Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_012674975.1 SULAZ_RS04740 diaminopimelate epimerase
Query= curated2:A8MH77 (280 letters) >NCBI__GCF_000021545.1:WP_012674975.1 Length = 288 Score = 224 bits (571), Expect = 2e-63 Identities = 111/274 (40%), Positives = 171/274 (62%), Gaps = 5/274 (1%) Query: 5 FKKMQGTGNDFIVVKYDDFPFEEKLSQLAEKICDRHFGIGADGLLIVNPSSIADIRMDYY 64 F K G GND+IV+ ++ FE +KICD H+GIG+DG+L+ PSS+AD ++ + Sbjct: 6 FVKSHGLGNDYIVIDSENITFEIT-QDFIKKICDVHYGIGSDGILVKYPSSVADFKLRIF 64 Query: 65 NSDGSIAAMCGNGIRCFSKFVFDEGFLRTKQFSVETLDGIKEIAIIEEK---GTVKSVEV 121 N DGS A GNG+R F KF++D G+ ++F+VET G+ A IEEK G K + V Sbjct: 65 NPDGSEAEKSGNGLRIFCKFLYDYGYTNKEEFTVETKGGLVR-AKIEEKNKFGKAKVITV 123 Query: 122 NMGQVTYDTEKIPVVSEDGYFINKKITVGGQDFIITAVSMGVPHVIIFTEKLDLEQIKFF 181 +MG+ ++ KIPV ++ F+ +K+ VG +++ + VS+G PH +I ++L+ E+IK + Sbjct: 124 DMGKAIFEASKIPVKTDKKEFLGEKVKVGDKEYEVNCVSVGNPHCVIIKKELNEEEIKTY 183 Query: 182 GPLIEKHAIFPKKTNVNFVHRIDKDNIAVRTWERGAGYTLACGTGSTSAVAVANKLGLVN 241 G LIE H +FP + NV FV I +D + WERGAG+T A G+ S + +V K GL Sbjct: 184 GSLIENHPLFPNRINVQFVKPISEDQAEILIWERGAGFTYASGSSSCAVASVLVKKGLAK 243 Query: 242 NNVNVEVEGGNIKIKIKESGNLFMEGPAENICSG 275 N++ +++ GG +KI + + N+ M G + IC G Sbjct: 244 NDITIKMIGGELKITVDKDWNIRMTGEVQEICRG 277 Lambda K H 0.321 0.140 0.407 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: 220 Number of extensions: 9 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: 280 Length of database: 288 Length adjustment: 26 Effective length of query: 254 Effective length of database: 262 Effective search space: 66548 Effective search space used: 66548 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_012674975.1 SULAZ_RS04740 (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.29472.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-81 259.4 0.6 2.2e-81 259.2 0.6 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012674975.1 SULAZ_RS04740 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674975.1 SULAZ_RS04740 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.2 0.6 2.2e-81 2.2e-81 3 268 .. 6 279 .. 4 281 .. 0.93 Alignments for each domain: == domain 1 score: 259.2 bits; conditional E-value: 2.2e-81 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeae 71 F+k hGlgNd++++d+ + ++ + +++++k+cd+h g+g+Dg+l+ p s+ ad+klrifN DGSeae lcl|NCBI__GCF_000021545.1:WP_012674975.1 6 FVKSHGLGNDYIVIDSENITFEIT-QDFIKKICDVHYGIGSDGILVKYP-SSVADFKLRIFNPDGSEAE 72 99*************998555555.8*****************999997.******************* PP TIGR00652 72 mCGNgiRcfakfvyekglkekkelsvetlaglikveveeen.....kkvkvdmgepkfkkeeipltvek 135 GNg+R+f kf+y+ g+++k+e++vet+ gl+ +++ee+n k ++vdmg++ f++++ip++++k lcl|NCBI__GCF_000021545.1:WP_012674975.1 73 KSGNGLRIFCKFLYDYGYTNKEEFTVETKGGLVRAKIEEKNkfgkaKVITVDMGKAIFEASKIPVKTDK 141 ********************************************9999******************877 PP TIGR00652 136 eeekeellalev......l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkked 197 +e e ++ v + +v+vGnPH+v++ +++++ ++++ g+l+e+h+ fp+++Nv+fv+ +ed lcl|NCBI__GCF_000021545.1:WP_012674975.1 142 KEFLGEKVK--VgdkeyeVnCVSVGNPHCVIIKKELNEEEIKTYGSLIENHPLFPNRINVQFVKPISED 208 765433333..222354547************************************************* PP TIGR00652 198 eiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvleg 266 + + ++ERGag+T a G+ ++A+a v +k+g+ k+++t+++ ggeL+i+v +d ++ +tG+++ +++g lcl|NCBI__GCF_000021545.1:WP_012674975.1 209 QAEILIWERGAGFTYASGSSSCAVASVLVKKGLAKNDITIKMIGGELKITVDKDWNIRMTGEVQEICRG 277 ********************************************************************9 PP TIGR00652 267 el 268 + lcl|NCBI__GCF_000021545.1:WP_012674975.1 278 II 279 87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (288 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: 8.23 // [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