Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_106299112.1 MGEO_RS00490 diaminopimelate epimerase
Query= curated2:Q3IZB6 (279 letters) >NCBI__GCF_002115805.1:WP_106299112.1 Length = 278 Score = 344 bits (882), Expect = 1e-99 Identities = 165/268 (61%), Positives = 208/268 (77%), Gaps = 2/268 (0%) Query: 10 LGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQEG-ADCAL 68 + FMKMHG GNDFVV+D+R + ++TA LA+A+GDRHRGVGFDQLA I G AD L Sbjct: 8 IAFMKMHGLGNDFVVLDARVQP-VVMTAALAQAIGDRHRGVGFDQLALIERGAGDADARL 66 Query: 69 DFWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVAVNMGAPQ 128 F+NSDGS +G CGNATRC++ +LM + G V L T RG+L AR +GL +VNMG PQ Sbjct: 67 VFYNSDGSTAGACGNATRCIARHLMDESGLTGVTLTTERGQLFARDAGNGLTSVNMGQPQ 126 Query: 129 LLWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVETDPLFPE 188 L W E+PLA M+T LP++G P+A GMGNPHC +FVEDAE+VDL RGA +E PL+P+ Sbjct: 127 LRWDEVPLAHEMDTLELPIDGAPTATGMGNPHCTFFVEDAESVDLETRGAEIEDHPLYPQ 186 Query: 189 RTNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRLEMDGGVL 248 RTNV+FASLIGPD LR+RVWERG G+TLA GS +CATAVAAARRGLTGR+V +++DGG + Sbjct: 187 RTNVQFASLIGPDHLRMRVWERGVGVTLASGSSSCATAVAAARRGLTGRRVSIDLDGGRI 246 Query: 249 EVDWRDEGVWLSGPVARVFEGHLSPEMM 276 E+DWR++GVW++GP A VF G + E + Sbjct: 247 EIDWREDGVWMTGPTAHVFSGTFTAEWL 274 Lambda K H 0.321 0.138 0.423 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: 328 Number of extensions: 13 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: 279 Length of database: 278 Length adjustment: 25 Effective length of query: 254 Effective length of database: 253 Effective search space: 64262 Effective search space used: 64262 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_106299112.1 MGEO_RS00490 (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.669643.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-75 240.2 0.0 1.5e-75 240.0 0.0 1.0 1 NCBI__GCF_002115805.1:WP_106299112.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_106299112.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 240.0 0.0 1.5e-75 1.5e-75 1 268 [. 8 269 .. 8 271 .. 0.95 Alignments for each domain: == domain 1 score: 240.0 bits; conditional E-value: 1.5e-75 TIGR00652 1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemC 73 ++F+kmhGlgNdFv++d + + +v + a+l++++ drh gvg+D++ l+e + +ad++l ++NsDGS a C NCBI__GCF_002115805.1:WP_106299112.1 8 IAFMKMHGLGNDFVVLDARVQPVVMT-AALAQAIGDRHRGVGFDQLALIERGAGDADARLVFYNSDGSTAGAC 79 57******************999999.9********************************************* PP TIGR00652 74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellale 146 GN+ Rc+a++++++ + + +++ t++g++ + ++ +v+mg+p+++ +e+pl +e ++ + + + NCBI__GCF_002115805.1:WP_106299112.1 80 GNATRCIARHLMDESGL--TGVTLTTERGQLFARDAGNG-LTSVNMGQPQLRWDEVPLAHEMDTLELPID-GA 148 **************999..79**********99999998.9******************97777744443.34 PP TIGR00652 147 vlvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGav 219 + +GnPH+ +fved e++dle+ g+++e h+ +p+++Nv+f+ ++d++++rv+ERG+g Tla G+ ++ NCBI__GCF_002115805.1:WP_106299112.1 149 PTATGMGNPHCTFFVEDAESVDLETRGAEIEDHPLYPQRTNVQFASLIGPDHLRMRVWERGVGVTLASGSSSC 221 469********************************************************************** PP TIGR00652 220 AsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 A+av+a++ g+t ++v + l+gg++ei+++edg v++tGp +v++g+ NCBI__GCF_002115805.1:WP_106299112.1 222 ATAVAAARRGLTGRRVSIDLDGGRIEIDWREDG-VWMTGPTAHVFSGTF 269 ********************************8.***********9975 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.50 // [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