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_013420687.1 RVAN_RS15655 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >NCBI__GCF_000166055.1:WP_013420687.1 Length = 279 Score = 341 bits (875), Expect = 9e-99 Identities = 177/275 (64%), Positives = 210/275 (76%), Gaps = 8/275 (2%) Query: 4 LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAV 63 L+ VI++AFE R I V +AV + LLD G RVAEK+ G+WV ++WLKKAV Sbjct: 5 LKAVIDAAFEDRQAIRFGQKGEVA-DAVEAALSLLDEGKARVAEKVGGEWVVNEWLKKAV 63 Query: 64 LLSFRINDNKVMDGAETR--YYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNT 121 LLSFR+NDN ++ E ++DKVP KF+ +DEARF+ GFR +P + VR+ AFI RN Sbjct: 64 LLSFRLNDNTLLGDGEAPGPWWDKVPSKFSGWDEARFRAAGFRALPGSIVRRSAFIERNV 123 Query: 122 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDN 181 VLMPS+VN+GAYV EGTMVDTWATVGSCAQIG++VHLSGG GIGGVLEPLQA P IIEDN Sbjct: 124 VLMPSFVNVGAYVGEGTMVDTWATVGSCAQIGRHVHLSGGAGIGGVLEPLQAGPVIIEDN 183 Query: 182 CFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSK 241 CFIGAR+EV EGV+V EGSV+SMGVYLGQST+I DR TGE+ YGRVP SVVVSG +P K Sbjct: 184 CFIGARAEVAEGVVVGEGSVLSMGVYLGQSTKIVDRATGEVFYGRVPPYSVVVSGAMPGK 243 Query: 242 -----DGSYSLYCAVIVKKVDAKTRGKVGINELLR 271 + SLYCAVIVK+VD KTR K IN+LLR Sbjct: 244 PLPNGEPGPSLYCAVIVKRVDEKTRSKTSINDLLR 278 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: 267 Number of extensions: 7 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: 279 Length adjustment: 25 Effective length of query: 249 Effective length of database: 254 Effective search space: 63246 Effective search space used: 63246 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_013420687.1 RVAN_RS15655 (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.9771.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-131 421.9 0.0 6.6e-131 421.7 0.0 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013420687.1 RVAN_RS15655 2,3,4,5-tetrahydrop Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013420687.1 RVAN_RS15655 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransfe # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 421.7 0.0 6.6e-131 6.6e-131 2 269 .. 5 278 .. 4 279 .] 0.95 Alignments for each domain: == domain 1 score: 421.7 bits; conditional E-value: 6.6e-131 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdn 70 l+ +i+ afe r+ i + + +v +av+ +++ ld+g+ rvaek++g+w+vnew+kkavllsfr++dn lcl|NCBI__GCF_000166055.1:WP_013420687.1 5 LKAVIDAAFEDRQAIRFGQ-KGEVADAVEAALSLLDEGKARVAEKVGGEWVVNEWLKKAVLLSFRLNDN 72 6789*********998765.57899******************************************** PP TIGR00965 71 qvlndavn..kyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtm 137 +l d+++ ++dkv++kf+ +de++f+ ag+r++pg++vrr afi +nvvlmps+vn+gayv egtm lcl|NCBI__GCF_000166055.1:WP_013420687.1 73 TLLGDGEApgPWWDKVPSKFSGWDEARFRAAGFRALPGSIVRRSAFIERNVVLMPSFVNVGAYVGEGTM 141 ***99886337********************************************************** PP TIGR00965 138 vdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfi 206 vdtwatvgscaqig+ vhlsgg+giggvleplqa pviiedncfigar+e++egv+v egsv+smgv++ lcl|NCBI__GCF_000166055.1:WP_013420687.1 142 VDTWATVGSCAQIGRHVHLSGGAGIGGVLEPLQAGPVIIEDNCFIGARAEVAEGVVVGEGSVLSMGVYL 210 ********************************************************************* PP TIGR00965 207 gqstkivdretgeiiygrvpagsvvvsgslpsk...dgk..kslycavivkkvdaktrgkvsinellr 269 gqstkivdr tge++ygrvp +svvvsg++p k +g+ +slycavivk+vd+ktr+k+sin+llr lcl|NCBI__GCF_000166055.1:WP_013420687.1 211 GQSTKIVDRATGEVFYGRVPPYSVVVSGAMPGKplpNGEpgPSLYCAVIVKRVDEKTRSKTSINDLLR 278 ******************************9864445652269************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (279 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: 00:00:00.00 # Mc/sec: 10.94 // [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