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_011737315.1 PPRO_RS17460 gamma-glutamyl-phosphate reductase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000015045.1:WP_011737315.1 Length = 418 Score = 374 bits (959), Expect = e-108 Identities = 203/415 (48%), Positives = 279/415 (67%), Gaps = 8/415 (1%) Query: 4 QMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAML 63 Q+ A+QAS+ L++LS+R KN +L +A+ LE Q+ ++ NA+D+ + + GLS AML Sbjct: 9 QIAHEARQASFVLSRLSTRVKNELLLAMAEALEQQAPHLIAENAKDLEEGKQKGLSSAML 68 Query: 64 DRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARP 123 DRL L R+ +AD +R+V L DPVG+V + L + + R+PLGVIG+I+EARP Sbjct: 69 DRLMLDAKRISAMADALREVAALPDPVGEVTKMWKRPNNLMVGKMRIPLGVIGIIFEARP 128 Query: 124 NVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRAL 183 NVT D A+LCLK GNAVILRGGKE +N A A++++A+ S G+PAGA+ I DR Sbjct: 129 NVTADAAALCLKAGNAVILRGGKEAINSNRAIAAILREAMVSKGVPAGALALIPFTDRQG 188 Query: 184 VSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIV 243 V EML+ ++ ID++IPRGG GL + E S IPVI GVCHI+VDES + A ++I+ Sbjct: 189 VLEMLKQEECIDLIIPRGGEGLIRFVTENSRIPVIKHYKGVCHIFVDESADFDMAERIII 248 Query: 244 NAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADA--AALAQLQAGPAKV 301 NAKTQRP CN +ETLL+++++A +F+P ++ + V L D ALA QA PA Sbjct: 249 NAKTQRPGVCNALETLLIHESVAAAFIPRIASILGGMQVELRGDERFRALAP-QAKPA-- 305 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 E++ E+L L L ++V DLD AI HI +G+ H+++I+T D AQRF+ EV+S Sbjct: 306 ---SEEDWYAEYLELILACRVVDDLDQAIDHINRYGSLHTESIITSDYGRAQRFIREVNS 362 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 S V VNASTRF DG Q GLGAE+ +ST KLH+ GPMGLE LTT K+I GD +R Sbjct: 363 SCVVVNASTRFADGNQLGLGAEIGISTTKLHSFGPMGLEDLTTTKFIVYGDGQVR 417 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: 422 Number of extensions: 10 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: 418 Length adjustment: 32 Effective length of query: 385 Effective length of database: 386 Effective search space: 148610 Effective search space used: 148610 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_011737315.1 PPRO_RS17460 (gamma-glutamyl-phosphate reductase)
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.6813.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-155 504.4 0.0 1.1e-155 504.2 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011737315.1 PPRO_RS17460 gamma-glutamyl-phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011737315.1 PPRO_RS17460 gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 504.2 0.0 1.1e-155 1.1e-155 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 504.2 bits; conditional E-value: 1.1e-155 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a++a++ l lst+ kne+l ++a++L+++a+ ++a+nakd++++k++Gl+ a+ldrL L+ +++ +a lcl|NCBI__GCF_000015045.1:WP_011737315.1 14 ARQASFVLSRLSTRVKNELLLAMAEALEQQAPHLIAENAKDLEEGKQKGLSSAMLDRLMLDAKRISAMA 82 89******************************************************************* PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 d++++v+ L+dPvG+v++ ++ + L++ ++r+PlGv+g+i+earP+v++d+a+Lclk+GnaviL+Ggk lcl|NCBI__GCF_000015045.1:WP_011737315.1 83 DALREVAALPDPVGEVTKMWKRPNNLMVGKMRIPLGVIGIIFEARPNVTADAAALCLKAGNAVILRGGK 151 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 ea++sn+a+++++++a+ + g+p++a+ li +dr+ v e+lk++e +dl+iPrGg++l++ + e+s+i lcl|NCBI__GCF_000015045.1:WP_011737315.1 152 EAINSNRAIAAILREAMVSKGVPAGALALIPFTDRQGVLEMLKQEECIDLIIPRGGEGLIRFVTENSRI 220 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pv++h +GvChi++desad +a+++i++aktqrP +Cna+etLL+++++a+ f++++++ l vel lcl|NCBI__GCF_000015045.1:WP_011737315.1 221 PVIKHYKGVCHIFVDESADFDMAERIIINAKTQRPGVCNALETLLIHESVAAAFIPRIASILGGMQVEL 289 ********************************************************************* PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+d+ + +l +++k +s+ed+ e+l+l+L+ ++v+dl++ai+hi++yg+ h+++i+t+d a+ lcl|NCBI__GCF_000015045.1:WP_011737315.1 290 RGDERFRALAPQAK----PASEEDWYAEYLELILACRVVDDLDQAIDHINRYGSLHTESIITSDYGRAQ 354 *********99983....45689********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f++ev+s+ v vnastrfadG + G+Gae+gist klh+ GP+GLe L+++k lcl|NCBI__GCF_000015045.1:WP_011737315.1 355 RFIREVNSSCVVVNASTRFADGNQLGLGAEIGISTTKLHSFGPMGLEDLTTTK 407 **************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (418 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: 11.37 // [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