Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate BPHYT_RS11065 BPHYT_RS11065 threonine dehydratase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__BFirm:BPHYT_RS11065 Length = 516 Score = 525 bits (1352), Expect = e-153 Identities = 268/504 (53%), Positives = 359/504 (71%), Gaps = 6/504 (1%) Query: 15 EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74 +YL+ L A VY+ A+ T L++ LS+RL N + +KRED QPV SFK+RGAY MA ++ Sbjct: 13 DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHIS 72 Query: 75 EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGG---EVLLH 131 E GVITASAGNHAQGVA S+AR+GVKA+IV+P T +KVDAVR GG EV+ Sbjct: 73 AEALERGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQF 132 Query: 132 GANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGG 190 G ++ +A A++L +++ T+V PFD P VIAGQGT+A+E+L Q + +FVP+GGG Sbjct: 133 GESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGG 192 Query: 191 GLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDE 250 GLAAGVA +K + P+IKVI V+ +DS + A+L AG V L VGLF++G AVK +G+E Sbjct: 193 GLAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEE 252 Query: 251 TFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERL 310 TFRLC EYLDD++ V++DA+CAA+KD+F+D R+V EP+G+LA+AG K+Y I + L Sbjct: 253 TFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTL 312 Query: 311 AHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYR 370 I SGAN+NF +R+V+ER E+GE REA+ AVTIPEE+GSF +FC+L+G RSVTEFNYR Sbjct: 313 IAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYR 372 Query: 371 FADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHP 430 ADA +A IFVGV++ R E +I G++ VDL+ DE++K H+RYMVGGR Sbjct: 373 IADANSAHIFVGVQI-RNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLA 431 Query: 431 LQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FE 489 ERL+ FEFPE PGAL++FL+++ WNISLFHYR+ G DY +L ++ D E + F Sbjct: 432 HDERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFN 491 Query: 490 TRLNELGYDCHDETNNPAFRFFLA 513 L LGY +ET NP +R FLA Sbjct: 492 KFLATLGYPNWEETQNPVYRLFLA 515 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: 655 Number of extensions: 27 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: 516 Length adjustment: 35 Effective length of query: 479 Effective length of database: 481 Effective search space: 230399 Effective search space used: 230399 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 BPHYT_RS11065 BPHYT_RS11065 (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.carbon/TIGR01124.hmm # target sequence database: /tmp/gapView.20431.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-251 820.8 0.4 2.1e-251 820.7 0.4 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS11065 BPHYT_RS11065 threonine dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS11065 BPHYT_RS11065 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 820.7 0.4 2.1e-251 2.1e-251 1 499 [] 13 514 .. 13 514 .. 1.00 Alignments for each domain: == domain 1 score: 820.7 bits; conditional E-value: 2.1e-251 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvia 70 dyl++ l+arvy++a et le+a +ls+rl+n v+lkred+qpvfsfk+rGaynkma++sae+ +Gvi+ lcl|FitnessBrowser__BFirm:BPHYT_RS11065 13 DYLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISAEALERGVIT 82 89******************************************************************** PP TIGR01124 71 asaGnhaqGvalsakklGvkavivmpettpeikvdavkafGg...evvlhGenydeakakalelaqekgl 137 asaGnhaqGvalsa+++Gvka+iv+p ttp++kvdav+a+Gg evv Ge+y++a+++a++l++e++l lcl|FitnessBrowser__BFirm:BPHYT_RS11065 83 ASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGptvEVVQFGESYSDAYEHAVKLQKERDL 152 *****************************************877789*********************** PP TIGR01124 138 tfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaal 207 tf++pfddp viaGqGtva+e+l+q++ +++a+fvp+GGGGl+aGvaa+vk ++peikvigv+++ds+a+ lcl|FitnessBrowser__BFirm:BPHYT_RS11065 153 TFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAYVKSVRPEIKVIGVQTDDSCAM 222 ********************************************************************** PP TIGR01124 208 kqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGa 277 +++l+aGerv+l++vGlf+dG+avk vG+etfrlc eyldd++lv+td++caaikdvf+dtr+vlepaG+ lcl|FitnessBrowser__BFirm:BPHYT_RS11065 223 AASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGS 292 ********************************************************************** PP TIGR01124 278 lalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlG 347 la+aG k+y++++gie++tl+ai+sGan+nfdr+r+v+erae+Ge rea++avtipee+Gs+++f+e++G lcl|FitnessBrowser__BFirm:BPHYT_RS11065 293 LAVAGAKQYAEREGIENQTLIAITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVG 362 ********************************************************************** PP TIGR01124 348 eraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGGraakve 417 r++tefnyr+ad+++ahifvGvq+++++e ++++ +e +g+++vdlt del+k h+ry+vGGr+ ++ lcl|FitnessBrowser__BFirm:BPHYT_RS11065 363 TRSVTEFNYRIADANSAHIFVGVQIRNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLAH 432 ********************************************************************** PP TIGR01124 418 nerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyrye 487 +erl++fefperpGal+kfl+++ ++wnislfhyrn Gady +lvg++vpd+e+e+f++fla+lgy + lcl|FitnessBrowser__BFirm:BPHYT_RS11065 433 DERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFNKFLATLGYPNW 502 ********************************************************************** PP TIGR01124 488 detenpayrlfl 499 +et+np+yrlfl lcl|FitnessBrowser__BFirm:BPHYT_RS11065 503 EETQNPVYRLFL 514 ***********8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (516 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: 10.61 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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