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_057687245.1 ABB28_RS15340 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_001431535.1:WP_057687245.1 Length = 418 Score = 354 bits (908), Expect = e-102 Identities = 189/415 (45%), Positives = 270/415 (65%), Gaps = 4/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 +E A + A+ +A L + ++ +L+ +A LE+ + IL ANA+D+A AR G+ A Sbjct: 4 IEGQARACRAAATVVAGLDTVQRTALLQSMAAALESHAGQILAANARDLAAARDKGIGSA 63 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 MLDRL L P RL +A +R V L DPVGQV V +G+R+++ RVPLGVI +IYEA Sbjct: 64 MLDRLMLDPPRLFAMAQALRDVAGLPDPVGQVTRDDVRPNGIRVQKVRVPLGVIAMIYEA 123 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVT + A+LCLK GN VILRGG E +N A A + AL + G+P AV + + R Sbjct: 124 RPNVTAEAAALCLKAGNGVILRGGSEAIHSNTAIAAALGSALPAHGVPEAAVTVLTDLRR 183 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 + E+L++ ID+ IPRGG GL + E + +PVI GVCH++VD S +I +A+ + Sbjct: 184 EAMLELLQLHDLIDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLFVDASADIDQAIDL 243 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 +V+ K RPS CN++ETLLV++++A FLP + +A GV L ADA +L L A Sbjct: 244 LVDGKCSRPSACNSLETLLVHRDVAAEFLPRAGQALAARGVELRADALSLPLL----AGS 299 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 A E+Y EFL L + VK+V DL+ AI HIR + + H++ I TRD +A+RF++ + S Sbjct: 300 TAATDEDYAAEFLDLVIAVKVVDDLEAAITHIRRYTSDHTEVIATRDADHAERFIHALQS 359 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 + V VNAS+RF+DGGQ GLG+E+ +ST +LHA GPMGLEALT +++ G+ +R Sbjct: 360 AVVMVNASSRFSDGGQLGLGSEIGISTTRLHAYGPMGLEALTVERFVVRGEGQVR 414 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: 437 Number of extensions: 18 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 WP_057687245.1 ABB28_RS15340 (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.2689281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-140 453.7 0.5 3.1e-140 453.4 0.5 1.0 1 NCBI__GCF_001431535.1:WP_057687245.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001431535.1:WP_057687245.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.4 0.5 3.1e-140 3.1e-140 2 396 .. 12 402 .. 11 404 .. 0.98 Alignments for each domain: == domain 1 score: 453.4 bits; conditional E-value: 3.1e-140 TIGR00407 2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkd 74 + aa+ +a l t ++ +l+ +a +L+ +a ilaana+d+aaa+++G+ a+ldrL L+ +l +a++++d NCBI__GCF_001431535.1:WP_057687245.1 12 RAAATVVAGLDTVQRTALLQSMAAALESHAGQILAANARDLAAARDKGIGSAMLDRLMLDPPRLFAMAQALRD 84 7899999****************************************************************** PP TIGR00407 75 vieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkal 147 v+ L+dPvG+v+ + +G+++++vrvPlGv+ +iyearP+v++++a+Lclk+Gn viL+Gg+ea++sn a+ NCBI__GCF_001431535.1:WP_057687245.1 85 VAGLPDPVGQVTRDDVRPNGIRVQKVRVPLGVIAMIYEARPNVTAEAAALCLKAGNGVILRGGSEAIHSNTAI 157 ************************************************************************* PP TIGR00407 148 veviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChiy 220 ++ + +al g+p av +++d re + ell+l + +dl iPrGg++l++ + e++++Pv++h +GvCh++ NCBI__GCF_001431535.1:WP_057687245.1 158 AAALGSALPAHGVPEAAVTVLTDLRREAMLELLQLHDLIDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLF 230 ************************************************************************* PP TIGR00407 221 ldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekate 293 +d+sad+ +a+ + vd k rPs+Cn++etLLv++++a+efl++ ++l++ gvelradal l ll + NCBI__GCF_001431535.1:WP_057687245.1 231 VDASADIDQAIDLLVDGKCSRPSACNSLETLLVHRDVAAEFLPRAGQALAARGVELRADALSLPLLAGS---- 299 ***************************************************************999887.... PP TIGR00407 294 aevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfad 366 +++++ed+ efl+l+++vk+v+dle+ai hir+y++ h++ i t+d ae+f+++ sa v vnas rf+d NCBI__GCF_001431535.1:WP_057687245.1 300 TAATDEDYAAEFLDLVIAVKVVDDLEAAITHIRRYTSDHTEVIATRDADHAERFIHALQSAVVMVNASSRFSD 372 456789******************************************************************* PP TIGR00407 367 GfrfGfGaevgistqklharGPvGLeaLvs 396 G++ G+G+e+gist +lha GP+GLeaL+ NCBI__GCF_001431535.1:WP_057687245.1 373 GGQLGLGSEIGISTTRLHAYGPMGLEALTV 402 ****************************95 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 14.55 // [ok]
This GapMind analysis is from Jul 25 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