Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Dyella79:N515DRAFT_0565 Length = 523 Score = 532 bits (1371), Expect = e-155 Identities = 276/503 (54%), Positives = 357/503 (70%), Gaps = 6/503 (1%) Query: 15 EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74 + LR L A VYE A+ T L+ LS+RL +L+KRED+QPV SFKLRGAY M GL Sbjct: 17 DLLRRTLAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLD 76 Query: 75 EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131 Q+A GVI ASAGNHAQGVA ++A+LG++A+IVMP +K+DAVR GG EV+L Sbjct: 77 AAQRARGVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGAWVEVVLA 136 Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGG 190 G ++ +A+A+A L QQ G+T+V PFD P VIAGQ T+ +E+L+Q L VFVPVGGG Sbjct: 137 GDSYSDAQAEAARLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGG 196 Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250 GL AGVA IK L P++KVI V+ DS + +L+ G V L VGLFA+G AVKR+G E Sbjct: 197 GLLAGVAAYIKALRPEVKVIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAE 256 Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310 TF LCQ ++D ++ VD+DAICAA++D+F++ R+V EPSGALALAG+K+Y A H + L Sbjct: 257 TFALCQRHVDAMLRVDTDAICAAIRDVFQETRSVPEPSGALALAGLKQYAATHQLDDATL 316 Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370 I+SGAN+NF LR+V+ER E+GEQREA+ AVTIPEE+GSF +FC LG RS+TEFNYR Sbjct: 317 VAIVSGANLNFDRLRFVAERAEVGEQREAVFAVTIPEERGSFRRFCATLGQRSITEFNYR 376 Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430 DA +A IFVG+++ R +ER+ + G+ V+DL+DDE+AKLH+R+M+GGR Sbjct: 377 IGDAASAHIFVGIQI-RQRDEREALTAAFAAEGFGVLDLTDDELAKLHLRHMIGGRSPLA 435 Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFE 489 E LY FEFPE PGAL RFL + WNISLFHYR+HG DYGR+L ++ FE Sbjct: 436 HDELLYRFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYGRILVGIQVPAGERAMFE 495 Query: 490 TRLNELGYDCHDETNNPAFRFFL 512 L +LGY C DE+ NPA+R L Sbjct: 496 QFLAQLGYPCRDESGNPAYRLLL 518 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: 737 Number of extensions: 40 Number of successful extensions: 6 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: 523 Length adjustment: 35 Effective length of query: 479 Effective length of database: 488 Effective search space: 233752 Effective search space used: 233752 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 N515DRAFT_0565 N515DRAFT_0565 (threonine dehydratase)
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.3277.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-250 815.6 0.3 8.5e-250 815.4 0.3 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 N515DRAFT_0565 threonine dehydra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 815.4 0.3 8.5e-250 8.5e-250 1 499 [] 17 518 .. 17 518 .. 0.99 Alignments for each domain: == domain 1 score: 815.4 bits; conditional E-value: 8.5e-250 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkak 66 d+lr+ l arvye+a et le a ls+rl+ rvllkred+qpvfsfklrGaynkm l a q+a+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 17 DLLRRTLAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLDAAQRAR 82 789*************************************************************** PP TIGR01124 67 GviaasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakal 129 GviaasaGnhaqGval+a+klG++avivmp t+p++k+dav+ Gg evvl G++y++a+a+a lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 83 GVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGawvEVVLAGDSYSDAQAEAA 148 ********************************************986668**************** PP TIGR01124 130 elaqekgltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeik 195 +l+q++g tf++pfddp viaGq tv++e+lrq+ +l+avfvpvGGGGl+aGvaa++k+l+pe+k lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 149 RLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGGGLLAGVAAYIKALRPEVK 214 ****************************************************************** PP TIGR01124 196 vigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaai 261 vigv++ ds+a++q+le+Gerv+ld+vGlfadG+avk+vG+etf+lc++++d +++vdtd++caai lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 215 VIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAETFALCQRHVDAMLRVDTDAICAAI 280 ****************************************************************** PP TIGR01124 262 kdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreal 327 +dvf++tr+v ep+GalalaGlk+y+a+++++d tlvai+sGanlnfdrlr+v+erae+Geqrea+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 281 RDVFQETRSVPEPSGALALAGLKQYAATHQLDDATLVAIVSGANLNFDRLRFVAERAEVGEQREAV 346 ****************************************************************** PP TIGR01124 328 lavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvv 393 +avtipee+Gs+++f+ lG+r+itefnyr++d+ +ahifvG+q+++++er+ l+a + +g+ v+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 347 FAVTIPEERGSFRRFCATLGQRSITEFNYRIGDAASAHIFVGIQIRQRDEREALTAAFAAEGFGVL 412 ****************************************************************** PP TIGR01124 394 dltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyG 459 dltddelaklh+r+++GGr+ +++e ly+fefperpGal++fl +++++wnislfhyrnhGadyG lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 413 DLTDDELAKLHLRHMIGGRSPLAHDELLYRFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYG 478 ****************************************************************** PP TIGR01124 460 rvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 r+lvg++vp e + feqfla+lgy + de+ npayrl+l lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 479 RILVGIQVPAGERAMFEQFLAQLGYPCRDESGNPAYRLLL 518 *************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (523 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: 8.78 // [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