Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_015739361.1 ADEG_RS06980 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >NCBI__GCF_000024605.1:WP_015739361.1 Length = 279 Score = 249 bits (637), Expect = 4e-71 Identities = 140/280 (50%), Positives = 175/280 (62%), Gaps = 14/280 (5%) Query: 6 FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRM 65 F KMHGLGN ++ V +P D +A KV + G+GADG++ I PS+ A + MR+ Sbjct: 3 FVKMHGLGNDFVVV--MARTLPP-DTPELARKVCRPHFGVGADGLVFILPSEEADITMRI 59 Query: 66 FNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKIDM 125 FN DGSE + CGN +RCVAK AYE +L+ I T AGI E+TV++GKV +DM Sbjct: 60 FNADGSEAEMCGNAIRCVAKLAYETRLIPYQRMRIATGAGIKPVELTVKDGKVVSCTVDM 119 Query: 126 GAPRLTRAEIPMLGEG----ETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPL 181 G P L R+ IPM G P I E+ L TA+S GNPH V+FV VE+AP+ Sbjct: 120 GEPILERSAIPMQGPPGKVVNEPLIFEDGLV----LRVTALSFGNPHCVLFVPAVEEAPV 175 Query: 182 TTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNG 241 LGP LE H FP R NVEF+E++ E+ RVWERG G T ACG+GACAA VASILNG Sbjct: 176 EELGPRLEHHPAFPHRTNVEFVEVVGPSEIRVRVWERGVGETLACGSGACAAAVASILNG 235 Query: 242 KMERGKEITVHLAGGDLMIAWTEE-GNVLMKGPAEVICRG 280 R EI VHL GGDL I W EE G+V ++GPA + +G Sbjct: 236 YTAR--EIVVHLPGGDLRIHWKEEDGHVYLQGPATTVFKG 273 Lambda K H 0.318 0.136 0.398 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: 270 Number of extensions: 15 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: 288 Length of database: 279 Length adjustment: 26 Effective length of query: 262 Effective length of database: 253 Effective search space: 66286 Effective search space used: 66286 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_015739361.1 ADEG_RS06980 (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.7666.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-97 311.7 0.0 2.4e-97 311.5 0.0 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015739361.1 ADEG_RS06980 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015739361.1 ADEG_RS06980 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 311.5 0.0 2.4e-97 2.4e-97 1 268 [. 1 275 [. 1 277 [. 0.94 Alignments for each domain: == domain 1 score: 311.5 bits; conditional E-value: 2.4e-97 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSe 69 m+F+kmhGlgNdFv+v ++ l+ ++el+rkvc+ h+gvgaDg++++ p seead+++rifN+DGSe lcl|NCBI__GCF_000024605.1:WP_015739361.1 1 MHFVKMHGLGNDFVVVMART--LPPDTPELARKVCRPHFGVGADGLVFILP-SEEADITMRIFNADGSE 66 89**************9888..88888***********************8.***************** PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeen...kkvkvdmgepkfkkeeipltvek 135 aemCGN+iRc+ak +ye+ l +++++ t ag+ ve++ ++ ++ +vdmgep +++++ip+++ + lcl|NCBI__GCF_000024605.1:WP_015739361.1 67 AEMCGNAIRCVAKLAYETRLIPYQRMRIATGAGIKPVELTVKDgkvVSCTVDMGEPILERSAIPMQGPP 135 *****************************************998777889****************777 PP TIGR00652 136 eeekeellalev...l...vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkede 198 ++ +e l +e l +++ GnPH+v+fv ve++++eelg+ le+h++fp ++Nvefvev++++e lcl|NCBI__GCF_000024605.1:WP_015739361.1 136 GKVVNEPLIFEDglvLrvtALSFGNPHCVLFVPAVEEAPVEELGPRLEHHPAFPHRTNVEFVEVVGPSE 204 7766666555555551446************************************************** PP TIGR00652 199 iklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvleg 266 i++rv+ERG+geTlaCG+Ga+A+av+++ g t +++ vhl+gg+L i++ke++ +vyl+Gpa++v++g lcl|NCBI__GCF_000024605.1:WP_015739361.1 205 IRVRVWERGVGETLACGSGACAAAVASILNGYTAREIVVHLPGGDLRIHWKEEDgHVYLQGPATTVFKG 273 **************************************************99877*************9 PP TIGR00652 267 el 268 e lcl|NCBI__GCF_000024605.1:WP_015739361.1 274 EW 275 85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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: 00:00:00.00 # Mc/sec: 10.68 // [ok]
This GapMind analysis is from Apr 10 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