Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_011386835.1 AMB_RS22725 diaminopimelate decarboxylase
Query= reanno::Korea:Ga0059261_2051 (419 letters) >NCBI__GCF_000009985.1:WP_011386835.1 Length = 424 Score = 406 bits (1044), Expect = e-118 Identities = 221/423 (52%), Positives = 285/423 (67%), Gaps = 7/423 (1%) Query: 1 MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNAL--AGLPSVHLAF 58 M+HF+ +NG L AE+V+I IA EVGTP Y YSTATL+RH + AL AGL + + F Sbjct: 1 MNHFHYQNGELFAEDVAIARIAREVGTPFYCYSTATLQRHYTVFAEALKAAGLDAT-ICF 59 Query: 59 AIKANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDE 118 A KANPN+AV+ A+ G GADVVS GEL++ALAAG+PA +VFSGVGKTR EL+ + + Sbjct: 60 AAKANPNMAVIRTFAQLGAGADVVSEGELRQALAAGVPAARIVFSGVGKTRHELEFAVAK 119 Query: 119 GIGQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDR 178 GI Q N+E E E E+L+++A A+G+ P +RVNPDVDAGTHAKI+TGK ENKFG+ R Sbjct: 120 GIFQINVESEPELEMLSEIAAARGQVMPIAIRVNPDVDAGTHAKITTGKKENKFGIEWTR 179 Query: 179 ALEIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLG 238 A E++ R PG+ +A HIGSQLTEL P A+ RV +LVA LRA G I +DLG Sbjct: 180 AREVYARAKALPGVEPVAIACHIGSQLTELTPFREAFLRVRDLVAMLRADGIDIRRLDLG 239 Query: 239 GGLGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAA 298 GGLGVPY +T + ++ +FEPGR + GNAG+LV+ +I VK + Sbjct: 240 GGLGVPYD-DETPPEPAAYAEVIKATLGDLGCRFVFEPGRLLVGNAGILVSRIIRVKEGS 298 Query: 299 GNPYVIVDAAMNDLARPALYDAYHE-FEAVEPTGEKFVA--NIAGPVCETGDTFAMGREI 355 ++IVDAAMNDLARP+LYDAYH F EP +A ++ GPVCETGDTFA R + Sbjct: 299 TRTFLIVDAAMNDLARPSLYDAYHSIFPVAEPKAGAALAEVDVVGPVCETGDTFAKQRRL 358 Query: 356 DVVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVP 415 +++ DL F TAGAYGA M+STYN+R L+PEVLV G +AV+ R E + E +P Sbjct: 359 PPMRTDDLLAFGTAGAYGAAMSSTYNTRPLIPEVLVKGGDYAVIRVRPSYEDMRSLESLP 418 Query: 416 EWV 418 W+ Sbjct: 419 GWL 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: 530 Number of extensions: 23 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: 424 Length adjustment: 32 Effective length of query: 387 Effective length of database: 392 Effective search space: 151704 Effective search space used: 151704 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_011386835.1 AMB_RS22725 (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.25086.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-145 470.6 0.0 2.1e-145 470.3 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386835.1 AMB_RS22725 diaminopimelate deca Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386835.1 AMB_RS22725 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 470.3 0.0 2.1e-145 2.1e-145 4 416 .. 6 415 .. 4 416 .. 0.97 Alignments for each domain: == domain 1 score: 470.3 bits; conditional E-value: 2.1e-145 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrlla 70 ++gel++e+v+++++a+e gtP+Y y+++tl+++++ ++ea ka ++++++A+KAn n+av+r++a lcl|NCBI__GCF_000009985.1:WP_011386835.1 6 YQNGELFAEDVAIARIAREVGTPFYCYSTATLQRHYTVFAEALKAagLDATICFAAKANPNMAVIRTFA 74 589****************************************9965556******************* PP TIGR01048 71 eeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelg 139 ++G+g+dvvs+GEl +alaAgv+a +ivfsg+gk+++ele a++ +i inv+s+ ele+l+eia+ g lcl|NCBI__GCF_000009985.1:WP_011386835.1 75 QLGAGADVVSEGELRQALAAGVPAARIVFSGVGKTRHELEFAVAKGIFQINVESEPELEMLSEIAAARG 143 ********************************************************************* PP TIGR01048 140 kkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepf 208 + +++++Rvnpdvda th +i+TG+ke+KFGie ++a+e+y +a++l+ +e+v i +HIGSq+++l pf lcl|NCBI__GCF_000009985.1:WP_011386835.1 144 QVMPIAIRVNPDVDAGTHAKITTGKKENKFGIEWTRAREVYARAKALPGVEPVAIACHIGSQLTELTPF 212 ********************************************************************* PP TIGR01048 209 veaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilE 277 +ea+ +v +l++ l+++gi+++ ldlGGGlg++y++e+ +p+++ yae+++++l + l + ++E lcl|NCBI__GCF_000009985.1:WP_011386835.1 213 REAFLRVRDLVAMLRADGIDIRRLDLGGGLGVPYDDET-PPEPAAYAEVIKATLGD-----LGCRFVFE 275 ************************************99.************99999.....7999**** PP TIGR01048 278 pGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrlee.eetetvdvvGp 345 pGR lv+nag+l+ r+ vKe ++r+f +vDa+mndl Rp+lY+ayh+i+++++ ++ ++ ++vdvvGp lcl|NCBI__GCF_000009985.1:WP_011386835.1 276 PGRLLVGNAGILVSRIIRVKEGSTRTFLIVDAAMNDLARPSLYDAYHSIFPVAEPKAgAALAEVDVVGP 344 ****************************************************99776155689****** PP TIGR01048 346 lCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414 +CE+gD++ak+r+lp ++++dlla aGAYga+mss+Yn+rp + evlv++g++ +ir r ++ed+ + lcl|NCBI__GCF_000009985.1:WP_011386835.1 345 VCETGDTFAKQRRLPPMRTDDLLAFGTAGAYGAAMSSTYNTRPLIPEVLVKGGDYAVIRVRPSYEDMRS 413 ******************************************************************977 PP TIGR01048 415 le 416 le lcl|NCBI__GCF_000009985.1:WP_011386835.1 414 LE 415 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (424 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: 8.97 // [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