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 N515DRAFT_0740 N515DRAFT_0740 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
Query= SwissProt::P56220 (274 letters) >FitnessBrowser__Dyella79:N515DRAFT_0740 Length = 275 Score = 372 bits (955), Expect = e-108 Identities = 187/275 (68%), Positives = 226/275 (82%), Gaps = 1/275 (0%) Query: 1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID-GQWVTHQWL 59 MQ ++++I AFERR D+T ++++T R AV QVI LL+SG RVAE G W +QW+ Sbjct: 1 MQSIESLINDAFERRNDLTQSDIETYLRPAVEQVIDLLESGERRVAEPDGHGGWTVNQWI 60 Query: 60 KKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119 KKAVLL FRIN N+V+DG +DKVP++FA ++A Q G RVVP A VR+GA +A+ Sbjct: 61 KKAVLLYFRINGNRVVDGGSALAFDKVPLRFAHGNDAELQGLGARVVPGALVRRGAHVAK 120 Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179 + VLMPSYVNIGAYV G+MVDTWATVGSCAQIG +VHLSGGVGIGGVLEPLQANPTIIE Sbjct: 121 DAVLMPSYVNIGAYVGAGSMVDTWATVGSCAQIGAHVHLSGGVGIGGVLEPLQANPTIIE 180 Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239 DNCFIGARSEVVEGV+VE+GSVI MGV+LGQSTRIY+R TG+I YGRVPAGSVVV+G+LP Sbjct: 181 DNCFIGARSEVVEGVVVEKGSVIGMGVFLGQSTRIYNRATGQISYGRVPAGSVVVAGSLP 240 Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274 +KDG++SLY A+IVK+VD KTR K INELLR+ + Sbjct: 241 AKDGTHSLYAAIIVKQVDEKTRSKTSINELLRSAE 275 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: 279 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: 275 Length adjustment: 25 Effective length of query: 249 Effective length of database: 250 Effective search space: 62250 Effective search space used: 62250 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 N515DRAFT_0740 N515DRAFT_0740 (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.19588.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-132 425.5 0.4 5.2e-132 425.3 0.4 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 N515DRAFT_0740 2,3,4,5-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 N515DRAFT_0740 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransf # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 425.3 0.4 5.2e-132 5.2e-132 2 270 .. 4 273 .. 3 274 .. 0.99 Alignments for each domain: == domain 1 score: 425.3 bits; conditional E-value: 5.2e-132 TIGR00965 2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfr 66 + i++aferr+++++++ ++ ++ av+++i l+sg rvae +g w vn+w+kkavll+fr lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 4 IESLINDAFERRNDLTQSDIETYLRPAVEQVIDLLESGERRVAEPDgHGGWTVNQWIKKAVLLYFR 69 66789***************************************98789***************** PP TIGR00965 67 itdnqvlndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayv 132 i+ n+v++++ + fdkv+ +fa +++e++ g r+vpga+vrrga++ak+ vlmpsyvnigayv lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 70 INGNRVVDGGSALAFDKVPLRFAHGNDAELQGLGARVVPGALVRRGAHVAKDAVLMPSYVNIGAYV 135 ****************************************************************** PP TIGR00965 133 degtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegs 198 g+mvdtwatvgscaqig vhlsggvgiggvleplqa+p+iiedncfigarse+vegv+ve+gs lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 136 GAGSMVDTWATVGSCAQIGAHVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVVVEKGS 201 ****************************************************************** PP TIGR00965 199 vismgvfigqstkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsi 264 vi mgvf+gqst+i++r tg+i ygrvpagsvvv+gslp+kdg +sly a+ivk+vd+ktr+k+si lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 202 VIGMGVFLGQSTRIYNRATGQISYGRVPAGSVVVAGSLPAKDGTHSLYAAIIVKQVDEKTRSKTSI 267 ****************************************************************** PP TIGR00965 265 nellrt 270 nellr+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0740 268 NELLRS 273 ****96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (271 nodes) Target sequences: 1 (275 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: 10.15 // [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