Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PP_5149 PP_5149 threonine deaminase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Putida:PP_5149 Length = 504 Score = 530 bits (1365), Expect = e-155 Identities = 263/500 (52%), Positives = 361/500 (72%), Gaps = 2/500 (0%) Query: 15 EYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLT 74 +Y++ +L + VY+ A TPLQ +LS RL N IL+KRED QPV SFK+RGAY +A L+ Sbjct: 4 QYVKKILTSRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYNKLAQLS 63 Query: 75 EEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGAN 134 E+ A GV+TASAGNHAQG+A ++ +G+KA IVMP T +IKV+ VR GG+V+LHG + Sbjct: 64 PEELARGVVTASAGNHAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKVVLHGDS 123 Query: 135 FDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQD-AHLDRVFVPVGGGGLA 193 F EA A +++L ++GF +V P+D P IAGQGT+A+E+L+Q LD +FVPVGGGGL Sbjct: 124 FPEALAYSLKLVDEKGFVYVHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGGLI 183 Query: 194 AGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFR 253 AG+A +K L P+IK+I VE +DS CL+AA+ AG V LP+VGLFA+GVAV +IG TF Sbjct: 184 AGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQIGQHTFD 243 Query: 254 LCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHI 313 +C+ ++D+++TV +D ICAA+KD+++D R++ EP+GAL +AG+KKY+ L+ + G+ L I Sbjct: 244 ICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVSGQTLVAI 303 Query: 314 LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFAD 373 SGANVNF LR+V+ER ELGE+REA++AVTIPE GSF FC+ +G R +TEFNYR Sbjct: 304 DSGANVNFDRLRHVAERAELGEKREAIIAVTIPERPGSFKAFCEAIGKRQITEFNYRKHT 363 Query: 374 AKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQE 433 + A IFVGV+ + R ++Q L + G+ V DL+D+E+AKLH+R+MVGG + E Sbjct: 364 SDEAHIFVGVQTHPENDPRAALVQQLTEQGFPVTDLTDNELAKLHIRHMVGGHSAGASDE 423 Query: 434 RLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDF-ETRL 492 + FEFPE PGAL FLN LG WNIS+FHYR+HG GRV+A ++ + E L Sbjct: 424 MVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPEDERHLVPAAL 483 Query: 493 NELGYDCHDETNNPAFRFFL 512 ++GY DET NPA++ FL Sbjct: 484 AKIGYPYWDETENPAYKLFL 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: 710 Number of extensions: 44 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 PP_5149 PP_5149 (threonine deaminase)
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.31839.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-247 805.8 0.0 7.6e-247 805.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_5149 PP_5149 threonine deaminase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_5149 PP_5149 threonine deaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 805.7 0.0 7.6e-247 7.6e-247 1 499 [] 4 503 .. 4 503 .. 0.99 Alignments for each domain: == domain 1 score: 805.7 bits; conditional E-value: 7.6e-247 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGn 75 +y+++il++rvy++avetpl+ a +ls+rl+n++llkredlqpvfsfk+rGaynk+aqls+e+ a+Gv++asaGn lcl|FitnessBrowser__Putida:PP_5149 4 QYVKKILTSRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYNKLAQLSPEELARGVVTASAGN 78 699************************************************************************ PP TIGR01124 76 haqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplvia 150 haqG+al+a+++G+ka+ivmp+ttpeikv+ v+++Gg+vvlhG+++ ea a++l+l +ekg+ +++p+ddp ia lcl|FitnessBrowser__Putida:PP_5149 79 HAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKVVLHGDSFPEALAYSLKLVDEKGFVYVHPYDDPHTIA 153 *************************************************************************** PP TIGR01124 151 GqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlf 225 GqGtva+e+lrq+ lda+fvpvGGGGliaG+aa+vk l+peik+igve++ds++l++a++aGerv l qvGlf lcl|FitnessBrowser__Putida:PP_5149 154 GQGTVAMEILRQHPGRLDAIFVPVGGGGLIAGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLF 228 *************************************************************************** PP TIGR01124 226 adGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvai 300 adGvav ++G++tf++c++++d++v+v tde+caaikd+++dtr+++epaGal++aG+kkyv+ g++++tlvai lcl|FitnessBrowser__Putida:PP_5149 229 ADGVAVAQIGQHTFDICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVSGQTLVAI 303 *************************************************************************** PP TIGR01124 301 lsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee 375 sGan+nfdrlr+v+eraelGe+rea++avtipe++Gs++ f+e +G+r+itefnyr +++ahifvGvq++ e lcl|FitnessBrowser__Putida:PP_5149 304 DSGANVNFDRLRHVAERAELGEKREAIIAVTIPERPGSFKAFCEAIGKRQITEFNYRKHTSDEAHIFVGVQTHPE 378 ************************************************************************987 PP TIGR01124 376 ee.rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislf 449 ++ r+ l+++l+e+g+ v dltd+elaklh+r++vGG +a +++e +++fefperpGal +fl++l ++wnis+f lcl|FitnessBrowser__Putida:PP_5149 379 NDpRAALVQQLTEQGFPVTDLTDNELAKLHIRHMVGGHSAGASDEMVLRFEFPERPGALFNFLNKLGGRWNISMF 453 553899********************************************************************* PP TIGR01124 450 hyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 hyrnhGa+ Grv++gl+vp++e + +la++gy y+detenpay+lfl lcl|FitnessBrowser__Putida:PP_5149 454 HYRNHGAADGRVVAGLQVPEDERHLVPAALAKIGYPYWDETENPAYKLFL 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.80 // [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