Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate BWI76_RS05835 BWI76_RS05835 gamma-glutamyl-phosphate reductase
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__Koxy:BWI76_RS05835 Length = 417 Score = 694 bits (1791), Expect = 0.0 Identities = 351/417 (84%), Positives = 386/417 (92%) Query: 1 MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60 MLEQMGIAAK ASYKLAQLSSREKN+VLEKIAD LEAQ++ IL ANA+D+A+ARANGLSE Sbjct: 1 MLEQMGIAAKAASYKLAQLSSREKNQVLEKIADYLEAQTDAILRANAEDLAEARANGLSE 60 Query: 61 AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120 A+LDRLAL PARL GIA+DVRQVC+LADPVGQVIDGG+LDSGLR+ERRRVPLGV+GVIYE Sbjct: 61 ALLDRLALNPARLSGIANDVRQVCSLADPVGQVIDGGLLDSGLRIERRRVPLGVVGVIYE 120 Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180 ARPNVTVDVASLCLKTGNA ILRGGKET RTNAATV VIQ AL+ CGLPA VQAI++PD Sbjct: 121 ARPNVTVDVASLCLKTGNAAILRGGKETWRTNAATVKVIQQALQECGLPAATVQAIESPD 180 Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240 RALV EML+MDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIY+D S ++AEALK Sbjct: 181 RALVGEMLKMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYIDHSADVAEALK 240 Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300 VIVNAK QRPS CN+VETLLV+++IA+ FLPALSKQMAESGV+LHADAA+L LQ GPA Sbjct: 241 VIVNAKVQRPSACNSVETLLVHQDIAERFLPALSKQMAESGVSLHADAASLPALQNGPAS 300 Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360 V VKAE+YD+E+LSLDLNVK+V+D D+A+AHIREHGTQHSDAILTR + NA RF+NEVD Sbjct: 301 VEPVKAEQYDNEYLSLDLNVKVVADQDEAVAHIREHGTQHSDAILTRTLGNANRFINEVD 360 Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIG GD TIRA Sbjct: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGFGDDTIRA 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: 627 Number of extensions: 15 Number of successful extensions: 1 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: 417 Length adjustment: 31 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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 BWI76_RS05835 BWI76_RS05835 (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.22373.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-194 629.6 1.8 1.1e-193 629.4 1.8 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS05835 BWI76_RS05835 gamma-glutamyl-pho Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS05835 BWI76_RS05835 gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.4 1.8 1.1e-193 1.1e-193 1 398 [] 9 406 .. 9 406 .. 1.00 Alignments for each domain: == domain 1 score: 629.4 bits; conditional E-value: 1.1e-193 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiadd 71 ak a++klaqls++ekn++l+kiad L+a++++il ana+d+a+a++nGl++alldrL+L+ ++l +ia+d lcl|FitnessBrowser__Koxy:BWI76_RS05835 9 AKAASYKLAQLSSREKNQVLEKIADYLEAQTDAILRANAEDLAEARANGLSEALLDRLALNPARLSGIAND 79 899******************************************************************** PP TIGR00407 72 vkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavr 142 v++v++LadPvG+vi+++ ld+GL++er+rvPlGv+gviyearP+v+vdvasLclktGna+iL+Ggke+ r lcl|FitnessBrowser__Koxy:BWI76_RS05835 80 VRQVCSLADPVGQVIDGGLLDSGLRIERRRVPLGVVGVIYEARPNVTVDVASLCLKTGNAAILRGGKETWR 150 *********************************************************************** PP TIGR00407 143 snkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvleha 213 +n+a+v+viq+al+++glp+ +vq+ie pdr+ v e+lk+d+y+d+liPrGg++l+kl++e+stiPv++++ lcl|FitnessBrowser__Koxy:BWI76_RS05835 151 TNAATVKVIQQALQECGLPAATVQAIESPDRALVGEMLKMDKYIDMLIPRGGAGLHKLCREQSTIPVITGG 221 *********************************************************************** PP TIGR00407 214 dGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlk 284 +GvChiy+d+sad+a+a kviv+ak qrPs+Cn++etLLv+++iae+fl++L+kq++e+gv+l+ada+ l lcl|FitnessBrowser__Koxy:BWI76_RS05835 222 IGVCHIYIDHSADVAEALKVIVNAKVQRPSACNSVETLLVHQDIAERFLPALSKQMAESGVSLHADAASLP 292 *********************************************************************** PP TIGR00407 285 llelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaa 355 l+ ++a++ v++e++d+e+lsldL+vk+v d +ea++hir++gt+hsdailt+ na++f++evds+a lcl|FitnessBrowser__Koxy:BWI76_RS05835 293 ALQNGPASVEPVKAEQYDNEYLSLDLNVKVVADQDEAVAHIREHGTQHSDAILTRTLGNANRFINEVDSSA 363 *********************************************************************** PP TIGR00407 356 vyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 vyvnastrf+dG++fG+Gaev++stqklharGP+GLeaL++yk lcl|FitnessBrowser__Koxy:BWI76_RS05835 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYK 406 ******************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (417 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: 12.48 // [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