Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate H281DRAFT_02200 H281DRAFT_02200 diaminopimelate epimerase
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__Burk376:H281DRAFT_02200 Length = 287 Score = 283 bits (725), Expect = 2e-81 Identities = 150/283 (53%), Positives = 184/283 (65%), Gaps = 9/283 (3%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 ++F+KMHG GNDF+V+D TQ V +P +R LADRH GVG DQLL+VE P +DF Y Sbjct: 3 LKFTKMHGAGNDFVVLDGYTQPVNLTPAQVRALADRHFGVGADQLLLVEKPTVEGVDFRY 62 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 RIFN DG EV CGNGARCF +FVR GLT++R +RV NG + LT+ ++ V V+MG Sbjct: 63 RIFNCDGGEVEHCGNGARCFVKFVRDSGLTDQRSVRVQVQNGTITLTMQENGEVLVDMGA 122 Query: 121 PNFEPSAVPF-------RANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVE 173 P F+P VPF R A+ + + T VVSMGNPH V V+DV+ V Sbjct: 123 PVFDPERVPFATKGLEGRREGADTLWPLDVNGTTRWISVVSMGNPHAVQVVEDVEQFPVL 182 Query: 174 TLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGL 233 GPV+E H RFP+R N GFMQ+V R I+LRVYERGAGET ACG+GACAAVA GI++GL Sbjct: 183 VEGPVIERHARFPQRVNAGFMQIVGRSEIKLRVYERGAGETLACGTGACAAVAAGIRRGL 242 Query: 234 LAEEVRVELPGGRLDIAW--KGPGHPLYMTGPAVHVYDGFIHL 274 L V V GG+L I+W K PL M GPA V+ G I L Sbjct: 243 LDAPVLVHTHGGKLTISWDSKQQNEPLLMAGPATTVFQGEIEL 285 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: 252 Number of extensions: 6 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: 287 Length adjustment: 26 Effective length of query: 248 Effective length of database: 261 Effective search space: 64728 Effective search space used: 64728 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 H281DRAFT_02200 H281DRAFT_02200 (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.11011.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-92 295.6 0.0 2e-92 295.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_02200 H281DRAFT_02200 diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_02200 H281DRAFT_02200 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 295.4 0.0 2e-92 2e-92 2 268 .. 4 283 .. 3 285 .. 0.93 Alignments for each domain: == domain 1 score: 295.4 bits; conditional E-value: 2e-92 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsD 66 +F+kmhG+gNdFv++d ++ + + +++vr+++drh+gvgaD++llve+ + e d+++rifN D lcl|FitnessBrowser__Burk376:H281DRAFT_02200 4 KFTKMHGAGNDFVVLDGYTQPVNLT-PAQVRALADRHFGVGADQLLLVEKpTVEGVDFRYRIFNCD 68 8******************766666.**********************9989999*********** PP TIGR00652 67 GSeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt 132 G e+e CGNg+Rcf+kfv+++gl+++++++v++++g+i+++++e++ +v vdmg p f +e +p+ lcl|FitnessBrowser__Burk376:H281DRAFT_02200 69 GGEVEHCGNGARCFVKFVRDSGLTDQRSVRVQVQNGTITLTMQENG-EVLVDMGAPVFDPERVPFA 133 **********************************************.******************* PP TIGR00652 133 vekeeekeellalev.........l..vvdvGnPHlvvfvedvekldleelgklleaheefpegvN 187 +++ e ++e + + + vv++GnPH+v +vedve++++ g+++e h +fp++vN lcl|FitnessBrowser__Burk376:H281DRAFT_02200 134 TKGLEGRREGADTLWpldvngttrWisVVSMGNPHAVQVVEDVEQFPVLVEGPVIERHARFPQRVN 199 777666666655333556577766268*************************************** PP TIGR00652 188 vefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg. 252 f+++++++eiklrvyERGageTlaCGtGa+A+++++++ g+++ v vh++gg+L+i++ ++ lcl|FitnessBrowser__Burk376:H281DRAFT_02200 200 AGFMQIVGRSEIKLRVYERGAGETLACGTGACAAVAAGIRRGLLDAPVLVHTHGGKLTISWDSKQq 265 *************************************************************87665 PP TIGR00652 253 ..kvyltGpavlvlegel 268 +++ Gpa++v++ge+ lcl|FitnessBrowser__Burk376:H281DRAFT_02200 266 nePLLMAGPATTVFQGEI 283 578*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (287 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: 00:00:00.00 # Mc/sec: 8.31 // [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