Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate N515DRAFT_3112 N515DRAFT_3112 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__Dyella79:N515DRAFT_3112 Length = 280 Score = 275 bits (702), Expect = 1e-78 Identities = 135/271 (49%), Positives = 181/271 (66%), Gaps = 1/271 (0%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++FSKMHG+GNDF++VDA E IR LADRH GVGFDQL+ +EPP D F+Y Sbjct: 3 LRFSKMHGIGNDFVMVDARAAGFALDAEEIRALADRHAGVGFDQLISIEPPRDASCRFYY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKG-LTNKRDIRVSTANGRMVLTVTDDDLVRVNMG 119 ++NADGS QCGNG RC A ++ G LT +R+ + +G + + + D V V+MG Sbjct: 63 GLWNADGSSANQCGNGVRCVAAWLHRAGELTLGETVRLESPSGPVTVRLLAADRVTVDMG 122 Query: 120 EPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVL 179 EP F P+ +PF A + Y + QT+ G VSMGNPH V+ VDD+ A+ LGP L Sbjct: 123 EPEFRPAQIPFDAAAPAERYALDTDGQTLEIGAVSMGNPHAVVTVDDLGAPALYRLGPAL 182 Query: 180 ESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVR 239 H RF + AN GF+++V R H+RLRV+ERG+G T+ACG+GACAA+AV +G + + V+ Sbjct: 183 TGHPRFAQGANAGFVRIVDRGHLRLRVHERGSGWTRACGTGACAAMAVLRLRGEVDDSVQ 242 Query: 240 VELPGGRLDIAWKGPGHPLYMTGPAVHVYDG 270 V+LPGGRL I W GPGH L+MTGPA ++G Sbjct: 243 VDLPGGRLQIDWAGPGHTLWMTGPAAFAFEG 273 Lambda K H 0.323 0.140 0.425 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: 285 Number of extensions: 14 Number of successful extensions: 2 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: 274 Length of database: 280 Length adjustment: 25 Effective length of query: 249 Effective length of database: 255 Effective search space: 63495 Effective search space used: 63495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 bits)
Align candidate N515DRAFT_3112 N515DRAFT_3112 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))
# 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/TIGR00652.hmm # target sequence database: /tmp/gapView.26854.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00652 [M=270] Accession: TIGR00652 Description: DapF: diaminopimelate epimerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-81 257.7 0.0 7.4e-81 257.5 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 N515DRAFT_3112 diaminopimelate e Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 N515DRAFT_3112 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.5 0.0 7.4e-81 7.4e-81 2 267 .. 4 274 .. 3 277 .. 0.91 Alignments for each domain: == domain 1 score: 257.5 bits; conditional E-value: 7.4e-81 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsD 66 +F+kmhG gNdFv+vd + + + ae++r+++drh gvg+D+++ +ep + + +++ ++N+D lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 4 RFSKMHGIGNDFVMVDARAAGFALD-AEEIRALADRHAGVGFDQLISIEPpRDASCRFYYGLWNAD 68 8******************877777.9**********************977778899999***** PP TIGR00652 67 GSeaemCGNgiRcfakfvyek.glkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipl 131 GS+a++CGNg+Rc+a+++ +l+ +++++e+ +g ++v + +++ +v+vdmgep+f++++ip+ lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 69 GSSANQCGNGVRCVAAWLHRAgELTLGETVRLESPSGPVTVRLLAAD-RVTVDMGEPEFRPAQIPF 133 *****************98761567789*******************.****************** PP TIGR00652 132 tvekeeekeellalev.l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvev 193 +++ +e++ l + l +v++GnPH+vv v+d+ +l +lg++l h++f++g N fv++ lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 134 DAAAPAERYALDTDGQtLeigAVSMGNPHAVVTVDDLGAPALYRLGPALTGHPRFAQGANAGFVRI 199 *55555544433322222335********************************************* PP TIGR00652 194 kkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltG 258 +++ +++lrv+ERG+g T+aCGtGa+A+++v + g+++++v+v l+gg+L+i++ g ++++tG lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 200 VDRGHLRLRVHERGSGWTRACGTGACAAMAVLRLRGEVDDSVQVDLPGGRLQIDWAGPGhTLWMTG 265 ***********************************************************99***** PP TIGR00652 259 pavlvlege 267 pa + +ege lcl|FitnessBrowser__Dyella79:N515DRAFT_3112 266 PAAFAFEGE 274 ******997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (280 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.45 // [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