Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate WP_029000548.1 H537_RS0128280 threonine ammonia-lyase, biosynthetic
Query= SwissProt::A0FKE6 (606 letters) >NCBI__GCF_000430725.1:WP_029000548.1 Length = 522 Score = 518 bits (1335), Expect = e-151 Identities = 267/504 (52%), Positives = 351/504 (69%), Gaps = 6/504 (1%) Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166 +YL IL++KVYDVA E+PL A LS RLG V LKRED QPVFSFK+RGAYN MA L Sbjct: 19 DYLKKILTAKVYDVAVESPLDLARNLSRRLGNQVLLKREDQQPVFSFKLRGAYNKMAHLS 78 Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGDS 226 EQL +GVIC+SAGNHAQGVAL A+RLGC AVIVMPVTTP +K +V++LG VVL GDS Sbjct: 79 AEQLARGVICASAGNHAQGVALGAKRLGCKAVIVMPVTTPRVKIDAVQQLGGEVVLHGDS 138 Query: 227 YDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGLI 286 Y +A +A + G TF+ PFD PDVI GQGT+ ME+ RQ + + A+FV +GGGGLI Sbjct: 139 YSDAALHASALEKERGLTFVHPFDDPDVIAGQGTIAMELLRQHQGPLDAVFVAIGGGGLI 198 Query: 287 AGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETYR 346 +G+AAY+K V P+I++IGV+ +D++A+ S+ +RV L VG FADG AVK+VGEET+R Sbjct: 199 SGVAAYIKAVRPEIQVIGVQSVDSDAMVRSVRAKKRVQLSDVGLFADGTAVKLVGEETFR 258 Query: 347 LCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENVVAI 406 + EL+D V+V D +CA+IKD+F++ RSI+EP+GA+ +A + Y + LKG AI Sbjct: 259 IARELVDDFVVVDNDEVCAAIKDVFQDTRSIVEPSGAMGVAAIKKYVDQHKLKGRTFAAI 318 Query: 407 TSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVG----PMNITEFKY 462 T GANMNFDRLR V E A+VG REA+ A +PE+ GSF++F E +G P +TEF Y Sbjct: 319 TCGANMNFDRLRFVAERAEVGEHREALFAVTIPEERGSFRRFCEAIGTPAHPRQVTEFNY 378 Query: 463 RYNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTNV 522 R SD++ A V +G+ E + + E T+NLTD++L K HLRH++GGR+ + Sbjct: 379 RI-SDQQVAHVFVGIGISKREEADKLARNFERHGFTTLNLTDDELAKQHLRHMVGGRSEL 437 Query: 523 -HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEF 581 +E L RFTFPE+PGAL++FL+A P WNISLFHYR QG +LVGIQVP + Sbjct: 438 ARDERLFRFTFPERPGALLRFLEAMQPDWNISLFHYRNQGADYGRILVGIQVPRGDRAAL 497 Query: 582 EGRADSLGYEYAMESLNEAYQLIM 605 + D+L Y E+ N Y+L + Sbjct: 498 KRFLDTLDYPCVDETDNPVYRLFL 521 Lambda K H 0.318 0.136 0.393 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: 713 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: 606 Length of database: 522 Length adjustment: 36 Effective length of query: 570 Effective length of database: 486 Effective search space: 277020 Effective search space used: 277020 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: 53 (25.0 bits)
Align candidate WP_029000548.1 H537_RS0128280 (threonine ammonia-lyase, biosynthetic)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))
# 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/TIGR01124.hmm # target sequence database: /tmp/gapView.1212569.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01124 [M=499] Accession: TIGR01124 Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-252 822.5 0.4 7e-252 822.3 0.4 1.0 1 NCBI__GCF_000430725.1:WP_029000548.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_029000548.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 822.3 0.4 7e-252 7e-252 1 499 [] 19 521 .. 19 521 .. 0.99 Alignments for each domain: == domain 1 score: 822.3 bits; conditional E-value: 7e-252 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasa 73 dyl++il+a+vy++ave+pl+ a++ls+rl+n+vllkred+qpvfsfklrGaynkma+lsaeq a+Gvi+asa NCBI__GCF_000430725.1:WP_029000548.1 19 DYLKKILTAKVYDVAVESPLDLARNLSRRLGNQVLLKREDQQPVFSFKLRGAYNKMAHLSAEQLARGVICASA 91 89*********************************************************************** PP TIGR01124 74 GnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddp 146 GnhaqGval+ak+lG+kavivmp ttp +k+dav++ GgevvlhG++y++a+ +a +l++e+gltf++pfddp NCBI__GCF_000430725.1:WP_029000548.1 92 GNHAQGVALGAKRLGCKAVIVMPVTTPRVKIDAVQQLGGEVVLHGDSYSDAALHASALEKERGLTFVHPFDDP 164 ************************************************************************* PP TIGR01124 147 lviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkl 219 +viaGqGt+a+ellrq++ +ldavfv++GGGGli+Gvaa++k+++pei+vigv++ ds+a+ +++ a +rv+l NCBI__GCF_000430725.1:WP_029000548.1 165 DVIAGQGTIAMELLRQHQGPLDAVFVAIGGGGLISGVAAYIKAVRPEIQVIGVQSVDSDAMVRSVRAKKRVQL 237 ************************************************************************* PP TIGR01124 220 dqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi 292 ++vGlfadG+avk vG+etfr+++e++dd+v vd devcaaikdvf+dtr+++ep+Ga+++a +kkyv+++++ NCBI__GCF_000430725.1:WP_029000548.1 238 SDVGLFADGTAVKLVGEETFRIARELVDDFVVVDNDEVCAAIKDVFQDTRSIVEPSGAMGVAAIKKYVDQHKL 310 ************************************************************************* PP TIGR01124 293 edktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGe....raitefnyrladd 361 +++t++ai++Gan+nfdrlr+v+erae+Ge+real+avtipee+Gs+++f+e +G r++tefnyr++d+ NCBI__GCF_000430725.1:WP_029000548.1 311 KGRTFAAITCGANMNFDRLRFVAERAEVGEHREALFAVTIPEERGSFRRFCEAIGTpahpRQVTEFNYRISDQ 383 *******************************************************7555589*********** PP TIGR01124 362 ekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGall 434 + ah+fvG+ ++++ee+++l++++e++g+++++ltddelak h+r++vGGr++ +++erl++f+fperpGall NCBI__GCF_000430725.1:WP_029000548.1 384 QVAHVFVGIGISKREEADKLARNFERHGFTTLNLTDDELAKQHLRHMVGGRSELARDERLFRFTFPERPGALL 456 ************************************************************************* PP TIGR01124 435 kfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 +fle +q++wnislfhyrn GadyGr+lvg++vp+ + ++++ fl++l+y ++det+np+yrlfl NCBI__GCF_000430725.1:WP_029000548.1 457 RFLEAMQPDWNISLFHYRNQGADYGRILVGIQVPRGDRAALKRFLDTLDYPCVDETDNPVYRLFL 521 ****************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (522 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 33.27 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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