Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_019557562.1 F612_RS0109645 diaminopimelate decarboxylase
Query= BRENDA::Q9KVL7 (417 letters) >NCBI__GCF_000381085.1:WP_019557562.1 Length = 417 Score = 496 bits (1276), Expect = e-145 Identities = 249/409 (60%), Positives = 313/409 (76%), Gaps = 2/409 (0%) Query: 8 EDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKANSNLG 67 ++G L AE V L LA +YGTPLYVYS+ E W AFD + G PHL+CYAVK NSN+ Sbjct: 8 KNGTLHAEDVSLDSLAKRYGTPLYVYSKTEFESRWLAFDTAFGSQPHLVCYAVKTNSNIA 67 Query: 68 VLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCFNVES 127 VL +LA++G+GFDIVS GELERVL AGGDP KVVFSGV K +E++RAL++ I+CFN+ES Sbjct: 68 VLQSLAKIGAGFDIVSQGELERVLRAGGDPKKVVFSGVAKQSSEIRRALEVGIRCFNLES 127 Query: 128 EPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQVYRLAH 187 EL R+ VA + + A IS+R+NPDVDAKTHPYISTGL+DNKFG+ + A ++Y A Sbjct: 128 HAELDRIQTVAESMDLIANISIRVNPDVDAKTHPYISTGLKDNKFGVDINTAPELYADAC 187 Query: 188 SLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGVVYRD 247 + +++ GIDCHIGSQLT + PF+DA +R+L L +L GI I HLD+GGGLG+ Y D Sbjct: 188 ACSHINPVGIDCHIGSQLTEITPFVDALERVLTLKATLAEMGIDIHHLDLGGGLGIQYTD 247 Query: 248 ELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHKNFAIIDA 307 E+PP +EY +AL+++L D+E+I EPGRAIA NAGVL+T+VE+LK TEHKNFAIIDA Sbjct: 248 EVPPPIAEYIQALINKL-NDPDIEVIIEPGRAIAGNAGVLLTEVEYLKPTEHKNFAIIDA 306 Query: 308 AMNDLIRPALYQAWQDIIPLRPRQGEAQT-YDLVGPVCETSDFLGKDRDLVLQEGDLLAV 366 AMNDLIRPALYQA+Q+I+ + PR +T +DLVGPVCET DFLGKDR L L+ GDLLAV Sbjct: 307 AMNDLIRPALYQAYQEIVAVTPRTDGLETNWDLVGPVCETGDFLGKDRALNLKAGDLLAV 366 Query: 367 RSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVL 415 SSGAYGFTMSSNYNTRPR AE+MV ++ +L+R RE L E ++ Sbjct: 367 MSSGAYGFTMSSNYNTRPRAAELMVQNDQAWLIRPRETYEDLMGSELLI 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: 499 Number of extensions: 17 Number of successful extensions: 3 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: 417 Length adjustment: 31 Effective length of query: 386 Effective length of database: 386 Effective search space: 148996 Effective search space used: 148996 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_019557562.1 F612_RS0109645 (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.30041.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-164 533.0 0.0 2.2e-164 532.8 0.0 1.0 1 lcl|NCBI__GCF_000381085.1:WP_019557562.1 F612_RS0109645 diaminopimelate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000381085.1:WP_019557562.1 F612_RS0109645 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.8 0.0 2.2e-164 2.2e-164 4 416 .. 7 412 .. 4 413 .. 0.98 Alignments for each domain: == domain 1 score: 532.8 bits; conditional E-value: 2.2e-164 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaee 72 k+g+l +e+v+l +la+++gtPlYvy+++++++r+ a+++af+++ +lv+YAvK nsn+avl+ la+ lcl|NCBI__GCF_000381085.1:WP_019557562.1 7 LKNGTLHAEDVSLDSLAKRYGTPLYVYSKTEFESRWLAFDTAFGSQPHLVCYAVKTNSNIAVLQSLAKI 75 6899***************************************************************** PP TIGR01048 73 GlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkk 141 G+g+d+vs+GEler+l Ag +++k+vfsg++k+++e+++ale++i+++n++s +el++++++a+++ lcl|NCBI__GCF_000381085.1:WP_019557562.1 76 GAGFDIVSQGELERVLRAGGDPKKVVFSGVAKQSSEIRRALEVGIRCFNLESHAELDRIQTVAESMDLI 144 ********************************************************************* PP TIGR01048 142 arvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfve 210 a++++Rvnpdvdakth+yisTGlk++KFG+++++a e y a + +++++vGi++HIGSq++++ pfv+ lcl|NCBI__GCF_000381085.1:WP_019557562.1 145 ANISIRVNPDVDAKTHPYISTGLKDNKFGVDINTAPELYADACACSHINPVGIDCHIGSQLTEITPFVD 213 ********************************************************************* PP TIGR01048 211 aaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpG 279 a+e+v++l ++l+e gi++++ldlGGGlgi+y++e +p ++ey ++l++kl++ + ++i+EpG lcl|NCBI__GCF_000381085.1:WP_019557562.1 214 ALERVLTLKATLAEMGIDIHHLDLGGGLGIQYTDEV-PPPIAEYIQALINKLND-----PDIEVIIEPG 276 **********************************99.*****************.....7********* PP TIGR01048 280 RslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCE 348 R++++nagvllt+Ve++K +e+++f+++Da+mndliRpalY+ay+ei+a++ ++ ++++d+vGp+CE lcl|NCBI__GCF_000381085.1:WP_019557562.1 277 RAIAGNAGVLLTEVEYLKPTEHKNFAIIDAAMNDLIRPALYQAYQEIVAVTPRTDGLETNWDLVGPVCE 345 ********************************************************************* PP TIGR01048 349 sgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 +gD+l+kdr+l+ ++Gdllav+s+GAYg++mssnYn+rpr+ae++v++++a lir ret+edl+ e lcl|NCBI__GCF_000381085.1:WP_019557562.1 346 TGDFLGKDRALNL-KAGDLLAVMSSGAYGFTMSSNYNTRPRAAELMVQNDQAWLIRPRETYEDLMGSE 412 ***********86.56************************************************9776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (417 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: 7.93 // [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