Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate WP_059152892.1 V474_RS18660 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_001046635.1:WP_059152892.1 Length = 429 Score = 344 bits (883), Expect = 3e-99 Identities = 186/407 (45%), Positives = 256/407 (62%), Gaps = 6/407 (1%) Query: 1 MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60 ++EQ+ + A LA++S +K L A L A IL ANAQD+A A GLS Sbjct: 19 LVEQLARDGRAAQRVLARISDADKAGALRAAAKALRAAESEILAANAQDIAAGEAKGLSA 78 Query: 61 AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120 A+LDRL L RL GIAD V QV L DPVG+VI +GL+L R RVP+G+IG+IYE Sbjct: 79 ALLDRLRLDAGRLAGIADAVEQVAALPDPVGEVISADERPNGLKLSRVRVPIGLIGIIYE 138 Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180 +RPNVT D A+LCL++GNAV+LRGG E +N A A + L+S G+PA A+Q + D Sbjct: 139 SRPNVTADAAALCLRSGNAVMLRGGTEALHSNRAIRAALAAGLESVGIPAAAIQLVPTQD 198 Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240 RA+V ML IDM++PRGG L + + +PV+ G+CH YV + + A K Sbjct: 199 RAVVGAMLTAAGLIDMIVPRGGKSLVARVQADARVPVLAHLDGICHTYVHAAADADMARK 258 Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300 + VNAK +R C +ETLL++ +S ++ + E+G + DA A QA ++ Sbjct: 259 LTVNAKLRRTGICGAMETLLLDTQFPES--ASVVGGLIEAGCEVRGDARA----QALDSR 312 Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360 V+ E++D E+L L+V +V LD AI HI H + H+DAI+T D A+RF++EVD Sbjct: 313 VLPASGEDWDTEYLDAVLSVAVVDGLDCAIEHIAAHSSHHTDAIVTDDAEAAERFLDEVD 372 Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKW 407 S+ V VNAS++F DGG+FGLGAE+ ++T +LHARGP+ LE LTTYKW Sbjct: 373 SAIVMVNASSQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYKW 419 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: 447 Number of extensions: 25 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: 429 Length adjustment: 32 Effective length of query: 385 Effective length of database: 397 Effective search space: 152845 Effective search space used: 152845 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 WP_059152892.1 V474_RS18660 (glutamate-5-semialdehyde dehydrogenase)
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.2288663.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-137 442.7 1.7 6.5e-137 442.5 1.7 1.0 1 NCBI__GCF_001046635.1:WP_059152892.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059152892.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.5 1.7 6.5e-137 6.5e-137 2 398 .] 28 418 .. 27 418 .. 0.98 Alignments for each domain: == domain 1 score: 442.5 bits; conditional E-value: 6.5e-137 TIGR00407 2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkd 74 + a la +s a+k al + a++L+a+ ++ilaana+diaa++++Gl+ alldrL L+ ++l +iad+v++ NCBI__GCF_001046635.1:WP_059152892.1 28 RAAQRVLARISDADKAGALRAAAKALRAAESEILAANAQDIAAGEAKGLSAALLDRLRLDAGRLAGIADAVEQ 100 5678899****************************************************************** PP TIGR00407 75 vieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkal 147 v+ L+dPvG+vi+a e+ +GLkl rvrvP+G +g+iye+rP+v++d+a+Lcl++Gnav+L+Gg ea +sn+a+ NCBI__GCF_001046635.1:WP_059152892.1 101 VAALPDPVGEVISADERPNGLKLSRVRVPIGLIGIIYESRPNVTADAAALCLRSGNAVMLRGGTEALHSNRAI 173 ************************************************************************* PP TIGR00407 148 veviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiy 220 + + le+ g+p+ a+ql+ ++dr+ v +l+ +d+++PrGg++lv ++ ++++Pvl h dG+Ch+y NCBI__GCF_001046635.1:WP_059152892.1 174 RAALAAGLESVGIPAAAIQLVPTQDRAVVGAMLTAAGLIDMIVPRGGKSLVARVQADARVPVLAHLDGICHTY 246 ************************************************************************* PP TIGR00407 221 ldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekate 293 + + ad +a+k++v+ak +r C a+etLL++ ++ e+ +++ l e+g e+r+da +++l + NCBI__GCF_001046635.1:WP_059152892.1 247 VHAAADADMARKLTVNAKLRRTGICGAMETLLLDTQFPES--ASVVGGLIEAGCEVRGDARAQALDSRV---- 313 *************************************964..6788999************99987654.... PP TIGR00407 294 aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfad 366 +s ed+d+e+l+ +Lsv +v+ l+ aiehi ++++h+dai+t+d ++ae+f++evdsa v vnas +fad NCBI__GCF_001046635.1:WP_059152892.1 314 LPASGEDWDTEYLDAVLSVAVVDGLDCAIEHIAAHSSHHTDAIVTDDAEAAERFLDEVDSAIVMVNASSQFAD 386 677889******************************************************************* PP TIGR00407 367 GfrfGfGaevgistqklharGPvGLeaLvsyk 398 G++fG+Gae+gi+t +lharGPv Le+L++yk NCBI__GCF_001046635.1:WP_059152892.1 387 GGEFGLGAEIGIATGRLHARGPVALEGLTTYK 418 *******************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (429 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 23.85 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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