Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_086508696.1 BZY95_RS04055 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_002151265.1:WP_086508696.1 Length = 433 Score = 362 bits (930), Expect = e-105 Identities = 192/412 (46%), Positives = 275/412 (66%), Gaps = 4/412 (0%) Query: 5 MGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLD 64 +G AA+ A+ ++ + + +KNR L +A L+ + IL ANA D+A RA+GL A+LD Sbjct: 25 LGQAARVAATQMRRAVTGDKNRALLAMAAHLQRRRSEILEANAADLARGRASGLEAALLD 84 Query: 65 RLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPN 124 RLAL AR+ + + + QV L DPVG++ SG+++ + RVPLGVIG+IYE+RPN Sbjct: 85 RLALNDARIDAMIEGLEQVAALPDPVGEIEGLRYRPSGIQVGQMRVPLGVIGIIYESRPN 144 Query: 125 VTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALV 184 VT++ ASLCLK+GNA ILRGG E +NAA A I+D L+ GLP AVQ + DRA V Sbjct: 145 VTMEAASLCLKSGNASILRGGSEARDSNAAIAACIRDGLRDAGLPETAVQVVATTDRAAV 204 Query: 185 SEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIVN 244 +++ M +Y+D++IPRGG L + ++ +PVI GVCH+Y+D + + +AL + VN Sbjct: 205 GQLIAMPEYVDVIIPRGGKSLIERISREARVPVIKHLDGVCHVYIDATADPEKALAIAVN 264 Query: 245 AKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVAV 304 AKT R TCNT+ETLLV+ +A++ LP L++ A GV L + A L + A Sbjct: 265 AKTHRYGTCNTMETLLVDAPVAEALLPRLAQAYAAHGVELRGCERSRAILD----DIAAA 320 Query: 305 KAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSAV 364 E++ E+L+ L V++V ++ AI HI +G+ H+DAI+T D A+RF+ EVDSS+V Sbjct: 321 SEEDWYAEYLAPVLAVRVVDGMEAAIEHIERYGSHHTDAIVTEDYGLARRFMAEVDSSSV 380 Query: 365 YVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 VNASTRF DG ++GLGAE+ +ST KLHARGP+GLE LTT K++ +GD +R Sbjct: 381 MVNASTRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTRKYVVLGDGQVR 432 Lambda K H 0.317 0.133 0.369 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: 452 Number of extensions: 8 Number of successful extensions: 2 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: 417 Length of database: 433 Length adjustment: 32 Effective length of query: 385 Effective length of database: 401 Effective search space: 154385 Effective search space used: 154385 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_086508696.1 BZY95_RS04055 (glutamate-5-semialdehyde dehydrogenase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))
# 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/TIGR00407.hmm # target sequence database: /tmp/gapView.24658.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00407 [M=398] Accession: TIGR00407 Description: proA: glutamate-5-semialdehyde dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-152 491.9 0.2 7.3e-152 491.7 0.2 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508696.1 BZY95_RS04055 glutamate-5-semial Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508696.1 BZY95_RS04055 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 491.7 0.2 7.3e-152 7.3e-152 1 398 [] 29 422 .. 29 422 .. 0.99 Alignments for each domain: == domain 1 score: 491.7 bits; conditional E-value: 7.3e-152 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a+ aa+++ t +kn+al ++a +L+++ ++il+ana d+a +++ Gl alldrL+L+++++ ++ lcl|NCBI__GCF_002151265.1:WP_086508696.1 29 ARVAATQMRRAVTGDKNRALLAMAAHLQRRRSEILEANAADLARGRASGLEAALLDRLALNDARIDAMI 97 789****************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 +++++v+ L+dPvG++ r + +G+++ ++rvPlGv+g+iye+rP+v++++asLclk+Gna iL+Gg+ lcl|NCBI__GCF_002151265.1:WP_086508696.1 98 EGLEQVAALPDPVGEIEGLRYRPSGIQVGQMRVPLGVIGIIYESRPNVTMEAASLCLKSGNASILRGGS 166 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea sn+a+++ i+d l+++glp +avq++ ++dr+ v +l+ + eyvd++iPrGg++l++ i +e+++ lcl|NCBI__GCF_002151265.1:WP_086508696.1 167 EARDSNAAIAACIRDGLRDAGLPETAVQVVATTDRAAVGQLIAMPEYVDVIIPRGGKSLIERISREARV 235 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv++h dGvCh+y+d++ad +ka + v+akt+r tCn++etLLv+ +ae l++L+++ +++gvel lcl|NCBI__GCF_002151265.1:WP_086508696.1 236 PVIKHLDGVCHVYIDATADPEKALAIAVNAKTHRYGTCNTMETLLVDAPVAEALLPRLAQAYAAHGVEL 304 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+ + ++l+ a++s+ed+ e+l+++L+v++v+ +e+aiehi++yg++h+dai+ted a+ lcl|NCBI__GCF_002151265.1:WP_086508696.1 305 RGCERSRAILDDI----AAASEEDWYAEYLAPVLAVRVVDGMEAAIEHIERYGSHHTDAIVTEDYGLAR 369 ****999999877....667899********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f+ evds++v vnastrfadGf++G+Gae+gist+klharGPvGLe+L++ k lcl|NCBI__GCF_002151265.1:WP_086508696.1 370 RFMAEVDSSSVMVNASTRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTRK 422 **************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (433 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: 9.83 // [ok]
This GapMind analysis is from Apr 10 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