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_057507868.1 ABB28_RS06515 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >NCBI__GCF_001431535.1:WP_057507868.1 Length = 352 Score = 337 bits (863), Expect = 3e-97 Identities = 171/272 (62%), Positives = 212/272 (77%), Gaps = 1/272 (0%) Query: 1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID-GQWVTHQWL 59 +++L+ IESAFERRA +T ++ T+ V +VI L+SG RVAE G W ++WL Sbjct: 77 VEELKFGIESAFERRATLTLHELEGSTKPLVGRVIDGLESGEFRVAEPDGHGGWKVNEWL 136 Query: 60 KKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119 KKAVLL FR+ND V+D ++DKV +FA +DEA+F++ G RVVP A R+G + + Sbjct: 137 KKAVLLYFRVNDMAVVDARPAPFWDKVESRFAGHDEAKFRRAGVRVVPGAIARRGTYFGK 196 Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179 + VLMPS+ NIGAYV EGTMVDTWATVGSCAQIG++ HLSGG GIGGVLEPLQA+PTIIE Sbjct: 197 DVVLMPSFTNIGAYVGEGTMVDTWATVGSCAQIGQHCHLSGGAGIGGVLEPLQASPTIIE 256 Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239 D+CFIGARSEVVEGV+V SVI MGV+L QSTRIY+R TGEI YG +P SVVVSG+LP Sbjct: 257 DHCFIGARSEVVEGVVVGHHSVIGMGVFLSQSTRIYNRATGEISYGYIPPYSVVVSGSLP 316 Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 S DG++SLYCAVIVK+VDA+TR K +N+LLR Sbjct: 317 SADGTHSLYCAVIVKQVDARTRSKTSVNDLLR 348 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: 304 Number of extensions: 5 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: 274 Length of database: 352 Length adjustment: 27 Effective length of query: 247 Effective length of database: 325 Effective search space: 80275 Effective search space used: 80275 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_057507868.1 ABB28_RS06515 (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.28394.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-129 414.8 0.0 1.2e-128 414.3 0.0 1.2 1 lcl|NCBI__GCF_001431535.1:WP_057507868.1 ABB28_RS06515 2,3,4,5-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507868.1 ABB28_RS06515 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 ! 414.3 0.0 1.2e-128 1.2e-128 5 270 .. 83 349 .. 79 350 .. 0.99 Alignments for each domain: == domain 1 score: 414.3 bits; conditional E-value: 1.2e-128 TIGR00965 5 iietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritdnqv 72 ie+aferra ++ + + +k v ++i l+sg +rvae +g wkvnew+kkavll+fr++d v lcl|NCBI__GCF_001431535.1:WP_057507868.1 83 GIESAFERRATLTLHELEGSTKPLVGRVIDGLESGEFRVAEPDgHGGWKVNEWLKKAVLLYFRVNDMAV 151 69***************************************98789*********************** PP TIGR00965 73 lndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtw 141 ++ + ++dkv ++fa +de++f++ag+r+vpga++rrg++ k+vvlmps+ nigayv egtmvdtw lcl|NCBI__GCF_001431535.1:WP_057507868.1 152 VDARPAPFWDKVESRFAGHDEAKFRRAGVRVVPGAIARRGTYFGKDVVLMPSFTNIGAYVGEGTMVDTW 220 ********************************************************************* PP TIGR00965 142 atvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqst 210 atvgscaqig+ +hlsgg+giggvleplqa+p+iied cfigarse+vegv+v svi mgvf+ qst lcl|NCBI__GCF_001431535.1:WP_057507868.1 221 ATVGSCAQIGQHCHLSGGAGIGGVLEPLQASPTIIEDHCFIGARSEVVEGVVVGHHSVIGMGVFLSQST 289 ********************************************************************* PP TIGR00965 211 kivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellrt 270 +i++r tgei yg +p +svvvsgslps dg +slycavivk+vda+tr+k+s+n+llr+ lcl|NCBI__GCF_001431535.1:WP_057507868.1 290 RIYNRATGEISYGYIPPYSVVVSGSLPSADGTHSLYCAVIVKQVDARTRSKTSVNDLLRG 349 ***********************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (352 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.03 // [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