Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate 3609846 Dshi_3228 Diaminopimelate epimerase (RefSeq)
Query= SwissProt::P0A6K1 (274 letters) >FitnessBrowser__Dino:3609846 Length = 282 Score = 199 bits (505), Expect = 7e-56 Identities = 114/270 (42%), Positives = 151/270 (55%), Gaps = 11/270 (4%) Query: 1 MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60 + F KMHGLGNDF+V+DA S L+ LADRH GVGFDQL V+ P PE D H Sbjct: 12 LPFFKMHGLGNDFVVIDARAAPRPVSDRLVAALADRHRGVGFDQLAVIAPA--PEADAHL 69 Query: 61 RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120 +NADGS A CGN RC AR + + T +R+ST G ++ D L RVNMG+ Sbjct: 70 TFYNADGSTSAACGNATRCIARMILDE--TGATALRLSTDRGLLLAEDAGDGLTRVNMGQ 127 Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180 P S VP +A T + G MGNPHC V D + ++T GP E Sbjct: 128 PQTLWSEVPLA--EAMDTLELPIEGTPTATG---MGNPHCTFFVADAEAIPLDTFGPRYE 182 Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240 H +P+R N+ Q+V +HIR+RV+ERG G T A GS +CA ++GL + R+ Sbjct: 183 HHPLYPQRTNVQVAQIVGPDHIRMRVWERGVGVTLASGSSSCATGVAAARRGLTGRKTRI 242 Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDG 270 +L GG L I W+ G ++MTGP + V++G Sbjct: 243 DLDGGTLWIDWREDG--VWMTGPNMTVFEG 270 Lambda K H 0.323 0.140 0.425 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: 223 Number of extensions: 8 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: 274 Length of database: 282 Length adjustment: 25 Effective length of query: 249 Effective length of database: 257 Effective search space: 63993 Effective search space used: 63993 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: 47 (22.7 bits)
Align candidate 3609846 Dshi_3228 (Diaminopimelate epimerase (RefSeq))
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.30306.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-74 234.6 0.0 8.1e-74 234.4 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609846 Dshi_3228 Diaminopimelate epimer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609846 Dshi_3228 Diaminopimelate epimerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 234.4 0.0 8.1e-74 8.1e-74 3 268 .. 14 272 .. 12 274 .. 0.95 Alignments for each domain: == domain 1 score: 234.4 bits; conditional E-value: 8.1e-74 TIGR00652 3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemCGNgiRc 79 F+kmhGlgNdFv++d + + + + +lv++++drh gvg+D++ ++ p +ead++l+++N+DGS + CGN+ Rc lcl|FitnessBrowser__Dino:3609846 14 FFKMHGLGNDFVVIDARAAPRPVS-DRLVAALADRHRGVGFDQLAVIAP-APEADAHLTFYNADGSTSAACGNATRC 88 9*****************999988.79*********************8.*************************** PP TIGR00652 80 fakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev..lvvdvGn 154 +a+ + +++++ + l+++t++gl+ +e ++ +v+mg+p+ +e+pl ++ ++ + + e + +Gn lcl|FitnessBrowser__Dino:3609846 89 IARMILDETGA--TALRLSTDRGLLLAEDAGDG-LTRVNMGQPQTLWSEVPLAEAMDTLELPI---EGtpTATGMGN 159 ***********..8**************99999.******************98777663333...332269***** PP TIGR00652 155 PHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgkt 231 PH+ +fv+d e ++l++ g+ e+h+ +p+++Nv++++++++d+i++rv+ERG+g Tla G+ ++A+ v+a++ g+t lcl|FitnessBrowser__Dino:3609846 160 PHCTFFVADAEAIPLDTFGPRYEHHPLYPQRTNVQVAQIVGPDHIRMRVWERGVGVTLASGSSSCATGVAAARRGLT 236 ***************************************************************************** PP TIGR00652 232 kkkvtvhleggeLeievkedgkvyltGpavlvlegel 268 +k ++ l+gg L i+++edg v++tGp +v+eg+l lcl|FitnessBrowser__Dino:3609846 237 GRKTRIDLDGGTLWIDWREDG-VWMTGPNMTVFEGRL 272 ********************8.*************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (282 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: 00:00:00.00 # Mc/sec: 9.69 // [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