Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_066920750.1 ACG33_RS09700 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_001579945.1:WP_066920750.1 Length = 281 Score = 389 bits (999), Expect = e-113 Identities = 193/268 (72%), Positives = 224/268 (83%) Query: 4 LQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAV 63 L + I +AFE RA +P NA R AV Q + LLD G +RVAEK D W +QWLKKAV Sbjct: 13 LADTIGSAFEDRARFSPDNAPQEVRTAVEQALDLLDRGQVRVAEKRDDGWQVNQWLKKAV 72 Query: 64 LLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVL 123 LLSFR+ DN+ ++ +R+FDKV +K+ADYDEARF+ +G RVVP A VR+GAF+ NTVL Sbjct: 73 LLSFRLQDNRPVDAGFTRFFDKVALKYADYDEARFRADGVRVVPHAIVRRGAFVGANTVL 132 Query: 124 MPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCF 183 MPSYVN+GAYV EGTMVDTWATVGSCAQIG+NVHLSGG GIGGVLEPLQANPTIIED+CF Sbjct: 133 MPSYVNVGAYVGEGTMVDTWATVGSCAQIGRNVHLSGGAGIGGVLEPLQANPTIIEDDCF 192 Query: 184 IGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDG 243 IGARSEVVEGVIVE+G+VISMGV+IG STRIYDRE E+ YGRVPAG+VVV G+LP+ +G Sbjct: 193 IGARSEVVEGVIVEQGAVISMGVFIGASTRIYDRERDEVLYGRVPAGAVVVPGSLPAANG 252 Query: 244 KYSLYCAVIVKKVDAKTRGKVGINELLR 271 KY LYCAVIVK+VDA+TR KVGINELLR Sbjct: 253 KYGLYCAVIVKRVDAQTRAKVGINELLR 280 Lambda K H 0.318 0.136 0.391 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: 319 Number of extensions: 6 Number of successful extensions: 1 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: 281 Length adjustment: 25 Effective length of query: 249 Effective length of database: 256 Effective search space: 63744 Effective search space used: 63744 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_066920750.1 ACG33_RS09700 (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.20788.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-140 450.8 0.2 1e-139 450.6 0.2 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066920750.1 ACG33_RS09700 2,3,4,5-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066920750.1 ACG33_RS09700 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 ! 450.6 0.2 1e-139 1e-139 2 269 .. 13 280 .. 12 281 .] 0.99 Alignments for each domain: == domain 1 score: 450.6 bits; conditional E-value: 1e-139 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdn 70 l + i +afe ra p ++ ++v+ av++++ ld+g++rvaek d+ w+vn+w+kkavllsfr++dn lcl|NCBI__GCF_001579945.1:WP_066920750.1 13 LADTIGSAFEDRARFSPDNAPQEVRTAVEQALDLLDRGQVRVAEKRDDGWQVNQWLKKAVLLSFRLQDN 81 567899*************************************************************** PP TIGR00965 71 qvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvd 139 + ++ + +++fdkva k+adyde++f+ +g+r+vp a+vrrgaf+ n+vlmpsyvn+gayv egtmvd lcl|NCBI__GCF_001579945.1:WP_066920750.1 82 RPVDAGFTRFFDKVALKYADYDEARFRADGVRVVPHAIVRRGAFVGANTVLMPSYVNVGAYVGEGTMVD 150 ********************************************************************* PP TIGR00965 140 twatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigq 208 twatvgscaqig+nvhlsgg+giggvleplqa+p+iied+cfigarse+vegvive+g+vismgvfig lcl|NCBI__GCF_001579945.1:WP_066920750.1 151 TWATVGSCAQIGRNVHLSGGAGIGGVLEPLQANPTIIEDDCFIGARSEVVEGVIVEQGAVISMGVFIGA 219 ********************************************************************* PP TIGR00965 209 stkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269 st+i+dre e+ ygrvpag+vvv+gslp+ +gk++lycavivk+vda+tr+kv+inellr lcl|NCBI__GCF_001579945.1:WP_066920750.1 220 STRIYDRERDEVLYGRVPAGAVVVPGSLPAANGKYGLYCAVIVKRVDAQTRAKVGINELLR 280 ************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (281 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: 8.46 // [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