Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 203422 SO4344 threonine dehydratase (NCBI ptt file)
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__MR1:203422 Length = 545 Score = 598 bits (1542), Expect = e-175 Identities = 303/523 (57%), Positives = 389/523 (74%), Gaps = 12/523 (2%) Query: 2 ADSQPLSGAPEGAE-------YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKRED 54 A+SQP +P E YL+ +L + VY+ A+VTPL + KLS+RL + +KRED Sbjct: 12 AESQPAQASPASVEKSQLAQHYLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKRED 71 Query: 55 RQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATA 114 QPVHSFKLRGAY +A L++ + GV+ ASAGNHAQGVA S+A GV A+IVMP T Sbjct: 72 MQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTP 131 Query: 115 DIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELL 174 DIKVDAVR GG V+LHG FD+A A+ ++QQ+G ++ PFD VIAGQGT+A E+L Sbjct: 132 DIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEML 191 Query: 175 QQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPR 234 QQ L+ +FVPVGGGGL AG+A K +MPQ+K++ VE ED+ACLKAA++AG PV L + Sbjct: 192 QQQRDLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQ 251 Query: 235 VGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALA 294 VGLFA+GVAVKRIG E FR+ + +D ++TV SD ICAA+KD+FED RA+AEP+GAL+LA Sbjct: 252 VGLFADGVAVKRIGTEPFRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLA 311 Query: 295 GMKKYIALH----NIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKG 350 G+KKY++ + + RGE++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE G Sbjct: 312 GLKKYVSTNATGESGRGEKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPG 371 Query: 351 SFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLS 410 SFL+FC+LL R +TEFNYRF+ A +F G+RL++G E ++I+ L D G+ V DLS Sbjct: 372 SFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLS 431 Query: 411 DDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGT 470 DE AKLHVRYMVGG P PL+ERL+SFEFPE PGALL+FL TL + WNISLFHYR+HG Sbjct: 432 GDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGA 491 Query: 471 DYGRVLAAFELGDHEP-DFETRLNELGYDCHDETNNPAFRFFL 512 +GRVLA FE+ + F+ L ELG+ +ET +PA++ FL Sbjct: 492 AFGRVLAGFEVPASDALPFQQFLTELGFVYQEETQSPAYQLFL 534 Lambda K H 0.321 0.138 0.403 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: 776 Number of extensions: 25 Number of successful extensions: 5 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: 514 Length of database: 545 Length adjustment: 35 Effective length of query: 479 Effective length of database: 510 Effective search space: 244290 Effective search space used: 244290 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 (21.8 bits) S2: 52 (24.6 bits)
Align candidate 203422 SO4344 (threonine dehydratase (NCBI ptt file))
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.6931.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-234 765.4 0.3 1.4e-234 765.2 0.3 1.0 1 lcl|FitnessBrowser__MR1:203422 SO4344 threonine dehydratase (NC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:203422 SO4344 threonine dehydratase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 765.2 0.3 1.4e-234 1.4e-234 2 499 .] 33 534 .. 32 534 .. 0.98 Alignments for each domain: == domain 1 score: 765.2 bits; conditional E-value: 1.4e-234 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaqGv 80 yl++il ++vy++a++tpl+ +kls+rl+ +v+lkred+qpv+sfklrGayn++aqls+ + +Gv++asaGnhaqGv lcl|FitnessBrowser__MR1:203422 33 YLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGV 111 99***************************************************************************** PP TIGR01124 81 alsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalel 159 a+sa+ Gv avivmpettp+ikvdav+ Gg+vvlhG+++d+a+ +a+ +aq++g +iapfdd+ viaGqGt+a e+ lcl|FitnessBrowser__MR1:203422 112 AMSAASRGVDAVIVMPETTPDIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEM 190 ******************************************************************************* PP TIGR01124 160 lrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdet 238 l+q++ dl+ +fvpvGGGGliaG+aa+ k+++p++k++gve+ed+a+lk+a+eaGe+v+l+qvGlfadGvavk++G+e lcl|FitnessBrowser__MR1:203422 191 LQQQR-DLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQVGLFADGVAVKRIGTEP 268 ***99.9************************************************************************ PP TIGR01124 239 frlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgi....edktlvailsGanlnfdrlry 313 fr++k +d +v+v +de+caa+kd+fedtra++epaGal+laGlkkyv ++ ++++++ailsGan+nf++lry lcl|FitnessBrowser__MR1:203422 269 FRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYVSTNATgesgRGEKVAAILSGANVNFHSLRY 347 *************************************************997653333789****************** PP TIGR01124 314 vseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagyk 391 vser+elGeq+ea+lav +pe++Gs+l+f+e+l +r +tefnyr++ ++ a +f G++l++ e ++++++le++g++ lcl|FitnessBrowser__MR1:203422 348 VSERCELGEQKEAVLAVKVPERPGSFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGhGELEQIINTLEDNGFE 426 **********************************************************99875899************* PP TIGR01124 392 vvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpde 470 v dl+ de aklhvry+vGG + + +erl+sfefpe+pGallkfl+tlq++wnislfhyrnhGa++Grvl+g+evp + lcl|FitnessBrowser__MR1:203422 427 VQDLSGDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGAAFGRVLAGFEVPAS 505 ******************************************************************************* PP TIGR01124 471 eaeefeqflaelgyryedetenpayrlfl 499 +a f+qfl elg+ y++et++pay+lfl lcl|FitnessBrowser__MR1:203422 506 DALPFQQFLTELGFVYQEETQSPAYQLFL 534 ****************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (545 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02 # Mc/sec: 10.37 // [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