Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_011160273.1 TX73_RS24240 diaminopimelate decarboxylase
Query= reanno::Korea:Ga0059261_2051 (419 letters) >NCBI__GCF_000195775.1:WP_011160273.1 Length = 421 Score = 438 bits (1126), Expect = e-127 Identities = 229/422 (54%), Positives = 293/422 (69%), Gaps = 5/422 (1%) Query: 1 MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60 M HF+ ++GVLHAE VS+ +IA +VGTP Y YS+ATLERH A AGL ++ + +A+ Sbjct: 1 MRHFDYRDGVLHAEGVSLASIAQDVGTPFYCYSSATLERHYRVFTEAFAGLDAL-VCYAM 59 Query: 61 KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120 KAN N +VL LA+ G GADVVSGGEL+RALAAG+P +VFSGVGKT AEL+ LD I Sbjct: 60 KANSNQSVLRTLAKLGAGADVVSGGELQRALAAGIPPSKIVFSGVGKTEAELRAALDHDI 119 Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180 N+E E E E L+ +A G+TA LRVNPDVD+GTHAKISTGK+ENKFG+ I A Sbjct: 120 KCLNVESEPELEQLSRIAVETGRTARISLRVNPDVDSGTHAKISTGKSENKFGIPIRHAR 179 Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240 E++ R AK PG+ + GV +HIGSQ+ +LAP+EAA+++V E + LR GHT+ HVD GGG Sbjct: 180 EVYARAAKLPGIQVTGVDVHIGSQIIDLAPMEAAFRKVAEFIHVLRGDGHTVNHVDFGGG 239 Query: 241 LGVPYHAGQTVSTAE-EFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299 LG+PY+ + + MV RVT TL+FEPGR I GNAG+LV +VI+VK G Sbjct: 240 LGIPYYEDRDAPPEPFAYAEMVKRVTHNLGCTLLFEPGRMIVGNAGILVAKVIYVKHGDG 299 Query: 300 NPYVIVDAAMNDLARPALYDAYHEF---EAVEPTGEKFVANIAGPVCETGDTFAMGREID 356 +VI+DAAMNDL RP LY+AYHE A P VA++ GPVCETGD A+ R++ Sbjct: 300 KTFVIIDAAMNDLIRPTLYEAYHEILPVAAPAPGVATMVADVVGPVCETGDYLALDRKLP 359 Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416 +K+GDL TAGAYGA A TYN+RALVPEVLV D+ AVV RI+ E ++ ++ Sbjct: 360 ELKAGDLIAIMTAGAYGAVQACTYNTRALVPEVLVKDDQVAVVRPRIEVEQLIAMDKPAP 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: 528 Number of extensions: 18 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: 421 Length adjustment: 32 Effective length of query: 387 Effective length of database: 389 Effective search space: 150543 Effective search space used: 150543 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 WP_011160273.1 TX73_RS24240 (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.12364.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-151 489.0 0.0 5.2e-151 488.8 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011160273.1 TX73_RS24240 diaminopimelate dec Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011160273.1 TX73_RS24240 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 488.8 0.0 5.2e-151 5.2e-151 5 416 .. 7 415 .. 4 416 .. 0.96 Alignments for each domain: == domain 1 score: 488.8 bits; conditional E-value: 5.2e-151 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 +dg l +egv+l+++a+ gtP+Y y+++tl+++++ ++eaf++ ++lv+YA+KAnsn +vlr+la++G lcl|NCBI__GCF_000195775.1:WP_011160273.1 7 RDGVLHAEGVSLASIAQDVGTPFYCYSSATLERHYRVFTEAFAGLDALVCYAMKANSNQSVLRTLAKLG 75 6899****************************************99*********************** PP TIGR01048 74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142 +g+dvvsgGEl+ralaAg++++kivfsg+gk+e+el+aal+++ik++nv+s+ ele+l++ia e+g +a lcl|NCBI__GCF_000195775.1:WP_011160273.1 76 AGADVVSGGELQRALAAGIPPSKIVFSGVGKTEAELRAALDHDIKCLNVESEPELEQLSRIAVETGRTA 144 ********************************************************************* PP TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211 r++lRvnpdvd th +isTG+ e+KFGi +++a+e+y +a+kl+ ++++G++vHIGSqi dl+p+++a lcl|NCBI__GCF_000195775.1:WP_011160273.1 145 RISLRVNPDVDSGTHAKISTGKSENKFGIPIRHAREVYARAAKLPGIQVTGVDVHIGSQIIDLAPMEAA 213 ********************************************************************* PP TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeee.apdleeyaeklleklekeaelglklklilEpG 279 ++kv+++++ l+ +g +++++d+GGGlgi+y e+ + +p++ yae+++ ++++ +l +l++EpG lcl|NCBI__GCF_000195775.1:WP_011160273.1 214 FRKVAEFIHVLRGDGHTVNHVDFGGGLGIPYYEDRDaPPEPFAYAEMVK-RVTH----NLGCTLLFEPG 277 ******************************9887651566677777655.5554....4899******* PP TIGR01048 280 RslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr.leeeetetvdvvGplC 347 R++v+nag+l+++V +vK+ + ++fv++Da+mndliRp lYeayhei ++++ +t+++dvvGp+C lcl|NCBI__GCF_000195775.1:WP_011160273.1 278 RMIVGNAGILVAKVIYVKHGDGKTFVIIDAAMNDLIRPTLYEAYHEILPVAApAPGVATMVADVVGPVC 346 ************************************************998834567899********* PP TIGR01048 348 EsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 E+gD la dr+lpe ++Gdl+a++ aGAYga + +Yn+r+ + evlv+++++ ++r r ++e+l+a + lcl|NCBI__GCF_000195775.1:WP_011160273.1 347 ETGDYLALDRKLPELKAGDLIAIMTAGAYGAVQACTYNTRALVPEVLVKDDQVAVVRPRIEVEQLIAMD 415 *****************************************************************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (421 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: 7.33 // [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