Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate GFF1182 HP15_1159 succinyl-diaminopimelate desuccinylase
Query= SwissProt::Q8ZN75 (375 letters) >FitnessBrowser__Marino:GFF1182 Length = 378 Score = 472 bits (1215), Expect = e-138 Identities = 233/373 (62%), Positives = 284/373 (76%), Gaps = 2/373 (0%) Query: 4 PVIELTQQLIRRPSLSPDDAGCQALMIERLRKIGFTIEHMDFGDTQNFWAWRG-RGETLA 62 P +EL LIRRPS++PDDAGCQ LM+ RL +GFT E++ FGDT N WA +G G LA Sbjct: 7 PTLELAVDLIRRPSVTPDDAGCQELMMSRLAPLGFTGENLRFGDTDNLWARKGSEGPVLA 66 Query: 63 FAGHTDVVPAGDVDRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQHPHHR 122 FAGHTDVVP G W +PPF+P IRDG L GRGAADMKGSLAA V A ERFVA +P HR Sbjct: 67 FAGHTDVVPTGPEKNWSHPPFDPVIRDGYLLGRGAADMKGSLAAFVTACERFVASYPDHR 126 Query: 123 GRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEIVGDVVKNGRRGSLT 182 G +A LITSDEE A++GTVKVVE L ARNE++D+CL+GEPSST VGDV+KNGRRGSL Sbjct: 127 GSIALLITSDEEGPAQHGTVKVVETLEARNEKIDWCLIGEPSSTREVGDVIKNGRRGSLH 186 Query: 183 CNLTIHGVQGHVAYPHLADNPVHRAAPFLNELVAIEWDRGNDFFPATSMQVANIQAGTGS 242 LT+HGVQGHVAYPHLA+NPVH AP L+ L WD GNDFFP T+ Q+ ++AGTGS Sbjct: 187 GYLTVHGVQGHVAYPHLAENPVHLVAPALDALAKEFWDNGNDFFPPTTFQITKLEAGTGS 246 Query: 243 NNVIPGELFVQFNFRFSTELTDEMIKERVHALLEKHQLRYTVDWWLSGQPFLTARGKLVD 302 N+IPGE V FNFR+ TE T E ++ERV A+L++H L+Y + W LSG+PFLT +G LV Sbjct: 247 -NIIPGECLVHFNFRYCTENTAESLEERVVAILDRHNLKYDLQWHLSGRPFLTDKGALVS 305 Query: 303 AVVNAIEHYNEIKPQLLTTGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQLL 362 A +AI + +L T+GGTSDGRFIA GAQVVELGP+NATIHK++ECV A DL L Sbjct: 306 ASQSAIRTVTGRETELSTSGGTSDGRFIAPTGAQVVELGPINATIHKVDECVKADDLNTL 365 Query: 363 ARMYQRIMEQLVA 375 + +Y++I+ +L+A Sbjct: 366 SEIYEQILIELLA 378 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: 445 Number of extensions: 8 Number of successful extensions: 4 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: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 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 GFF1182 HP15_1159 (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.25585.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-170 551.2 0.0 6.2e-170 551.0 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1182 HP15_1159 succinyl-diaminopimela Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1182 HP15_1159 succinyl-diaminopimelate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 551.0 0.0 6.2e-170 6.2e-170 2 370 .] 9 376 .. 8 376 .. 0.99 Alignments for each domain: == domain 1 score: 551.0 bits; conditional E-value: 6.2e-170 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWs 76 lela +Li+r+svtP+dag+qel+++rL lgf+ e l+f+dt nlwa++g e pvl+faGhtDvvP+G++++Ws lcl|FitnessBrowser__Marino:GFF1182 9 LELAVDLIRRPSVTPDDAGCQELMMSRLAPLGFTGENLRFGDTDNLWARKGSEGPVLAFAGHTDVVPTGPEKNWS 83 689************************************************************************ PP TIGR01246 77 sdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdel 151 +pf+p++rdG+l grGaaDmkgslaafv+a+erfv++++dh+Gs++llitsDeeg a +Gt+kvvetl++r+e+ lcl|FitnessBrowser__Marino:GFF1182 84 HPPFDPVIRDGYLLGRGAADMKGSLAAFVTACERFVASYPDHRGSIALLITSDEEGPAQHGTVKVVETLEARNEK 158 *************************************************************************** PP TIGR01246 152 idyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffpps 226 id++++gePss++++GDvik+GrrGs+ g l+++G+qGhvaYPh+aenPvh ++p+l +l+++ +D+Gn+ffpp+ lcl|FitnessBrowser__Marino:GFF1182 159 IDWCLIGEPSSTREVGDVIKNGRRGSLHGYLTVHGVQGHVAYPHLAENPVHLVAPALDALAKEFWDNGNDFFPPT 233 *************************************************************************** PP TIGR01246 227 slqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkv 301 +qi+ +eagtg sn+iPge v+fn+r+++e ++e+l+++v++ild+h+l+Y+l+w+lsg+pflt++g l+++ lcl|FitnessBrowser__Marino:GFF1182 234 TFQITKLEAGTG-SNIIPGECLVHFNFRYCTENTAESLEERVVAILDRHNLKYDLQWHLSGRPFLTDKGALVSAS 307 ***********9.69************************************************************ PP TIGR01246 302 aeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370 ++ai+ v+++++elstsGGtsD+rfia ga+vvelG++n+tihkv+e+vk +dl+ lse+ye++l+el lcl|FitnessBrowser__Marino:GFF1182 308 QSAIRTVTGRETELSTSGGTSDGRFIAPTGAQVVELGPINATIHKVDECVKADDLNTLSEIYEQILIEL 376 *****************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (378 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.46 // [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