Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate WP_051939867.1 BS73_RS12745 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= BRENDA::P9WP21 (317 letters) >NCBI__GCF_000744815.1:WP_051939867.1 Length = 333 Score = 412 bits (1060), Expect = e-120 Identities = 219/321 (68%), Positives = 244/321 (76%), Gaps = 7/321 (2%) Query: 4 VTGAAGIGLATLAADGSVLDTWFPAPELTESGT--SATSRLAVSDVPVEL----AALIGR 57 ++GA GLATLAADG+VLDTWFPAPELT S + + T RL L A IG Sbjct: 12 LSGAVAAGLATLAADGTVLDTWFPAPELTASPSEPAGTERLTAEQAVAALGEGAAEAIGP 71 Query: 58 DDDRRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWT 117 D R E +AVRT I SL + AD YD YLRLHLLSHRLV P+ + G+F L NV WT Sbjct: 72 DPRRGVEVVAVRTTISSLSEEPADAYDVYLRLHLLSHRLVRPNVQSLEGIFAHLANVAWT 131 Query: 118 NHGPCAIDGFEAVRARLRRRG-PVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAP 176 + GP +D E+ R +R +G +TVYGVDKFPRM+DYVVP GVRIADADRVRLGAHLA Sbjct: 132 SVGPVPVDRIESTRLAVRAQGGSLTVYGVDKFPRMLDYVVPAGVRIADADRVRLGAHLAA 191 Query: 177 GTTVMHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGK 236 GTTVMHEGFVN+NAGTLG SMVEGRIS GVVVGD SD+GGGASIMGTLSGGG V+SIG+ Sbjct: 192 GTTVMHEGFVNFNAGTLGTSMVEGRISQGVVVGDSSDIGGGASIMGTLSGGGKEVVSIGE 251 Query: 237 RCLLGANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVSG 296 RCLLGAN+G+GISLGDDCVVEAGLYVTAGTRVT PD KA ELSG SNLLFRRNS +G Sbjct: 252 RCLLGANAGIGISLGDDCVVEAGLYVTAGTRVTTPDGQVAKAAELSGQSNLLFRRNSQTG 311 Query: 297 AVEVLARDGQGIALNEDLHAN 317 AVEVLAR G LNE LHA+ Sbjct: 312 AVEVLARKGSWGGLNEVLHAH 332 Lambda K H 0.318 0.136 0.397 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: 367 Number of extensions: 13 Number of successful extensions: 3 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: 317 Length of database: 333 Length adjustment: 28 Effective length of query: 289 Effective length of database: 305 Effective search space: 88145 Effective search space used: 88145 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: 48 (23.1 bits)
Align candidate WP_051939867.1 BS73_RS12745 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR03535 (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/TIGR03535.hmm # target sequence database: /tmp/gapView.2140041.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03535 [M=320] Accession: TIGR03535 Description: DapD_actino: 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-156 505.8 7.3 2.5e-156 505.6 7.3 1.0 1 NCBI__GCF_000744815.1:WP_051939867.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_051939867.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.6 7.3 2.5e-156 2.5e-156 2 320 .] 14 332 .. 13 332 .. 0.96 Alignments for each domain: == domain 1 score: 505.6 bits; conditional E-value: 2.5e-156 TIGR03535 2 salglGlatvtadgtvldvWypelelgea..aeagterleae..leelaa....lagedeargvervvvttki 66 +a+++Glat++adgtvld+W+p++el++ ++agterl+ae +++l + ++g d +rgve+v+v+t+i NCBI__GCF_000744815.1:WP_051939867.1 14 GAVAAGLATLAADGTVLDTWFPAPELTASpsEPAGTERLTAEqaVAALGEgaaeAIGPDPRRGVEVVAVRTTI 86 699***********************998668999**99998663334334444899**************** PP TIGR03535 67 adldeapadaadaylrlhllshrlvkPntvnldGifgllanvvWtnlGPvavedlektraklraeg.pvtvys 138 ++l+e pada+d+ylrlhllshrlv+Pn ++l+Gif++lanv+Wt++GPv v+ +e+tr+++ra+g ++tvy+ NCBI__GCF_000744815.1:WP_051939867.1 87 SSLSEEPADAYDVYLRLHLLSHRLVRPNVQSLEGIFAHLANVAWTSVGPVPVDRIESTRLAVRAQGgSLTVYG 159 *****************************************************************65****** PP TIGR03535 139 vdkfPrmvdyvvPtgvrigdadrvrlGaylaeGttvmheGfvnfnaGtlGasmveGrisaGvvvgdGsdiGGG 211 vdkfPrm+dyvvP+gvri+dadrvrlGa+la+GttvmheGfvnfnaGtlG+smveGris+Gvvvgd sdiGGG NCBI__GCF_000744815.1:WP_051939867.1 160 VDKFPRMLDYVVPAGVRIADADRVRLGAHLAAGTTVMHEGFVNFNAGTLGTSMVEGRISQGVVVGDSSDIGGG 232 ************************************************************************* PP TIGR03535 212 asimGtlsGGGkevisiGercllGansGvGislGddcvveaGlyvtaGtkvtlvdkakeaageegevvkaael 284 asimGtlsGGGkev+siGercllGan+G+GislGddcvveaGlyvtaGt+vt+ ++g+v kaael NCBI__GCF_000744815.1:WP_051939867.1 233 ASIMGTLSGGGKEVVSIGERCLLGANAGIGISLGDDCVVEAGLYVTAGTRVTT---------PDGQVAKAAEL 296 *****************************************************.........99********* PP TIGR03535 285 sGasnllfrrnsvsGaveavarkgkaielnealhan 320 sG+snllfrrns++Gave++arkg++ lne lha+ NCBI__GCF_000744815.1:WP_051939867.1 297 SGQSNLLFRRNSQTGAVEVLARKGSWGGLNEVLHAH 332 **********************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (320 nodes) Target sequences: 1 (333 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 15.28 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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