Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate AZOBR_RS14160 AZOBR_RS14160 diaminopimelate epimerase
Query= SwissProt::Q81XR2 (288 letters) >FitnessBrowser__azobra:AZOBR_RS14160 Length = 278 Score = 197 bits (501), Expect = 2e-55 Identities = 117/277 (42%), Positives = 155/277 (55%), Gaps = 14/277 (5%) Query: 6 FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPS--DVAPVKM 63 F KMHGLGN ++ ++ + P +++ TG+G D I+I P+ D M Sbjct: 5 FLKMHGLGNDFVVIDA--RKTPYSPAEAEVRAIADRKTGVGCDQFIVIEPAKTDGTAGFM 62 Query: 64 RMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEEGKVTLAKI 123 R+ N DG E +CGN RCV E E F ET AGI+ A + G++T + Sbjct: 63 RIRNADGGEVSACGNASRCVGWLLMEEAGAERVAF--ETNAGILQAS-RADNGRIT---V 116 Query: 124 DMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTT 183 DMG L +IP+ +T +R + + + TAVSMGNPHAV FVDD E PL Sbjct: 117 DMGPANLDWTQIPLAEPADT--LRLDAVSHGGFAGPTAVSMGNPHAVFFVDDAEAVPLAE 174 Query: 184 LGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKM 243 +GPV E H FP+R NVEF+++L+ + RVWERG+GVTQACGTGACA VA+I G Sbjct: 175 VGPVFENHPAFPQRTNVEFVQVLSPTAVRMRVWERGAGVTQACGTGACATAVAAIRRGLT 234 Query: 244 ERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRG 280 R ++ V L GG L I W E+G VLM GP + G Sbjct: 235 NR--KVDVILDGGTLTIEWREDGRVLMTGPVALSYTG 269 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: 218 Number of extensions: 14 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 AZOBR_RS14160 AZOBR_RS14160 (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.19844.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-88 281.4 0.0 4.4e-88 281.2 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS14160 AZOBR_RS14160 diaminopimelate ep Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS14160 AZOBR_RS14160 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.2 0.0 4.4e-88 4.4e-88 2 268 .. 4 271 .. 3 273 .. 0.92 Alignments for each domain: == domain 1 score: 281.2 bits; conditional E-value: 4.4e-88 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSe 69 eFlkmhGlgNdFv++d ++ +++vr+++dr+tgvg+D+++++ep + + + +ri+N+DG e lcl|FitnessBrowser__azobra:AZOBR_RS14160 4 EFLKMHGLGNDFVVIDARKTPYSPA-EAEVRAIADRKTGVGCDQFIVIEPaKTDGTAGFMRIRNADGGE 71 7*****************9655555.799*********************6566677789********* PP TIGR00652 70 aemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeee 138 ++ CGN++Rc+ ++e++++ +++ +et+ag++++ +++ +++vdmg +++ ++ipl + ++ lcl|FitnessBrowser__azobra:AZOBR_RS14160 72 VSACGNASRCVGWLLMEEAGA--ERVAFETNAGILQASRADNG-RITVDMGPANLDWTQIPLAEPADTL 137 *********************..7**************99999.******************9766665 PP TIGR00652 139 keellalevl....vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrv 203 + + + + +v++GnPH+v+fv+d e ++l e+g+++e+h++fp+++Nvefv+v+++ ++++rv lcl|FitnessBrowser__azobra:AZOBR_RS14160 138 RLDAVSHGGFagptAVSMGNPHAVFFVDDAEAVPLAEVGPVFENHPAFPQRTNVEFVQVLSPTAVRMRV 206 44444333323556******************************************************* PP TIGR00652 204 yERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 +ERGag T+aCGtGa+A+av+a++ g+t++kv+v l+gg L+ie++edg+v++tGp+ l + g+l lcl|FitnessBrowser__azobra:AZOBR_RS14160 207 WERGAGVTQACGTGACATAVAAIRRGLTNRKVDVILDGGTLTIEWREDGRVLMTGPVALSYTGRL 271 ***********************************************************999987 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: 00:00:00.01 # Mc/sec: 6.99 // [ok]
This GapMind analysis is from Apr 09 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