Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate 350076 BT0548 diaminopimelate epimerase (NCBI ptt file)
Query= SwissProt::Q81XR2 (288 letters) >FitnessBrowser__Btheta:350076 Length = 267 Score = 228 bits (582), Expect = 9e-65 Identities = 125/283 (44%), Positives = 169/283 (59%), Gaps = 20/283 (7%) Query: 2 SQFSFTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPV 61 ++ FTKMHG GN YIYV+ I + + + S +TGIG+DG+ILI SD A Sbjct: 3 TKIKFTKMHGAGNDYIYVDTTRYPIAAPEKKAI--EWSKFHTGIGSDGLILIGSSDKADF 60 Query: 62 KMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLA 121 MR+FN DGSE CGNG RCV KY YE+ L T++T +GI ++ VE GKVT Sbjct: 61 SMRIFNADGSEAMMCGNGSRCVGKYVYEYGLTAKKEITLDTRSGIKVLKLHVEGGKVTAV 120 Query: 122 KIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPL 181 +DMG+P E E + F + + T VSMGNPH V FV+D+ Q L Sbjct: 121 TVDMGSPL----------ETEAVDFGDQFPFQS-----TRVSMGNPHLVTFVEDITQINL 165 Query: 182 TTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNG 241 +GP LE + +FP+R NVEF +I+ ++ + RVWERGSG+TQACGTGACA VA++L+G Sbjct: 166 PEIGPQLENYHLFPDRTNVEFAQIVGKDTIRMRVWERGSGITQACGTGACATAVAAVLHG 225 Query: 242 KMERGKEITVHLAGGDLMIAWTE-EGNVLMKGPAEVICRGVYE 283 G++ + + GG + I W E G++LM GPA + G E Sbjct: 226 L--AGRKCDIIMDGGTVTIEWEEATGHILMTGPATKVFDGEME 266 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: 247 Number of extensions: 14 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: 288 Length of database: 267 Length adjustment: 25 Effective length of query: 263 Effective length of database: 242 Effective search space: 63646 Effective search space used: 63646 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 350076 BT0548 (diaminopimelate epimerase (NCBI ptt file))
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.14379.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-91 290.3 0.1 8.4e-91 290.1 0.1 1.0 1 lcl|FitnessBrowser__Btheta:350076 BT0548 diaminopimelate epimerase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350076 BT0548 diaminopimelate epimerase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.1 0.1 8.4e-91 8.4e-91 1 268 [. 5 265 .. 5 267 .] 0.93 Alignments for each domain: == domain 1 score: 290.1 bits; conditional E-value: 8.4e-91 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemCGNg 76 ++F+kmhG+gNd+++vd+ + ++ + + +++htg+g+Dg++l+ ss++ad+ +rifN+DGSea mCGNg lcl|FitnessBrowser__Btheta:350076 5 IKFTKMHGAGNDYIYVDTTRYPIAAP-EKKAIEWSKFHTGIGSDGLILIG-SSDKADFSMRIFNADGSEAMMCGNG 78 68****************99666666.78999******************.5************************ PP TIGR00652 77 iRcfakfvyekglkekkelsvetlaglikveveeen...kkvkvdmgepkfkkeeipltvekeeekeellalevlv 149 +Rc+ k+vye gl+ kke+++ t +g+ +++++ e+ + v+vdmg+p +++e++ + +++ + + ++ lcl|FitnessBrowser__Btheta:350076 79 SRCVGKYVYEYGLTAKKEITLDTRSGIKVLKLHVEGgkvTAVTVDMGSP-LETEAVDF---GDQFPFQSTR----- 145 ************************************99999********.44444333...3344445555..... PP TIGR00652 150 vdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavva 225 v++GnPHlv+fved+ +++l e+g++le+ + fp+++Nvef++++++d+i++rv+ERG+g+T+aCGtGa+A+av+a lcl|FitnessBrowser__Btheta:350076 146 VSMGNPHLVTFVEDITQINLPEIGPQLENYHLFPDRTNVEFAQIVGKDTIRMRVWERGSGITQACGTGACATAVAA 221 9*************************************************************************** PP TIGR00652 226 lklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 + g+ +k+++ ++gg ++ie++e++ ++++tGpa++v++ge+ lcl|FitnessBrowser__Btheta:350076 222 VLHGLAGRKCDIIMDGGTVTIEWEEATgHILMTGPATKVFDGEM 265 *************************999**************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (267 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: 6.13 // [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