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 WP_086509350.1 BZY95_RS07625 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::G3XD76 (344 letters) >NCBI__GCF_002151265.1:WP_086509350.1 Length = 341 Score = 464 bits (1193), Expect = e-135 Identities = 234/341 (68%), Positives = 269/341 (78%), Gaps = 1/341 (0%) Query: 5 LFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQAYQL 64 + S AFG+GTQN Q WLE++Y PL KP + +V AV +L +GN A++F + + Sbjct: 1 MLSFAFGIGTQNTQGDWLEIYYPAPLFKPDASLVEAVGKVLDIPSGNAAVSFLPEHCSDI 60 Query: 65 ADALKGID-AAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKPHAV 123 A+ALK AQ+ L LA SQ+PLVAT + D P S E YLKLHLLSHRLVKPH + Sbjct: 61 AEALKAAGHVAQAELAEALAGSQRPLVATFIDSDVPPQSVPEVYLKLHLLSHRLVKPHGL 120 Query: 124 NLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPAGVR 183 +L+G+F LL NVAWT+ G +D+ EL +L+ARL+G+ L V VDKFPKMTDYVVP+GVR Sbjct: 121 DLTGMFGLLRNVAWTSEGPIDIEELPARRLKARLEGRALSVDCVDKFPKMTDYVVPSGVR 180 Query: 184 IADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGCSTM 243 IADTARVRLGAY+GEGTTVMHEGFVNFNAG EGPGMIEGR+SAGV VGKGSDLGGGCSTM Sbjct: 181 IADTARVRLGAYLGEGTTVMHEGFVNFNAGAEGPGMIEGRISAGVLVGKGSDLGGGCSTM 240 Query: 244 GTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALVKVV 303 GTLSGGGNIVI VGEGCLIGANAGIGIPLGDR VEAGLYITAG KV LLD+Q VK V Sbjct: 241 GTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRCTVEAGLYITAGAKVTLLDDQGQEVKTV 300 Query: 304 KARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344 AR+LAGQ DLL RRNSQNG +EC TNK+AI LNEALHA+N Sbjct: 301 AARELAGQSDLLLRRNSQNGRIECLTNKSAIALNEALHANN 341 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: 400 Number of extensions: 13 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: 344 Length of database: 341 Length adjustment: 29 Effective length of query: 315 Effective length of database: 312 Effective search space: 98280 Effective search space used: 98280 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 WP_086509350.1 BZY95_RS07625 (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.6389.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-190 617.7 0.2 2.5e-190 617.5 0.2 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509350.1 BZY95_RS07625 2,3,4,5-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509350.1 BZY95_RS07625 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransf # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.5 0.2 2.5e-190 2.5e-190 1 341 [] 1 341 [] 1 341 [] 1.00 Alignments for each domain: == domain 1 score: 617.5 bits; conditional E-value: 2.5e-190 TIGR03536 1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagl 69 +ls+a+G+gt+n++g+wle+++p+pl+ pd++lveav ++l+ +Gn+a+++ +e+++++a+alk+ag+ lcl|NCBI__GCF_002151265.1:WP_086509350.1 1 MLSFAFGIGTQNTQGDWLEIYYPAPLFKPDASLVEAVGKVLDIPSGNAAVSFLPEHCSDIAEALKAAGH 69 689****************************************************************** PP TIGR03536 70 eeqaelaaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneG 138 +qaela++l+ s+rplva+++++d p svpe+ylkl+llshrlvkphg++l+G+fgll+nvawt+eG lcl|NCBI__GCF_002151265.1:WP_086509350.1 70 VAQAELAEALAGSQRPLVATFIDSDVPPQSVPEVYLKLHLLSHRLVKPHGLDLTGMFGLLRNVAWTSEG 138 ********************************************************************* PP TIGR03536 139 aidleelaerqlearlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnf 207 +id+eel++r+l+arl+G++l+vd+vdkfpkmtdyvvp+GvriadtarvrlGay+GeGttvmheGfvnf lcl|NCBI__GCF_002151265.1:WP_086509350.1 139 PIDIEELPARRLKARLEGRALSVDCVDKFPKMTDYVVPSGVRIADTARVRLGAYLGEGTTVMHEGFVNF 207 ********************************************************************* PP TIGR03536 208 naGteGasmveGrisaGvlvGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctve 276 naG+eG++m+eGrisaGvlvGkGsdlGGG+stmGtlsGGGnivi+vGe+cl+GanaGiGiplGdrctve lcl|NCBI__GCF_002151265.1:WP_086509350.1 208 NAGAEGPGMIEGRISAGVLVGKGSDLGGGCSTMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRCTVE 276 ********************************************************************* PP TIGR03536 277 aGlyitaGtkvallddkgelvevvkardlaGksdllfrrnslnGavecltnksaielneelhann 341 aGlyitaG+kv+lldd+g+ v++v ar+laG+sdll+rrns+nG++ecltnksai+lne+lhann lcl|NCBI__GCF_002151265.1:WP_086509350.1 277 AGLYITAGAKVTLLDDQGQEVKTVAARELAGQSDLLLRRNSQNGRIECLTNKSAIALNEALHANN 341 ***************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (341 nodes) Target sequences: 1 (341 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: 00:00:00.01 # Mc/sec: 11.27 // [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