Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate NP_662896.1 CT2021 diaminopimelate epimerase
Query= curated2:Q8KAX9 (257 letters) >NCBI__GCF_000006985.1:NP_662896.1 Length = 257 Score = 527 bits (1358), Expect = e-155 Identities = 257/257 (100%), Positives = 257/257 (100%) Query: 1 MSGAGNDFIVIDNRQGLFNLTHEQVRAMCTRRTGIGADGLILLETSETADFRMNYHNADG 60 MSGAGNDFIVIDNRQGLFNLTHEQVRAMCTRRTGIGADGLILLETSETADFRMNYHNADG Sbjct: 1 MSGAGNDFIVIDNRQGLFNLTHEQVRAMCTRRTGIGADGLILLETSETADFRMNYHNADG 60 Query: 61 FPGTMCGNGGRCAVWFAHLIGIRPTGKHYRFEAGPSTYEAEVTGEESVRLHMLPPSDFRD 120 FPGTMCGNGGRCAVWFAHLIGIRPTGKHYRFEAGPSTYEAEVTGEESVRLHMLPPSDFRD Sbjct: 61 FPGTMCGNGGRCAVWFAHLIGIRPTGKHYRFEAGPSTYEAEVTGEESVRLHMLPPSDFRD 120 Query: 121 GLQAGAWNCHFVDTGSPHAIAYVNNLDQLDVLTEGGNIRHNKELFPDGTNVNFLEITAPD 180 GLQAGAWNCHFVDTGSPHAIAYVNNLDQLDVLTEGGNIRHNKELFPDGTNVNFLEITAPD Sbjct: 121 GLQAGAWNCHFVDTGSPHAIAYVNNLDQLDVLTEGGNIRHNKELFPDGTNVNFLEITAPD 180 Query: 181 ALSIRTFERGVEDETLACGTGTVAAALMSFRLGKVTSSLVRVKVKSGETLMVGFNEMMDE 240 ALSIRTFERGVEDETLACGTGTVAAALMSFRLGKVTSSLVRVKVKSGETLMVGFNEMMDE Sbjct: 181 ALSIRTFERGVEDETLACGTGTVAAALMSFRLGKVTSSLVRVKVKSGETLMVGFNEMMDE 240 Query: 241 IYLEGPARAVYRGTITL 257 IYLEGPARAVYRGTITL Sbjct: 241 IYLEGPARAVYRGTITL 257 Lambda K H 0.320 0.138 0.417 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: 393 Number of extensions: 9 Number of successful extensions: 1 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: 257 Length of database: 257 Length adjustment: 24 Effective length of query: 233 Effective length of database: 233 Effective search space: 54289 Effective search space used: 54289 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 NP_662896.1 CT2021 (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.24628.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-68 216.2 0.0 4.8e-68 215.5 0.0 1.3 1 lcl|NCBI__GCF_000006985.1:NP_662896.1 CT2021 diaminopimelate epimerase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000006985.1:NP_662896.1 CT2021 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.5 0.0 4.8e-68 4.8e-68 6 268 .. 1 255 [. 1 257 [] 0.91 Alignments for each domain: == domain 1 score: 215.5 bits; conditional E-value: 4.8e-68 TIGR00652 6 mhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemCGNgi 77 m+G+gNdF+++d+++ l++ + e+vr++c+r+tg+gaDg++l+e+ se+ad+++++ N+DG +mCGNg lcl|NCBI__GCF_000006985.1:NP_662896.1 1 MSGAGNDFIVIDNRQ-GLFNLTHEQVRAMCTRRTGIGADGLILLET-SETADFRMNYHNADGFPGTMCGNGG 70 89************9.5556669**********************6.************************* PP TIGR00652 78 Rcfakfvyekglke.kkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalevl 148 Rc++ f+ g+ k++++e+ ++++ev+ e+ +v+ m p+ ++ ++ +++ + lcl|NCBI__GCF_000006985.1:NP_662896.1 71 RCAVWFAHLIGIRPtGKHYRFEAGPSTYEAEVTGEE-SVRLHMLPPSDFRDGLQAGAWNCHF---------- 131 ********99997414889*****************.*********7777777766654444.......... PP TIGR00652 149 vvdvGnPHlvvfvedvekldleelgklleah.eefpegvNvefvevkkedeiklrvyERG.ageTlaCGtGa 218 vd+G PH++ v+++++ld+ + g ++++ e fp+g+Nv+f+e++ +d++ +r++ERG ++eTlaCGtG+ lcl|NCBI__GCF_000006985.1:NP_662896.1 132 -VDTGSPHAIAYVNNLDQLDVLTEGGNIRHNkELFPDGTNVNFLEITAPDALSIRTFERGvEDETLACGTGT 202 .9*******************99988888761567************************************* PP TIGR00652 219 vAsavvalklgktkkk.vtvhlegg.eLeievkedg.kvyltGpavlvlegel 268 vA+a+++ +lgk+ ++ v+v++++g L++ ++e ++yl+Gpa+ v++g++ lcl|NCBI__GCF_000006985.1:NP_662896.1 203 VAAALMSFRLGKVTSSlVRVKVKSGeTLMVGFNEMMdEIYLEGPARAVYRGTI 255 ****************9****9988689*****9999**************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (257 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2.50 // [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