Align N-acetylglutamylphosphate reductase (EC 1.2.1.38) (characterized)
to candidate Ga0059261_0351 Ga0059261_0351 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
Query= reanno::Korea:Ga0059261_0351 (310 letters) >FitnessBrowser__Korea:Ga0059261_0351 Length = 310 Score = 613 bits (1580), Expect = e-180 Identities = 310/310 (100%), Positives = 310/310 (100%) Query: 1 MSVSVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPD 60 MSVSVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPD Sbjct: 1 MSVSVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPD 60 Query: 61 DAAREAVALIANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTG 120 DAAREAVALIANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTG Sbjct: 61 DAAREAVALIANDTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTG 120 Query: 121 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEPTGFRAYGLDLEHKHL 180 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEPTGFRAYGLDLEHKHL Sbjct: 121 FLALVRPLVRAGLIPPDWVLTAGGASGYSGGGKSMIAEFEDGSEPTGFRAYGLDLEHKHL 180 Query: 181 PEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSPIV 240 PEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSPIV Sbjct: 181 PEMQKHARIDHAPIFQPAVARSYRGMLIEVPLPLQMLPRKPAPAQIEQVLADAYRDSPIV 240 Query: 241 RVLPSDDVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAVQNLNIMA 300 RVLPSDDVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAVQNLNIMA Sbjct: 241 RVLPSDDVSLVRIEDDAGTDRLTIRVFGNAERGQARLVATLDNLGKGAGGAAVQNLNIMA 300 Query: 301 GFDQTAGLVL 310 GFDQTAGLVL Sbjct: 301 GFDQTAGLVL 310 Lambda K H 0.319 0.136 0.400 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: 494 Number of extensions: 3 Number of successful extensions: 1 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: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 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: 48 (23.1 bits)
Align candidate Ga0059261_0351 Ga0059261_0351 (N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))
to HMM TIGR01851 (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/TIGR01851.hmm # target sequence database: /tmp/gapView.30796.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01851 [M=310] Accession: TIGR01851 Description: argC_other: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-119 383.4 0.0 4.8e-119 383.2 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0351 Ga0059261_0351 N-acetyl-gamma-gl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0351 Ga0059261_0351 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 ! 383.2 0.0 4.8e-119 4.8e-119 3 309 .. 4 301 .. 2 302 .. 0.97 Alignments for each domain: == domain 1 score: 383.2 bits; conditional E-value: 4.8e-119 TIGR01851 3 kvfidGeaGttGlqirerlaerddlellsidedkrkdaderakllnaadvailclpddaareavslvdn 71 vfidG aGttGl+irerla r+d+ l+ +d+ +rkda +ra+ +n+ad +ilclpddaareav+l+ n lcl|FitnessBrowser__Korea:Ga0059261_0351 4 SVFIDGAAGTTGLEIRERLATRSDISLIGLDDAHRKDAGKRAEAINSADFVILCLPDDAAREAVALIAN 72 69******************************************************************* PP TIGR01851 72 pntkildastayrtaedwvyGfpelaaeqrekianakrvanPGcyatgaiallrPlveaGilPadfPvt 140 t+++dasta+r+a++w+yGf+el++ q ia+a++v+nPGc++tg++al+rPlv aG++P d+ +t lcl|FitnessBrowser__Korea:Ga0059261_0351 73 DTTRVIDASTAHRVADGWTYGFAELEPAQAAAIAEARYVSNPGCWPTGFLALVRPLVRAGLIPPDWVLT 141 ********************************************************************* PP TIGR01851 141 inavsGysGGGkaliakyeeesaddskkaafiiyglalehkhlpemrkhsglaskPiftPavGdfaqGl 209 + + sGysGGGk++ia++e++s+ + f++ygl lehkhlpem+kh+++ + Pif Pav + +G+ lcl|FitnessBrowser__Korea:Ga0059261_0351 142 AGGASGYSGGGKSMIAEFEDGSEP----TGFRAYGLDLEHKHLPEMQKHARIDHAPIFQPAVARSYRGM 206 *******************66543....57*************************************** PP TIGR01851 210 lveiplhlaeldskvsaedihkalaeyykGekfvkvaelddaellddtildaqglngtnrlelfvfgsd 278 l+e+pl+l+ l k+++++i+++la+ y+ v+v + dd++l+ + gt+rl + vfg++ lcl|FitnessBrowser__Korea:Ga0059261_0351 207 LIEVPLPLQMLPRKPAPAQIEQVLADAYRDSPIVRVLPSDDVSLV-----RIEDDAGTDRLTIRVFGNA 270 *******************************************66.....4566679************ PP TIGR01851 279 dgerallvarldnlGkGasGaavqnlnialG 309 + ++a+lva ldnlGkGa Gaavqnlni+ G lcl|FitnessBrowser__Korea:Ga0059261_0351 271 ERGQARLVATLDNLGKGAGGAAVQNLNIMAG 301 *****************************88 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (310 nodes) Target sequences: 1 (310 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: 7.31 // [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