Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_013429569.1 CALKRO_RS02625 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >NCBI__GCF_000166775.1:WP_013429569.1 Length = 278 Score = 252 bits (644), Expect = 6e-72 Identities = 121/278 (43%), Positives = 187/278 (67%), Gaps = 5/278 (1%) Query: 6 FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRM 65 F+KMHGLGN +I ++ ++ + D L+A+++ + + G+GADG++L+ S +A ++MR+ Sbjct: 3 FSKMHGLGNDFIVIDARGKE--DIDYNLLAKRMCHRHIGVGADGLLLVLDSKLADIRMRI 60 Query: 66 FNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEE-GKVTLAKID 124 N+DGSE + CGNG+RC AKY +E +V+ T F +ETLAGI+ E+ + E G V K++ Sbjct: 61 INSDGSEAEMCGNGIRCFAKYVFERGIVKATKFKVETLAGIIEPELFINEYGLVDKVKVN 120 Query: 125 MGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTL 184 MG P R +IPM G+ ++ I + + + + Y T++ MG PH ++FVDD+E+ + TL Sbjct: 121 MGKPSFKRKDIPMQGDPKSDAINTSIVVDGNEYRITSLLMGVPHTILFVDDLEKVDIYTL 180 Query: 185 GPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKME 244 GP +E HE+FP + NV F++++++ + R WERG+G T ACGTG+CA+V+A+ LNG E Sbjct: 181 GPKIEKHEIFPRKTNVNFVQVIDKNNIKVRTWERGAGATFACGTGSCASVIAANLNGLTE 240 Query: 245 RGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVY 282 R + VHL G L I W E+G V M GPAE + G Y Sbjct: 241 R--KANVHLYFGILEIEWREDGIVFMTGPAEEVFVGEY 276 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: 237 Number of extensions: 13 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: 288 Length of database: 278 Length adjustment: 26 Effective length of query: 262 Effective length of database: 252 Effective search space: 66024 Effective search space used: 66024 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 WP_013429569.1 CALKRO_RS02625 (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.659850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-100 320.2 0.1 6.3e-100 320.0 0.1 1.0 1 NCBI__GCF_000166775.1:WP_013429569.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013429569.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 320.0 0.1 6.3e-100 6.3e-100 1 268 [. 1 276 [. 1 278 [] 0.93 Alignments for each domain: == domain 1 score: 320.0 bits; conditional E-value: 6.3e-100 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemC 73 m F+kmhGlgNdF+++d + +e + + l++++c+rh gvgaDg+llv +s+ ad+++ri NsDGSeaemC NCBI__GCF_000166775.1:WP_013429569.1 1 MLFSKMHGLGNDFIVIDARGKEDIDY-NLLAKRMCHRHIGVGADGLLLVL-DSKLADIRMRIINSDGSEAEMC 71 78*********************999.79*********************.5********************* PP TIGR00652 74 GNgiRcfakfvyekglkekkelsvetlaglikveveeen....kkvkvdmgepkfkkeeipltvekeeekeel 142 GNgiRcfak+v e+g+++ ++++vetlag+i+ e+ ++ kvkv+mg+p+fk+++ip+++++++ + NCBI__GCF_000166775.1:WP_013429569.1 72 GNGIRCFAKYVFERGIVKATKFKVETLAGIIEPELFINEyglvDKVKVNMGKPSFKRKDIPMQGDPKSDAINT 144 ************************************99999*99*******************7655442222 PP TIGR00652 143 lalev.......l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERG 207 v + + +G+PH ++fv+d+ek+d+ +lg+++e+he fp ++Nv+fv+v ++++ik+r++ERG NCBI__GCF_000166775.1:WP_013429569.1 145 SI--VvdgneyrItSLLMGVPHTILFVDDLEKVDIYTLGPKIEKHEIFPRKTNVNFVQVIDKNNIKVRTWERG 215 11..1123454526999******************************************************** PP TIGR00652 208 ageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 ag T aCGtG++As+++a+ g+t++k++vhl g Leie++edg v++tGpa+ v+ ge+ NCBI__GCF_000166775.1:WP_013429569.1 216 AGATFACGTGSCASVIAANLNGLTERKANVHLYFGILEIEWREDGIVFMTGPAEEVFVGEY 276 *********************************************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (278 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.31 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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