Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_019866655.1 METMI_RS0112590 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >NCBI__GCF_000384075.1:WP_019866655.1 Length = 415 Score = 559 bits (1440), Expect = e-164 Identities = 271/417 (64%), Positives = 339/417 (81%), Gaps = 3/417 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 MDYFNY+ D +L+AE V + D+ ++G+P Y+YSRATLERHW AFD + G+ PHL+CYAV Sbjct: 1 MDYFNYR-DNELFAEDVAVQDIVYKFGSPCYIYSRATLERHWKAFDGAFGNTPHLVCYAV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KANSNLG+LN LARLGSGFDIVS+GE+ERVLAAGGD K+VFSGVGK E E+ AL+ I Sbjct: 60 KANSNLGLLNVLARLGSGFDIVSLGEMERVLAAGGDAKKIVFSGVGKREDEILAALKTGI 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 +CFN+E EL R+N +AG+LGV AP+S R+NPDVDAKTHPYISTGL++NKFGI D A Sbjct: 120 RCFNIEVSGELDRINTLAGQLGVAAPVSFRVNPDVDAKTHPYISTGLKENKFGIDIDTAI 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 YR A ++PN++V GIDCHIGSQLT PF+DA D+LL L+ +L+ EGI ++HLD+GGG Sbjct: 180 AEYRRAAAMPNINVVGIDCHIGSQLTETRPFLDALDKLLELVANLQKEGIRLQHLDLGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 LG+ Y+DE PP+PSEY +A+L RL +H D E++ EPGRAI NAG+LVT+VE+LK T +K Sbjct: 240 LGICYKDEQPPEPSEYIQAVLARLGQH-DYEILLEPGRAIVGNAGILVTQVEYLKPTANK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQ-TYDLVGPVCETSDFLGKDRDLVLQ 359 NFAI+DAAMNDL+RP+LY AWQ+IIP+ P + +D+VGPVCET DFLGK R L L Sbjct: 299 NFAIVDAAMNDLLRPSLYSAWQNIIPVSPHDDAPEIQWDIVGPVCETGDFLGKGRVLKLA 358 Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416 +GDLLA+RS+GAYGF+MSSNYN+RPRVAEVMVDG + +LVR RE L+ LWA E +LP Sbjct: 359 QGDLLAIRSAGAYGFSMSSNYNSRPRVAEVMVDGGQCHLVRARETLAQLWAGERLLP 415 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: 541 Number of extensions: 17 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: 415 Length adjustment: 31 Effective length of query: 386 Effective length of database: 384 Effective search space: 148224 Effective search space used: 148224 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_019866655.1 METMI_RS0112590 (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.576.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-165 535.2 0.0 5.1e-165 534.9 0.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019866655.1 METMI_RS0112590 diaminopimelate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019866655.1 METMI_RS0112590 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.9 0.0 5.1e-165 5.1e-165 5 416 .. 7 411 .. 4 412 .. 0.99 Alignments for each domain: == domain 1 score: 534.9 bits; conditional E-value: 5.1e-165 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 +d el++e+v++++++ +fg+P Y+y+++tl+++++a++ af+++ +lv+YAvKAnsnl +l++la++G lcl|NCBI__GCF_000384075.1:WP_019866655.1 7 RDNELFAEDVAVQDIVYKFGSPCYIYSRATLERHWKAFDGAFGNTPHLVCYAVKANSNLGLLNVLARLG 75 67899**************************************************************** PP TIGR01048 74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142 +g+d+vs GE+er+laAg +a+kivfsg+gk+e+e+ aal+++i+++n++ el++++++a++lg a lcl|NCBI__GCF_000384075.1:WP_019866655.1 76 SGFDIVSLGEMERVLAAGGDAKKIVFSGVGKREDEILAALKTGIRCFNIEVSGELDRINTLAGQLGVAA 144 ********************************************************************* PP TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211 +v++Rvnpdvdakth+yisTGlke+KFGi++++a + y++a++++++++vGi++HIGSq++++ pf +a lcl|NCBI__GCF_000384075.1:WP_019866655.1 145 PVSFRVNPDVDAKTHPYISTGLKENKFGIDIDTAIAEYRRAAAMPNINVVGIDCHIGSQLTETRPFLDA 213 ********************************************************************* PP TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGR 280 ++k+++l+++l++egi+l++ldlGGGlgi+y++e+ +p+++ey +++l++l + ++ +++lEpGR lcl|NCBI__GCF_000384075.1:WP_019866655.1 214 LDKLLELVANLQKEGIRLQHLDLGGGLGICYKDEQ-PPEPSEYIQAVLARLGQ-----HDYEILLEPGR 276 ********************************999.**************999.....7********** PP TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEs 349 ++v+nag+l+t+Ve++K + +++f++vDa+mndl+Rp+lY+a+++i++++ +++++ ++d+vGp+CE+ lcl|NCBI__GCF_000384075.1:WP_019866655.1 277 AIVGNAGILVTQVEYLKPTANKNFAIVDAAMNDLLRPSLYSAWQNIIPVSPHDDAPEIQWDIVGPVCET 345 ********************************************************************* PP TIGR01048 350 gDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 gD+l+k r l+ ++ Gdlla++saGAYg+smssnYnsrpr+aev+v++g+++l+r retl++l+a e lcl|NCBI__GCF_000384075.1:WP_019866655.1 346 GDFLGKGRVLKLAQ-GDLLAIRSAGAYGFSMSSNYNSRPRVAEVMVDGGQCHLVRARETLAQLWAGE 411 **********9998.*************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (415 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # 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