Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate GFF1211 PS417_06155 succinyl-diaminopimelate desuccinylase
Query= BRENDA::Q9KQ52 (377 letters) >FitnessBrowser__WCS417:GFF1211 Length = 383 Score = 458 bits (1178), Expect = e-133 Identities = 230/375 (61%), Positives = 277/375 (73%), Gaps = 2/375 (0%) Query: 4 SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQS-PL 62 SP L LA +LI R SVTP DA CQ LM++RL GF +E M ED NFWA G P+ Sbjct: 8 SPTLQLAIDLIRRPSVTPIDADCQKLMMQRLGDAGFALEPMRIEDVDNFWATHGKHDGPV 67 Query: 63 FVFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHP 121 FAGHTDVVP GP+ W PF+ + + G L GRGAADMKGSLA M+VA ERF+ ++P Sbjct: 68 LCFAGHTDVVPTGPVQAWQNDPFDALIDENGMLCGRGAADMKGSLAAMLVAAERFVTDYP 127 Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181 DH+GS+ FLITSDEEGP +GT V+E L AR E +D CIVGEPSST VGDVVKNGRRG Sbjct: 128 DHKGSVAFLITSDEEGPAHHGTKAVIERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRG 187 Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241 S+ L V+G QGHVAYPHLA NP+H A PALAELAA WD+GNA+FPPTSFQI NL +G Sbjct: 188 SLGATLTVRGIQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFPPTSFQISNLNSG 247 Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301 TGA+NVIPG+ FNFRFSTE T E +++RV +LD HGLD+ V+W LSG PFLT+ G Sbjct: 248 TGATNVIPGDLKAVFNFRFSTESTVEGLQQRVAEILDKHGLDWHVEWALSGLPFLTEPGA 307 Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361 LL AV A+++ + + T+GGTSDGRFIA +G QVVELGPVNATIH+VNE + +DL Sbjct: 308 LLDAVSASIKAITGRETQASTSGGTSDGRFIATLGTQVVELGPVNATIHQVNERILASDL 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: 517 Number of extensions: 24 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 GFF1211 PS417_06155 (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.9448.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-166 538.1 0.0 6.2e-166 537.9 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF1211 PS417_06155 succinyl-diaminopime Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1211 PS417_06155 succinyl-diaminopimelate desuccinylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 537.9 0.0 6.2e-166 6.2e-166 2 370 .] 11 381 .. 10 381 .. 0.98 Alignments for each domain: == domain 1 score: 537.9 bits; conditional E-value: 6.2e-166 TIGR01246 2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGhtDvvPaGelekW 75 l+la++Li+r+svtP da++q+l+++rL gf+ e +++ed+ n+wat+g + pvl+faGhtDvvP+G++++W lcl|FitnessBrowser__WCS417:GFF1211 11 LQLAIDLIRRPSVTPIDADCQKLMMQRLGDAGFALEPMRIEDVDNFWATHGKhDGPVLCFAGHTDVVPTGPVQAW 85 5899**********************************************98789******************** PP TIGR01246 76 ssdpfepee.rdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerd 149 ++dpf++ + ++G+l grGaaDmkgslaa++vaaerfv++++dhkGs+++litsDeeg a +Gtk+v+e l +r+ lcl|FitnessBrowser__WCS417:GFF1211 86 QNDPFDALIdENGMLCGRGAADMKGSLAAMLVAAERFVTDYPDHKGSVAFLITSDEEGPAHHGTKAVIERLAARK 160 *****9876267*************************************************************** PP TIGR01246 150 elidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffp 224 e +d+++vgePss+ +GDv+k+GrrGs+ ++l+++GiqGhvaYPh+a+nP+h a+p+l+el+a+++D+Gn+ffp lcl|FitnessBrowser__WCS417:GFF1211 161 ERLDWCIVGEPSSTTLVGDVVKNGRRGSLGATLTVRGIQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFP 235 *************************************************************************** PP TIGR01246 225 psslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklik 299 p+s+qi+n+++gtga+nviPg+lk+ fn+rfs+e+++e l+++v++ildkh+ld+++ew lsg pflt+ g l++ lcl|FitnessBrowser__WCS417:GFF1211 236 PTSFQISNLNSGTGATNVIPGDLKAVFNFRFSTESTVEGLQQRVAEILDKHGLDWHVEWALSGLPFLTEPGALLD 310 *************************************************************************** PP TIGR01246 300 kvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370 +v ++i+ ++++++++stsGGtsD+rfia+lg++vvelG+vn+tih+vne++ +dl+ l+e+y+++l++l lcl|FitnessBrowser__WCS417:GFF1211 311 AVSASIKAITGRETQASTSGGTSDGRFIATLGTQVVELGPVNATIHQVNERILASDLDVLTEIYYQTLIKL 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.67 // [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