Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 207423 DVU1953 gamma-glutamyl phosphate reductase
Query= SwissProt::P07004 (417 letters) >MicrobesOnline__882:207423 Length = 419 Score = 354 bits (909), Expect = e-102 Identities = 189/415 (45%), Positives = 268/415 (64%), Gaps = 3/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 +E MG A+ A +LA S K L+ +A LE + + IL ANA D+A A G+ Sbjct: 7 IEDMGRRARAAGRRLAAASPAAKAGALDHLATLLEQRQDAILAANAADLAAAAEAGMDAP 66 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 +DRL LTPA + +A R V L DPVG + +GL + + R+PLGVI +IYE+ Sbjct: 67 RMDRLRLTPATIAEMAAACRHVAALPDPVGAIETQWQRPNGLLVGKMRIPLGVIAMIYES 126 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVT+D A LCLK GNAVILRGG E +N A A+I +AL S GLPA AVQ + DR Sbjct: 127 RPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAALITEALSSVGLPAEAVQVVSTTDR 186 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 A+++E+ +++++ID++IPRGG L + + + +PV+ GVCH Y+D ++A+A+++ Sbjct: 187 AVIAELCKLEEHIDVIIPRGGETLIRAVVDMARMPVLKHYKGVCHAYIDSGADLAQAVEI 246 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 I NAK QRP CN +E LLV+++ A +FLPA+++++ GV A A+L L Sbjct: 247 IHNAKVQRPGVCNALEGLLVHRDEAAAFLPAIAERLGNDGVEFRACPASLPLL---GDSA 303 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 + +K E+ EF L L V+IV D+D+A+AHI +G+ H++ I TRD NA RF+ E D+ Sbjct: 304 IPMKDEDNGQEFHDLILLVRIVDDMDEALAHIAAYGSNHTEIICTRDHGNAMRFLREADA 363 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 S V VNAS+RF DGGQ GLGAE+ +ST KLH+ GPMG++ LTT K++ G IR Sbjct: 364 SMVAVNASSRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELTTTKFVVFGAGQIR 418 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: 440 Number of extensions: 14 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: 419 Length adjustment: 32 Effective length of query: 385 Effective length of database: 387 Effective search space: 148995 Effective search space used: 148995 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 207423 DVU1953 (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.28331.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-137 442.6 0.4 6.6e-137 442.5 0.4 1.0 1 lcl|MicrobesOnline__882:207423 DVU1953 gamma-glutamyl phosphate Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207423 DVU1953 gamma-glutamyl phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.5 0.4 6.6e-137 6.6e-137 1 398 [] 14 408 .. 14 408 .. 0.99 Alignments for each domain: == domain 1 score: 442.5 bits; conditional E-value: 6.6e-137 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieLa 79 a+ a+ +la s a k al +a L+++ ++ilaana d+aaa e G+ + +drL Lt + + ++a++ ++v+ L+ lcl|MicrobesOnline__882:207423 14 ARAAGRRLAAASPAAKAGALDHLATLLEQRQDAILAANAADLAAAAEAGMDAPRMDRLRLTPATIAEMAAACRHVAALP 92 899**************************************************************************** PP TIGR00407 80 dPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdaleqt 158 dPvG + ++ ++ +GL + ++r+PlGv+ +iye+rP+v++d a Lclk+GnaviL+Gg+ea++sn al+++i +al + lcl|MicrobesOnline__882:207423 93 DPVGAIETQWQRPNGLLVGKMRIPLGVIAMIYESRPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAALITEALSSV 171 ******************************************************************************* PP TIGR00407 159 glpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadlakakkvivda 237 glp+eavq++ ++dr+ + el kl+e +d++iPrGg+ l++ + + +++Pvl+h +GvCh y+d adla+a ++i +a lcl|MicrobesOnline__882:207423 172 GLPAEAVQVVSTTDRAVIAELCKLEEHIDVIIPRGGETLIRAVVDMARMPVLKHYKGVCHAYIDSGADLAQAVEIIHNA 250 ******************************************************************************* PP TIGR00407 238 ktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdkeflsldLsvkive 316 k qrP +Cna+e LLv+++ a+ fl++++++l + gve+ra + l ll + + +++ed +ef +l+L v+iv+ lcl|MicrobesOnline__882:207423 251 KVQRPGVCNALEGLLVHRDEAAAFLPAIAERLGNDGVEFRACPASLPLLGDS---AIPMKDEDNGQEFHDLILLVRIVD 326 *****************************************99999988877...456788999*************** PP TIGR00407 317 dleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLv 395 d++ea++hi yg++h++ i t+d+ na +f++e d++ v vnas rf dG++ G+Gae+gist+klh+ GP+G++ L+ lcl|MicrobesOnline__882:207423 327 DMDEALAHIAAYGSNHTEIICTRDHGNAMRFLREADASMVAVNASSRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELT 405 ******************************************************************************* PP TIGR00407 396 syk 398 ++k lcl|MicrobesOnline__882:207423 406 TTK 408 997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (419 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.08 // [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