Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_012506052.1 PAES_RS07495 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >NCBI__GCF_000020625.1:WP_012506052.1 Length = 416 Score = 313 bits (803), Expect = 5e-90 Identities = 176/408 (43%), Positives = 254/408 (62%), Gaps = 4/408 (0%) Query: 3 YFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKA 62 +F+Y+ D L E V L LA +Y TPL+V SR L + AF+++ H CY+VKA Sbjct: 6 FFSYK-DTVLSCEGVALDALAAEYSTPLFVVSRNALVEQYRAFEEAFSSLSHFTCYSVKA 64 Query: 63 NSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKC 122 N N+ V+ L+ G G D+ S GEL R L AG DP K++ +GVGK++ +++ ALQ I Sbjct: 65 NFNIHVIKALSDQGCGCDVNSGGELFRALKAGVDPQKIIMAGVGKSDQDIEYALQSGIFM 124 Query: 123 FNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQV 182 ES EL+ + VA LGV A + +RINP+V A+THPYI+TG KFGI ++ Sbjct: 125 LKAESLSELRHIEAVARRLGVTASVGVRINPNVTAETHPYITTGDSKEKFGIDEGSLDEM 184 Query: 183 YRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLG 242 + L S+ +++ +D HIGSQ+ + AT++LL ++D+ +A+G I +LD+GGG Sbjct: 185 FDLFKSMKHVNFMCLDMHIGSQIFDTEFYHAATEKLLDVLDAARAKGFSIDYLDIGGGFP 244 Query: 243 VVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTE-HKN 301 V Y + P P E ++L + + +IFEPGR IAAN+GV+VTKV + K K Sbjct: 245 VTYEPQKPATPIEQFASVLIPVLKKTGTTIIFEPGRFIAANSGVMVTKVLYRKRNHIGKE 304 Query: 302 FAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL-VLQE 360 F I+DA M +LIRPALYQ++ +II ++ +Q D+VGPVCE+ DF + R + + E Sbjct: 305 FVIVDAGMTELIRPALYQSYHEIIGVK-QQEATIVADVVGPVCESGDFFARGRTIDAVGE 363 Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSL 408 G+ LA+ S+GAYG MS+NYN R R AEVMVD +T L+R+R+ L Sbjct: 364 GEYLAILSAGAYGAVMSNNYNGRLRPAEVMVDNGRTSLIRKRDTFEQL 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: 413 Number of extensions: 15 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: 416 Length adjustment: 31 Effective length of query: 386 Effective length of database: 385 Effective search space: 148610 Effective search space used: 148610 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_012506052.1 PAES_RS07495 (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.21882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-146 472.0 0.0 7.3e-146 471.8 0.0 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012506052.1 PAES_RS07495 diaminopimelate dec Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012506052.1 PAES_RS07495 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.8 0.0 7.3e-146 7.3e-146 4 417 .] 9 416 .] 6 416 .] 0.98 Alignments for each domain: == domain 1 score: 471.8 bits; conditional E-value: 7.3e-146 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaee 72 kd+ l++egv+l +la+e+ tPl+v+++++l e+++a++eaf++ ++ +Y vKAn n++v++ l+++ lcl|NCBI__GCF_000020625.1:WP_012506052.1 9 YKDTVLSCEGVALDALAAEYSTPLFVVSRNALVEQYRAFEEAFSSLSHFTCYSVKANFNIHVIKALSDQ 77 67899****************************************99********************** PP TIGR01048 73 GlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkk 141 G+g dv sgGEl ral+Agv+++ki+ +g+gks++++e al+++i ++ ++s++el+++e++a++lg + lcl|NCBI__GCF_000020625.1:WP_012506052.1 78 GCGCDVNSGGELFRALKAGVDPQKIIMAGVGKSDQDIEYALQSGIFMLKAESLSELRHIEAVARRLGVT 146 ********************************************************************* PP TIGR01048 142 arvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfve 210 a v +R+np+v+a+th+yi+TG ++KFGi+ + e++ l +++++++ + +++HIGSqi+d+e +++ lcl|NCBI__GCF_000020625.1:WP_012506052.1 147 ASVGVRINPNVTAETHPYITTGDSKEKFGIDEGSLDEMFDLFKSMKHVNFMCLDMHIGSQIFDTEFYHA 215 ********************************************************************* PP TIGR01048 211 aaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpG 279 a+ek++++l+ +++g+++ ld+GGG+ ++ye+++ a +e++a++l+ l+k + ++i+EpG lcl|NCBI__GCF_000020625.1:WP_012506052.1 216 ATEKLLDVLDAARAKGFSIDYLDIGGGFPVTYEPQKPATPIEQFASVLIPVLKK-----TGTTIIFEPG 279 *****************************************************9.....5899****** PP TIGR01048 280 RslvanagvlltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplC 347 R+++an+gv++t+V ++K+++ ++fv+vDagm++liRpalY++yhei+ +k+ +e+t ++dvvGp+C lcl|NCBI__GCF_000020625.1:WP_012506052.1 280 RFIAANSGVMVTKVLYRKRNHIgKEFVIVDAGMTELIRPALYQSYHEIIGVKQ--QEATIVADVVGPVC 346 ********************989****************************54..7779********** PP TIGR01048 348 EsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 EsgD++a+ r++++v eG++la+ saGAYga ms+nYn r rpaev+v++g+++lir+r+t+e+l+++e lcl|NCBI__GCF_000020625.1:WP_012506052.1 347 ESGDFFARGRTIDAVGEGEYLAILSAGAYGAVMSNNYNGRLRPAEVMVDNGRTSLIRKRDTFEQLIENE 415 ******************************************************************998 PP TIGR01048 417 l 417 + lcl|NCBI__GCF_000020625.1:WP_012506052.1 416 V 416 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (416 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: 10.82 // [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