Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase
Query= SwissProt::A0FKE6 (606 letters) >FitnessBrowser__Cup4G11:RR42_RS02315 Length = 508 Score = 512 bits (1319), Expect = e-149 Identities = 266/503 (52%), Positives = 354/503 (70%), Gaps = 5/503 (0%) Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166 +YL IL++KVYDVA ET L A LS R G VW KRED QPVFSFK+RGAYN MA L Sbjct: 6 DYLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLS 65 Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGAT---VVLV 223 E+L++GVI +SAGNHAQGVALSA RL C A+I MPVTTP +K +V+ G +VL Sbjct: 66 PEELKRGVIAASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLH 125 Query: 224 GDSYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGG 283 GDSY +A +A + TFI PFD P+VI GQGT+ MEI RQ +HA+FV +GGG Sbjct: 126 GDSYSDAYNHAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGG 185 Query: 284 GLIAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEE 343 GLI+GIA+Y+K V P+IK+IGV+ +D++A+ S+ G+RV L +VG F+DG AVK+VG+E Sbjct: 186 GLISGIASYIKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKE 245 Query: 344 TYRLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENV 403 T+R+ EL+D ++LV DAICA +KD+F++ RSILEPAGA+A+AG + Y + LKG+++ Sbjct: 246 TFRITRELVDEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHL 305 Query: 404 VAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFKYR 463 VAI GANMNFDRLR V E A+VG REAV A +PE+ GSFK+F E +G N+TEF YR Sbjct: 306 VAIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRFCEQLGTRNVTEFNYR 365 Query: 464 YNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTNV- 522 +DK A + V + + E E + T++L++++L K H+R+++GG + + Sbjct: 366 I-ADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGGHSPLA 424 Query: 523 HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEFE 582 H+ELL RF FPE+PGALM+FL + SP WNISLFHYR QG +N+LVGIQVP +E F Sbjct: 425 HDELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFR 484 Query: 583 GRADSLGYEYAMESLNEAYQLIM 605 +LGY + E+ N Y+L + Sbjct: 485 DFLATLGYVHWEETENPVYKLFL 507 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: 704 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: 508 Length adjustment: 36 Effective length of query: 570 Effective length of database: 472 Effective search space: 269040 Effective search space used: 269040 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 RR42_RS02315 RR42_RS02315 (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.21903.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-245 801.1 0.1 2.1e-245 800.9 0.1 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS02315 RR42_RS02315 threonine dehydrata Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS02315 RR42_RS02315 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 800.9 0.1 2.1e-245 2.1e-245 1 499 [] 6 507 .. 6 507 .. 0.99 Alignments for each domain: == domain 1 score: 800.9 bits; conditional E-value: 2.1e-245 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGvi 69 dylr+il+a+vy++a+et l a+ ls+r +n+v++kred qpvfsfklrGaynkma+ls+e+ +Gvi lcl|FitnessBrowser__Cup4G11:RR42_RS02315 6 DYLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLSPEELKRGVI 74 89******************************************************************* PP TIGR01124 70 aasaGnhaqGvalsakklGvkavivmpettpeikvdavkafGge...vvlhGenydeakakalelaqek 135 aasaGnhaqGvalsa++l +ka+i mp ttp++k+dav+++Gge +vlhG++y++a+++a l++++ lcl|FitnessBrowser__Cup4G11:RR42_RS02315 75 AASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEwveIVLHGDSYSDAYNHAAVLEKKH 143 ******************************************9544489******************** PP TIGR01124 136 gltfiapfddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaeds 204 ltfi+pfddp viaGqGt+a+e+lrq+ +l+avfv++GGGGli+G+a+++k+++peikvigv++ ds lcl|FitnessBrowser__Cup4G11:RR42_RS02315 144 KLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGGGLISGIASYIKAVRPEIKVIGVQTVDS 212 ********************************************************************* PP TIGR01124 205 aalkqaleaGervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravle 273 +a+k++++aG+rv+l++vGlf+dG+avk vG+etfr+++e++d+i+lvdtd++ca +kdvf+dtr++le lcl|FitnessBrowser__Cup4G11:RR42_RS02315 213 DAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKETFRITRELVDEIILVDTDAICAGLKDVFQDTRSILE 281 ********************************************************************* PP TIGR01124 274 paGalalaGlkkyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkf 342 paGa+a+aGlk y++++++++++lvai++Gan+nfdrlr+v+erae+Ge rea++av+ipee+Gs+++f lcl|FitnessBrowser__Cup4G11:RR42_RS02315 282 PAGAMAVAGLKLYAEREKLKGQHLVAIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRF 350 ********************************************************************* PP TIGR01124 343 vevlGeraitefnyrladdekahifvGvqlaeeeerkellarleeagykvvdltddelaklhvrylvGG 411 +e lG r++tefnyr+ad++ ahifvGvq+a+++e+++++a ++++g++++dl++delak h+ry+vGG lcl|FitnessBrowser__Cup4G11:RR42_RS02315 351 CEQLGTRNVTEFNYRIADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGG 419 ********************************************************************* PP TIGR01124 412 raakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqfla 480 + +++e ly+fefperpGal++fl+++ ++wnislfhyrn G+d ++lvg++vp++e+ +f +fla lcl|FitnessBrowser__Cup4G11:RR42_RS02315 420 HSPLAHDELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFRDFLA 488 ********************************************************************* PP TIGR01124 481 elgyryedetenpayrlfl 499 +lgy ++etenp+y+lfl lcl|FitnessBrowser__Cup4G11:RR42_RS02315 489 TLGYVHWEETENPVYKLFL 507 ******************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (508 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: 00:00:00.03 # Mc/sec: 7.67 // [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