Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_027179250.1 G496_RS0110460 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >NCBI__GCF_000429985.1:WP_027179250.1 Length = 412 Score = 424 bits (1089), Expect = e-123 Identities = 216/413 (52%), Positives = 291/413 (70%), Gaps = 3/413 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 M+YF ++ D +L+AE + + +LA++YGTPLYVYS ATL RH+ AFD + HL C++V Sbjct: 1 MNYFEFK-DNELFAENISVTELAHEYGTPLYVYSAATLRRHFDAFDSAFSGLEHLTCFSV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KANSNL VL LA G+G DIVS GEL R L AG ++V+SGVGK E+ AL+ I Sbjct: 60 KANSNLSVLKLLAEKGAGMDIVSGGELYRALKAGVPSDRIVYSGVGKKAYEIAEALKADI 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 FNVES EL R+N+VAG +G KA IS RINPDVD KTHPYISTG++ NKFG+ + A Sbjct: 120 LMFNVESVGELHRINEVAGSMGKKARISFRINPDVDPKTHPYISTGMKKNKFGLEIENAF 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 + Y+ A LPN+D G+DCHIGSQLT +APF++A ++LL LK GI+I LD+GGG Sbjct: 180 EAYKTAKDLPNVDPVGMDCHIGSQLTEIAPFLEALEKLLKFNQRLKDIGINISTLDLGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 LG+ Y +E PP P E+ +AL L + + L++I EPGR IA N+G+LVT+V + K + K Sbjct: 240 LGITYDEEEPPHPKEFGEALTKAL-KDQGLKVILEPGRVIAGNSGILVTEVVYTKKSPTK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL-VLQ 359 NF I+DA MNDLIRP+LY ++ + + + D+VGP+CE+ DF+ +DR+L ++ Sbjct: 299 NFLIVDAGMNDLIRPSLYGSYHRLEEVVKKGRPEIECDVVGPICESGDFIARDRNLPEME 358 Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALE 412 +G+LLA S+GAYGFTM+SNYN+RPR AEV+VDG+ + R+RE L LE Sbjct: 359 QGELLAAYSAGAYGFTMASNYNSRPRAAEVIVDGDDVIVARRRESYEDLVNLE 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: 488 Number of extensions: 23 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: 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 WP_027179250.1 G496_RS0110460 (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.1195.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-168 546.1 0.0 2.4e-168 545.9 0.0 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027179250.1 G496_RS0110460 diaminopimelate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027179250.1 G496_RS0110460 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 545.9 0.0 2.4e-168 2.4e-168 5 417 .] 7 412 .] 4 412 .] 0.99 Alignments for each domain: == domain 1 score: 545.9 bits; conditional E-value: 2.4e-168 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 kd el++e+++++ela+e+gtPlYvy+++tlr+++ a+++af++ e+l ++ vKAnsnl+vl+llae+G lcl|NCBI__GCF_000429985.1:WP_027179250.1 7 KDNELFAENISVTELAHEYGTPLYVYSAATLRRHFDAFDSAFSGLEHLTCFSVKANSNLSVLKLLAEKG 75 6789*****************************************9*********************** PP TIGR01048 74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142 +g+d+vsgGEl+ral+Agv++++iv+sg+gk+ e+++al+++i ++nv+sv el++++e+a+++gkka lcl|NCBI__GCF_000429985.1:WP_027179250.1 76 AGMDIVSGGELYRALKAGVPSDRIVYSGVGKKAYEIAEALKADILMFNVESVGELHRINEVAGSMGKKA 144 ********************************************************************* PP TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211 r+++R+npdvd+kth+yisTG+k++KFG+e+e+a eay++a++l+++++vG+++HIGSq+++++pf ea lcl|NCBI__GCF_000429985.1:WP_027179250.1 145 RISFRINPDVDPKTHPYISTGMKKNKFGLEIENAFEAYKTAKDLPNVDPVGMDCHIGSQLTEIAPFLEA 213 ********************************************************************* PP TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGR 280 +ek++k+ ++lk+ gi++++ldlGGGlgi+y+eee +p+++e+ e+l+++l++ + lk+ilEpGR lcl|NCBI__GCF_000429985.1:WP_027179250.1 214 LEKLLKFNQRLKDIGINISTLDLGGGLGITYDEEE-PPHPKEFGEALTKALKD-----QGLKVILEPGR 276 ********************************999.*****************.....599******** PP TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEs 349 +++n+g+l+t+V ++K++++++f +vDagmndliRp+lY++yh++ ++ + +++ ++dvvGp+CEs lcl|NCBI__GCF_000429985.1:WP_027179250.1 277 VIAGNSGILVTEVVYTKKSPTKNFLIVDAGMNDLIRPSLYGSYHRLEEV-VKKGRPEIECDVVGPICES 344 *************************************************.558899************* PP TIGR01048 350 gDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllalel 417 gD++a+dr+lpe+e+G+lla saGAYg++m+snYnsrpr+aev+v+++++ + rrre++edl++le+ lcl|NCBI__GCF_000429985.1:WP_027179250.1 345 GDFIARDRNLPEMEQGELLAAYSAGAYGFTMASNYNSRPRAAEVIVDGDDVIVARRRESYEDLVNLEC 412 ****************************************************************9985 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: 7.89 // [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