Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate AO353_09035 AO353_09035 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >FitnessBrowser__pseudo3_N2E3:AO353_09035 Length = 415 Score = 555 bits (1430), Expect = e-163 Identities = 278/417 (66%), Positives = 337/417 (80%), Gaps = 2/417 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 MD FNY+ DG+L+AE V L+ +A ++GTP YVYSRA +E + AF ++ PHL+C+AV Sbjct: 1 MDAFNYR-DGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYLAFADALAGTPHLVCFAV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KANSNLGVLN LARLG+GFDIVS GELERVLAAGG P K+VFSGVGKT +M+RAL++ + Sbjct: 60 KANSNLGVLNVLARLGAGFDIVSGGELERVLAAGGQPDKIVFSGVGKTREDMRRALEVGV 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 CFNVES EL+RL VA ELGV+APISLR+NPDVDA THPYISTGL++NKFGI A Sbjct: 120 HCFNVESTDELERLQVVAAELGVRAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAE 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 VY A LPNL+V G+DCHIGSQLT L PF+DA DRLLALID L GI++RH+D+GGG Sbjct: 180 DVYVRAAQLPNLEVVGVDCHIGSQLTTLPPFLDALDRLLALIDRLGDCGIYLRHIDLGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 LGV YRDE PP ++Y KA+ +R++ RDL L+FEPGR I ANAGVL+T+VE+LKHTEHK Sbjct: 240 LGVRYRDEEPPLAADYIKAVRERID-GRDLTLVFEPGRFIVANAGVLLTEVEYLKHTEHK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360 +FAI+DAAMNDLIRPALYQAW D+ +RPR A+ YD+VGP+CET DFL KDR L L+E Sbjct: 299 DFAIVDAAMNDLIRPALYQAWMDVTAVRPRATPARAYDIVGPICETGDFLAKDRQLALEE 358 Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417 GDLLAV S+GAYGF MSSNYNTR R AEV+VDG++ VR+RE ++ L+A ES+LPE Sbjct: 359 GDLLAVHSAGAYGFVMSSNYNTRGRAAEVLVDGDQAIEVRRRETVAELFAGESLLPE 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: 553 Number of extensions: 13 Number of successful extensions: 2 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 AO353_09035 AO353_09035 (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.17045.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-163 528.6 0.0 5.2e-163 528.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 AO353_09035 diaminopimelate deca Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 AO353_09035 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 528.3 0.0 5.2e-163 5.2e-163 5 416 .. 7 410 .. 4 411 .. 0.98 Alignments for each domain: == domain 1 score: 528.3 bits; conditional E-value: 5.2e-163 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrll 69 +dgel++egv+l ++ae+fgtP+Yvy+++++++++ a++ a +++ +lv++AvKAnsnl vl++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 7 RDGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYLAFADALAGTPHLVCFAVKANSNLGVLNVL 71 799******************************************9******************* PP TIGR01048 70 aeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleei 134 a++G+g+d+vsgGEler+laAg +++kivfsg+gk++e++++ale++++++nv+s++ele+l+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 72 ARLGAGFDIVSGGELERVLAAGGQPDKIVFSGVGKTREDMRRALEVGVHCFNVESTDELERLQVV 136 ***************************************************************** PP TIGR01048 135 akelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIG 199 a+elg +a+++lRvnpdvda th+yisTGlke+KFGi++++ae++y +a++l++le+vG+++HIG lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 137 AAELGVRAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYVRAAQLPNLEVVGVDCHIG 201 ***************************************************************** PP TIGR01048 200 SqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklek 264 Sq++ l pf +a+++++ l+++l + gi l+++dlGGGlg++y++ee +p +++y +++ e++ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 202 SQLTTLPPFLDALDRLLALIDRLGDCGIYLRHIDLGGGLGVRYRDEE-PPLAADYIKAVRERIDG 265 **********************************************9.999*******9999888 PP TIGR01048 265 eaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaal 329 ++l+l++EpGR++vanagvllt+Ve++K++e++ f++vDa+mndliRpalY+a+++++a+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 266 -----RDLTLVFEPGRFIVANAGVLLTEVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAV 325 .....7*********************************************************** PP TIGR01048 330 krleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevl 394 r +++++ +d+vGp+CE+gD+lakdr+l e Gdllav+saGAYg+ mssnYn+r+r+aevl lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 326 -RPRATPARAYDIVGPICETGDFLAKDRQLALEE-GDLLAVHSAGAYGFVMSSNYNTRGRAAEVL 388 .89***************************8776.****************************** PP TIGR01048 395 veegkarlirrretledllale 416 v++++a +rrret+++l+a e lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 389 VDGDQAIEVRRRETVAELFAGE 410 ******************9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.06 // [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