Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 6938396 Sama_2515 gamma-glutamyl phosphate reductase (RefSeq)
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__SB2B:6938396 Length = 420 Score = 479 bits (1234), Expect = e-140 Identities = 243/415 (58%), Positives = 315/415 (75%), Gaps = 1/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 L Q+G AAK + + LA L KNR+L ++A EL++ + IL ANA+DVA ARA+GL +A Sbjct: 7 LLQLGQAAKSSGFALANLGVMAKNRLLGRVAAELKSAFDEILAANAKDVAAARASGLGDA 66 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 M+DRL L RLKGI D+ V +LADP+G+ D +LD+G+RL RRRVPLGVIGVIYEA Sbjct: 67 MVDRLLLNDDRLKGIIADIDNVISLADPIGEEFDSRLLDNGMRLCRRRVPLGVIGVIYEA 126 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVTV++A L LKTGNAVILRGGKET +N A A I+ AL GLP VQ IDNPDR Sbjct: 127 RPNVTVEIAVLALKTGNAVILRGGKETLESNLALAAAIRRALAGEGLPEDCVQLIDNPDR 186 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 ALV+ +L++DK++DM++PRGG GL +LC EQ+TIPVI GGIG+CH+Y+D +I+ A V Sbjct: 187 ALVTGLLKLDKFVDMIVPRGGQGLQRLCAEQATIPVILGGIGICHLYLDRDADISRAANV 246 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 I+NAK QRP+ CN ++TLL++++ D +LP L++ + + GV L A +L L A + Sbjct: 247 IINAKVQRPTVCNALDTLLIHRDKLD-WLPTLARALQQQGVKLVACEQSLGALAAAGIEA 305 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 A E + E+LSL L VK+V+D+D+AIAHIR + + HS+AILT ++ A F+NEV+S Sbjct: 306 EAASDESFGTEWLSLTLGVKVVADIDEAIAHIRHYSSGHSEAILTDNLAAATHFMNEVNS 365 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 +AVY+NASTRFTDGGQFG GAEVAVSTQKLHARGPMGLEALTTYKW+G+GDY+ R Sbjct: 366 AAVYLNASTRFTDGGQFGFGAEVAVSTQKLHARGPMGLEALTTYKWLGVGDYSCR 420 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: 499 Number of extensions: 20 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: 420 Length adjustment: 32 Effective length of query: 385 Effective length of database: 388 Effective search space: 149380 Effective search space used: 149380 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 6938396 Sama_2515 (gamma-glutamyl phosphate reductase (RefSeq))
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.25445.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-164 531.2 0.4 8.4e-164 531.0 0.4 1.0 1 lcl|FitnessBrowser__SB2B:6938396 Sama_2515 gamma-glutamyl phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938396 Sama_2515 gamma-glutamyl phosphate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 531.0 0.4 8.4e-164 8.4e-164 1 398 [] 14 410 .. 14 410 .. 0.99 Alignments for each domain: == domain 1 score: 531.0 bits; conditional E-value: 8.4e-164 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvie 77 ak +++ la+l kn++l +a eLk + ++ilaanakd+aaa++ Gl da++drLlL++++lk+i++d+ +vi+ lcl|FitnessBrowser__SB2B:6938396 14 AKSSGFALANLGVMAKNRLLGRVAAELKSAFDEILAANAKDVAAARASGLGDAMVDRLLLNDDRLKGIIADIDNVIS 90 78999************************************************************************ PP TIGR00407 78 LadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154 LadP+G+ ++r ld+G++l r+rvPlGv+gviyearP+v+v++a L+lktGnaviL+Ggke+ +sn al++ i++a lcl|FitnessBrowser__SB2B:6938396 91 LADPIGEEFDSRLLDNGMRLCRRRVPLGVIGVIYEARPNVTVEIAVLALKTGNAVILRGGKETLESNLALAAAIRRA 167 ***************************************************************************** PP TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakak 231 l+ glp +vqli++pdr+ v+ llkld++vd+++PrGg++l +l+ e++tiPv+ +++G+Ch+yld++ad+++a lcl|FitnessBrowser__SB2B:6938396 168 LAGEGLPEDCVQLIDNPDRALVTGLLKLDKFVDMIVPRGGQGLQRLCAEQATIPVILGGIGICHLYLDRDADISRAA 244 ***************************************************************************** PP TIGR00407 232 kvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsl 308 +vi++ak qrP++Cna++tLL++++ ++l++L+++l+++gv+l a ++ l l +++++ ++s+e f +e+lsl lcl|FitnessBrowser__SB2B:6938396 245 NVIINAKVQRPTVCNALDTLLIHRDKL-DWLPTLARALQQQGVKLVACEQSLGALAAAGIEAEAASDESFGTEWLSL 320 ************************988.9******************999988888888988899999********* PP TIGR00407 309 dLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385 L vk+v d++eai+hir+y++ hs+ailt++ ++a++f++ev+saavy nastrf+dG++fGfGaev++stqklha lcl|FitnessBrowser__SB2B:6938396 321 TLGVKVVADIDEAIAHIRHYSSGHSEAILTDNLAAATHFMNEVNSAAVYLNASTRFTDGGQFGFGAEVAVSTQKLHA 397 ***************************************************************************** PP TIGR00407 386 rGPvGLeaLvsyk 398 rGP+GLeaL++yk lcl|FitnessBrowser__SB2B:6938396 398 RGPMGLEALTTYK 410 ************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (420 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: 10.67 // [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