Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_043879608.1 AZC_RS19115 diaminopimelate epimerase
Query= curated2:B2IEM1 (297 letters) >NCBI__GCF_000010525.1:WP_043879608.1 Length = 283 Score = 292 bits (747), Expect = 7e-84 Identities = 160/285 (56%), Positives = 193/285 (67%), Gaps = 13/285 (4%) Query: 4 LANRFVTKMNGLGNAIVVLDLRGTGIVISAAEARAIGQGKGLHFDQLMVLHDPLSPGSAA 63 LA+R KMNGLGN I+VLDLR + AA ARA+ + L FDQ MVL+ P +AA Sbjct: 2 LAHRPFVKMNGLGNEILVLDLRHEPEDVPAAAARALARPGVLPFDQAMVLYPPRRADTAA 61 Query: 64 FMRIYNIDGSLAGACGNGTRCVAWTLLREDHRIGAE-LMLETAAGQLACLKLAEDRFSVD 122 F+RI N DGS +GACGNGTRC+A E RIG ++ E+AAG L C+ + + +VD Sbjct: 62 FVRILNSDGSESGACGNGTRCIA---AYEAGRIGERHVLFESAAGLLDCVMQPDGQVTVD 118 Query: 123 MGKPAFAWDAIPLAHPVPDTNAVDLARDLAVLPPVDPDALRKASMVNMGNPHAVLFVADQ 182 MG P WDAIPLA PV DT+AV + A L P ASMV+MGNPHAV FV D Sbjct: 119 MGAPRLGWDAIPLARPVADTSAVQI-EGFASLGP--------ASMVSMGNPHAVFFVPDA 169 Query: 183 DACDLALVGPVLEHHPLFPDRANISIATVVSPDHIVLKVWERGAGATLACGSAACATLVA 242 +A D+ +G LEHHPLFP+RANIS A V+SPDHI+L VWERGAG T ACG+AACAT V+ Sbjct: 170 NAVDVEALGATLEHHPLFPERANISFAQVLSPDHILLHVWERGAGRTRACGTAACATGVS 229 Query: 243 AVRHGLAAREARISLPGGDLTIAWRAADDHVIMTGPVTFEFTTRL 287 R G R+ R++LPGGDL I WRA+D HV+MTGPV EFT L Sbjct: 230 TARTGRTGRKVRVTLPGGDLVIDWRASDGHVLMTGPVALEFTGTL 274 Lambda K H 0.323 0.137 0.418 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: 306 Number of extensions: 11 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: 297 Length of database: 283 Length adjustment: 26 Effective length of query: 271 Effective length of database: 257 Effective search space: 69647 Effective search space used: 69647 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_043879608.1 AZC_RS19115 (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.15798.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-68 217.0 0.0 1.9e-68 216.8 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_043879608.1 AZC_RS19115 diaminopimelate epim Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_043879608.1 AZC_RS19115 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.8 0.0 1.9e-68 1.9e-68 3 268 .. 7 274 .. 5 276 .. 0.89 Alignments for each domain: == domain 1 score: 216.8 bits; conditional E-value: 1.9e-68 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSea 70 F+km+GlgN+ +++d ++ +++ ++ +++ +r + +D+ +++ p ++ + +ri NsDGSe lcl|NCBI__GCF_000010525.1:WP_043879608.1 7 FVKMNGLGNEILVLDLRH--EPEDVPAAAARALARPGVLPFDQAMVLYPpRRADTAAFVRILNSDGSES 73 9*************9998..34444567777777888899***9999884666677778********** PP TIGR00652 71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt..vekee 137 CGNg Rc+a++ + + ++ +++ +e+ agl+ + ++ ++ +v+vdmg p++ ++ipl v ++ lcl|NCBI__GCF_000010525.1:WP_043879608.1 74 GACGNGTRCIAAYEAGRIGE--RHVLFESAAGLLDCVMQPDG-QVTVDMGAPRLGWDAIPLArpV-ADT 138 *************9999999..8*******************.******************9542.233 PP TIGR00652 138 ekeellalevl....vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklr 202 + +++ ++ l +v++GnPH+v+fv d + +d+e lg++le+h+ fpe+ N+ f++v+++d+i l+ lcl|NCBI__GCF_000010525.1:WP_043879608.1 139 SAVQIEGFASLgpasMVSMGNPHAVFFVPDANAVDVEALGATLEHHPLFPERANISFAQVLSPDHILLH 207 333444444434557****************************************************** PP TIGR00652 203 vyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268 v+ERGag T+aCGt a+A+ v +++g+t +kv+v+l+gg+L+i+++ ++ +v++tGp+ l + g+l lcl|NCBI__GCF_000010525.1:WP_043879608.1 208 VWERGAGRTRACGTAACATGVSTARTGRTGRKVRVTLPGGDLVIDWRASDgHVLMTGPVALEFTGTL 274 **********************************************98777*********9999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (283 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: 10.86 // [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