Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate Ga0059261_0797 Ga0059261_0797 succinyldiaminopimelate desuccinylase (EC 3.5.1.18)
Query= SwissProt::Q9JYL2 (381 letters) >FitnessBrowser__Korea:Ga0059261_0797 Length = 373 Score = 262 bits (669), Expect = 1e-74 Identities = 152/377 (40%), Positives = 214/377 (56%), Gaps = 14/377 (3%) Query: 7 LELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKN------IWLRRGTKA 60 +EL K LI+ PS+TP +L L +GF + G+ + + +R Sbjct: 5 VELTKALIAAPSITPAHGSVFDVLEAALRPLGFTVDRFVAGEAPDGPVENLLAVRNAGPG 64 Query: 61 PVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKH 120 P FAGH DVVP G E W S FEP R LYGRGA DMK SIA F A A Sbjct: 65 PHFAFAGHLDVVPPG--EGWTSGAFEPEVRGDLLYGRGAVDMKGSIAAFAAAVAALPAS- 121 Query: 121 PNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRR 180 G+++L+IT DEEG A GT ++D + A D C+VGEPT+ +LGD IK GRR Sbjct: 122 ----GTLSLIITGDEEGPATYGTLALMDRMAAAGLTPDMCLVGEPTSAHRLGDTIKIGRR 177 Query: 181 GSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNING 240 GS ++ V G+QGH+AYPHLA NP+ AL E+ DEG ++F P++ + ++ Sbjct: 178 GSTVIDIEVPGRQGHVAYPHLADNPIPRLVRALAEIDAIELDEGTDWFQPSNIETIDLTV 237 Query: 241 GTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAG 300 G ATNVIPG+ + + + RF+ + L +R+ I+ H ++ G+ FLT+ G Sbjct: 238 GNPATNVIPGKASARLSIRFNDQHRGQDLIERIERIVHAHAPAGIVRGRVYGEAFLTEPG 297 Query: 301 KLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLND 360 L+ + AI GI ELST+GGTSD RF+ I ++E G NAT+H+++E V L+D Sbjct: 298 TLSTLISDAIEVETGIRPELSTSGGTSDARFLSRIC-PVVEFGLLNATMHKLDEAVALDD 356 Query: 361 IPKLSAVYEGILARLLA 377 + KL+A+YE +L R+ A Sbjct: 357 LHKLTAIYETLLRRVYA 373 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: 392 Number of extensions: 27 Number of successful extensions: 5 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: 373 Length adjustment: 30 Effective length of query: 351 Effective length of database: 343 Effective search space: 120393 Effective search space used: 120393 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 Ga0059261_0797 Ga0059261_0797 (succinyldiaminopimelate 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.21709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-113 365.4 0.0 1.8e-113 365.2 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0797 Ga0059261_0797 succinyldiaminopi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0797 Ga0059261_0797 succinyldiaminopimelate desuccinylase (EC 3.5.1.18) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 365.2 0.0 1.8e-113 1.8e-113 1 369 [. 4 370 .. 4 371 .. 0.96 Alignments for each domain: == domain 1 score: 365.2 bits; conditional E-value: 1.8e-113 TIGR01246 1 vlelakeLisrksvtPndagaqeliaerLkklgfeieilefed.....tknlwatrgt.eepvlvfaGh 63 v+el+k Li +s+tP+ + +++++ L+ lgf++++ ++ ++nl+a r+ p+++faGh lcl|FitnessBrowser__Korea:Ga0059261_0797 4 VVELTKALIAAPSITPAHGSVFDVLEAALRPLGFTVDRFVAGEapdgpVENLLAVRNAgPGPHFAFAGH 72 5799********************************9988876233336888887777679******** PP TIGR01246 64 tDvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeeg 132 DvvP G e W+s +fepe+r lygrGa+Dmkgs+aaf +a+ G+lsl+it Deeg lcl|FitnessBrowser__Korea:Ga0059261_0797 73 LDVVPPG--EGWTSGAFEPEVRGDLLYGRGAVDMKGSIAAFAAAVA-----ALPASGTLSLIITGDEEG 134 *******..9*******************************99987.....44568************* PP TIGR01246 133 eaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPv 201 a +Gt ++++ + + ++d+++vgeP+s+++lGD+ikiGrrGs ++++ G qGhvaYPh+a+nP+ lcl|FitnessBrowser__Korea:Ga0059261_0797 135 PATYGTLALMDRMAAAGLTPDMCLVGEPTSAHRLGDTIKIGRRGSTVIDIEVPGRQGHVAYPHLADNPI 203 ********************************************************************* PP TIGR01246 202 hkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvek 270 +++v++l+e+ ai+lDeG++ f+ps+++ ++++g+ a+nviPg+++++ +rf+ ++ ++l +++e+ lcl|FitnessBrowser__Korea:Ga0059261_0797 204 PRLVRALAEIDAIELDEGTDWFQPSNIETIDLTVGNPATNVIPGKASARLSIRFNDQHRGQDLIERIER 272 ********************************************************************* PP TIGR01246 271 ildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGl 339 i+++h ++ ++ ge+flt+ g l + + +aie ++++pelstsGGtsDarf+ ++ + vve+Gl lcl|FitnessBrowser__Korea:Ga0059261_0797 273 IVHAHAPAGIVRGRVYGEAFLTEPGTLSTLISDAIEVETGIRPELSTSGGTSDARFLSRI-CPVVEFGL 340 ************************************************************.******** PP TIGR01246 340 vndtihkvneavkiedleklsevyekllee 369 +n+t+hk++eav ++dl+kl+++ye+ll++ lcl|FitnessBrowser__Korea:Ga0059261_0797 341 LNATMHKLDEAVALDDLHKLTAIYETLLRR 370 ***************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (370 nodes) Target sequences: 1 (373 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: 9.80 // [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