Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate WP_028998830.1 H537_RS0117020 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= CharProtDB::CH_024869 (274 letters) >NCBI__GCF_000430725.1:WP_028998830.1 Length = 274 Score = 399 bits (1025), Expect = e-116 Identities = 201/271 (74%), Positives = 224/271 (82%), Gaps = 1/271 (0%) Query: 2 QQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKID-GQWVTHQWLK 60 QQLQ +I+ A+E RA ++PANA +EAV VIA L++G LRVA + GQW HQW+K Sbjct: 3 QQLQAVIDAAWEDRASLSPANAPAEVKEAVETVIADLNAGRLRVATREGVGQWTVHQWIK 62 Query: 61 KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120 KAVLLSFR+ DNQ+I + ++DKV KFA + + G RVVPPA R+G+FI R Sbjct: 63 KAVLLSFRLKDNQIIRAGDLGFYDKVDTKFATAPDEEMRASGVRVVPPAVARRGSFIGRG 122 Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180 VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED Sbjct: 123 AVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 182 Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240 NCFIGARSEVVEGVIVEE SVISMGVYIGQST+IYDR TGE+ YGR+PAGSVVVSGNLPS Sbjct: 183 NCFIGARSEVVEGVIVEENSVISMGVYIGQSTKIYDRATGEVSYGRIPAGSVVVSGNLPS 242 Query: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLR 271 DGKYSLYCAVIVKKVDA+TR K INELLR Sbjct: 243 ADGKYSLYCAVIVKKVDAQTRAKTSINELLR 273 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: 305 Number of extensions: 6 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: 274 Length adjustment: 25 Effective length of query: 249 Effective length of database: 249 Effective search space: 62001 Effective search space used: 62001 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_028998830.1 H537_RS0117020 (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.5027.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-145 469.5 1.9 2e-145 469.3 1.9 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028998830.1 H537_RS0117020 2,3,4,5-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028998830.1 H537_RS0117020 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltrans # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.3 1.9 2e-145 2e-145 1 269 [. 4 273 .. 4 274 .] 0.99 Alignments for each domain: == domain 1 score: 469.3 bits; conditional E-value: 2e-145 TIGR00965 1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfrit 68 +lq +i+ a+e ra + pa++ ++vkeav+ +ia l+ g lrva + +gqw v++w+kkavllsfr++ lcl|NCBI__GCF_000430725.1:WP_028998830.1 4 QLQAVIDAAWEDRASLSPANAPAEVKEAVETVIADLNAGRLRVATREgVGQWTVHQWIKKAVLLSFRLK 72 6899******************************************989******************** PP TIGR00965 69 dnqvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtm 137 dnq++ + ++dkv tkfa ++e++ +g+r+vp+av+rrg+fi + vlmpsyvnigayvdegtm lcl|NCBI__GCF_000430725.1:WP_028998830.1 73 DNQIIRAGDLGFYDKVDTKFATAPDEEMRASGVRVVPPAVARRGSFIGRGAVLMPSYVNIGAYVDEGTM 141 ********************************************************************* PP TIGR00965 138 vdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfi 206 vdtwatvgscaqigknvhlsggvgiggvleplqa+p+iiedncfigarse+vegvivee svismgv+i lcl|NCBI__GCF_000430725.1:WP_028998830.1 142 VDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEENSVISMGVYI 210 ********************************************************************* PP TIGR00965 207 gqstkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269 gqstki+dr tge+ ygr+pagsvvvsg+lps dgk+slycavivkkvda+tr+k+sinellr lcl|NCBI__GCF_000430725.1:WP_028998830.1 211 GQSTKIYDRATGEVSYGRIPAGSVVVSGNLPSADGKYSLYCAVIVKKVDAQTRAKTSINELLR 273 **************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (274 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: 7.49 // [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