Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate Ga0059261_2506 Ga0059261_2506 glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41)
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__Korea:Ga0059261_2506 Length = 422 Score = 345 bits (884), Expect = 2e-99 Identities = 191/408 (46%), Positives = 259/408 (63%), Gaps = 6/408 (1%) Query: 1 MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60 ++ ++G A+ A+ LA L + K + L A + A ++ IL ANA+DVA ANGLS Sbjct: 12 LIAELGARARAAAVTLAGLPAPAKAQGLRAAAAAIRADADAILAANARDVAAGEANGLSG 71 Query: 61 AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120 A+LDRL L PARL+G A V V LADPVG+VI +GL+L R RVP+GVIG+IYE Sbjct: 72 ALLDRLRLDPARLEGAAAGVEAVAALADPVGEVISTSERPNGLQLSRVRVPIGVIGIIYE 131 Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180 +RPNVT D A+LC+ +GNA ILRGG E +N A A L GLP AVQ + D Sbjct: 132 SRPNVTADAAALCVMSGNAAILRGGSEAVHSNRAIHAAFACGLADAGLPEDAVQLVPTTD 191 Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240 RA V ML+ D ID+++PRGG L +E++ +PV+ G+ H Y+D + + A Sbjct: 192 RAAVGAMLKADGAIDLVVPRGGKSLVARVQEEARVPVLAHLDGINHTYIDGAADPDMARD 251 Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300 + VNAK +R C ETLL++ AD P LS +A++G L D A ++A + Sbjct: 252 LAVNAKMRRTGICGATETLLIDTAFADP-APILS-ALADTGCELRGD----ADIRAIDPR 305 Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360 VVA AE++D E+L L+VK V + A+AHI HG+ H+DAI+T D A+RF+N VD Sbjct: 306 VVAANAEDWDTEYLDSILSVKRVDGVVGAMAHIAAHGSHHTDAIVTGDAATAERFLNGVD 365 Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 408 S+ V NAST+F DGG+FGLGAE+ ++T +LHARGP+ LE LTTYKW+ Sbjct: 366 SAIVMWNASTQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYKWV 413 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: 431 Number of extensions: 16 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 Ga0059261_2506 Ga0059261_2506 (glutamate-5-semialdehyde dehydrogenase (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.10172.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-138 445.3 0.4 1e-137 445.1 0.4 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2506 Ga0059261_2506 glutamate-5-semia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2506 Ga0059261_2506 glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.1 0.4 1e-137 1e-137 1 398 [] 20 411 .. 20 411 .. 0.98 Alignments for each domain: == domain 1 score: 445.1 bits; conditional E-value: 1e-137 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a+ aa++la l + k + l + a +++a+a++ilaana+d+aa+++nGl+ alldrL L+ ++l++ a lcl|FitnessBrowser__Korea:Ga0059261_2506 20 ARAAAVTLAGLPAPAKAQGLRAAAAAIRADADAILAANARDVAAGEANGLSGALLDRLRLDPARLEGAA 88 899****************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 ++v+ v+ LadPvG+vi++ e+ +GL+l rvrvP+Gv+g+iye+rP+v++d+a+Lc+ +Gna+iL+Gg+ lcl|FitnessBrowser__Korea:Ga0059261_2506 89 AGVEAVAALADPVGEVISTSERPNGLQLSRVRVPIGVIGIIYESRPNVTADAAALCVMSGNAAILRGGS 157 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 eav+sn+a+ + l+++glp avql+ ++dr+ v +lk d +dl++PrGg++lv ++ee+++ lcl|FitnessBrowser__Korea:Ga0059261_2506 158 EAVHSNRAIHAAFACGLADAGLPEDAVQLVPTTDRAAVGAMLKADGAIDLVVPRGGKSLVARVQEEARV 226 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pvl h dG+ h+y+d ad +a+ + v+ak +r C a etLL++ a+a+ + ++l+++g el lcl|FitnessBrowser__Korea:Ga0059261_2506 227 PVLAHLDGINHTYIDGAADPDMARDLAVNAKMRRTGICGATETLLIDTAFAD--PAPILSALADTGCEL 293 ***************************************************5..3567789******** PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+da + ++ + +++ +ed+d+e+l+ +Lsvk v+ + a++hi +g++h+dai+t d ++ae lcl|FitnessBrowser__Korea:Ga0059261_2506 294 RGDADIRAIDPRV----VAANAEDWDTEYLDSILSVKRVDGVVGAMAHIAAHGSHHTDAIVTGDAATAE 358 ****999988766....566679********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f++ vdsa v +nast+fadG++fG+Gae+gi+t +lharGPv Le+L++yk lcl|FitnessBrowser__Korea:Ga0059261_2506 359 RFLNGVDSAIVMWNASTQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYK 411 ****************************************************8 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: 00:00:00.02 # Mc/sec: 6.96 // [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