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_010440698.1 G7G_RS0109130 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >NCBI__GCF_000192475.1:WP_010440698.1 Length = 275 Score = 342 bits (876), Expect = 7e-99 Identities = 177/272 (65%), Positives = 212/272 (77%), Gaps = 5/272 (1%) Query: 3 QLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEK-IDGQWVTHQWLKK 61 QL+ IE+A++ R ITPA REA+ + LDSG+LRVAEK DG W +QW KK Sbjct: 5 QLEAAIEAAWDMRDTITPATTGE-QREAIEDTLNALDSGSLRVAEKQADGNWHVNQWAKK 63 Query: 62 AVLLSFRINDNKVMDGAETR--YYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119 AVLL FRI D ++ +G ++DKV KFA +DE +++ GFR VP VR+ A+IA Sbjct: 64 AVLLGFRIKDMEIQNGGPQAGGWWDKVDSKFAGWDENQWRAAGFRAVPNCVVRKSAYIAP 123 Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179 VLMPS+VN+GAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTIIE Sbjct: 124 GAVLMPSFVNLGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIE 183 Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239 DNCFIGARSEVVEG IV EGSV+ MGV++G+ST+I DRETGE+ YG VP SVVV+G++P Sbjct: 184 DNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRETGEVMYGEVPPYSVVVAGSMP 243 Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 SK+ + SLYCAVIVK+VD KTR K GIN+LLR Sbjct: 244 SKN-NVSLYCAVIVKRVDEKTRSKTGINDLLR 274 Lambda K H 0.318 0.136 0.393 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: 284 Number of extensions: 11 Number of successful extensions: 5 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: 274 Length of database: 275 Length adjustment: 25 Effective length of query: 249 Effective length of database: 250 Effective search space: 62250 Effective search space used: 62250 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: 47 (22.7 bits)
Align candidate WP_010440698.1 G7G_RS0109130 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR00965 (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/TIGR00965.hmm # target sequence database: /tmp/gapView.2097017.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00965 [M=271] Accession: TIGR00965 Description: dapD: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-133 429.6 0.8 3e-133 429.4 0.8 1.0 1 NCBI__GCF_000192475.1:WP_010440698.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010440698.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.4 0.8 3e-133 3e-133 2 269 .. 6 274 .. 5 275 .] 0.97 Alignments for each domain: == domain 1 score: 429.4 bits; conditional E-value: 3e-133 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritdnqvl 73 l ie a+++r+ i+pa++ + +ea++++++ ldsg lrvaek+ dg+w+vn+w+kkavll fri+d ++ NCBI__GCF_000192475.1:WP_010440698.1 6 LEAAIEAAWDMRDTITPATT-GEQREAIEDTLNALDSGSLRVAEKQaDGNWHVNQWAKKAVLLGFRIKDMEIQ 77 6788*************975.678*********************999************************* PP TIGR00965 74 nda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatv 144 n++ ++dkv +kfa +de++++ ag+r+vp+ vvr+ a+ia vlmps+vn+gayvdegtmvdtwatv NCBI__GCF_000192475.1:WP_010440698.1 78 NGGpqAGGWWDKVDSKFAGWDENQWRAAGFRAVPNCVVRKSAYIAPGAVLMPSFVNLGAYVDEGTMVDTWATV 150 *9722457***************************************************************** PP TIGR00965 145 gscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdret 217 gscaqigknvhlsggvgiggvlep+qa p+iiedncfigarse+veg iv egsv+ mgvfig+stkivdret NCBI__GCF_000192475.1:WP_010440698.1 151 GSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRET 223 ************************************************************************* PP TIGR00965 218 geiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269 ge++yg vp +svvv+gs+psk+ + slycavivk+vd+ktr+k++in+llr NCBI__GCF_000192475.1:WP_010440698.1 224 GEVMYGEVPPYSVVVAGSMPSKN-NVSLYCAVIVKRVDEKTRSKTGINDLLR 274 *********************97.68*************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (275 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: 00:00:00.00 # Mc/sec: 17.34 // [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