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_029133656.1 A3GO_RS0112365 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000428045.1:WP_029133656.1 Length = 423 Score = 368 bits (945), Expect = e-106 Identities = 187/415 (45%), Positives = 270/415 (65%), Gaps = 4/415 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 + +G A+ AS +LA S+ KN L+ IA +++A E +++ N +D+ A GL A Sbjct: 12 MADLGRRARAASRRLAAASTASKNAALQAIAADIQANREALMSENRRDLEAGAAKGLDSA 71 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 +LDRL LTPAR+ + + ++Q+ LADP+G++ D SG+++ R RVPLGV+G+IYE+ Sbjct: 72 LLDRLELTPARIDSMIEGIQQIIALADPIGEIFDMNYRPSGIQVGRMRVPLGVVGIIYES 131 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVT D A+LCLK+GNA +LRGG E +N A A IQ L+ GLP +VQ + DR Sbjct: 132 RPNVTADAAALCLKSGNATVLRGGSEAFHSNQAIAASIQRGLEQAGLPGDSVQVVATTDR 191 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 A V M+ M + ID++IPRGG GL + + + +PVI G+CH+Y+D+ + A+A + Sbjct: 192 AAVGAMITMPEAIDVIIPRGGKGLIERIAKDARVPVIKHLDGICHVYIDDQADTAKAFDI 251 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301 +NAKTQR TCNT+ETLLV IA+ LP L+ E V L A L+ + Sbjct: 252 AINAKTQRYGTCNTMETLLVADAIAEDVLPMLAAAYTEQAVELRGCARCREILE----EC 307 Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361 ++D E+L L++++V DLD+AI HI H + H+++I+T + A+RF+ EVDS Sbjct: 308 NEATDSDWDTEYLGPILSIRVVRDLDEAIEHINTHSSGHTESIVTENYTRARRFLTEVDS 367 Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 S+V VNASTRF DG ++GLGAE+ +ST K HARGP+GLE LT+ K+I +GD IR Sbjct: 368 SSVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSVKYIVLGDGHIR 422 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: 417 Number of extensions: 16 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: 423 Length adjustment: 32 Effective length of query: 385 Effective length of database: 391 Effective search space: 150535 Effective search space used: 150535 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_029133656.1 A3GO_RS0112365 (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.3692482.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-155 502.3 1.0 5.2e-155 502.1 1.0 1.0 1 NCBI__GCF_000428045.1:WP_029133656.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000428045.1:WP_029133656.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.1 1.0 5.2e-155 5.2e-155 1 398 [] 19 412 .. 19 412 .. 0.99 Alignments for each domain: == domain 1 score: 502.1 bits; conditional E-value: 5.2e-155 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 a+ a+ +la sta kn al++ia +++a+ e+++ +n++d++a+ ++Gl alldrL+Lt +++ s++++++ NCBI__GCF_000428045.1:WP_029133656.1 19 ARAASRRLAAASTASKNAALQAIAADIQANREALMSENRRDLEAGAAKGLDSALLDRLELTPARIDSMIEGIQ 91 899********************************************************************** PP TIGR00407 74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146 ++i LadP+G++ + + + +G+++ r+rvPlGv+g+iye+rP+v++d+a+Lclk+Gna +L+Gg+ea +sn+a NCBI__GCF_000428045.1:WP_029133656.1 92 QIIALADPIGEIFDMNYRPSGIQVGRMRVPLGVVGIIYESRPNVTADAAALCLKSGNATVLRGGSEAFHSNQA 164 ************************************************************************* PP TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219 +++ iq+ leq+glp +vq++ ++dr+ v ++++ e +d++iPrGg++l++ i +++++Pv++h dG+Ch+ NCBI__GCF_000428045.1:WP_029133656.1 165 IAASIQRGLEQAGLPGDSVQVVATTDRAAVGAMITMPEAIDVIIPRGGKGLIERIAKDARVPVIKHLDGICHV 237 ************************************************************************* PP TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekat 292 y+d++ad+aka + ++aktqr tCn++etLLv aiae+ l+ L+ + +e+ velr+ a ++le + NCBI__GCF_000428045.1:WP_029133656.1 238 YIDDQADTAKAFDIAINAKTQRYGTCNTMETLLVADAIAEDVLPMLAAAYTEQAVELRGCARCREILEEC--N 308 **************************************************************99998866..4 PP TIGR00407 293 eaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfa 365 e +++ d+d+e+l ++Ls+++v dl+eaiehi+++++ h+++i+te+ + a++f++evds++v vnastrfa NCBI__GCF_000428045.1:WP_029133656.1 309 E--ATDSDWDTEYLGPILSIRVVRDLDEAIEHINTHSSGHTESIVTENYTRARRFLTEVDSSSVMVNASTRFA 379 4..5667****************************************************************** PP TIGR00407 366 dGfrfGfGaevgistqklharGPvGLeaLvsyk 398 dGf++G+Gae+gist+k+harGPvGLe+L+s k NCBI__GCF_000428045.1:WP_029133656.1 380 DGFEYGLGAEIGISTDKFHARGPVGLEGLTSVK 412 ******************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (423 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: 16.35 // [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