Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate AO356_12740 AO356_12740 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_12740 Length = 415 Score = 545 bits (1405), Expect = e-160 Identities = 272/417 (65%), Positives = 334/417 (80%), Gaps = 2/417 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 MD FNY+ G+L+AE V L+ +A ++GTP YVYSRA +E + F ++ PHL+C+AV Sbjct: 1 MDAFNYR-GGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYRTFADALDGMPHLVCFAV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KANSNLGVLN LARLG+GFDIVS GELERVLAAGG K+VFSGVGKT +M+RAL++ + Sbjct: 60 KANSNLGVLNVLARLGAGFDIVSGGELERVLAAGGSADKIVFSGVGKTREDMRRALEVGV 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 CFN+ES EL+RL VA ELGV+AP+SLR+NPDVDA THPYISTGL++NKFGI A Sbjct: 120 HCFNIESTDELERLQVVAAELGVRAPVSLRVNPDVDAGTHPYISTGLKENKFGIAIADAE 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 VY A LPNL+V G+DCHIGSQLT L PFIDA DRLLAL+D L GI++RH+D+GGG Sbjct: 180 DVYVRAAQLPNLEVLGVDCHIGSQLTTLEPFIDALDRLLALVDRLGDCGIYLRHIDLGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 +GV YRDE PP ++Y K + +RLE RDL L+FEPGR I ANAGVL+T+VE+LKHTEHK Sbjct: 240 VGVRYRDEEPPLVADYIKTVRERLE-GRDLALMFEPGRYIVANAGVLLTQVEYLKHTEHK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360 +FAI+DAAMNDLIRPALYQAW D+ +RPR A+ YD+VGP+CET DFL K R+L L+E Sbjct: 299 DFAIVDAAMNDLIRPALYQAWMDVTAVRPRATAARPYDIVGPICETGDFLAKGRELALEE 358 Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417 GDLLAV S+GAYGF MSSNYNTR R AEV+VDG++ + VR+RE ++ L+A ES+LPE Sbjct: 359 GDLLAVHSAGAYGFVMSSNYNTRGRCAEVLVDGDQAFEVRRRETVAELFAGESLLPE 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: 542 Number of extensions: 12 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 AO356_12740 AO356_12740 (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.30377.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-162 525.3 0.0 5e-162 525.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 AO356_12740 diaminopimelate deca Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 AO356_12740 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.1 0.0 5e-162 5e-162 6 416 .. 8 410 .. 4 411 .. 0.98 Alignments for each domain: == domain 1 score: 525.1 bits; conditional E-value: 5e-162 TIGR01048 6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrl 68 gel++egv+l ++ae+fgtP+Yvy+++++++++++++ a + +lv++AvKAnsnl vl++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 8 GGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYRTFADALDGMPHLVCFAVKANSNLGVLNV 70 689*****************************************9****************** PP TIGR01048 69 laeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelell 131 la++G+g+d+vsgGEler+laAg +a+kivfsg+gk++e++++ale++++++n++s++ele+l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 71 LARLGAGFDIVSGGELERVLAAGGSADKIVFSGVGKTREDMRRALEVGVHCFNIESTDELERL 133 *************************************************************** PP TIGR01048 132 eeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGi 194 + +a+elg +a+v+lRvnpdvda th+yisTGlke+KFGi++++ae++y +a++l++le++G+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 134 QVVAAELGVRAPVSLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYVRAAQLPNLEVLGV 196 *************************************************************** PP TIGR01048 195 hvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaek 257 ++HIGSq++ lepf++a+++++ l+++l + gi l+++dlGGG+g++y++ee +p +++y ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 197 DCHIGSQLTTLEPFIDALDRLLALVDRLGDCGIYLRHIDLGGGVGVRYRDEE-PPLVADYIKT 258 ***************************************************9.********** PP TIGR01048 258 lleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalY 320 + e+le+ ++l l++EpGR++vanagvllt+Ve++K++e++ f++vDa+mndliRpalY lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 259 VRERLEG-----RDLALMFEPGRYIVANAGVLLTQVEYLKHTEHKDFAIVDAAMNDLIRPALY 316 ***9999.....6************************************************** PP TIGR01048 321 eayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssn 383 +a+++++a+ r +++++ +d+vGp+CE+gD+lak rel e Gdllav+saGAYg+ mssn lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 317 QAWMDVTAV-RPRATAARPYDIVGPICETGDFLAKGRELALEE-GDLLAVHSAGAYGFVMSSN 377 *********.889999***********************8776.******************* PP TIGR01048 384 Ynsrprpaevlveegkarlirrretledllale 416 Yn+r+r+aevlv++++a +rrret+++l+a e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_12740 378 YNTRGRCAEVLVDGDQAFEVRRRETVAELFAGE 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: 10.84 // [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