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 CCNA_00283 CCNA_00283 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >FitnessBrowser__Caulo:CCNA_00283 Length = 286 Score = 360 bits (924), Expect = e-104 Identities = 185/276 (67%), Positives = 214/276 (77%), Gaps = 6/276 (2%) Query: 1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60 + LQ IE+A+E RADI+ A V R AV++ + LLDSG RVAEKIDG+W THQWLK Sbjct: 11 LADLQTEIEAAWEARADISAATTGPV-RTAVDEALRLLDSGEARVAEKIDGEWFTHQWLK 69 Query: 61 KAVLLSFRINDNKVM-----DGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGA 115 KAVLLSFR+N N VM G ++DKVP KF +D +F+ GFR VP A VR+GA Sbjct: 70 KAVLLSFRLNPNTVMRSGALGGGVGPWWDKVPNKFDGWDAPQFEAGGFRAVPGAIVRRGA 129 Query: 116 FIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANP 175 I +N +LMPS+VNIG YVDEGTMVDTW TVGSCAQIGKNVHLSGGVGIGGVLEPLQANP Sbjct: 130 HIGKNVILMPSFVNIGGYVDEGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANP 189 Query: 176 TIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVS 235 TIIEDNCFIGARSEVVEGV+V EGSV+SMGV++ ST+I DR+TG +H G+VP SVVV Sbjct: 190 TIIEDNCFIGARSEVVEGVVVGEGSVLSMGVFISASTKIVDRKTGAVHIGKVPPYSVVVP 249 Query: 236 GNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 GNLP +G LYCAVIVK VDA+TR K IN+LLR Sbjct: 250 GNLPDPNGGPGLYCAVIVKTVDAQTRSKTSINDLLR 285 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: 276 Number of extensions: 4 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: 286 Length adjustment: 26 Effective length of query: 248 Effective length of database: 260 Effective search space: 64480 Effective search space used: 64480 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 CCNA_00283 CCNA_00283 (2,3,4,5-tetrahydropyridine-2-carboxylate 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.17324.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-134 431.6 0.1 7.3e-134 431.4 0.1 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00283 CCNA_00283 2,3,4,5-tetrahydropyr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00283 CCNA_00283 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.4 0.1 7.3e-134 7.3e-134 2 269 .. 14 285 .. 13 286 .] 0.96 Alignments for each domain: == domain 1 score: 431.4 bits; conditional E-value: 7.3e-134 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnqvln 74 lq +ie a+e ra+i a++ v+ av e+++ ldsg rvaek+dg+w +++w+kkavllsfr++ n v+ lcl|FitnessBrowser__Caulo:CCNA_00283 14 LQTEIEAAWEARADISAATT-GPVRTAVDEALRLLDSGEARVAEKIDGEWFTHQWLKKAVLLSFRLNPNTVMR 85 799************98765.568*********************************************9987 PP TIGR00965 75 .....davnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwa 142 ++v ++dkv+ kf +d +f+ g+r+vpga+vrrga+i knv+lmps+vnig yvdegtmvdtw lcl|FitnessBrowser__Caulo:CCNA_00283 86 sgalgGGVGPWWDKVPNKFDGWDAPQFEAGGFRAVPGAIVRRGAHIGKNVILMPSFVNIGGYVDEGTMVDTWV 158 2222256889*************************************************************** PP TIGR00965 143 tvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdr 215 tvgscaqigknvhlsggvgiggvleplqa+p+iiedncfigarse+vegv+v egsv+smgvfi stkivdr lcl|FitnessBrowser__Caulo:CCNA_00283 159 TVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVVVGEGSVLSMGVFISASTKIVDR 231 ************************************************************************* PP TIGR00965 216 etgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269 +tg ++ g+vp +svvv+g+lp +g ++lycavivk vda+tr+k+sin+llr lcl|FitnessBrowser__Caulo:CCNA_00283 232 KTGAVHIGKVPPYSVVVPGNLPDPNGGPGLYCAVIVKTVDAQTRSKTSINDLLR 285 *****************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (286 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.02 // [ok]
This GapMind analysis is from Apr 09 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