvtkHrHtpEieqelsklaekkvkvsftphlvpmtrGilatiyaklkkelte 255 l++e++e++k+Y+v++HrH pEi+q l+++a+k+v ++f+phl+pm+rGi++t+ya++ + ++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 193 LYSETSESMKAYAVKGHRHLPEIRQGLRRAAGKDVGLTFVPHLTPMIRGIHSTLYATVVD--RS 254 ***********************************************************9..78 PP TIGR01850 256 eelrklyeevYedepfvrvlkegelPstkavlgsnfvdigvavdeetkrvvvvsaiDNLvKGaa 319 +l++l+e++Y++epfv+v+++g+ P+t++v+g n+++i+v+ ++ + vvv+s+iDNLvKGa+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 255 VDLQALFEKRYANEPFVDVMPAGSHPETRSVRGANVCRIAVHRPQDGDLVVVLSVIDNLVKGAS 318 9*************************************************************** PP TIGR01850 320 gqAvqnlNlmlgfdetegLeklpllp 345 gqAvqnlN+ +g+de+ gL++ ++lp lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2559 319 GQAVQNLNILFGLDERLGLSHAGMLP 344 *********************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (345 nodes) Target sequences: 1 (344 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.69 // [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