Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate Pf1N1B4_2688 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 Length = 415 Score = 366 bits (939), Expect = e-106 Identities = 186/415 (44%), Positives = 273/415 (65%), Gaps = 5/415 (1%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 + ++G AA++AS + + S+ +KNR L+ A+ L+A + AN D+A RANGL A Sbjct: 1 MTRLGRAAREASRVIGRASTAQKNRALQAAANALDAARAELTAANELDLAAGRANGLEPA 60 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 +L+RLALTP R+ G+ +RQV L DPVG + D SG+++ + RVPLGVIG+IYE+ Sbjct: 61 LLERLALTPERIDGMIVGLRQVAALPDPVGAIRDMSYRPSGIQVGKMRVPLGVIGIIYES 120 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVT+D ASLCLK+GNA ILRGG E +N A A IQ L GLPA VQ ++ DR Sbjct: 121 RPNVTIDAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEAGLPAAVVQVVETTDR 180 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 A V ++ M +Y+D+++PRGG GL + + +PVI G+CH+YV ++ +A ++ Sbjct: 181 AAVGALITMPEYVDVIVPRGGRGLIERVSRDARVPVIKHLDGICHVYVSAHADLPKAQRI 240 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 NAKT R C +ETLLV++ +A FLP+++ Q+ E GV L A ++A Sbjct: 241 AFNAKTYRYGICGAMETLLVDQAVAKDFLPSMAAQLREKGVELRGCERTRAIIEA----- 295 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 VA E++ E+L+ L++++V LD AI HI ++G+ H+D+I++ ++ + +RFV EVDS Sbjct: 296 VAATEEDWHTEYLAPILSIRVVDGLDQAIEHINKYGSHHTDSIVSENLADTRRFVAEVDS 355 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 S+V +N T F DG ++GLGAE+ +ST KLHARGP+GLE LT K+I +GD +R Sbjct: 356 SSVMINTPTCFADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYIVVGDGQLR 410 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: 414 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: 415 Length adjustment: 31 Effective length of query: 386 Effective length of database: 384 Effective search space: 148224 Effective search space used: 148224 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 Pf1N1B4_2688 (Gamma-glutamyl phosphate reductase (EC 1.2.1.41))
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.21152.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-150 487.8 0.1 1.3e-150 487.6 0.1 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 Gamma-glutamyl phosphate reducta Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 Gamma-glutamyl phosphate reductase (EC 1.2.1.41) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.6 0.1 1.3e-150 1.3e-150 1 397 [. 8 399 .. 8 400 .. 0.99 Alignments for each domain: == domain 1 score: 487.6 bits; conditional E-value: 1.3e-150 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteek 64 a+ea+ + sta+kn+al++ a++L a+ ++ aan+ d+aa+++nGl +all+rL+Lt e+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 8 AREASRVIGRASTAQKNRALQAAANALDAARAELTAANELDLAAGRANGLEPALLERLALTPER 71 89************************************************************** PP TIGR00407 65 lksiaddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclkt 128 + +++ ++++v+ L+dPvG + + + +G+++ ++rvPlGv+g+iye+rP+v++d+asLclk+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 72 IDGMIVGLRQVAALPDPVGAIRDMSYRPSGIQVGKMRVPLGVIGIIYESRPNVTIDAASLCLKS 135 **************************************************************** PP TIGR00407 129 GnaviLkGgkeavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPr 192 Gna iL+Gg+ea++sn+a+++ iq+ l+++glp+ vq++e++dr+ v l+++ eyvd+++Pr lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 136 GNATILRGGSEAIHSNRAIAACIQRGLAEAGLPAAVVQVVETTDRAAVGALITMPEYVDVIVPR 199 **************************************************************** PP TIGR00407 193 GgnelvklikeestiPvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnka 256 Gg++l++ + +++++Pv++h dG+Ch+y+ ++adl ka+++ +akt r C a+etLLv++a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 200 GGRGLIERVSRDARVPVIKHLDGICHVYVSAHADLPKAQRIAFNAKTYRYGICGAMETLLVDQA 263 **************************************************************** PP TIGR00407 257 iaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsvkivedlee 320 +a++fl++++ ql ekgvelr+ + + +++e+ a ++ed+++e+l+++Ls+++v+ l++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 264 VAKDFLPSMAAQLREKGVELRGCERTRAIIEAVAA-----TEEDWHTEYLAPILSIRVVDGLDQ 322 *****************************998855.....4599******************** PP TIGR00407 321 aiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklh 384 aiehi++yg++h+d+i++e+ + ++fv evds++v n+ t fadGf++G+Gae+gist+klh lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 323 AIEHINKYGSHHTDSIVSENLADTRRFVAEVDSSSVMINTPTCFADGFEYGLGAEIGISTDKLH 386 **************************************************************** PP TIGR00407 385 arGPvGLeaLvsy 397 arGPvGLe+L+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 387 ARGPVGLEGLTCE 399 **********976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (415 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.04 // [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