Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate Dsui_1220 Dsui_1220 gamma-glutamyl phosphate reductase
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__PS:Dsui_1220 Length = 418 Score = 363 bits (933), Expect = e-105 Identities = 183/415 (44%), Positives = 280/415 (67%), Gaps = 4/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 ++ +G A+ AS ++A+ + KNR L IA + +L AN +D+A ARA GL A Sbjct: 7 MQNLGRRARAASRQMAKADTNAKNRALLAIAAAIRRDEAKLLAANGEDLAAARAAGLEPA 66 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 M+DRL L+P + +A+ + Q+ +L DP+G++ D SG+++ RVPLGVIG+IYEA Sbjct: 67 MVDRLTLSPKTVATMAEGLEQIASLPDPIGEMTDLRFRPSGIQVGHMRVPLGVIGIIYEA 126 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVTVD A LC+K+GNA ILRGG E R N A ++++ L+S GLPA AVQ ++ DR Sbjct: 127 RPNVTVDAAGLCIKSGNASILRGGSEAIRCNQALATLVKEGLQSAGLPADAVQVVETTDR 186 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 A V E++ M +++D+++PRGG GL +S +P+I G CH+Y+D+S + A+A+ V Sbjct: 187 AAVGELITMREFVDVIVPRGGKGLIARLLAESRVPMIQHLDGNCHVYLDDSADAAKAMAV 246 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 + N+KTQR TCNT E+LLV +++A + LP ++ + GV + A A + P Sbjct: 247 VENSKTQRYGTCNTAESLLVARSVAATLLPPIAAMLTAKGVEIRGCAETRALV---PNAK 303 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 A +A ++ +E+L+ + VK+V+ LD+AI HI ++ + H++AI+T + +A RF+ EVDS Sbjct: 304 EATEA-DWGEEYLAPIIAVKVVAGLDEAIEHINKYSSSHTEAIVTENHTHAMRFLREVDS 362 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 ++V VNASTRF DG ++GLGAE+ +ST K+HARGP+GLE LT+ KW+ +G+ +R Sbjct: 363 ASVMVNASTRFADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKWVVLGNGQVR 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: 402 Number of extensions: 12 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 Dsui_1220 Dsui_1220 (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.4872.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-150 485.9 1.6 4.8e-150 485.7 1.6 1.0 1 lcl|FitnessBrowser__PS:Dsui_1220 Dsui_1220 gamma-glutamyl phospha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1220 Dsui_1220 gamma-glutamyl phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.7 1.6 4.8e-150 4.8e-150 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 485.7 bits; conditional E-value: 4.8e-150 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvie 77 a+ a+ ++a+ t+ kn+al +ia +++++ +laan +d+aaa++ Gl +a++drL+L+ + + ++a++++++++ lcl|FitnessBrowser__PS:Dsui_1220 14 ARAASRQMAKADTNAKNRALLAIAAAIRRDEAKLLAANGEDLAAARAAGLEPAMVDRLTLSPKTVATMAEGLEQIAS 90 899************************************************************************** PP TIGR00407 78 LadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqda 154 L+dP+G++++ r + +G+++ ++rvPlGv+g+iyearP+v+vd+a Lc+k+Gna iL+Gg+ea+r n+al+ ++++ lcl|FitnessBrowser__PS:Dsui_1220 91 LPDPIGEMTDLRFRPSGIQVGHMRVPLGVIGIIYEARPNVTVDAAGLCIKSGNASILRGGSEAIRCNQALATLVKEG 167 ***************************************************************************** PP TIGR00407 155 leqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakak 231 l+++glp+ avq++e++dr+ v el+++ e+vd+++PrGg++l+ + es++P+++h dG+Ch+yld+sad aka+ lcl|FitnessBrowser__PS:Dsui_1220 168 LQSAGLPADAVQVVETTDRAAVGELITMREFVDVIVPRGGKGLIARLLAESRVPMIQHLDGNCHVYLDDSADAAKAM 244 ***************************************************************************** PP TIGR00407 232 kvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsl 308 v+ ++ktqr tCn+ e+LLv +++a+ l+ ++ l++kgve+r+ a + +l++ + + e+++ d+ +e+l++ lcl|FitnessBrowser__PS:Dsui_1220 245 AVVENSKTQRYGTCNTAESLLVARSVAATLLPPIAAMLTAKGVEIRGCAETRALVPNA--K--EATEADWGEEYLAP 317 ******************************************************9987..4..466789******** PP TIGR00407 309 dLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklha 385 +++vk+v l+eaiehi++y++ h++ai+te+++ a +f++evdsa+v vnastrfadGf++G+Gae+gist+k+ha lcl|FitnessBrowser__PS:Dsui_1220 318 IIAVKVVAGLDEAIEHINKYSSSHTEAIVTENHTHAMRFLREVDSASVMVNASTRFADGFEYGLGAEIGISTDKIHA 394 ***************************************************************************** PP TIGR00407 386 rGPvGLeaLvsyk 398 rGPvGLe+L+s k lcl|FitnessBrowser__PS:Dsui_1220 395 RGPVGLEGLTSQK 407 **********986 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.30 // [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