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_068461962.1 APY04_RS09380 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >NCBI__GCF_001541235.1:WP_068461962.1 Length = 284 Score = 317 bits (813), Expect = 1e-91 Identities = 171/276 (61%), Positives = 201/276 (72%), Gaps = 8/276 (2%) Query: 3 QLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKA 62 +L I++ +E R I+ A V R+ V + LLD G +RVAEK W +QWLKKA Sbjct: 9 ELATAIDAMWEERDGIS-AGTTGVIRDTVETALNLLDKGEVRVAEKGADGWTVNQWLKKA 67 Query: 63 VLLSFRINDNKVMDGAE--TRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARN 120 VLLSFR+ND + GA ++DKVP KFA + F++ GFR VP + VR+ A+IA Sbjct: 68 VLLSFRLNDMAAISGAPGGANWWDKVPSKFAGMTDDDFRRAGFRAVPGSIVRRSAYIAPT 127 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 VLMPS+VN+GAYVD GTMVDTWATVGSCAQIGKN H+SGG GIGGVLEPLQA P IIED Sbjct: 128 VVLMPSFVNLGAYVDAGTMVDTWATVGSCAQIGKNCHISGGAGIGGVLEPLQAGPVIIED 187 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNL-- 238 NCFIGAR+EV EGVIV EGSV+SMGVYLG ST I DR TGE +G+VP SVVVSG++ Sbjct: 188 NCFIGARAEVAEGVIVGEGSVLSMGVYLGASTTIIDRATGEKFFGKVPPYSVVVSGSMAG 247 Query: 239 -PSKDGS--YSLYCAVIVKKVDAKTRGKVGINELLR 271 P DG+ +LYCAVIVKKVDAKTR K INELLR Sbjct: 248 KPLPDGTPGPNLYCAVIVKKVDAKTRSKTSINELLR 283 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: 271 Number of extensions: 12 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: 274 Length of database: 284 Length adjustment: 26 Effective length of query: 248 Effective length of database: 258 Effective search space: 63984 Effective search space used: 63984 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_068461962.1 APY04_RS09380 (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.8126.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-125 401.5 0.1 1.1e-124 401.3 0.1 1.0 1 lcl|NCBI__GCF_001541235.1:WP_068461962.1 APY04_RS09380 2,3,4,5-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001541235.1:WP_068461962.1 APY04_RS09380 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 ! 401.3 0.1 1.1e-124 1.1e-124 3 269 .. 11 283 .. 9 284 .] 0.94 Alignments for each domain: == domain 1 score: 401.3 bits; conditional E-value: 1.1e-124 TIGR00965 3 qkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnq 71 i+ +e+r+ i ++ ++++ v+ +++ ld+g +rvaek ++ w vn+w+kkavllsfr++d lcl|NCBI__GCF_001541235.1:WP_068461962.1 11 ATAIDAMWEERDGISA-GTTGVIRDTVETALNLLDKGEVRVAEKGADGWTVNQWLKKAVLLSFRLNDMA 78 6679999****99976.557789********************************************** PP TIGR00965 72 vlnda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmv 138 + +a ++++dkv++kfa + +d f++ag+r+vpg++vrr a+ia vvlmps+vn+gayvd gtmv lcl|NCBI__GCF_001541235.1:WP_068461962.1 79 AISGApgGANWWDKVPSKFAGMTDDDFRRAGFRAVPGSIVRRSAYIAPTVVLMPSFVNLGAYVDAGTMV 147 *998622589*********************************************************** PP TIGR00965 139 dtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfig 207 dtwatvgscaqigkn+h+sgg+giggvleplqa pviiedncfigar+e++egviv egsv+smgv++g lcl|NCBI__GCF_001541235.1:WP_068461962.1 148 DTWATVGSCAQIGKNCHISGGAGIGGVLEPLQAGPVIIEDNCFIGARAEVAEGVIVGEGSVLSMGVYLG 216 ********************************************************************* PP TIGR00965 208 qstkivdretgeiiygrvpagsvvvsgslpsk...dgkk..slycavivkkvdaktrgkvsinellr 269 st i+dr tge ++g+vp +svvvsgs+ k dg + +lycavivkkvdaktr+k+sinellr lcl|NCBI__GCF_001541235.1:WP_068461962.1 217 ASTTIIDRATGEKFFGKVPPYSVVVSGSMAGKplpDGTPgpNLYCAVIVKKVDAKTRSKTSINELLR 283 ****************************96543337875227************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (284 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: 6.21 // [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