Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate Dsui_0728 Dsui_0728 threonine ammonia-lyase, biosynthetic, long form
Query= SwissProt::A0FKE6 (606 letters) >FitnessBrowser__PS:Dsui_0728 Length = 503 Score = 553 bits (1425), Expect = e-162 Identities = 283/501 (56%), Positives = 365/501 (72%), Gaps = 2/501 (0%) Query: 106 YEYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKL 165 ++YLT IL+++VY+ A ETPL+ AP LS RLG + KRED+QPVFSFK+RGAYN +A L Sbjct: 3 HDYLTKILNARVYEAAVETPLELAPNLSHRLGNRFYFKREDMQPVFSFKLRGAYNKIAHL 62 Query: 166 PKEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGATVVLVGD 225 QL++GVIC+SAGNHAQGVALSA ++GC AVIVMP TTP IK ++V G VVL G+ Sbjct: 63 TPAQLQRGVICASAGNHAQGVALSAAKIGCRAVIVMPTTTPQIKVQAVASRGGEVVLAGE 122 Query: 226 SYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGGGL 285 SYDEA A+A + ++E TF+ PFD P VI GQGT+GMEI RQ IHA+FV +GGGGL Sbjct: 123 SYDEAYAHAVELEKAEKLTFVHPFDDPYVIAGQGTIGMEILRQHGKPIHAVFVAIGGGGL 182 Query: 286 IAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEETY 345 AG+AAY+K V P+IK+IGVE DA+A+ S+ G+RV LD VG FADG AVK VGEET+ Sbjct: 183 AAGVAAYIKAVRPEIKVIGVETFDADAMKQSIAAGKRVRLDNVGLFADGTAVKFVGEETF 242 Query: 346 RLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENVVA 405 R+C E +D ++LV DAICA+IKD+FE+ RSILEP+GALA+AGA+ Y K + LK +++VA Sbjct: 243 RVCREYLDDIILVDTDAICAAIKDVFEDTRSILEPSGALAIAGAKEYAKQHKLKDKSLVA 302 Query: 406 ITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFKYRYN 465 + SGAN NFDRLR V E A+VG QREAVLA +PE PG++K+F ++G NITEF YR++ Sbjct: 303 VASGANTNFDRLRFVAERAEVGEQREAVLAVTLPEKPGAYKRFVSLIGSRNITEFNYRFH 362 Query: 466 SDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRT-NVHN 524 +E A V V + E +VE ++ T++LTD+++ K H+RH++GG V N Sbjct: 363 EARE-AHVFVGVQVANRAESTKLVESLKKHGYATLDLTDDEMGKLHVRHMVGGHAPQVEN 421 Query: 525 ELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEFEGR 584 ELL RF FPE+PGALM FL+ S WNISLFHYR G VLVG+QVPP E+ EF+ Sbjct: 422 ELLYRFEFPERPGALMNFLNRMSSGWNISLFHYRNHGADYGRVLVGMQVPPAEMGEFQTF 481 Query: 585 ADSLGYEYAMESLNEAYQLIM 605 LGY + E+ N AY+L + Sbjct: 482 LQELGYHHWDETANPAYKLFL 502 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: 697 Number of extensions: 31 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: 606 Length of database: 503 Length adjustment: 36 Effective length of query: 570 Effective length of database: 467 Effective search space: 266190 Effective search space used: 266190 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 Dsui_0728 Dsui_0728 (threonine ammonia-lyase, biosynthetic, long form)
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.5428.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-260 850.6 0.9 2.1e-260 850.4 0.9 1.0 1 lcl|FitnessBrowser__PS:Dsui_0728 Dsui_0728 threonine ammonia-lyas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0728 Dsui_0728 threonine ammonia-lyase, biosynthetic, long form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 850.4 0.9 2.1e-260 2.1e-260 1 499 [] 4 502 .. 4 502 .. 1.00 Alignments for each domain: == domain 1 score: 850.4 bits; conditional E-value: 2.1e-260 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnha 77 dyl++il+arvyeaavetple a +ls+rl+nr ++kred+qpvfsfklrGaynk+a+l++ q +Gvi+asaGnha lcl|FitnessBrowser__PS:Dsui_0728 4 DYLTKILNARVYEAAVETPLELAPNLSHRLGNRFYFKREDMQPVFSFKLRGAYNKIAHLTPAQLQRGVICASAGNHA 80 89*************************************************************************** PP TIGR01124 78 qGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGt 154 qGvalsa+k+G++avivmp+ttp+ikv+av ++Ggevvl Ge+ydea+a+a+el++ + ltf++pfddp viaGqGt lcl|FitnessBrowser__PS:Dsui_0728 81 QGVALSAAKIGCRAVIVMPTTTPQIKVQAVASRGGEVVLAGESYDEAYAHAVELEKAEKLTFVHPFDDPYVIAGQGT 157 ***************************************************************************** PP TIGR01124 155 valellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvav 231 +++e+lrq+ ++++avfv++GGGGl+aGvaa++k+++peikvigve+ d++a+kq+++aG+rv+ld+vGlfadG+av lcl|FitnessBrowser__PS:Dsui_0728 158 IGMEILRQHGKPIHAVFVAIGGGGLAAGVAAYIKAVRPEIKVIGVETFDADAMKQSIAAGKRVRLDNVGLFADGTAV 234 ***************************************************************************** PP TIGR01124 232 kevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvailsGanlnf 308 k vG+etfr+c+eylddi+lvdtd++caaikdvfedtr++lep+Gala+aG k+y+++++++dk+lva++sGan nf lcl|FitnessBrowser__PS:Dsui_0728 235 KFVGEETFRVCREYLDDIILVDTDAICAAIKDVFEDTRSILEPSGALAIAGAKEYAKQHKLKDKSLVAVASGANTNF 311 ***************************************************************************** PP TIGR01124 309 drlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeeeerkellarl 385 drlr+v+erae+Geqrea+lavt+pe++G++++fv+++G+r+itefnyr+ ++ +ah+fvGvq+a+++e ++l+++l lcl|FitnessBrowser__PS:Dsui_0728 312 DRLRFVAERAEVGEQREAVLAVTLPEKPGAYKRFVSLIGSRNITEFNYRFHEAREAHVFVGVQVANRAESTKLVESL 388 ***************************************************************************** PP TIGR01124 386 eeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvl 462 +++gy+++dltdde+ klhvr++vGG a +vene ly+fefperpGal++fl+ + + wnislfhyrnhGadyGrvl lcl|FitnessBrowser__PS:Dsui_0728 389 KKHGYATLDLTDDEMGKLHVRHMVGGHAPQVENELLYRFEFPERPGALMNFLNRMSSGWNISLFHYRNHGADYGRVL 465 ***************************************************************************** PP TIGR01124 463 vglevpdeeaeefeqflaelgyryedetenpayrlfl 499 vg++vp++e+ ef++fl+elgy+ +det npay+lfl lcl|FitnessBrowser__PS:Dsui_0728 466 VGMQVPPAEMGEFQTFLQELGYHHWDETANPAYKLFL 502 ************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (503 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: 9.54 // [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