Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF5275 PS417_27010 threonine dehydratase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__WCS417:GFF5275 Length = 504 Score = 525 bits (1351), Expect = e-153 Identities = 261/500 (52%), Positives = 355/500 (71%), Gaps = 2/500 (0%) Query: 15 EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74 +Y++ +L + VY+ A TPLQ +LS RL N + +KRED QPV SFK+RGAY + LT Sbjct: 4 QYVKKILTSRVYDVAVETPLQTARQLSERLGNQVWLKREDLQPVFSFKIRGAYNKLTQLT 63 Query: 75 EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134 E++A GV+TASAGNHAQG+A ++ LGVKA IVMP T +IKV+ VR GG+V+LHG + Sbjct: 64 AEERARGVVTASAGNHAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDS 123 Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193 F EA A +++L ++G+ ++ P+D P IAGQGT+A+E+L+Q LD +FVPVGGGGL Sbjct: 124 FPEALAYSLKLVDEKGYVYIHPYDDPHTIAGQGTVAMEILRQHPGPLDAIFVPVGGGGLI 183 Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253 AG+A +K L P IK+I VE +DS CL+AAL AG V LP VG+FA+GVAV +IG TF Sbjct: 184 AGIAAYVKYLRPDIKIIGVEPDDSNCLQAALAAGERVVLPTVGIFADGVAVAQIGQHTFD 243 Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313 +C++Y+D++ITV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+ + G+ L I Sbjct: 244 ICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVETRGVTGQTLVAI 303 Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373 SGANVNF LR+V+ER ELGE REA++AVTIPE GSF FC+ +G R +TEFNYRF Sbjct: 304 DSGANVNFDRLRHVAERAELGEGREAIIAVTIPERPGSFKAFCEAVGKRQITEFNYRFHS 363 Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433 A IFVGV+ + R ++ L G+ V+DL+++E+AKLH+R+MVGG +H E Sbjct: 364 GSEAHIFVGVQTHPENDPRSALIASLTRQGFPVLDLTENELAKLHIRHMVGGHAAHVSNE 423 Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETRL 492 ++ FEFPE PGAL FLN LG WNIS+FHYR+HG GRV+A ++ D L Sbjct: 424 VVFRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPADERHLVPAAL 483 Query: 493 NELGYDCHDETNNPAFRFFL 512 +GY DE++NPA+ FL Sbjct: 484 EAIGYPYWDESDNPAYTLFL 503 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: 707 Number of extensions: 39 Number of successful extensions: 4 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: 504 Length adjustment: 34 Effective length of query: 480 Effective length of database: 470 Effective search space: 225600 Effective search space used: 225600 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 GFF5275 PS417_27010 (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.5831.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-249 812.5 0.0 7.3e-249 812.3 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF5275 PS417_27010 threonine dehydratas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF5275 PS417_27010 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 812.3 0.0 7.3e-249 7.3e-249 1 499 [] 4 503 .. 4 503 .. 0.99 Alignments for each domain: == domain 1 score: 812.3 bits; conditional E-value: 7.3e-249 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGn 75 +y+++il++rvy++avetpl++a++lserl+n+v+lkredlqpvfsfk+rGaynk++ql+ae++a+Gv++asaGn lcl|FitnessBrowser__WCS417:GFF5275 4 QYVKKILTSRVYDVAVETPLQTARQLSERLGNQVWLKREDLQPVFSFKIRGAYNKLTQLTAEERARGVVTASAGN 78 699************************************************************************ PP TIGR01124 76 haqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplvia 150 haqG+al+ak lGvka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a++l+l +ekg +i+p+ddp ia lcl|FitnessBrowser__WCS417:GFF5275 79 HAQGLALAAKVLGVKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALAYSLKLVDEKGYVYIHPYDDPHTIA 153 *************************************************************************** PP TIGR01124 151 GqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlf 225 GqGtva+e+lrq+ +lda+fvpvGGGGliaG+aa+vk l+p+ik+igve++ds++l++al+aGerv l +vG+f lcl|FitnessBrowser__WCS417:GFF5275 154 GQGTVAMEILRQHPGPLDAIFVPVGGGGLIAGIAAYVKYLRPDIKIIGVEPDDSNCLQAALAAGERVVLPTVGIF 228 *************************************************************************** PP TIGR01124 226 adGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvai 300 adGvav ++G++tf++ck+y+d++++v tde+caaikd+++dtr+++epaGal++aG+kkyv+++g++++tlvai lcl|FitnessBrowser__WCS417:GFF5275 229 ADGVAVAQIGQHTFDICKDYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVETRGVTGQTLVAI 303 *************************************************************************** PP TIGR01124 301 lsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee 375 sGan+nfdrlr+v+eraelGe rea++avtipe++Gs++ f+e +G+r+itefnyr+ ++ahifvGvq++ e lcl|FitnessBrowser__WCS417:GFF5275 304 DSGANVNFDRLRHVAERAELGEGREAIIAVTIPERPGSFKAFCEAVGKRQITEFNYRFHSGSEAHIFVGVQTHPE 378 ************************************************************************988 PP TIGR01124 376 ee.rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislf 449 ++ r+ l+a+l+++g+ v+dlt++elaklh+r++vGG aa+v+ne +++fefperpGal +fl++l ++wnis+f lcl|FitnessBrowser__WCS417:GFF5275 379 NDpRSALIASLTRQGFPVLDLTENELAKLHIRHMVGGHAAHVSNEVVFRFEFPERPGALFNFLNKLGGRWNISMF 453 553899********************************************************************* PP TIGR01124 450 hyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 hyrnhGa+ Grv++gl+vp +e + +l+ +gy y+de++npay lfl lcl|FitnessBrowser__WCS417:GFF5275 454 HYRNHGAADGRVVAGLQVPADERHLVPAALEAIGYPYWDESDNPAYTLFL 503 *************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (504 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 12.55 // [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