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_026186090.1 THITHI_RS0105635 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000378965.1:WP_026186090.1 Length = 427 Score = 375 bits (963), Expect = e-108 Identities = 196/413 (47%), Positives = 275/413 (66%), Gaps = 4/413 (0%) Query: 4 QMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAML 63 +MG A+ AS LA+ + K+ L +A+ +EA++ ++ N +D+ + NGL +A+L Sbjct: 18 EMGRRARAASRALARAETGVKDAALLGMAEIIEARAAALMAENRKDLEAGQQNGLDDALL 77 Query: 64 DRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARP 123 DRLA TP R+ +A+ +RQ+ LADPVG + D SG+++ R RVPLGVIG+IYE+RP Sbjct: 78 DRLAFTPERIAVMAEGLRQIAALADPVGAISDLNYRPSGIQVGRMRVPLGVIGIIYESRP 137 Query: 124 NVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRAL 183 NVTVD A LCLK+GNA ILRGG E +N A I+D L+ GLP AVQ + DRA Sbjct: 138 NVTVDAAGLCLKSGNACILRGGSEAFHSNGALADCIRDGLERAGLPMDAVQVVATTDRAA 197 Query: 184 VSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIV 243 V +LR+ +D+++PRGG GL E+S IPVI GVCH+YVD+ + +A++V V Sbjct: 198 VGALLRLKDSVDVIVPRGGKGLIARVSEESLIPVIKHLDGVCHVYVDDGADPDKAVRVAV 257 Query: 244 NAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVA 303 NAKTQR TCNT+ETLLV++ +A+ LP L A+ GV L A+ A L + Sbjct: 258 NAKTQRYGTCNTMETLLVSRGVAERILPRLGDAFADKGVELRGCEASRAILSG----IKE 313 Query: 304 VKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSA 363 +++ +E+L+ L V++V LD AI HI +G+ H+D+I+T D A+RF+ EVDSS+ Sbjct: 314 ATEQDWSEEYLAPVLAVRVVDGLDAAIEHINTYGSHHTDSIVTEDYTRARRFLREVDSSS 373 Query: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIR 416 V VNASTRF DG ++GLGAE+ +ST KLHARGP+GLE LTT K++ +GD +R Sbjct: 374 VMVNASTRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTLKYVVLGDGHVR 426 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: 457 Number of extensions: 19 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: 427 Length adjustment: 32 Effective length of query: 385 Effective length of database: 395 Effective search space: 152075 Effective search space used: 152075 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_026186090.1 THITHI_RS0105635 (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.2392494.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-153 496.6 0.1 2.7e-153 496.4 0.1 1.0 1 NCBI__GCF_000378965.1:WP_026186090.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000378965.1:WP_026186090.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 496.4 0.1 2.7e-153 2.7e-153 1 398 [] 23 416 .. 23 416 .. 0.98 Alignments for each domain: == domain 1 score: 496.4 bits; conditional E-value: 2.7e-153 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 a+ a+ la t k+ al +a+ ++a+a +++a+n+kd++a+++nGl dalldrL++t e++ ++a++++ NCBI__GCF_000378965.1:WP_026186090.1 23 ARAASRALARAETGVKDAALLGMAEIIEARAAALMAENRKDLEAGQQNGLDDALLDRLAFTPERIAVMAEGLR 95 799********************************************************************** PP TIGR00407 74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146 +++ LadPvG + + + + +G+++ r+rvPlGv+g+iye+rP+v+vd+a Lclk+Gna iL+Gg+ea +sn a NCBI__GCF_000378965.1:WP_026186090.1 96 QIAALADPVGAISDLNYRPSGIQVGRMRVPLGVIGIIYESRPNVTVDAAGLCLKSGNACILRGGSEAFHSNGA 168 ************************************************************************* PP TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219 l++ i+d le++glp+ avq++ ++dr+ v ll+l + vd+++PrGg++l+ + ees iPv++h dGvCh+ NCBI__GCF_000378965.1:WP_026186090.1 169 LADCIRDGLERAGLPMDAVQVVATTDRAAVGALLRLKDSVDVIVPRGGKGLIARVSEESLIPVIKHLDGVCHV 241 ************************************************************************* PP TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlkllelekat 292 y+d+ ad ka +v v+aktqr tCn++etLLv + +ae+ l++L ++ ++kgvelr+ ++ ++l+ ++ NCBI__GCF_000378965.1:WP_026186090.1 242 YVDDGADPDKAVRVAVNAKTQRYGTCNTMETLLVSRGVAERILPRLGDAFADKGVELRGCEASRAILSG--IK 312 ***********************************************************9999988764..45 PP TIGR00407 293 eaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfa 365 e ++++d+ +e+l+++L+v++v+ l++aiehi++yg++h+d+i+ted + a++f++evds++v vnastrfa NCBI__GCF_000378965.1:WP_026186090.1 313 E--ATEQDWSEEYLAPVLAVRVVDGLDAAIEHINTYGSHHTDSIVTEDYTRARRFLREVDSSSVMVNASTRFA 383 5..6778****************************************************************** PP TIGR00407 366 dGfrfGfGaevgistqklharGPvGLeaLvsyk 398 dGf++G+Gae+gist+klharGPvGLe+L++ k NCBI__GCF_000378965.1:WP_026186090.1 384 DGFEYGLGAEIGISTDKLHARGPVGLEGLTTLK 416 ******************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (427 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: 00:00:00.00 # Mc/sec: 28.05 // [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