Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3271 HP15_3213 threonine dehydratase biosynthetic
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Marino:GFF3271 Length = 511 Score = 543 bits (1400), Expect = e-159 Identities = 275/499 (55%), Positives = 369/499 (73%), Gaps = 2/499 (0%) Query: 16 YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75 Y++ +L A VY+ A TPL + LS R N IL+KRED QPV SFK+RGAY +A L+E Sbjct: 5 YIKKILDARVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLSE 64 Query: 76 EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135 EQKA GVI ASAGNHAQGVA ++ LG+KA+IVMP T +IKV +VR G +V+L G F Sbjct: 65 EQKAKGVICASAGNHAQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDAF 124 Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH-LDRVFVPVGGGGLAA 194 DEA A A EL + G+T++PP+D P VIAGQGT+A+E++ Q + + +F+ VGGGGL A Sbjct: 125 DEAAAHAQELIAKHGYTYIPPYDDPDVIAGQGTVAMEIMWQFSKPIHAIFICVGGGGLIA 184 Query: 195 GVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRL 254 G+A IK L P+IKVI VE EDS CL+AA+ AG V L VG+FA+GVAVK+IG + + Sbjct: 185 GMAAYIKYLRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFADGVAVKQIGKYPWEI 244 Query: 255 CQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHIL 314 C++++D++ITV +D ICAA+KD+FED R++AEP+GAL +AG+KKYI + GE L L Sbjct: 245 CKDHVDEVITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIATL 304 Query: 315 SGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADA 374 SGAN+NF LRY+SER E+GE+REA+LAVTIPE+ G+F F L RS+TEFNYR+ADA Sbjct: 305 SGANMNFDRLRYISERTEVGEKREAILAVTIPEKPGAFKTFINALHKRSITEFNYRYADA 364 Query: 375 KNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQER 434 NA IFVG++++ G R++++Q L + GYSVVDL+D ++AK H+R+MVGG E+ Sbjct: 365 TNATIFVGIQIAAGGHGREDLVQDLRESGYSVVDLTDSDLAKQHIRHMVGGHAPTITNEK 424 Query: 435 LYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHE-PDFETRLN 493 ++ FEFPE PGALL+FL +LGT WNIS+FHYR+HG Y RVL ++ DHE DFE L+ Sbjct: 425 VFQFEFPERPGALLKFLMSLGTRWNISMFHYRNHGAAYSRVLLGAQVDDHEVQDFEKMLD 484 Query: 494 ELGYDCHDETNNPAFRFFL 512 ++G+ + T+N A++ FL Sbjct: 485 KVGFRYENMTDNEAYQLFL 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: 691 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: 514 Length of database: 511 Length adjustment: 35 Effective length of query: 479 Effective length of database: 476 Effective search space: 228004 Effective search space used: 228004 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 GFF3271 HP15_3213 (threonine dehydratase biosynthetic)
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.13282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-247 808.5 1.2 1.2e-247 808.3 1.2 1.0 1 lcl|FitnessBrowser__Marino:GFF3271 HP15_3213 threonine dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3271 HP15_3213 threonine dehydratase biosynthetic # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 808.3 1.2 1.2e-247 1.2e-247 2 499 .] 5 503 .. 4 503 .. 0.99 Alignments for each domain: == domain 1 score: 808.3 bits; conditional E-value: 1.2e-247 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 y+++il arvy++a+etpl +a++ls+r +n++llkredlqpvfsfk+rGayn++aqls+eqkakGvi+asaGnh lcl|FitnessBrowser__Marino:GFF3271 5 YIKKILDARVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLSEEQKAKGVICASAGNH 79 89************************************************************************* PP TIGR01124 77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151 aqGval+ak+lG+kavivmp+ttpeikv +v+ +G++vvl+G+++dea+a+a+el ++g t+i+p+ddp+viaG lcl|FitnessBrowser__Marino:GFF3271 80 AQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDAFDEAAAHAQELIAKHGYTYIPPYDDPDVIAG 154 *************************************************************************** PP TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226 qGtva+e++ q +++++a+f+ vGGGGliaG+aa++k l+peikvigve+eds++l++a++aG+rv ld+vG+fa lcl|FitnessBrowser__Marino:GFF3271 155 QGTVAMEIMWQFSKPIHAIFICVGGGGLIAGMAAYIKYLRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFA 229 *************************************************************************** PP TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301 dGvavk++G++ +++ck+++d++++v tde+caaikdvfedtr+++epaGal++aG+kky++++++e+++l+a l lcl|FitnessBrowser__Marino:GFF3271 230 DGVAVKQIGKYPWEICKDHVDEVITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIATL 304 *************************************************************************** PP TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee. 375 sGan+nfdrlry+ser+e+Ge+rea+lavtipe++G+++ f++ l +r+itefnyr+ad+ +a+ifvG+q+a lcl|FitnessBrowser__Marino:GFF3271 305 SGANMNFDRLRYISERTEVGEKREAILAVTIPEKPGAFKTFINALHKRSITEFNYRYADATNATIFVGIQIAAGg 379 **********************************************************************99875 PP TIGR01124 376 eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450 + r++l+++l+e+gy+vvdltd +lak h+r++vGG a +++ne++++fefperpGallkfl +l ++wnis+fh lcl|FitnessBrowser__Marino:GFF3271 380 HGREDLVQDLRESGYSVVDLTDSDLAKQHIRHMVGGHAPTITNEKVFQFEFPERPGALLKFLMSLGTRWNISMFH 454 889************************************************************************ PP TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 yrnhGa+y rvl+g +v+d+e ++fe++l+++g+rye+ t+n+ay+lfl lcl|FitnessBrowser__Marino:GFF3271 455 YRNHGAAYSRVLLGAQVDDHEVQDFEKMLDKVGFRYENMTDNEAYQLFL 503 ************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (511 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: 12.56 // [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