Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_011972928.1 MAEO_RS01020 diaminopimelate epimerase
Query= curated2:Q58519 (295 letters) >NCBI__GCF_000017185.1:WP_011972928.1 Length = 295 Score = 468 bits (1203), Expect = e-137 Identities = 218/290 (75%), Positives = 259/290 (89%) Query: 1 MEFTKMHALGNDYIVINEFDGEKVKEEEKAEFSRKICRRGFSVGADGVIFIQKPTSDEYD 60 + FTKMH LGNDYIVINEFDGEK+KE+EKAEFS+KIC+RGFS+GADGVIF+Q T ++YD Sbjct: 3 LNFTKMHGLGNDYIVINEFDGEKIKEDEKAEFSKKICKRGFSIGADGVIFVQPATDEKYD 62 Query: 61 VRFRIFNSDGSEAEMCGNGIRCFSKYVYERIMKKNPLKVETKGGLRVSEMEIEGDEVKKI 120 +RFRIFNSDGSEAEMCGNGIRCFSK+VYER+M+KNPL VET GGLRVSEM IE + VK I Sbjct: 63 IRFRIFNSDGSEAEMCGNGIRCFSKFVYERVMQKNPLNVETMGGLRVSEMNIENNIVKSI 122 Query: 121 KVYMGVPKFKLKDIPMVVDGYKEDDEFLNGELKLKNPYLPKVKLSVVNVGNPHAVIFVED 180 KV+MG P F+LKDIPMVV+G E+D FL+ E++LKN L VKLSVVNVGNPHAVIF++D Sbjct: 123 KVFMGAPTFELKDIPMVVEGKSENDVFLDEEIELKNALLNSVKLSVVNVGNPHAVIFMKD 182 Query: 181 NNIDLDFVREHLDVIGKEIEHHEAFPERINVHFVKVLNPNEIRIVTWERGAGYTTACGTG 240 NN+ F+R HL+++GKEIEHH FPE+INVHFV+++NP EI+I+TWERGAGYTTACGTG Sbjct: 183 NNLKAPFIRTHLNILGKEIEHHSVFPEKINVHFVEIVNPQEIKIITWERGAGYTTACGTG 242 Query: 241 TTASVIMAHKLGKTNNRVLAHLDGGDLEIEIKDDGVYMIGDAVMVYDAKL 290 TT+SVI+A+KLGKT N+VLAHLDGGDLEIEIK+DGVYM GDAV+VYD +L Sbjct: 243 TTSSVIIANKLGKTGNKVLAHLDGGDLEIEIKEDGVYMEGDAVIVYDGEL 292 Lambda K H 0.319 0.140 0.411 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: 450 Number of extensions: 16 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: 295 Length of database: 295 Length adjustment: 26 Effective length of query: 269 Effective length of database: 269 Effective search space: 72361 Effective search space used: 72361 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_011972928.1 MAEO_RS01020 (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.850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-105 336.2 1.8 8.5e-105 336.0 1.8 1.0 1 lcl|NCBI__GCF_000017185.1:WP_011972928.1 MAEO_RS01020 diaminopimelate epi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017185.1:WP_011972928.1 MAEO_RS01020 diaminopimelate epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 336.0 1.8 8.5e-105 8.5e-105 2 269 .. 4 293 .. 3 294 .. 0.97 Alignments for each domain: == domain 1 score: 336.0 bits; conditional E-value: 8.5e-105 TIGR00652 2 eFlkmhGlgNdFvlvdevdeelvkee..aelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDG 67 +F+kmhGlgNd+++++e+d e++ke+ ae+ +k+c+r +++gaDgv++v+p ++e++d+++rifNsDG lcl|NCBI__GCF_000017185.1:WP_011972928.1 4 NFTKMHGLGNDYIVINEFDGEKIKEDekAEFSKKICKRGFSIGADGVIFVQPaTDEKYDIRFRIFNSDG 72 8**********************999899***********************89999************ PP TIGR00652 68 SeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeen...kkvkvdmgepkfkkeeipltv 133 SeaemCGNgiRcf+kfvye+ ++ k+ l+vet gl+++e++ en k++kv mg p+f+ ++ip++v lcl|NCBI__GCF_000017185.1:WP_011972928.1 73 SEAEMCGNGIRCFSKFVYERVMQ-KNPLNVETMGGLRVSEMNIENnivKSIKVFMGAPTFELKDIPMVV 140 ***********************.7*******************99999******************** PP TIGR00652 134 ekeeekeellalev.........l...vvdvGnPHlvvfved......vekldleelgklleaheefpe 184 e+++e++++l e+ + vv+vGnPH+v+f++d + + +l+ lgk++e+h fpe lcl|NCBI__GCF_000017185.1:WP_011972928.1 141 EGKSENDVFLDEEIelknallnsVklsVVNVGNPHAVIFMKDnnlkapFIRTHLNILGKEIEHHSVFPE 209 *********999989999887662668***************9999998899***************** PP TIGR00652 185 gvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgk 253 ++Nv+fve+++++eik+ ++ERGag+T+aCGtG++ s+++a+klgkt +kv hl+gg+Leie+kedg lcl|NCBI__GCF_000017185.1:WP_011972928.1 210 KINVHFVEIVNPQEIKIITWERGAGYTTACGTGTTSSVIIANKLGKTGNKVLAHLDGGDLEIEIKEDG- 277 *******************************************************************8. PP TIGR00652 254 vyltGpavlvlegela 269 vy++G+av v++gel+ lcl|NCBI__GCF_000017185.1:WP_011972928.1 278 VYMEGDAVIVYDGELY 293 *************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (295 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: 00:00:00.01 # Mc/sec: 6.67 // [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