Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_050762303.1 DEBA_RS09375 diaminopimelate epimerase
Query= curated2:O67693 (279 letters) >NCBI__GCF_000143965.1:WP_050762303.1 Length = 294 Score = 217 bits (553), Expect = 2e-61 Identities = 128/282 (45%), Positives = 175/282 (62%), Gaps = 21/282 (7%) Query: 1 MEFWKLQGSGNDFVVIDDRDEKLESFLKERGVSKEDFVRKVCAFHTGVGADGLILIKNPD 60 +EF K+ G+GNDF++ID+R +L L + +C VGADGLI++ Sbjct: 13 VEFCKMTGTGNDFILIDNRRARLAPALMPA------LAKALCCRRRSVGADGLIVLSPSQ 66 Query: 61 NPEN-----DFKWEFFNSDGSVAEMCGNGSRCAVRFAYERGIVGNKVRFETLAGVIKAEV 115 + DF+W+FFN+DGS AEMCGNG RCA RFA G+ G ++ F+TLAG I+A V Sbjct: 67 RVDAALGKIDFRWDFFNADGSSAEMCGNGGRCAARFAVSIGLAGPELIFDTLAGPIRAWV 126 Query: 116 YENGRK-VKVQLTPPSK-PEEKTLTVDGEEVIGVFINTGVPHFVVPVEDVEKVNVIKLGR 173 GR+ V ++LTPP+ ++ L + G + +NTGVPH VVPV+D+ +V GR Sbjct: 127 ---GRQTVTLELTPPTGWYDDLRLEIGGRTMTIHGVNTGVPHAVVPVDDLSSADVKNWGR 183 Query: 174 AIRFHEEFQPKGTNVNFVQPVSEDTIKVRTYERGVESETLACGTGATACAIVSYLKGLVK 233 IRFH F P GTNVNF+ ++VRTYERGVE ETLACGTGA A A+++ G + Sbjct: 184 EIRFHRHFAPAGTNVNFI-AARHGRLEVRTYERGVEDETLACGTGAVASALMAGRLGWL- 241 Query: 234 KKPVNVLTRSGEVLTIDFSED---LKEVFLTGSVYKVFEGRL 272 K P+ V RSGE LTI FS+D +++V L G+ V++G L Sbjct: 242 KSPITVAVRSGEKLTIHFSQDESGVRQVRLEGAADHVYDGVL 283 Lambda K H 0.317 0.138 0.399 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: 232 Number of extensions: 13 Number of successful extensions: 6 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: 279 Length of database: 294 Length adjustment: 26 Effective length of query: 253 Effective length of database: 268 Effective search space: 67804 Effective search space used: 67804 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_050762303.1 DEBA_RS09375 (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.20970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-74 236.2 0.0 2.6e-74 236.0 0.0 1.0 1 lcl|NCBI__GCF_000143965.1:WP_050762303.1 DEBA_RS09375 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_050762303.1 DEBA_RS09375 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 236.0 0.0 2.6e-74 2.6e-74 2 268 .. 14 283 .. 13 285 .. 0.94 Alignments for each domain: == domain 1 score: 236.0 bits; conditional E-value: 2.6e-74 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkee.aelvrkvcdrhtgvgaDgvllvep......sseeadvklrif 63 eF km G+gNdF+l+d++ ++l ++l++++c r+ +vgaDg++++ p + + d+++++f lcl|NCBI__GCF_000143965.1:WP_050762303.1 14 EFCKMTGTGNDFILIDNRRARLAPALmPALAKALCCRRRSVGADGLIVLSPsqrvdaALGKIDFRWDFF 82 8******************98887767************************88888778899******* PP TIGR00652 64 NsDGSeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt 132 N+DGS+aemCGNg Rc+a+f+++ gl+ el + tlag i + v ++ v+ +++ p+ ++ +l+ lcl|NCBI__GCF_000143965.1:WP_050762303.1 83 NADGSSAEMCGNGGRCAARFAVSIGLAG-PELIFDTLAGPIRAWVGRQT--VTLELTPPTGWYDDLRLE 148 ***************************7.9***************9998..********9999999999 PP TIGR00652 133 vekeeekeellalevlvvdvGnPHlvvfvedvekldleelgklleaheef.pegvNvefvevkkedeik 200 + + ++ ++ v++G+PH+vv+v+d++++d++++g+++++h +f p+g+Nv+f+ + + ++ lcl|NCBI__GCF_000143965.1:WP_050762303.1 149 IGGRTM--TIH-----GVNTGVPHAVVPVDDLSSADVKNWGREIRFHRHFaPAGTNVNFIAARH-GRLE 209 866655..333.....49******************************************9988.**** PP TIGR00652 201 lrvyERG.ageTlaCGtGavAsavvalklgktkkkvtvhlegg.eLeievkedg....kvyltGpavlv 263 +r+yERG ++eTlaCGtGavAsa++a +lg +k+ +tv +++g +L+i++++d+ +v l+G+a +v lcl|NCBI__GCF_000143965.1:WP_050762303.1 210 VRTYERGvEDETLACGTGAVASALMAGRLGWLKSPITVAVRSGeKLTIHFSQDEsgvrQVRLEGAADHV 278 ***************************************998879*****9997778899********* PP TIGR00652 264 legel 268 ++g+l lcl|NCBI__GCF_000143965.1:WP_050762303.1 279 YDGVL 283 ***87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (294 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: 8.55 // [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