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_019895556.1 A377_RS0107085 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000384235.1:WP_019895556.1 Length = 422 Score = 363 bits (931), Expect = e-105 Identities = 185/416 (44%), Positives = 276/416 (66%), Gaps = 4/416 (0%) Query: 1 MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60 ++ Q+G AA+ A+ +L+ + +KN LE IA E+E ++E + + NA+D+ +ANGL Sbjct: 10 LMHQLGQAARTAATQLSVADTAQKNAALEAIAVEIERRAEFLQSENARDLDAGKANGLDA 69 Query: 61 AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120 AMLDRL L+ L G+ +RQ+ L DP+G+V D L SG+ + + RVPLGV+G+IYE Sbjct: 70 AMLDRLTLSDKALNGMVTGLRQIAALKDPIGEVSDLSPLPSGIEVGKMRVPLGVVGIIYE 129 Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180 +RPNVT+D A+LCLK+GNA ILRGG E +N A IQ LK+ LP AVQ + D Sbjct: 130 SRPNVTIDAAALCLKSGNAAILRGGSEARHSNQALAQCIQAGLKAADLPEAAVQVVPTTD 189 Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240 RA V E++ M +++D++IPRGG GL + + +PVI G+CH+Y+D++ + +A + Sbjct: 190 RAAVGELIAMPQFVDVIIPRGGKGLIERISADARVPVIKHLDGICHVYIDDAADAEKAHR 249 Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300 V NAKT R CN +ETLLV ++ A LP L++ + GV L A+ + A+ Sbjct: 250 VAFNAKTHRYGVCNAMETLLVAESRAAEILPRLAQAFEQKGVELR----GCARTREIIAE 305 Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360 + A E++ E+L L++K+V+D A+AHI ++ + H+++I+T ++ A+RF+ +VD Sbjct: 306 MKAATDEDWATEYLDAILSIKVVADASAAMAHIAQYSSGHTESIITENLTTARRFLAQVD 365 Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 SS+V VNASTRF DG ++GLGAE+ +ST K HARGP+GLE LT+ K+I GD TIR Sbjct: 366 SSSVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSQKYIVFGDGTIR 421 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: 423 Number of extensions: 14 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: 422 Length adjustment: 32 Effective length of query: 385 Effective length of database: 390 Effective search space: 150150 Effective search space used: 150150 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: 50 (23.9 bits)
Align candidate WP_019895556.1 A377_RS0107085 (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.19725.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-152 492.7 2.8 4.1e-152 492.5 2.8 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019895556.1 A377_RS0107085 glutamate-5-semia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895556.1 A377_RS0107085 glutamate-5-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 492.5 2.8 4.1e-152 4.1e-152 1 398 [] 18 411 .. 18 411 .. 0.99 Alignments for each domain: == domain 1 score: 492.5 bits; conditional E-value: 4.1e-152 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a+ aa++l ta+kn al++ia e++++ae++ +na+d+ a+k+nGl a+ldrL+L+++ l++++ lcl|NCBI__GCF_000384235.1:WP_019895556.1 18 ARTAATQLSVADTAQKNAALEAIAVEIERRAEFLQSENARDLDAGKANGLDAAMLDRLTLSDKALNGMV 86 899****************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 ++++++ L+dP+G+v + l +G+ + ++rvPlGv+g+iye+rP+v++d+a+Lclk+Gna+iL+Gg+ lcl|NCBI__GCF_000384235.1:WP_019895556.1 87 TGLRQIAALKDPIGEVSDLSPLPSGIEVGKMRVPLGVVGIIYESRPNVTIDAAALCLKSGNAAILRGGS 155 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea +sn+al++ iq l+ + lp avq++ ++dr+ v el+ + ++vd++iPrGg++l++ i ++++ lcl|NCBI__GCF_000384235.1:WP_019895556.1 156 EARHSNQALAQCIQAGLKAADLPEAAVQVVPTTDRAAVGELIAMPQFVDVIIPRGGKGLIERISADARV 224 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv++h dG+Ch+y+d+ ad +ka++v +akt+r +Cna+etLLv ++ a+e l++L+++ e+kgvel lcl|NCBI__GCF_000384235.1:WP_019895556.1 225 PVIKHLDGICHVYIDDAADAEKAHRVAFNAKTHRYGVCNAMETLLVAESRAAEILPRLAQAFEQKGVEL 293 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+ a + +++ ka +++ed+ +e+l+ +Ls+k+v d +a++hi qy++ h+++i+te+ ++a+ lcl|NCBI__GCF_000384235.1:WP_019895556.1 294 RGCARTREIIAEMKA----ATDEDWATEYLDAILSIKVVADASAAMAHIAQYSSGHTESIITENLTTAR 358 ********9987744....4589********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f+ +vds++v vnastrfadGf++G+Gae+gist+k+harGPvGLe+L+s k lcl|NCBI__GCF_000384235.1:WP_019895556.1 359 RFLAQVDSSSVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSQK 411 **************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (422 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.05 // [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