Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate Pf1N1B4_3071 N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)
Query= BRENDA::Q9KQ52 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 Length = 383 Score = 454 bits (1168), Expect = e-132 Identities = 229/375 (61%), Positives = 275/375 (73%), Gaps = 2/375 (0%) Query: 4 SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGT-QSPL 62 SP L LA +LI R SVTP DA CQ M++RL GF++E M ED NFWA G + P+ Sbjct: 8 SPTLQLAIDLIRRPSVTPVDADCQKQMMQRLGDAGFKLEPMRIEDVDNFWATHGKHEGPV 67 Query: 63 FVFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHP 121 FAGHTDVVP GP++ W PF + + G L GRGAADMKGSLA M VA ERF+A++P Sbjct: 68 LCFAGHTDVVPTGPVTAWQIDPFNAVIDEHGMLCGRGAADMKGSLASMTVAAERFVADYP 127 Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181 DH+G + FLITSDEEGP +GT V+E L AR E +D CIVGEPSST VGDVVKNGRRG Sbjct: 128 DHKGKVAFLITSDEEGPAHHGTKAVIERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRG 187 Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241 S+ L V+G QGHVAYPHLA NP+H A PALAELAA WD GN +FPPTSFQI N+ +G Sbjct: 188 SLGAKLTVRGVQGHVAYPHLAKNPIHLAAPALAELAAEHWDHGNDFFPPTSFQISNVNSG 247 Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301 TGA+NVIPG+ FNFRFSTE T E +++RV +LD HGLD+ + W LSG PFLT+ G Sbjct: 248 TGATNVIPGDLVAVFNFRFSTESTVEGLQKRVADILDKHGLDWHIDWALSGLPFLTEPGA 307 Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361 LL AV A+++++ + T+GGTSDGRFIA MG QVVELGPVNATIH+VNE V ADL Sbjct: 308 LLDAVSASIKDITGRETQASTSGGTSDGRFIATMGTQVVELGPVNATIHQVNERVLAADL 367 Query: 362 EKLTDMYQKTLNHLL 376 + LT++Y +TL LL Sbjct: 368 DVLTEIYYQTLIKLL 382 Lambda K H 0.318 0.135 0.403 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: 509 Number of extensions: 27 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: 377 Length of database: 383 Length adjustment: 30 Effective length of query: 347 Effective length of database: 353 Effective search space: 122491 Effective search space used: 122491 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate Pf1N1B4_3071 (N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18))
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.30571.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-164 531.0 0.0 8.6e-164 530.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 N-succinyl-L,L-diaminopimelate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 530.8 0.0 8.6e-164 8.6e-164 2 370 .] 11 381 .. 10 381 .. 0.98 Alignments for each domain: == domain 1 score: 530.8 bits; conditional E-value: 8.6e-164 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGht 64 l+la++Li+r+svtP da++q+ +++rL gf+ e +++ed+ n+wat+g e pvl+faGht lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 11 LQLAIDLIRRPSVTPVDADCQKQMMQRLGDAGFKLEPMRIEDVDNFWATHGKhEGPVLCFAGHT 74 5899**********************************************98789********* PP TIGR01246 65 DvvPaGelekWssdpfepeerd.GklygrGaaDmkgslaafvvaaerfvkknadhkGslsllit 127 DvvP+G++ +W+ dpf++++ + G+l grGaaDmkgsla++ vaaerfv++++dhkG++++lit lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 75 DVVPTGPVTAWQIDPFNAVIDEhGMLCGRGAADMKGSLASMTVAAERFVADYPDHKGKVAFLIT 138 *****************997544***************************************** PP TIGR01246 128 sDeegeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhv 191 sDeeg a +Gtk+v+e l +r+e +d+++vgePss+ +GDv+k+GrrGs+ +kl+++G+qGhv lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 139 SDEEGPAHHGTKAVIERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRGSLGAKLTVRGVQGHV 202 **************************************************************** PP TIGR01246 192 aYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrf 255 aYPh+a+nP+h a+p+l+el+a+++D+Gn+ffpp+s+qi+n+++gtga+nviPg+l + fn+rf lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 203 AYPHLAKNPIHLAAPALAELAAEHWDHGNDFFPPTSFQISNVNSGTGATNVIPGDLVAVFNFRF 266 **************************************************************** PP TIGR01246 256 ssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsG 319 s+e+++e l+++v++ildkh+ld++++w lsg pflt+ g l+++v ++i+ ++++++++stsG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 267 STESTVEGLQKRVADILDKHGLDWHIDWALSGLPFLTEPGALLDAVSASIKDITGRETQASTSG 330 **************************************************************** PP TIGR01246 320 GtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370 GtsD+rfia++g++vvelG+vn+tih+vne+v +dl+ l+e+y+++l++l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3071 331 GTSDGRFIATMGTQVVELGPVNATIHQVNERVLAADLDVLTEIYYQTLIKL 381 **********************************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (383 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: 7.67 // [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