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_011443723.1 SARO_RS00300 gamma-glutamyl-phosphate reductase
Query= SwissProt::P07004 (417 letters) >NCBI__GCF_000013325.1:WP_011443723.1 Length = 425 Score = 337 bits (864), Expect = 4e-97 Identities = 184/408 (45%), Positives = 253/408 (62%), Gaps = 6/408 (1%) Query: 1 MLEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSE 60 ++E + AA+ A +LA++ S K R L A L A IL ANAQD+A+ ANGLS Sbjct: 15 LVEGLARAARSAQRQLARMDSPVKERALTLAAAALRAAEAEILAANAQDMANGAANGLSS 74 Query: 61 AMLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYE 120 AMLDRL LTP RL GIAD V QV LADPVG+VI +G+ L+R R+P+GVIG+IYE Sbjct: 75 AMLDRLKLTPERLAGIADAVAQVAGLADPVGEVISEAARPNGMVLQRVRIPVGVIGIIYE 134 Query: 121 ARPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPD 180 +RPNVT D A+LC+++GNA ILRGG E +N A + L G+PA AVQ + D Sbjct: 135 SRPNVTADAAALCVRSGNAAILRGGSEAVHSNRAIHKALVAGLAEGGVPAEAVQLVPTQD 194 Query: 181 RALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALK 240 RA V ML IDM++PRGG L + + +PV+ G+ H +V S + A A Sbjct: 195 RAAVGAMLGAAGLIDMIVPRGGKSLVARVQADARVPVLAHLDGINHTFVHASADPAMAQA 254 Query: 241 VIVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAK 300 +++NAK +R C +ETLL++ D L + + ++G L DA A +A + Sbjct: 255 IVLNAKMRRTGVCGAMETLLIDATYPDPH--GLVEPLLDAGCELRGDARA----RAIDPR 308 Query: 301 VVAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVD 360 + ++D E+L L+V +V LD+A+AHI H + H+DAI+ D A RF+ EVD Sbjct: 309 IAPAADNDWDTEYLEAILSVAVVDGLDEALAHIARHASGHTDAIVAADQDVADRFLAEVD 368 Query: 361 SSAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 408 S+ V NAS++F DGG+FGLGAE+ ++T +LHARGP+ LE LTTYKW+ Sbjct: 369 SAIVMHNASSQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYKWL 416 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: 466 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: 425 Length adjustment: 32 Effective length of query: 385 Effective length of database: 393 Effective search space: 151305 Effective search space used: 151305 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_011443723.1 SARO_RS00300 (gamma-glutamyl-phosphate reductase)
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.4506.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-135 437.5 1.0 2.5e-135 437.3 1.0 1.0 1 lcl|NCBI__GCF_000013325.1:WP_011443723.1 SARO_RS00300 gamma-glutamyl-phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_011443723.1 SARO_RS00300 gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.3 1.0 2.5e-135 2.5e-135 1 398 [] 23 414 .. 23 414 .. 0.98 Alignments for each domain: == domain 1 score: 437.3 bits; conditional E-value: 2.5e-135 TIGR00407 1 akeaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksia 69 a+ a +la + + k++al++ a +L+a+ +ilaana+d+a++ +nGl+ a+ldrL+Lt e+l +ia lcl|NCBI__GCF_000013325.1:WP_011443723.1 23 ARSAQRQLARMDSPVKERALTLAAAALRAAEAEILAANAQDMANGAANGLSSAMLDRLKLTPERLAGIA 91 7999***************************************************************** PP TIGR00407 70 ddvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgk 138 d+v +v+ LadPvG+vi++ + +G++l+rvr+P+Gv+g+iye+rP+v++d+a+Lc+++Gna+iL+Gg+ lcl|NCBI__GCF_000013325.1:WP_011443723.1 92 DAVAQVAGLADPVGEVISEAARPNGMVLQRVRIPVGVIGIIYESRPNVTADAAALCVRSGNAAILRGGS 160 ********************************************************************* PP TIGR00407 139 eavrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeesti 207 eav+sn+a+ + + l++ g+p+eavql+ ++dr+ v +l +d+++PrGg++lv ++ ++++ lcl|NCBI__GCF_000013325.1:WP_011443723.1 161 EAVHSNRAIHKALVAGLAEGGVPAEAVQLVPTQDRAAVGAMLGAAGLIDMIVPRGGKSLVARVQADARV 229 ********************************************************************* PP TIGR00407 208 PvlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvel 276 Pvl h dG+ h+++ +sad a+a+ ++++ak +r +C a+etLL++ ++ + + L++ l ++g el lcl|NCBI__GCF_000013325.1:WP_011443723.1 230 PVLAHLDGINHTFVHASADPAMAQAIVLNAKMRRTGVCGAMETLLIDATYPDPH--GLVEPLLDAGCEL 296 ***************************************************887..599********** PP TIGR00407 277 radalvlkllelekateaevskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknae 345 r+da + ++ + a ++++d+d+e+l+ +Lsv +v+ l+ea++hi ++++ h+dai++ d+ a+ lcl|NCBI__GCF_000013325.1:WP_011443723.1 297 RGDARARAIDPRI----APAADNDWDTEYLEAILSVAVVDGLDEALAHIARHASGHTDAIVAADQDVAD 361 ******9998876....566789********************************************** PP TIGR00407 346 kfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 +f+ evdsa v +nas +fadG++fG+Gae+gi+t +lharGPv Le+L++yk lcl|NCBI__GCF_000013325.1:WP_011443723.1 362 RFLAEVDSAIVMHNASSQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYK 414 ****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (425 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: 12.60 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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