Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_012334564.1 M446_RS23310 diaminopimelate decarboxylase
Query= reanno::Korea:Ga0059261_2051 (419 letters) >NCBI__GCF_000019365.1:WP_012334564.1 Length = 423 Score = 415 bits (1067), Expect = e-120 Identities = 220/422 (52%), Positives = 279/422 (66%), Gaps = 5/422 (1%) Query: 1 MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60 M HF ++G LHAE V + +A VGTP Y Y++ATLERH A AG + + FA+ Sbjct: 1 MHHFTYRDGTLHAEEVDLARLAEAVGTPFYCYASATLERHFRVFAEAFAGDDPL-VCFAV 59 Query: 61 KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120 KAN N AVL LAR G G D+VS GEL+RALAAG+P E +VFSGV KTRAE+ + LD GI Sbjct: 60 KANSNQAVLASLARLGAGMDIVSEGELRRALAAGVPGERIVFSGVAKTRAEMAVALDAGI 119 Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180 FN+E E E E L+++A A+G+TAP +RVNPDVDA THAKISTGK+ENKFG+ I RA Sbjct: 120 LCFNVESEPELEALSEVARARGQTAPVSIRVNPDVDARTHAKISTGKSENKFGIPISRAR 179 Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240 E++ R A PGL + GV +HIGSQ+T+LAP + A + EL L AAGH + H+D GGG Sbjct: 180 EVYARAAALPGLAVAGVDMHIGSQITDLAPYDNAASLLAELARDLMAAGHRLHHIDFGGG 239 Query: 241 LGVPYHAGQT-VSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299 LG+PY F A++ + + +FE GR I GNAG+LVT V++VK G Sbjct: 240 LGIPYRDDNAPPPDPAAFAAVIRPHFRPLGLRPVFEIGRMIAGNAGILVTRVVYVKEGEG 299 Query: 300 NPYVIVDAAMNDLARPALYDAYHEFEAV---EPTGEKFVANIAGPVCETGDTFAMGREID 356 +VIVDA MNDL RP LY+AYH V +P + A++ GPVCE+GD A+GRE+ Sbjct: 300 RSFVIVDAGMNDLIRPTLYEAYHALRPVRQPDPEAPRLTADVVGPVCESGDYLALGREMP 359 Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416 V GDL +AGAYGA A TYN+R LVPEVLV G AVV R E ++G +RVP+ Sbjct: 360 AVAPGDLLAVMSAGAYGAVQAGTYNTRRLVPEVLVRGAAHAVVRPRQSYEELIGLDRVPD 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: 549 Number of extensions: 21 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: 423 Length adjustment: 32 Effective length of query: 387 Effective length of database: 391 Effective search space: 151317 Effective search space used: 151317 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_012334564.1 M446_RS23310 (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.12103.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-145 469.1 0.0 6.2e-145 468.8 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334564.1 M446_RS23310 diaminopimelate dec Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012334564.1 M446_RS23310 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.8 0.0 6.2e-145 6.2e-145 5 415 .. 7 414 .. 4 416 .. 0.97 Alignments for each domain: == domain 1 score: 468.8 bits; conditional E-value: 6.2e-145 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 +dg+l +e+vdl++lae gtP+Y y ++tl+++++ ++eaf++ + lv++AvKAnsn avl la++G lcl|NCBI__GCF_000019365.1:WP_012334564.1 7 RDGTLHAEEVDLARLAEAVGTPFYCYASATLERHFRVFAEAFAGDDPLVCFAVKANSNQAVLASLARLG 75 7899***************************************9999********************** PP TIGR01048 74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142 +g+d+vs+GEl ralaAgv+ e+ivfsg++k+++e++ al+++i ++nv+s+ ele l+e+a+ g++a lcl|NCBI__GCF_000019365.1:WP_012334564.1 76 AGMDIVSEGELRRALAAGVPGERIVFSGVAKTRAEMAVALDAGILCFNVESEPELEALSEVARARGQTA 144 ********************************************************************* PP TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211 +v++Rvnpdvda+th +isTG+ e+KFGi +++a+e+y +a++l+ l + G+++HIGSqi+dl+p+ +a lcl|NCBI__GCF_000019365.1:WP_012334564.1 145 PVSIRVNPDVDARTHAKISTGKSENKFGIPISRAREVYARAAALPGLAVAGVDMHIGSQITDLAPYDNA 213 ********************************************************************* PP TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeee.apdleeyaeklleklekeaelglklklilEpG 279 a+ +++l+++l ++g +l+++d+GGGlgi+y++++ +pd++ +a+++ +++ l l+ ++E+G lcl|NCBI__GCF_000019365.1:WP_012334564.1 214 ASLLAELARDLMAAGHRLHHIDFGGGLGIPYRDDNApPPDPAAFAAVIRPHFRP-----LGLRPVFEIG 277 ********************************9987256899999999999998.....567779**** PP TIGR01048 280 RslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrle.eeetetvdvvGplC 347 R++++nag+l+trV +vKe e r fv+vDagmndliRp lYeayh ++++++ + e+++ t+dvvGp+C lcl|NCBI__GCF_000019365.1:WP_012334564.1 278 RMIAGNAGILVTRVVYVKEGEGRSFVIVDAGMNDLIRPTLYEAYHALRPVRQPDpEAPRLTADVVGPVC 346 **************************************************9865367889********* PP TIGR01048 348 EsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllal 415 EsgD la re+p+v +Gdllav+saGAYga + +Yn+r + evlv++ ++r r+++e+l+ l lcl|NCBI__GCF_000019365.1:WP_012334564.1 347 ESGDYLALGREMPAVAPGDLLAVMSAGAYGAVQAGTYNTRRLVPEVLVRGAAHAVVRPRQSYEELIGL 414 *****************************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (423 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: 00:00:00.01 # Mc/sec: 10.76 // [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