Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate YP_426271.1 Rru_A1183 diaminopimelate epimerase
Query= curated2:B6IP82 (291 letters) >NCBI__GCF_000013085.1:YP_426271.1 Length = 280 Score = 305 bits (780), Expect = 1e-87 Identities = 153/270 (56%), Positives = 183/270 (67%), Gaps = 3/270 (1%) Query: 5 FLKMHGLGNDFVVLDARRDPLPLTTAAARAIADRHTGVGCDQIVLLEPPRHPAADLFMRI 64 FLKMHGLGNDF+V+DAR PL LT RA+ADRH+GVGCDQ V +EP R FM + Sbjct: 8 FLKMHGLGNDFIVIDARTRPLDLTPERVRALADRHSGVGCDQFVTIEPARGGGV-AFMGL 66 Query: 65 LNPDGSESGACGNATRCVASLVADGSGRAEVTVETATGLLRCRLRADGSVTVDMGPARLD 124 N DG +CGNA+RCV L+ + V +ET G++ R + + VDMGPARL Sbjct: 67 RNADGEIVESCGNASRCVGRLLLEEREAESVLIETLGGMVEARRASGELIEVDMGPARLT 126 Query: 125 WTQIPLAAAHDTLRVPAGAGPLQDACCVGMGNPHAVFFVDDAEAVDLATLGPVLEHHSLF 184 W +IPLA A DTL + GPL D C V MGNPHAVFFVDDA+A+DLAT GP++EHH LF Sbjct: 127 WQEIPLAGAADTLHIELSVGPLSDPCAVSMGNPHAVFFVDDADAIDLATWGPLIEHHGLF 186 Query: 185 PQRCNIEVAQVLAPDHIRMRVWERGAGITRACGSGSCATLVAAARRGL-TGRAAWIELDG 243 P R N+E + A +RMRVWERG GITRACG+G+CA+ VAA RRGL GR A + LDG Sbjct: 187 PNRTNVEAVHLRADGRLRMRVWERGVGITRACGTGACASAVAAMRRGLIAGRTAEVVLDG 246 Query: 244 GRLWIEW-HGDGHVLMTGPVATAFTGELSE 272 G L I W DGHVLMTG A++G L E Sbjct: 247 GTLGIVWRESDGHVLMTGSATLAYSGVLDE 276 Lambda K H 0.322 0.137 0.435 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: 350 Number of extensions: 17 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: 291 Length of database: 280 Length adjustment: 26 Effective length of query: 265 Effective length of database: 254 Effective search space: 67310 Effective search space used: 67310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate YP_426271.1 Rru_A1183 (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.6564.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-79 251.5 0.0 5.7e-79 251.3 0.0 1.0 1 lcl|NCBI__GCF_000013085.1:YP_426271.1 Rru_A1183 diaminopimelate epimer Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_426271.1 Rru_A1183 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.3 0.0 5.7e-79 5.7e-79 2 268 .. 7 274 .. 6 276 .. 0.95 Alignments for each domain: == domain 1 score: 251.3 bits; conditional E-value: 5.7e-79 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemC 73 +FlkmhGlgNdF+++d +++ l + +e+vr+++drh gvg+D+++++ep+ + + ++N+DG +e C lcl|NCBI__GCF_000013085.1:YP_426271.1 7 HFLKMHGLGNDFIVIDARTRPLDLT-PERVRALADRHSGVGCDQFVTIEPARGGGVAFMGLRNADGEIVESC 77 6******************766666.************************99999999************** PP TIGR00652 74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellal 145 GN++Rc+ + + e+ + +++ +etl g++++ + + ++vdmg ++++ +eipl ++ ++ + el lcl|NCBI__GCF_000013085.1:YP_426271.1 78 GNASRCVGRLLLEEREA--ESVLIETLGGMVEARRASGE-LIEVDMGPARLTWQEIPLAGAADTLHIELSVG 146 *************9999..7**************99999.*******************9999998888877 PP TIGR00652 146 ev...lvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaC 214 + ++v++GnPH+v+fv+d + +dl ++g+l+e+h fp+++Nve v+ + ++++rv+ERG+g+T+aC lcl|NCBI__GCF_000013085.1:YP_426271.1 147 PLsdpCAVSMGNPHAVFFVDDADAIDLATWGPLIEHHGLFPNRTNVEAVHLRADGRLRMRVWERGVGITRAC 218 775555****************************************************************** PP TIGR00652 215 GtGavAsavvalklgktkkk.vtvhleggeLeievkedg.kvyltGpavlvlegel 268 GtGa+Asav+a++ g+ + ++v+l+gg L i ++e++ +v++tG+a+l ++g+l lcl|NCBI__GCF_000013085.1:YP_426271.1 219 GTGACASAVAAMRRGLIAGRtAEVVLDGGTLGIVWRESDgHVLMTGSATLAYSGVL 274 **************9999888**************99877************9987 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: 8.32 // [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