Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate SMc00723 SMc00723 diaminopimelate DAP decarboxylase
Query= reanno::Korea:Ga0059261_2051 (419 letters) >FitnessBrowser__Smeli:SMc00723 Length = 422 Score = 406 bits (1044), Expect = e-118 Identities = 213/422 (50%), Positives = 280/422 (66%), Gaps = 5/422 (1%) Query: 1 MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60 M+HF ++G+L+AE+V + IA VGTP Y YSTATLERH A A + ++ + +A+ Sbjct: 1 MNHFQYRDGILYAEDVPLTEIARAVGTPFYCYSTATLERHYKVFSQAFADVDAM-VCYAM 59 Query: 61 KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120 KAN N AVL L R G G DVVS GEL+RALAAG+PA ++FSGVGKT E+ L+ GI Sbjct: 60 KANSNQAVLKTLGRLGAGLDVVSEGELRRALAAGIPAGRIMFSGVGKTAREMDFALEAGI 119 Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180 FN+E E E EVL A G+ AP R+NPDVDA THAKISTGK ENKFG++ +RA Sbjct: 120 YCFNVESEPELEVLNQRAVRAGRRAPVSFRINPDVDARTHAKISTGKKENKFGISWERAR 179 Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240 ++ A+ PG+ + G+ +HIGSQ+TEL P + A+K + ELV LR+ GH I HVD+GGG Sbjct: 180 GVYAHAAELPGIEVTGIDMHIGSQITELQPFDDAFKLLRELVDTLRSDGHVIEHVDIGGG 239 Query: 241 LGVPYHA-GQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299 LG+PY + + +V +G + ++ EPGR I GNAG+LVTEV++VK Sbjct: 240 LGIPYREDNNPPPLPDAYADIVKNQLKGLDCKIVTEPGRLIVGNAGILVTEVVYVKDGGD 299 Query: 300 NPYVIVDAAMNDLARPALYDAYHEFEAVE---PTGEKFVANIAGPVCETGDTFAMGREID 356 +VIVD AMNDL RP LY+AYHE V+ + + A++ GPVCETGD A+ RE+ Sbjct: 300 KTFVIVDGAMNDLIRPTLYEAYHEIRPVKISAASAPRIKADVVGPVCETGDYLALDREMA 359 Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416 + K GDL +AGAYGA A TYNSR LVPEVLV GDRF V+ R + ++G + VP+ Sbjct: 360 MPKPGDLFAIGSAGAYGAVQAGTYNSRLLVPEVLVKGDRFHVIRPRRDYDELIGLDSVPD 419 Query: 417 WV 418 W+ Sbjct: 420 WL 421 Lambda K H 0.318 0.135 0.389 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: 535 Number of extensions: 22 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: 419 Length of database: 422 Length adjustment: 32 Effective length of query: 387 Effective length of database: 390 Effective search space: 150930 Effective search space used: 150930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate SMc00723 SMc00723 (diaminopimelate DAP 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.21535.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-148 478.8 0.0 6.3e-148 478.6 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc00723 SMc00723 diaminopimelate DAP dec Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc00723 SMc00723 diaminopimelate DAP decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.6 0.0 6.3e-148 6.3e-148 4 415 .. 6 414 .. 3 416 .. 0.96 Alignments for each domain: == domain 1 score: 478.6 bits; conditional E-value: 6.3e-148 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldv 78 +dg l++e+v+l+e+a+ gtP+Y y+++tl+++++ +++af++ +++v+YA+KAnsn avl++l ++G+gldv lcl|FitnessBrowser__Smeli:SMc00723 6 YRDGILYAEDVPLTEIARAVGTPFYCYSTATLERHYKVFSQAFADVDAMVCYAMKANSNQAVLKTLGRLGAGLDV 80 57899****************************************999*************************** PP TIGR01048 79 vsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvd 153 vs+GEl ralaAg++a +i+fsg+gk+ +e+ ale++i ++nv+s+ ele l++ a ++g +a+v++R+npdvd lcl|FitnessBrowser__Smeli:SMc00723 81 VSEGELRRALAAGIPAGRIMFSGVGKTAREMDFALEAGIYCFNVESEPELEVLNQRAVRAGRRAPVSFRINPDVD 155 *************************************************************************** PP TIGR01048 154 aktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegie 228 a+th +isTG+ke+KFGi+ e+a+ +y a++l+ +e++Gi++HIGSqi++l+pf +a++ + +l+++l+++g lcl|FitnessBrowser__Smeli:SMc00723 156 ARTHAKISTGKKENKFGISWERARGVYAHAAELPGIEVTGIDMHIGSQITELQPFDDAFKLLRELVDTLRSDGHV 230 *************************************************************************** PP TIGR01048 229 leeldlGGGlgisyeeeeeapdlee.yaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesr 302 +e++d+GGGlgi+y+e++++p l + ya+ ++++l++ l+ k++ EpGR +v+nag+l+t+V +vK+ + + lcl|FitnessBrowser__Smeli:SMc00723 231 IEHVDIGGGLGIPYREDNNPPPLPDaYADIVKNQLKG-----LDCKIVTEPGRLIVGNAGILVTEVVYVKDGGDK 300 *****************99988766155555556655.....9******************************** PP TIGR01048 303 kfvlvDagmndliRpalYeayheiaalkr.leeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAY 376 +fv+vD++mndliRp lYeayhei+++k +++ ++dvvGp+CE+gD la dre+ ++Gdl a+ saGAY lcl|FitnessBrowser__Smeli:SMc00723 301 TFVIVDGAMNDLIRPTLYEAYHEIRPVKIsAASAPRIKADVVGPVCETGDYLALDREMAMPKPGDLFAIGSAGAY 375 ***************************75356778999************************************* PP TIGR01048 377 gasmssnYnsrprpaevlveegkarlirrretledllal 415 ga + +Ynsr + evlv++++ ++ir r +++l+ l lcl|FitnessBrowser__Smeli:SMc00723 376 GAVQAGTYNSRLLVPEVLVKGDRFHVIRPRRDYDELIGL 414 ***********************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (422 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.93 // [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