Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 6939152 Sama_3250 diaminopimelate decarboxylase (RefSeq)
Query= BRENDA::Q9KVL7 (417 letters) >FitnessBrowser__SB2B:6939152 Length = 414 Score = 546 bits (1406), Expect = e-160 Identities = 276/416 (66%), Positives = 324/416 (77%), Gaps = 2/416 (0%) Query: 1 MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60 MD+F Y+E+ +L+AE+ +A LA ++GTPLYVYSRATLERHWHAFD +V +PHLICYAV Sbjct: 1 MDHFLYREE-RLFAEECDVAGLAAEHGTPLYVYSRATLERHWHAFDGAVASHPHLICYAV 59 Query: 61 KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120 KANSNL VLN LARLGSGFDIVS GEL RVL AGGDP+KVVFSGVGKT AEM+ AL I Sbjct: 60 KANSNLAVLNVLARLGSGFDIVSGGELSRVLEAGGDPAKVVFSGVGKTVAEMELALNTGI 119 Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180 CFN+ES EL+ LN+VAG LG AP+SLR+NPDVDA THPYISTGL++NKFGI + A Sbjct: 120 MCFNLESGAELELLNEVAGRLGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIPMEEAE 179 Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240 ++ A +LPNL V G+DCHIGSQLT L PF+DA DR+LALID L +GI I H DVGGG Sbjct: 180 ALFARAAALPNLAVKGVDCHIGSQLTELKPFLDAMDRMLALIDRLAEQGIVIEHFDVGGG 239 Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300 LGV Y E PP P YA A+L++L R L+LIFEPGRAIAANAG+ VT+V + K K Sbjct: 240 LGVTYNGETPPHPDVYAAAILEKL-NGRPLKLIFEPGRAIAANAGIFVTQVLYTKDNGDK 298 Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360 F I+D AMNDLIRP+LY AWQ+IIP D+VGPVCET DFLGKDR+L Sbjct: 299 RFVIVDGAMNDLIRPSLYGAWQNIIPAVKTNEPTTRCDVVGPVCETGDFLGKDRELAAGS 358 Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416 GDLL VRS+GAYGFTM+SNYNTRPR AE+MVDG+K Y+VR+RE+LS LW E +LP Sbjct: 359 GDLLVVRSAGAYGFTMASNYNTRPRAAELMVDGDKAYVVREREKLSQLWQGEQLLP 414 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: 510 Number of extensions: 16 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: 414 Length adjustment: 31 Effective length of query: 386 Effective length of database: 383 Effective search space: 147838 Effective search space used: 147838 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 6939152 Sama_3250 (diaminopimelate decarboxylase (RefSeq))
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.18633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-162 525.5 0.0 4.7e-162 525.2 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6939152 Sama_3250 diaminopimelate decarb Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6939152 Sama_3250 diaminopimelate decarboxylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.2 0.0 4.7e-162 4.7e-162 6 416 .. 8 410 .. 5 411 .. 0.98 Alignments for each domain: == domain 1 score: 525.2 bits; conditional E-value: 4.7e-162 TIGR01048 6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 + +l++e++d++ la+e+gtPlYvy+++tl+++++a++ a++++ +l++YAvKAnsnlavl++la++G+g+d+vsgG lcl|FitnessBrowser__SB2B:6939152 8 EERLFAEECDVAGLAAEHGTPLYVYSRATLERHWHAFDGAVASHPHLICYAVKANSNLAVLNVLARLGSGFDIVSGG 84 56899************************************************************************ PP TIGR01048 83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthey 159 El r+l+Ag ++ k+vfsg+gk+ +e+e al+++i ++n++s +elell+e+a++lgk a+v+lRvnpdvda th+y lcl|FitnessBrowser__SB2B:6939152 85 ELSRVLEAGGDPAKVVFSGVGKTVAEMELALNTGIMCFNLESGAELELLNEVAGRLGKVAPVSLRVNPDVDAGTHPY 161 ***************************************************************************** PP TIGR01048 160 isTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGG 236 isTGlke+KFGi +eeae+ + +a++l++l + G+++HIGSq+++l+pf +a+++++ l+++l+e+gi +e++d+GG lcl|FitnessBrowser__SB2B:6939152 162 ISTGLKENKFGIPMEEAEALFARAAALPNLAVKGVDCHIGSQLTELKPFLDAMDRMLALIDRLAEQGIVIEHFDVGG 238 ***************************************************************************** PP TIGR01048 237 GlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmnd 313 Glg++y+ e+ +p+++ ya+++lekl++ + lkli+EpGR+++anag+++t+V ++K+++ ++fv+vD++mnd lcl|FitnessBrowser__SB2B:6939152 239 GLGVTYNGET-PPHPDVYAAAILEKLNG-----RPLKLIFEPGRAIAANAGIFVTQVLYTKDNGDKRFVIVDGAMND 309 ********99.***************99.....6******************************************* PP TIGR01048 314 liRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprp 390 liRp+lY+a+++i+++ + ++e+t+++dvvGp+CE+gD+l+kdrel + Gdll+v+saGAYg++m+snYn+rpr+ lcl|FitnessBrowser__SB2B:6939152 310 LIRPSLYGAWQNIIPAVK-TNEPTTRCDVVGPVCETGDFLGKDRELAAGS-GDLLVVRSAGAYGFTMASNYNTRPRA 384 ****************66.6677***********************9887.************************** PP TIGR01048 391 aevlveegkarlirrretledllale 416 ae++v+++ka+++r+re+l++l++ e lcl|FitnessBrowser__SB2B:6939152 385 AELMVDGDKAYVVREREKLSQLWQGE 410 ***********************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (414 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.97 // [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