Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 207105 DVU1647 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >MicrobesOnline__882:207105 Length = 412 Score = 423 bits (1088), Expect = e-123 Identities = 218/413 (52%), Positives = 289/413 (69%), Gaps = 3/413 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 M F Y+E G L+AE V + DLA+ YGTPLYVYS TLERH+ AFD + G HL C++V Sbjct: 1 MHLFQYRE-GSLFAEDVSIIDLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KA SN+ +L L LG+G DIVS GEL R L AG ++V+SGVGK E++ AL+ I Sbjct: 60 KACSNIHILKLLGSLGAGVDIVSGGELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADI 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 FNVES EL+ + +VA +G A +SLRINPDVD THPYISTGL+ NKFGI +A Sbjct: 120 LMFNVESLQELRTIEEVAASMGTTARVSLRINPDVDPHTHPYISTGLQKNKFGIEMTQAL 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 + Y LA LP++D GIDCHIGSQLT+L+PF++A D++L + L G+ I +LD+GGG Sbjct: 180 EGYMLARDLPHIDPIGIDCHIGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 LG+ Y +E PP P ++ +A+L+R + +L L+ EPGR IA NAG+LVT+V + K T K Sbjct: 240 LGITYGEETPPHPRDFGRAVLER-TKGLNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL-VLQ 359 F I+DAAMNDL+RP+LY ++ I + P QT D+VGP+CE+ DFL +DR L ++ Sbjct: 299 QFVIVDAAMNDLVRPSLYASYHRIAEVLPHGRTEQTVDVVGPICESGDFLARDRVLPAVE 358 Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALE 412 +G+LLAV S+GAYGF+MSS YN+RPR AEV+V G+ +R+RE L ALE Sbjct: 359 QGELLAVFSAGAYGFSMSSQYNSRPRAAEVLVRGDTAKSIRRRETYDDLTALE 411 Lambda K H 0.319 0.137 0.405 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: 475 Number of extensions: 23 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: 417 Length of database: 412 Length adjustment: 31 Effective length of query: 386 Effective length of database: 381 Effective search space: 147066 Effective search space used: 147066 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: 50 (23.9 bits)
Align candidate 207105 DVU1647 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))
# 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/TIGR01048.hmm # target sequence database: /tmp/gapView.476.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01048 [M=417] Accession: TIGR01048 Description: lysA: diaminopimelate decarboxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-164 532.9 0.0 2.6e-164 532.6 0.0 1.0 1 lcl|MicrobesOnline__882:207105 DVU1647 diaminopimelate decarbox Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207105 DVU1647 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.6 0.0 2.6e-164 2.6e-164 4 416 .. 6 411 .. 4 412 .] 0.98 Alignments for each domain: == domain 1 score: 532.6 bits; conditional E-value: 2.6e-164 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 ++g+l++e+v++ +la ++gtPlYvy++ tl+++++a+++af+++ +l ++ vKA+sn+++l+ll ++G+g+d+vsgG lcl|MicrobesOnline__882:207105 6 YREGSLFAEDVSIIDLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSVKACSNIHILKLLGSLGAGVDIVSGG 84 57899****************************************99******************************** PP TIGR01048 83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyis 161 El ral Ag++ +iv+sg+gk+ +e++ ale++i ++nv+s++el+++ee+a+++g++arv+lR+npdvd++th+yis lcl|MicrobesOnline__882:207105 85 ELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADILMFNVESLQELRTIEEVAASMGTTARVSLRINPDVDPHTHPYIS 163 ******************************************************************************* PP TIGR01048 162 TGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgi 240 TGl+++KFGie+++a+e y la +l++++++Gi++HIGSq++ l+pf ea++kv+++ e+l+ g++++ ldlGGGlgi lcl|MicrobesOnline__882:207105 164 TGLQKNKFGIEMTQALEGYMLARDLPHIDPIGIDCHIGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGGLGI 242 ******************************************************************************* PP TIGR01048 241 syeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpal 319 +y ee+ +p+++++ +++le+ ++ l+l+l+lEpGR +++nag+l+t+V ++K+++s++fv+vDa+mndl+Rp+l lcl|MicrobesOnline__882:207105 243 TYGEET-PPHPRDFGRAVLERTKG-----LNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSKQFVIVDAAMNDLVRPSL 315 ***999.**********9987777.....8************************************************* PP TIGR01048 320 YeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveeg 398 Y +yh+ia++ + ++++tvdvvGp+CEsgD+la+dr lp+ve+G+llav+saGAYg+smss+Ynsrpr+aevlv+++ lcl|MicrobesOnline__882:207105 316 YASYHRIAEV-LPHGRTEQTVDVVGPICESGDFLARDRVLPAVEQGELLAVFSAGAYGFSMSSQYNSRPRAAEVLVRGD 393 **********.5577789************************************************************* PP TIGR01048 399 karlirrretledllale 416 a+ irrret++dl ale lcl|MicrobesOnline__882:207105 394 TAKSIRRRETYDDLTALE 411 **************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (412 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: 00:00:00.02 # Mc/sec: 7.59 // [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