Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_057507870.1 ABB28_RS06525 succinyl-diaminopimelate desuccinylase
Query= SwissProt::Q9JYL2 (381 letters) >NCBI__GCF_001431535.1:WP_057507870.1 Length = 375 Score = 418 bits (1075), Expect = e-121 Identities = 203/371 (54%), Positives = 259/371 (69%) Query: 7 LELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFA 66 L+LA +LI+RPSVTPDD CQ+LLA RL GF E L G+ N+W G+ PV+ Sbjct: 5 LDLACDLIARPSVTPDDAGCQQLLATRLQAAGFQCEHLRLGEVDNLWATHGSGGPVLVLL 64 Query: 67 GHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGS 126 GHTDVVPTGPV W S PF P RDG LYGRGAADMK S+A FV A E+FVA HP H G+ Sbjct: 65 GHTDVVPTGPVADWASDPFVPTVRDGVLYGRGAADMKGSVAAFVVAAEQFVAAHPEHPGT 124 Query: 127 IALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGN 186 +A+L+TSDEEGDA+DG V + R E ID+CI GEP++ +LGD+++ GRRGSLS Sbjct: 125 LAVLLTSDEEGDAIDGVRHVARLFAERGERIDWCITGEPSSTARLGDLLRVGRRGSLSAR 184 Query: 187 LTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATN 246 L V+G QGH+AYP A NP+H APAL ELT WDEG E FPPTS Q+SN++ GTGA N Sbjct: 185 LLVQGVQGHVAYPDKARNPIHQAAPALAELTARRWDEGFESFPPTSLQVSNVHAGTGANN 244 Query: 247 VIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVA 306 VIPG+L V FN R++ L+ + A+LD+HG++Y ++W SG+PF T G L VA Sbjct: 245 VIPGQLQVDFNLRYNPHWNADKLETEIAALLDRHGLEYTVKWHRSGEPFHTPEGTLRRVA 304 Query: 307 RAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLSA 366 R + E G E ST GGTSD RFI + + IE+GP NA+IHQ++ENVR++D+ +L A Sbjct: 305 REVLGEFAGAPPEESTGGGTSDARFIAPLGAQCIEVGPVNASIHQVDENVRVDDLEQLPA 364 Query: 367 VYEGILARLLA 377 +Y+ ++ RLLA Sbjct: 365 LYQRLIERLLA 375 Lambda K H 0.317 0.135 0.400 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: 444 Number of extensions: 15 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: 381 Length of database: 375 Length adjustment: 30 Effective length of query: 351 Effective length of database: 345 Effective search space: 121095 Effective search space used: 121095 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_057507870.1 ABB28_RS06525 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))
# 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/TIGR01246.hmm # target sequence database: /tmp/gapView.24190.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01246 [M=370] Accession: TIGR01246 Description: dapE_proteo: succinyl-diaminopimelate desuccinylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-169 549.0 0.0 2.9e-169 548.8 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507870.1 ABB28_RS06525 succinyl-diaminopi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507870.1 ABB28_RS06525 succinyl-diaminopimelate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.8 0.0 2.9e-169 2.9e-169 2 370 .] 5 373 .. 4 373 .. 1.00 Alignments for each domain: == domain 1 score: 548.8 bits; conditional E-value: 2.9e-169 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaG 70 l+la++Li r+svtP+dag+q+l+a+rL++ gf++e+l+ +++ nlwat+g + pvlv+ GhtDvvP+G lcl|NCBI__GCF_001431535.1:WP_057507870.1 5 LDLACDLIARPSVTPDDAGCQQLLATRLQAAGFQCEHLRLGEVDNLWATHGSGGPVLVLLGHTDVVPTG 73 789****************************************************************** PP TIGR01246 71 elekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtk 139 ++ +W sdpf p++rdG+lygrGaaDmkgs+aafvvaae+fv+++++h G+l++l+tsDeeg+aidG++ lcl|NCBI__GCF_001431535.1:WP_057507870.1 74 PVADWASDPFVPTVRDGVLYGRGAADMKGSVAAFVVAAEQFVAAHPEHPGTLAVLLTSDEEGDAIDGVR 142 ********************************************************************* PP TIGR01246 140 kvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvl 208 +v+ + er e id++++gePss+ +lGD++++GrrGs++++l ++G+qGhvaYP+ka+nP+h+a+p+l lcl|NCBI__GCF_001431535.1:WP_057507870.1 143 HVARLFAERGERIDWCITGEPSSTARLGDLLRVGRRGSLSARLLVQGVQGHVAYPDKARNPIHQAAPAL 211 ********************************************************************* PP TIGR01246 209 keliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkl 277 +el+a+++DeG e+fpp+slq++n++agtga+nviPg+l+v fnlr+++++++++l+ +++++ld+h+l lcl|NCBI__GCF_001431535.1:WP_057507870.1 212 AELTARRWDEGFESFPPTSLQVSNVHAGTGANNVIPGQLQVDFNLRYNPHWNADKLETEIAALLDRHGL 280 ********************************************************************* PP TIGR01246 278 dYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihk 346 +Y+++w++sgepf t eg l ++++e++ e+ ++ pe st+GGtsDarfia lga+++e+G+vn++ih+ lcl|NCBI__GCF_001431535.1:WP_057507870.1 281 EYTVKWHRSGEPFHTPEGTLRRVAREVLGEFAGAPPEESTGGGTSDARFIAPLGAQCIEVGPVNASIHQ 349 ********************************************************************* PP TIGR01246 347 vneavkiedleklsevyeklleel 370 v+e+v+++dle+l ++y++l+e+l lcl|NCBI__GCF_001431535.1:WP_057507870.1 350 VDENVRVDDLEQLPALYQRLIERL 373 *********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (375 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.95 // [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