Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate BWI76_RS20870 BWI76_RS20870 succinyl-diaminopimelate desuccinylase
Query= SwissProt::Q8ZN75 (375 letters) >FitnessBrowser__Koxy:BWI76_RS20870 Length = 375 Score = 711 bits (1835), Expect = 0.0 Identities = 347/375 (92%), Positives = 362/375 (96%) Query: 1 MSCPVIELTQQLIRRPSLSPDDAGCQALMIERLRKIGFTIEHMDFGDTQNFWAWRGRGET 60 MSCPVIEL QQLIRRPSLSPDDAGCQALMIERLR IGFT+E MDFGDTQNFWAWRGRGET Sbjct: 1 MSCPVIELAQQLIRRPSLSPDDAGCQALMIERLRAIGFTVEPMDFGDTQNFWAWRGRGET 60 Query: 61 LAFAGHTDVVPAGDVDRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQHPH 120 LAFAGHTDVVP+GD DRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQ+P Sbjct: 61 LAFAGHTDVVPSGDADRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQYPD 120 Query: 121 HRGRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEIVGDVVKNGRRGS 180 H+GRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTE+VGDVVKNGRRGS Sbjct: 121 HKGRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEVVGDVVKNGRRGS 180 Query: 181 LTCNLTIHGVQGHVAYPHLADNPVHRAAPFLNELVAIEWDRGNDFFPATSMQVANIQAGT 240 LTCNLTIHGVQGHVAYPHLADNPVHRAAP L ELV IEWD+GN+FFP TSMQ+AN+Q+GT Sbjct: 181 LTCNLTIHGVQGHVAYPHLADNPVHRAAPMLAELVTIEWDKGNEFFPPTSMQIANVQSGT 240 Query: 241 GSNNVIPGELFVQFNFRFSTELTDEMIKERVHALLEKHQLRYTVDWWLSGQPFLTARGKL 300 GSNNVIPG++FVQFNFRFSTELTDEMIK RV ALLEK+ LRY+VDWWLSGQPFLT+RGKL Sbjct: 241 GSNNVIPGDMFVQFNFRFSTELTDEMIKARVVALLEKYALRYSVDWWLSGQPFLTSRGKL 300 Query: 301 VDAVVNAIEHYNEIKPQLLTTGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ 360 VDAVVNAIEHYNEIKPQLLT GGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ Sbjct: 301 VDAVVNAIEHYNEIKPQLLTNGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ 360 Query: 361 LLARMYQRIMEQLVA 375 LLARMYQRIMEQLVA Sbjct: 361 LLARMYQRIMEQLVA 375 Lambda K H 0.322 0.136 0.415 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: 604 Number of extensions: 13 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: 375 Length of database: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
Align candidate BWI76_RS20870 BWI76_RS20870 (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.26770.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-177 574.0 0.0 7.2e-177 573.9 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS20870 BWI76_RS20870 succinyl-diaminopi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS20870 BWI76_RS20870 succinyl-diaminopimelate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 573.9 0.0 7.2e-177 7.2e-177 2 370 .] 6 373 .. 5 373 .. 0.99 Alignments for each domain: == domain 1 score: 573.9 bits; conditional E-value: 7.2e-177 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGel 72 +ela++Li+r+s++P+dag+q+l++erL+++gf++e + f+dt+n+wa rg +e +l+faGhtDvvP+G+ lcl|FitnessBrowser__Koxy:BWI76_RS20870 6 IELAQQLIRRPSLSPDDAGCQALMIERLRAIGFTVEPMDFGDTQNFWAWRGRGE-TLAFAGHTDVVPSGDA 75 79*************************************************987.9*************** PP TIGR01246 73 ekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvve 143 ++W ++pfep++rdG+l+grGaaDmkgslaa+vvaaerfv++++dhkG+l++litsDee++a++Gt+kvve lcl|FitnessBrowser__Koxy:BWI76_RS20870 76 DRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQYPDHKGRLAFLITSDEEASAKNGTVKVVE 146 *********************************************************************** PP TIGR01246 144 tlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliai 214 l++r+e +dy++vgePss++ +GDv+k+GrrGs+t +l+i+G+qGhvaYPh+a+nPvh+a+p+l+el++i lcl|FitnessBrowser__Koxy:BWI76_RS20870 147 ALMARNERLDYCLVGEPSSTEVVGDVVKNGRRGSLTCNLTIHGVQGHVAYPHLADNPVHRAAPMLAELVTI 217 *********************************************************************** PP TIGR01246 215 klDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewkl 285 ++D+Gneffpp+s+qian+++gtg++nviPg++ v+fn+rfs+e+++e +k +v+++l+k+ l Y+++w l lcl|FitnessBrowser__Koxy:BWI76_RS20870 218 EWDKGNEFFPPTSMQIANVQSGTGSNNVIPGDMFVQFNFRFSTELTDEMIKARVVALLEKYALRYSVDWWL 288 *********************************************************************** PP TIGR01246 286 sgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedl 356 sg+pflt++gkl+++v++aie+ +++kp+l t+GGtsD+rfia++ga+vvelG+vn+tihk+ne+v+ +dl lcl|FitnessBrowser__Koxy:BWI76_RS20870 289 SGQPFLTSRGKLVDAVVNAIEHYNEIKPQLLTNGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADL 359 *********************************************************************** PP TIGR01246 357 eklsevyeklleel 370 + l+++y++++e+l lcl|FitnessBrowser__Koxy:BWI76_RS20870 360 QLLARMYQRIMEQL 373 ***********986 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: 10.42 // [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