Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate GFF1428 Psest_1465 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::G3XD76 (344 letters) >FitnessBrowser__psRCH2:GFF1428 Length = 344 Score = 587 bits (1514), Expect = e-172 Identities = 298/344 (86%), Positives = 318/344 (92%) Query: 1 MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60 MS +LFSLAFGVGTQNRQ WLEVFYA PLLKP+ E+VAAVAP+LGYA GNQA+T T+ Q Sbjct: 1 MSATLFSLAFGVGTQNRQGDWLEVFYAQPLLKPAGELVAAVAPLLGYAGGNQAITITTSQ 60 Query: 61 AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120 A QLADALK +DA Q ALL+RLAESQ+PLVATLLAEDA SST EAYLKLHLLSHRL KP Sbjct: 61 AAQLADALKPLDATQYALLTRLAESQRPLVATLLAEDAPLSSTPEAYLKLHLLSHRLAKP 120 Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180 H +NL+GIFPLLPNVAWTN GAVDL ELAE QLEARLKG LLEVFSVDKFPKMTDYVVPA Sbjct: 121 HGLNLTGIFPLLPNVAWTNQGAVDLGELAERQLEARLKGDLLEVFSVDKFPKMTDYVVPA 180 Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240 GVRIADTARVRLGAY+GEGTTVMHEGF+NFNAGT+GPGMIEGRVSAGVFVGKGSDLGGGC Sbjct: 181 GVRIADTARVRLGAYVGEGTTVMHEGFINFNAGTQGPGMIEGRVSAGVFVGKGSDLGGGC 240 Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRN VE+GLYITAGTKV+LLDE + LV Sbjct: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNTVESGLYITAGTKVSLLDENDQLV 300 Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344 KVVKAR+LAGQ DLLFRRNSQ GAVECKT+K+AIELNEALHAHN Sbjct: 301 KVVKARELAGQSDLLFRRNSQTGAVECKTHKSAIELNEALHAHN 344 Lambda K H 0.317 0.134 0.380 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: 473 Number of extensions: 17 Number of successful extensions: 1 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: 344 Length of database: 344 Length adjustment: 29 Effective length of query: 315 Effective length of database: 315 Effective search space: 99225 Effective search space used: 99225 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate GFF1428 Psest_1465 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR03536 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))
# 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/TIGR03536.hmm # target sequence database: /tmp/gapView.12667.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03536 [M=341] Accession: TIGR03536 Description: DapD_gpp: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-191 622.0 0.4 1.2e-191 621.9 0.4 1.0 1 lcl|FitnessBrowser__psRCH2:GFF1428 Psest_1465 2,3,4,5-tetrahydropyr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1428 Psest_1465 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 621.9 0.4 1.2e-191 1.2e-191 1 341 [] 5 344 .] 5 344 .] 0.99 Alignments for each domain: == domain 1 score: 621.9 bits; conditional E-value: 1.2e-191 TIGR03536 1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagleeqael 75 l+sla+Gvgt+nr+g+wlevf+++pll p+ elv+ava lgy+gGnqai++t++++++la alk +++q +l lcl|FitnessBrowser__psRCH2:GFF1428 5 LFSLAFGVGTQNRQGDWLEVFYAQPLLKPAGELVAAVAPLLGYAGGNQAITITTSQAAQLADALKPL-DATQYAL 78 59**************************************************************999.6778889 PP TIGR03536 76 aaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneGaidleelaerql 150 +++l+es+rplva+ll+eda +s+peaylkl+llshrl+kphg+nl+Gif+ll+nvawtn+Ga+dl elaerql lcl|FitnessBrowser__psRCH2:GFF1428 79 LTRLAESQRPLVATLLAEDAPLSSTPEAYLKLHLLSHRLAKPHGLNLTGIFPLLPNVAWTNQGAVDLGELAERQL 153 9************************************************************************** PP TIGR03536 151 earlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnfnaGteGasmveGrisaGv 225 earl+G++lev+svdkfpkmtdyvvp+GvriadtarvrlGayvGeGttvmheGf+nfnaGt+G++m+eGr+saGv lcl|FitnessBrowser__psRCH2:GFF1428 154 EARLKGDLLEVFSVDKFPKMTDYVVPAGVRIADTARVRLGAYVGEGTTVMHEGFINFNAGTQGPGMIEGRVSAGV 228 *************************************************************************** PP TIGR03536 226 lvGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevv 300 +vGkGsdlGGG+stmGtlsGGGnivisvGe+cl+GanaGiGiplGdr+tve+GlyitaGtkv+lld++++lv+vv lcl|FitnessBrowser__psRCH2:GFF1428 229 FVGKGSDLGGGCSTMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNTVESGLYITAGTKVSLLDENDQLVKVV 303 *************************************************************************** PP TIGR03536 301 kardlaGksdllfrrnslnGavecltnksaielneelhann 341 kar+laG+sdllfrrns++Gavec+t+ksaielne+lha+n lcl|FitnessBrowser__psRCH2:GFF1428 304 KARELAGQSDLLFRRNSQTGAVECKTHKSAIELNEALHAHN 344 ****************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (341 nodes) Target sequences: 1 (344 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: 7.92 // [ok]
This GapMind analysis is from Apr 09 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