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_038203754.1 Q392_RS07075 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000745855.1:WP_038203754.1 Length = 427 Score = 360 bits (923), Expect = e-104 Identities = 189/418 (45%), Positives = 271/418 (64%), Gaps = 2/418 (0%) Query: 2 LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61 ++ +G+ AK AS ++A+ + KN L +A L + ANAQD+A A A GL Sbjct: 10 MQALGLQAKTASAQMARADAATKNVALRALARRLREAGPALAEANAQDLARAEAAGLPAP 69 Query: 62 MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121 M DRL LTP ++ +A Q+ + D +G+VI +SG+R+ + RVP+GV G+IYE+ Sbjct: 70 MQDRLRLTPKVIETVALGCEQLAAMPDVIGEVIGMKQQESGIRVGQMRVPIGVFGMIYES 129 Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181 RPNVT++ ASL +K+GNA ILRGG E +N A A+++ AL GLP AVQ + DR Sbjct: 130 RPNVTIEAASLAIKSGNAAILRGGSEAIDSNKALAALVRAALAEAGLPEDAVQLVQTTDR 189 Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241 V ++ M +++D++IPRGG GL + + +PVI G CH+YVD++ ++ A+KV Sbjct: 190 EAVGHLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHVYVDDTADLDMAVKV 249 Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHAD--AAALAQLQAGPA 299 NAKTQ+ S CN E LLV + +A FLP + A GV + D AAAL Q AG Sbjct: 250 ADNAKTQKYSPCNAAEGLLVARAVAAQFLPRIGAVFAAKGVEMRCDGEAAALLQGLAGQP 309 Query: 300 KVVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEV 359 KVV +++ +E+L+ +++K+V+ LD+AI HI + + H+DAILTRD NAQRF+ EV Sbjct: 310 KVVPATEQDWSEEYLAPIISIKVVAGLDEAIDHINRYSSHHTDAILTRDHVNAQRFLREV 369 Query: 360 DSSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417 DS++V VNASTRF DG ++GLGAE+ +ST K HARGP+G+E LT+ K+I +G IRA Sbjct: 370 DSASVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLKYIVLGQGEIRA 427 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: 431 Number of extensions: 12 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_038203754.1 Q392_RS07075 (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.2735878.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-150 485.2 1.0 7.8e-150 485.0 1.0 1.0 1 NCBI__GCF_000745855.1:WP_038203754.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038203754.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.0 1.0 7.8e-150 7.8e-150 1 398 [] 17 416 .. 17 416 .. 0.98 Alignments for each domain: == domain 1 score: 485.0 bits; conditional E-value: 7.8e-150 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvk 73 ak a++++a +a kn al ++a L+++ +++ +ana+d+a a++ Gl ++ drL Lt + ++++a + + NCBI__GCF_000745855.1:WP_038203754.1 17 AKTASAQMARADAATKNVALRALARRLREAGPALAEANAQDLARAEAAGLPAPMQDRLRLTPKVIETVALGCE 89 899********************************************************************** PP TIGR00407 74 dvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnka 146 +++ ++d +G+vi ++ ++G+++ ++rvP+Gv g+iye+rP+v++++asL++k+Gna+iL+Gg+ea+ snka NCBI__GCF_000745855.1:WP_038203754.1 90 QLAAMPDVIGEVIGMKQQESGIRVGQMRVPIGVFGMIYESRPNVTIEAASLAIKSGNAAILRGGSEAIDSNKA 162 ************************************************************************* PP TIGR00407 147 lveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiPvlehadGvChi 219 l+++++ al+++glp avql++++dre v +l+ + ++vd++iPrGg++l++ i +++++Pv++h dG+Ch+ NCBI__GCF_000745855.1:WP_038203754.1 163 LAALVRAALAEAGLPEDAVQLVQTTDREAVGHLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHV 235 ************************************************************************* PP TIGR00407 220 yldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelradalvlklle..lek 290 y+d++adl +a kv ++aktq+ s Cna e LLv +a+a++fl+++ ++kgve+r d + +ll+ +++ NCBI__GCF_000745855.1:WP_038203754.1 236 YVDDTADLDMAVKVADNAKTQKYSPCNAAEGLLVARAVAAQFLPRIGAVFAAKGVEMRCDGEAAALLQglAGQ 308 ***********************************************************98888887744678 PP TIGR00407 291 ateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastr 363 +++ ++++d+ +e+l++++s+k+v l+eai+hi++y+++h+dailt+d+ na++f++evdsa+v vnastr NCBI__GCF_000745855.1:WP_038203754.1 309 PKVVPATEQDWSEEYLAPIISIKVVAGLDEAIDHINRYSSHHTDAILTRDHVNAQRFLREVDSASVMVNASTR 381 89999******************************************************************** PP TIGR00407 364 fadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 fadGf++G+Gae+gist+k+harGPvG+e+L+s k NCBI__GCF_000745855.1:WP_038203754.1 382 FADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLK 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: 28.91 // [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