Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate GFF618 HP15_601 gamma-glutamyl phosphate reductase
Query= SwissProt::P07004 (417 letters) >FitnessBrowser__Marino:GFF618 Length = 418 Score = 365 bits (936), Expect = e-105 Identities = 189/415 (45%), Positives = 270/415 (65%), Gaps = 4/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 + ++G A+ A+ +A+ ++ +N+ L A+ L+A E + AN +D+ R NGL A Sbjct: 7 MAEVGQQARAAATGVARSTTAVRNQALLATAEALDAAREELALANGKDLQMGRENGLDAA 66 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 MLDRL LTP R+ + + +RQV +L DP+G + D SG+++ + RVPLGVIG+IYE+ Sbjct: 67 MLDRLELTPQRIDTMIEGLRQVASLPDPIGAITDMNYRPSGIQVGKMRVPLGVIGIIYES 126 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVTV+ ASLCLK+GNA ILRGG E+ +N A + L GLP AVQ I DR Sbjct: 127 RPNVTVEAASLCLKSGNATILRGGSESIHSNQAIARCLSAGLAKAGLPENAVQVIKTTDR 186 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 A V E++ M Y+D+++PRGG GL + + +PVI GVCH+Y+D + +ALKV Sbjct: 187 AAVGELITMPDYVDVIVPRGGKGLIERISRDARVPVIKHLDGVCHVYIDSHADPEKALKV 246 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 +NAKT R TCNT+ETLLV+ IA+ LP L++ E GV L A ++ V Sbjct: 247 AINAKTHRYGTCNTMETLLVDAEIAEDILPLLAQAFVEKGVELRGCERTRAIVEG----V 302 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 V +++ E+L+ L V++V L+ AIAHI + +QH+D+I+T + A+RF+ EVDS Sbjct: 303 VEATEADWEAEYLAPVLAVRVVDGLEGAIAHINRYSSQHTDSIITENYTRARRFITEVDS 362 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 S+V VNASTRF DG ++GLGAE+ +ST K+HARGP+GLE LT+ K++ GD IR Sbjct: 363 SSVMVNASTRFADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKYVVFGDGHIR 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: 415 Number of extensions: 10 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 GFF618 HP15_601 (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.9178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-156 507.4 0.7 1.5e-156 507.2 0.7 1.0 1 lcl|FitnessBrowser__Marino:GFF618 HP15_601 gamma-glutamyl phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF618 HP15_601 gamma-glutamyl phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 507.2 0.7 1.5e-156 1.5e-156 1 398 [] 14 407 .. 14 407 .. 0.99 Alignments for each domain: == domain 1 score: 507.2 bits; conditional E-value: 1.5e-156 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvi 76 a+ aa+ +a +ta +n+al + a++L a+ e++ an kd++ ++enGl a+ldrL+Lt +++ ++++++++v+ lcl|FitnessBrowser__Marino:GFF618 14 ARAAATGVARSTTAVRNQALLATAEALDAAREELALANGKDLQMGRENGLDAAMLDRLELTPQRIDTMIEGLRQVA 89 799************************************************************************* PP TIGR00407 77 eLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviq 152 +L+dP+G +++ + + +G+++ ++rvPlGv+g+iye+rP+v+v++asLclk+Gna iL+Gg+e+++sn+a+++ + lcl|FitnessBrowser__Marino:GFF618 90 SLPDPIGAITDMNYRPSGIQVGKMRVPLGVIGIIYESRPNVTVEAASLCLKSGNATILRGGSESIHSNQAIARCLS 165 **************************************************************************** PP TIGR00407 153 daleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228 l+++glp +avq+i+++dr+ v el+++ +yvd+++PrGg++l++ i +++++Pv++h dGvCh+y+d +ad + lcl|FitnessBrowser__Marino:GFF618 166 AGLAKAGLPENAVQVIKTTDRAAVGELITMPDYVDVIVPRGGKGLIERISRDARVPVIKHLDGVCHVYIDSHADPE 241 **************************************************************************** PP TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekateaevskedfdke 304 ka kv ++akt+r tCn++etLLv+ +iae+ l+ L+++ ekgvelr+ + + +++e +e+++ d++ e lcl|FitnessBrowser__Marino:GFF618 242 KALKVAINAKTHRYGTCNTMETLLVDAEIAEDILPLLAQAFVEKGVELRGCERTRAIVEGV----VEATEADWEAE 313 *****************************************************99998865....788999***** PP TIGR00407 305 flsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGaevgist 380 +l+++L+v++v+ le ai+hi++y+++h+d+i+te+ + a++f++evds++v vnastrfadGf++G+Gae+gist lcl|FitnessBrowser__Marino:GFF618 314 YLAPVLAVRVVDGLEGAIAHINRYSSQHTDSIITENYTRARRFITEVDSSSVMVNASTRFADGFEYGLGAEIGIST 389 **************************************************************************** PP TIGR00407 381 qklharGPvGLeaLvsyk 398 +k+harGPvGLe+L+s k lcl|FitnessBrowser__Marino:GFF618 390 DKIHARGPVGLEGLTSQK 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.22 // [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