Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3797 Psest_3866 threonine ammonia-lyase, biosynthetic, long form
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__psRCH2:GFF3797 Length = 504 Score = 523 bits (1347), Expect = e-153 Identities = 262/499 (52%), Positives = 359/499 (71%), Gaps = 2/499 (0%) Query: 16 YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75 Y++ +L + VY+ A TPLQ +LS R+ N IL+KRED QPV SFK+RGAY +A L+ Sbjct: 5 YVKKILTSRVYDVAIETPLQPARQLSERIGNQILLKREDLQPVFSFKVRGAYNKLAQLSA 64 Query: 76 EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135 E+ A GV+TASAGNHAQGVA ++ +LG+KA IVMP T ++KV VR GG+V+LHG F Sbjct: 65 EELARGVVTASAGNHAQGVALAAKQLGIKATIVMPRTTPELKVQGVRARGGKVVLHGDAF 124 Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGLAA 194 EA A +++L +++G+ ++ P+D P VIAGQGT+A+E+L+Q +D +FVPVGGGGL A Sbjct: 125 PEALAYSLKLVEEKGYVYIHPYDDPDVIAGQGTVAMEILRQHQGPIDAIFVPVGGGGLVA 184 Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254 G+A +K L PQ KVI VE +DS CL+AA+ AG V L +VGLFA+GVAV +IG TF + Sbjct: 185 GIAAYVKYLYPQTKVIGVEPDDSNCLQAAMAAGERVVLEQVGLFADGVAVAQIGQHTFEI 244 Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314 C+ Y+D++ITV +D ICAA+KD+++D R++ EP+GAL++AG+KKY+ + G+ L I Sbjct: 245 CRHYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALSVAGIKKYVEREGVSGQVLVGID 304 Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374 SGANVNF LR+V+ER ELGE+REA++AVTIPE+ GSF FC+ +G R +TEFNYR+ Sbjct: 305 SGANVNFDRLRHVAERAELGEKREAIIAVTIPEQPGSFKAFCEAIGKRQITEFNYRYHTD 364 Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434 + A IFVGV+ + R ++Q L D G+ V+DL+D+E+AKLH R+MVGG E Sbjct: 365 REAHIFVGVQTHPENDPRAALVQGLRDKGFPVLDLTDNELAKLHTRHMVGGHAVGVSNEM 424 Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETRLN 493 + FEFPE PGAL FLN LG WNIS+FHYR+HG GRV+A ++ D L+ Sbjct: 425 VLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPADERHLVPAALD 484 Query: 494 ELGYDCHDETNNPAFRFFL 512 ++GY DE+ NPA++ FL Sbjct: 485 KIGYRYWDESENPAYKLFL 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: 709 Number of extensions: 46 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: 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 GFF3797 Psest_3866 (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.carbon/TIGR01124.hmm # target sequence database: /tmp/gapView.25458.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-249 813.8 0.3 3.1e-249 813.6 0.3 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3797 Psest_3866 threonine ammonia-lya Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3797 Psest_3866 threonine ammonia-lyase, biosynthetic, long form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 813.6 0.3 3.1e-249 3.1e-249 2 499 .] 5 503 .. 4 503 .. 0.99 Alignments for each domain: == domain 1 score: 813.6 bits; conditional E-value: 3.1e-249 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 y+++il++rvy++a+etpl++a++lser++n++llkredlqpvfsfk+rGaynk+aqlsae+ a+Gv++asaGnh lcl|FitnessBrowser__psRCH2:GFF3797 5 YVKKILTSRVYDVAIETPLQPARQLSERIGNQILLKREDLQPVFSFKVRGAYNKLAQLSAEELARGVVTASAGNH 79 899************************************************************************ PP TIGR01124 77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151 aqGval+ak+lG+ka+ivmp+ttpe+kv+ v+a+Gg+vvlhG+++ ea a++l+l +ekg +i+p+ddp+viaG lcl|FitnessBrowser__psRCH2:GFF3797 80 AQGVALAAKQLGIKATIVMPRTTPELKVQGVRARGGKVVLHGDAFPEALAYSLKLVEEKGYVYIHPYDDPDVIAG 154 *************************************************************************** PP TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226 qGtva+e+lrq++ ++da+fvpvGGGGl+aG+aa+vk l+p+ kvigve++ds++l++a++aGerv l+qvGlfa lcl|FitnessBrowser__psRCH2:GFF3797 155 QGTVAMEILRQHQGPIDAIFVPVGGGGLVAGIAAYVKYLYPQTKVIGVEPDDSNCLQAAMAAGERVVLEQVGLFA 229 *************************************************************************** PP TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301 dGvav ++G++tf++c++y+d++++v tde+caaikd+++dtr+++epaGal++aG+kkyv+++g++++ lv i lcl|FitnessBrowser__psRCH2:GFF3797 230 DGVAVAQIGQHTFEICRHYVDEVITVSTDEICAAIKDIYDDTRSITEPAGALSVAGIKKYVEREGVSGQVLVGID 304 *************************************************************************** PP TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaeee 376 sGan+nfdrlr+v+eraelGe+rea++avtipe++Gs++ f+e +G+r+itefnyr+ d +ahifvGvq++ e+ lcl|FitnessBrowser__psRCH2:GFF3797 305 SGANVNFDRLRHVAERAELGEKREAIIAVTIPEQPGSFKAFCEAIGKRQITEFNYRYHTDREAHIFVGVQTHPEN 379 ***********************************************************************9875 PP TIGR01124 377 e.rkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450 + r+ l++ l+++g+ v+dltd+elaklh r++vGG a v+ne +++fefperpGal +fl++l ++wnis+fh lcl|FitnessBrowser__psRCH2:GFF3797 380 DpRAALVQGLRDKGFPVLDLTDNELAKLHTRHMVGGHAVGVSNEMVLRFEFPERPGALFNFLNKLGGRWNISMFH 454 53899********************************************************************** PP TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 yrnhGa+ Grv++gl+vp +e + +l+++gyry+de+enpay+lfl lcl|FitnessBrowser__psRCH2:GFF3797 455 YRNHGAADGRVVAGLQVPADERHLVPAALDKIGYRYWDESENPAYKLFL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 11.58 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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