Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate Ac3H11_1993 Diaminopimelate epimerase (EC 5.1.1.7)
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1993 Length = 286 Score = 273 bits (697), Expect = 4e-78 Identities = 146/281 (51%), Positives = 182/281 (64%), Gaps = 12/281 (4%) Query: 6 MHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNA 65 M G GNDF+V+D + S R LADRH GVG DQ+L V P +DF Y I NA Sbjct: 1 MQGAGNDFVVLDETQGRLGLSAAQYRFLADRHFGVGADQILTVRPSPAEGIDFEYVIHNA 60 Query: 66 DGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNFEP 125 DG EV QCGNGARCFARFV KGLT K IRV T +G + +T D V V+MG P F+P Sbjct: 61 DGGEVEQCGNGARCFARFVHDKGLTGKDQIRVQTQSGVIAPRLTADGRVTVDMGRPEFDP 120 Query: 126 SAVPFRANK--------AEKTYIM---RAAEQTILCGVVSMGNPHCVIQVDDVDTAAVET 174 + VPF A+ +K + +A +L +VSMGNPH V VD+VDTA V+ Sbjct: 121 AKVPFDASGLVPVAQGLGQKWPLPPDGKALSAIVLVAIVSMGNPHAVQLVDNVDTAPVQE 180 Query: 175 LGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLL 234 GP++ESH RFP+R N G++Q+V R H+RLRV+ERG GET ACG+GACAAVA GI+ GLL Sbjct: 181 TGPLIESHPRFPQRVNAGYLQIVDRAHVRLRVFERGVGETLACGTGACAAVAAGIRLGLL 240 Query: 235 AEEVRVELPGGRLDIAWKG-PGHPLYMTGPAVHVYDGFIHL 274 EV+V+ GGRL IAW G ++MTGPA V++G I + Sbjct: 241 DPEVQVDTRGGRLTIAWSGQEADSVFMTGPATTVFEGQIDI 281 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: 272 Number of extensions: 11 Number of successful extensions: 4 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: 286 Length adjustment: 26 Effective length of query: 248 Effective length of database: 260 Effective search space: 64480 Effective search space used: 64480 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 Ac3H11_1993 (Diaminopimelate epimerase (EC 5.1.1.7))
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.6828.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-86 274.3 0.0 7e-86 274.0 0.0 1.1 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 Diaminopimelate epimerase (EC 5. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 Diaminopimelate epimerase (EC 5.1.1.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 274.0 0.0 7e-86 7e-86 6 268 .. 1 279 [. 1 281 [. 0.93 Alignments for each domain: == domain 1 score: 274.0 bits; conditional E-value: 7e-86 TIGR00652 6 mhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsD 66 m+G+gNdFv++de + +l + a++ r ++drh+gvgaD++l+v+p e d+++ i N+D lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 1 MQGAGNDFVVLDETQGRLGLS-AAQYRFLADRHFGVGADQILTVRPsPAEGIDFEYVIHNAD 61 89*************888888.9**********************9777889********** PP TIGR00652 67 GSeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkee 128 G e+e+CGNg+Rcfa+fv +kgl+ k++++v+t++g+i +++++ +v+vdmg+p+f +++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 62 GGEVEQCGNGARCFARFVHDKGLTGKDQIRVQTQSGVIAPRLTADG-RVTVDMGRPEFDPAK 122 **********************************************.*************** PP TIGR00652 129 ipltvekeeekeellalev.............l..vvdvGnPHlvvfvedvekldleelgkl 175 +p+++++ + l ++ l +v++GnPH+v v++v++++++e+g+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 123 VPFDASGLVPVAQGLGQKWplppdgkalsaivLvaIVSMGNPHAVQLVDNVDTAPVQETGPL 184 ****76665555555545466777888777651689************************** PP TIGR00652 176 leaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtv 237 +e+h++fp++vN +++++++ +++lrv+ERG+geTlaCGtGa+A+++++++lg+++ +v+v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 185 IESHPRFPQRVNAGYLQIVDRAHVRLRVFERGVGETLACGTGACAAVAAGIRLGLLDPEVQV 246 ************************************************************** PP TIGR00652 238 hleggeLeievkedg..kvyltGpavlvlegel 268 ++gg+L+i ++ ++ +v++tGpa++v+eg++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1993 247 DTRGGRLTIAWSGQEadSVFMTGPATTVFEGQI 279 ***********9888789*************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (286 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: 9.63 // [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