Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_012502796.1 CPAR_RS07940 gamma-glutamyl-phosphate reductase
Query= BRENDA::A7Y114 (420 letters) >NCBI__GCF_000020505.1:WP_012502796.1 Length = 420 Score = 312 bits (799), Expect = 1e-89 Identities = 180/409 (44%), Positives = 248/409 (60%), Gaps = 11/409 (2%) Query: 18 KKASKSLMILSDKEKNDALHHIADVLERDFEAILAANEKDLRNGREQGFTEAFMDRLSLS 77 + AS+ ++ L + N L+ +AD + E IL AN KDL + DRL L+ Sbjct: 15 QNASRKIVTLDEDAINALLNDLADRIPDAAETILEANRKDLER---MDPADPRYDRLLLN 71 Query: 78 QERIRDFAQGLRDVAELEDPTGKKLSDWTLENGLQVEKVTVPLGVIGMIYEARPNVTVDA 137 + R+ A LR+VA L P + L + TL NGL++ KV+VPLGVIG+IYE+RPNVT D Sbjct: 72 ESRLNSIASDLRNVAALPSPLDRVLEERTLPNGLELRKVSVPLGVIGIIYESRPNVTFDV 131 Query: 138 TGLALKSGNAIVLKGGSSAINSNQAIVEVIHKALAETKIPQESVQFIASTDRAATNQLFT 197 L LKSGNA VLKGGS A SN AIVE+I + + + E + ++ +R A + L Sbjct: 132 FALCLKSGNATVLKGGSDAAFSNIAIVELIQTVIRDRGLDPEMI-YLLPAEREAAHILLN 190 Query: 198 MKEHVDVLIPRGGGKLIQAVVENATVPVLETGVGNCHIYIDKDADVEKAISILVNAKTDR 257 ++DV+IPRG LI +++TVPV+ETG G H Y D+ D+ I+ NAKT R Sbjct: 191 AVGYIDVIIPRGSQALIDFARKHSTVPVIETGAGIVHTYFDESGDLAMGRDIIFNAKTRR 250 Query: 258 PAVCNAAETLIVHKDWLAQHSDELISALKKENIHVHGDE----HVLTIIPDAVP--AGED 311 P+VCNA +TLIVHK + L+ L+++ + + DE +L PD + A + Sbjct: 251 PSVCNALDTLIVHKSRI-DDLPVLVEQLEEKLVQIFADEPAYYKLLNRYPDELLQIATPE 309 Query: 312 DWKNEYLSTDIAVKAVDDLVDAIAHIETYGTKHSEAIVTENQEAADKFLAIVDAAAIYHN 371 ++ EYLS +++K V+ +A+ HI + +KHSEAIV +Q D F+ VDAAA+Y N Sbjct: 310 NFGTEYLSLKMSIKTVETFEEALDHIAHHSSKHSEAIVASDQATIDAFMKRVDAAAVYAN 369 Query: 372 ASTRFTDGGALGFGAEIGISTQKLHARGPMGLPALTTVKFLMKGTGQIR 420 ST FTDG G GAEIGISTQKLHARGPM L L T K+L++G GQ+R Sbjct: 370 TSTAFTDGAQFGLGAEIGISTQKLHARGPMALKELCTYKWLIEGQGQVR 418 Lambda K H 0.315 0.131 0.365 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: 472 Number of extensions: 30 Number of successful extensions: 4 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: 420 Length of database: 420 Length adjustment: 32 Effective length of query: 388 Effective length of database: 388 Effective search space: 150544 Effective search space used: 150544 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: 42 (22.0 bits) S2: 50 (23.9 bits)
Align candidate WP_012502796.1 CPAR_RS07940 (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.8100.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-131 422.9 0.0 6.7e-131 422.7 0.0 1.0 1 lcl|NCBI__GCF_000020505.1:WP_012502796.1 CPAR_RS07940 gamma-glutamyl-phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012502796.1 CPAR_RS07940 gamma-glutamyl-phosphate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.7 0.0 6.7e-131 6.7e-131 2 398 .] 15 408 .. 14 408 .. 0.96 Alignments for each domain: == domain 1 score: 422.7 bits; conditional E-value: 6.7e-131 TIGR00407 2 keaalklaqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiad 70 ++a+ k+ +l ++ n +l+ +ad + +ae+il+an+kd++ + ad+ +drLlL+e++l+sia lcl|NCBI__GCF_000020505.1:WP_012502796.1 15 QNASRKIVTLDEDAINALLNDLADRIPDAAETILEANRKDLER---MDPADPRYDRLLLNESRLNSIAS 80 57999999********************************975...6679******************* PP TIGR00407 71 dvkdvieLadPvGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgke 139 d+++v+ L+ P+ +v+e+r+l +GL l++v+vPlGv+g+iye+rP+v+ dv +Lclk+Gna +LkGg++ lcl|NCBI__GCF_000020505.1:WP_012502796.1 81 DLRNVAALPSPLDRVLEERTLPNGLELRKVSVPLGVIGIIYESRPNVTFDVFALCLKSGNATVLKGGSD 149 ********************************************************************* PP TIGR00407 140 avrsnkalveviqdaleqtglpveavqliedpdreevkellkldeyvdlliPrGgnelvklikeestiP 208 a +sn a+ve+iq+ +++ gl e + l+ +re ++ ll+ y+d++iPrG+++l++ +++st+P lcl|NCBI__GCF_000020505.1:WP_012502796.1 150 AAFSNIAIVELIQTVIRDRGLDPEMIYLLPA-EREAAHILLNAVGYIDVIIPRGSQALIDFARKHSTVP 217 *****************************98.9************************************ PP TIGR00407 209 vlehadGvChiyldesadlakakkvivdaktqrPstCnaietLLvnkaiaeefleeLekqleekgvelr 277 v+e+++G+ h+y des dla+ + +i +akt+rPs+Cna++tL+v+k+ + l++L++qleek v++ lcl|NCBI__GCF_000020505.1:WP_012502796.1 218 VIETGAGIVHTYFDESGDLAMGRDIIFNAKTRRPSVCNALDTLIVHKSRI-DDLPVLVEQLEEKLVQIF 285 ***********************************************998.669*************** PP TIGR00407 278 adalv.lkllelekateae.vskedfdkeflsldLsvkivedleeaiehirqygtkhsdailtedkkna 344 ad+ + kll+ + + + ++ e+f +e+lsl++s+k+ve eea++hi ++++khs+ai+++d+++ lcl|NCBI__GCF_000020505.1:WP_012502796.1 286 ADEPAyYKLLNRYPDELLQiATPENFGTEYLSLKMSIKTVETFEEALDHIAHHSSKHSEAIVASDQATI 354 *875425777776665544155689******************************************** PP TIGR00407 345 ekfvkevdsaavyvnastrfadGfrfGfGaevgistqklharGPvGLeaLvsyk 398 + f+k+vd+aavy n+st f+dG +fG+Gae+gistqklharGP+ L+ L +yk lcl|NCBI__GCF_000020505.1:WP_012502796.1 355 DAFMKRVDAAAVYANTSTAFTDGAQFGLGAEIGISTQKLHARGPMALKELCTYK 408 *****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (398 nodes) Target sequences: 1 (420 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: 00:00:00.02 # Mc/sec: 7.67 // [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