Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate BWI76_RS00980 BWI76_RS00980 PLP-dependent threonine dehydratase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Koxy:BWI76_RS00980 Length = 514 Score = 988 bits (2554), Expect = 0.0 Identities = 491/514 (95%), Positives = 510/514 (99%) Query: 1 MADSQPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHS 60 MA+SQPLS APEGAEYLRAVLRAPVYEAAQ+TPLQKMEKLSSRLDNV+LVKREDRQPVHS Sbjct: 1 MAESQPLSAAPEGAEYLRAVLRAPVYEAAQITPLQKMEKLSSRLDNVVLVKREDRQPVHS 60 Query: 61 FKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDA 120 FKLRGAYAMMAGLTEEQK+HGVITASAGNHAQGVAFS++RLGVKALIVMPTATADIKVDA Sbjct: 61 FKLRGAYAMMAGLTEEQKSHGVITASAGNHAQGVAFSASRLGVKALIVMPTATADIKVDA 120 Query: 121 VRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHL 180 VRGFGGEVLLHGANFDEAKAKAIEL+QQQGFTWVPPFDHPMVIAGQGTLALELLQQDAH+ Sbjct: 121 VRGFGGEVLLHGANFDEAKAKAIELAQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHI 180 Query: 181 DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE 240 DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE Sbjct: 181 DRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAE 240 Query: 241 GVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI 300 GVAVKRIGDETFRLCQEYLDDI+TVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI Sbjct: 241 GVAVKRIGDETFRLCQEYLDDIVTVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYI 300 Query: 301 ALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG 360 A HNIRGERLAH+LSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG Sbjct: 301 AQHNIRGERLAHVLSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLG 360 Query: 361 GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVR 420 GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEIL +L++GGYSVVDLSDDEMAKLHVR Sbjct: 361 GRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILNLLHEGGYSVVDLSDDEMAKLHVR 420 Query: 421 YMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE 480 YMVGGRPS PLQERL+SFEFPESPGALL+FL+TLGT+WNISLFHYRSHGTDYGRVLAAFE Sbjct: 421 YMVGGRPSQPLQERLFSFEFPESPGALLKFLHTLGTHWNISLFHYRSHGTDYGRVLAAFE 480 Query: 481 LGDHEPDFETRLNELGYDCHDETNNPAFRFFLAG 514 LGDHEPDFETRL+ELGYDCHDE+NNPAFRFFLAG Sbjct: 481 LGDHEPDFETRLHELGYDCHDESNNPAFRFFLAG 514 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: 928 Number of extensions: 25 Number of successful extensions: 3 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: 514 Length adjustment: 35 Effective length of query: 479 Effective length of database: 479 Effective search space: 229441 Effective search space used: 229441 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 BWI76_RS00980 BWI76_RS00980 (PLP-dependent 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.aa/TIGR01124.hmm # target sequence database: /tmp/gapView.11617.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-271 886.2 0.0 3.3e-271 886.0 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS00980 BWI76_RS00980 PLP-dependent thre Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS00980 BWI76_RS00980 PLP-dependent threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 886.0 0.0 3.3e-271 3.3e-271 1 499 [] 15 512 .. 15 512 .. 1.00 Alignments for each domain: == domain 1 score: 886.0 bits; conditional E-value: 3.3e-271 TIGR01124 1 dylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaa 71 +ylra+l+a vyeaa+ tpl+k++kls+rl+n vl+kred+qpv+sfklrGay++ma l++eqk++Gvi+a lcl|FitnessBrowser__Koxy:BWI76_RS00980 15 EYLRAVLRAPVYEAAQITPLQKMEKLSSRLDNVVLVKREDRQPVHSFKLRGAYAMMAGLTEEQKSHGVITA 85 69********************************************************************* PP TIGR01124 72 saGnhaqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiap 142 saGnhaqGva+sa++lGvka+ivmp++t++ikvdav++fGgev+lhG+n+deakaka+elaq++g+t+++p lcl|FitnessBrowser__Koxy:BWI76_RS00980 86 SAGNHAQGVAFSASRLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELAQQQGFTWVPP 156 *********************************************************************** PP TIGR01124 143 fddplviaGqGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqalea 213 fd+p+viaGqGt+alell+q++ ++d+vfvpvGGGGl+aGva+l+kql+p+ikvi+veaedsa+lk+al+a lcl|FitnessBrowser__Koxy:BWI76_RS00980 157 FDHPMVIAGQGTLALELLQQDA-HIDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDA 226 *********************9.************************************************ PP TIGR01124 214 GervkldqvGlfadGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlk 284 G++v+l +vGlfa+Gvavk++Gdetfrlc+eylddiv+vd+d++caa+kd+fed+rav+ep+GalalaG+k lcl|FitnessBrowser__Koxy:BWI76_RS00980 227 GHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIVTVDSDAICAAMKDLFEDVRAVAEPSGALALAGMK 297 *********************************************************************** PP TIGR01124 285 kyvakkgiedktlvailsGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefn 355 ky+a+++i++++l+++lsGan+nf+ lryvser+elGeqreallavtipeekGs+lkf+++lG r++tefn lcl|FitnessBrowser__Koxy:BWI76_RS00980 298 KYIAQHNIRGERLAHVLSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFN 368 *********************************************************************** PP TIGR01124 356 yrladdekahifvGvqlaee.eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfe 425 yr+ad+++a+ifvGv+l++ eerke+l+ l+e gy+vvdl+dde+aklhvry+vGGr+++ +erl+sfe lcl|FitnessBrowser__Koxy:BWI76_RS00980 369 YRFADAKNACIFVGVRLSRGlEERKEILNLLHEGGYSVVDLSDDEMAKLHVRYMVGGRPSQPLQERLFSFE 439 *****************998899************************************************ PP TIGR01124 426 fperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayr 496 fpe+pGallkfl+tl ++wnislfhyr+hG+dyGrvl+++e+ d+e + fe++l+elgy+++de++npa+r lcl|FitnessBrowser__Koxy:BWI76_RS00980 440 FPESPGALLKFLHTLGTHWNISLFHYRSHGTDYGRVLAAFELGDHEPD-FETRLHELGYDCHDESNNPAFR 509 **********************************************99.********************** PP TIGR01124 497 lfl 499 +fl lcl|FitnessBrowser__Koxy:BWI76_RS00980 510 FFL 512 **8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (514 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.43 // [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