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 PP_1530 PP_1530 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::G3XD76 (344 letters) >FitnessBrowser__Putida:PP_1530 Length = 344 Score = 598 bits (1541), Expect = e-176 Identities = 304/344 (88%), Positives = 322/344 (93%) Query: 1 MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60 MS +LFSLAFGVG+QNRQ AWLEVFYA PLL PS+E+VAAVAP+LGY GNQA+ F++ Q Sbjct: 1 MSNTLFSLAFGVGSQNRQGAWLEVFYAQPLLNPSAELVAAVAPVLGYEGGNQAIAFSNAQ 60 Query: 61 AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120 A QLA+ALKG+DAAQ+ALL+RLAES KPLVATLLAEDAA SST EAYLKLHLLSHRLVKP Sbjct: 61 AAQLAEALKGVDAAQAALLTRLAESHKPLVATLLAEDAALSSTPEAYLKLHLLSHRLVKP 120 Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180 H V+L+GIFPLLPNVAWTN GAVDL ELAELQLEARLKG+LLEVFSVDKFPKMTDYVVPA Sbjct: 121 HGVSLAGIFPLLPNVAWTNQGAVDLGELAELQLEARLKGELLEVFSVDKFPKMTDYVVPA 180 Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240 GVRIADTARVRLGAYIGEGTT+MHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC Sbjct: 181 GVRIADTARVRLGAYIGEGTTIMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240 Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300 STMGTLSGGGNIVI VGEGCLIGANAGIGIPLGDRN VEAGLYITAGTKV LLDE N LV Sbjct: 241 STMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVEAGLYITAGTKVNLLDENNELV 300 Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344 KVVKARDLAGQ DLLFRRNS NGAVECKT+K+AIELNEALHAHN Sbjct: 301 KVVKARDLAGQTDLLFRRNSLNGAVECKTHKSAIELNEALHAHN 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: 474 Number of extensions: 16 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 PP_1530 PP_1530 (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.9459.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-197 638.6 2.4 1.1e-196 638.5 2.4 1.0 1 lcl|FitnessBrowser__Putida:PP_1530 PP_1530 2,3,4,5-tetrahydropyridi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1530 PP_1530 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 ! 638.5 2.4 1.1e-196 1.1e-196 1 341 [] 5 344 .] 5 344 .] 0.99 Alignments for each domain: == domain 1 score: 638.5 bits; conditional E-value: 1.1e-196 TIGR03536 1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagleeqael 75 l+sla+Gvg++nr+g+wlevf+++pllnp++elv+ava +lgyegGnqai+++++++++la+alk + +++qa+l lcl|FitnessBrowser__Putida:PP_1530 5 LFSLAFGVGSQNRQGAWLEVFYAQPLLNPSAELVAAVAPVLGYEGGNQAIAFSNAQAAQLAEALKGV-DAAQAAL 78 59***************************************************************99.8899*** PP TIGR03536 76 aaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneGaidleelaerql 150 +++l+es++plva+ll+edaa +s+peaylkl+llshrlvkphgv+l+Gif+ll+nvawtn+Ga+dl elae ql lcl|FitnessBrowser__Putida:PP_1530 79 LTRLAESHKPLVATLLAEDAALSSTPEAYLKLHLLSHRLVKPHGVSLAGIFPLLPNVAWTNQGAVDLGELAELQL 153 *************************************************************************** PP TIGR03536 151 earlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnfnaGteGasmveGrisaGv 225 earl+Ge+lev+svdkfpkmtdyvvp+GvriadtarvrlGay+GeGtt+mheGfvnfnaGteG++m+eGr+saGv lcl|FitnessBrowser__Putida:PP_1530 154 EARLKGELLEVFSVDKFPKMTDYVVPAGVRIADTARVRLGAYIGEGTTIMHEGFVNFNAGTEGPGMIEGRVSAGV 228 *************************************************************************** PP TIGR03536 226 lvGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevv 300 +vGkGsdlGGG+stmGtlsGGGnivi+vGe+cl+GanaGiGiplGdr+tveaGlyitaGtkv+lld+++elv+vv lcl|FitnessBrowser__Putida:PP_1530 229 FVGKGSDLGGGCSTMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVEAGLYITAGTKVNLLDENNELVKVV 303 *************************************************************************** PP TIGR03536 301 kardlaGksdllfrrnslnGavecltnksaielneelhann 341 kardlaG++dllfrrnslnGavec+t+ksaielne+lha+n lcl|FitnessBrowser__Putida:PP_1530 304 KARDLAGQTDLLFRRNSLNGAVECKTHKSAIELNEALHAHN 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.80 // [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