Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3437 PGA1_c34900 threonine dehydratase biosynthetic
Query= BRENDA::Q04513 (436 letters) >FitnessBrowser__Phaeo:GFF3437 Length = 408 Score = 307 bits (786), Expect = 4e-88 Identities = 173/398 (43%), Positives = 246/398 (61%), Gaps = 16/398 (4%) Query: 24 ADIQT----AQARISSVIAPTPLQYCPRLSEETGAEIYLKREDLQDVRSYKIRGALNSGA 79 +D QT A+ + ++ TPLQ LSE GAEIYLKREDL VRSYKIRGA N+ Sbjct: 2 SDFQTQARAAEQAMRAIFPATPLQRSALLSERFGAEIYLKREDLSPVRSYKIRGAFNA-- 59 Query: 80 QLTQEQRDAGIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSL 139 + ++ + V ASAGNHAQGVAY+C+ LG +G I++PV TP+QK + + GG+ V + Sbjct: 60 -MRKQLEQSLFVCASAGNHAQGVAYMCRELGKRGVIFMPVTTPQQKIQKTRMFGGDSVEI 118 Query: 140 VVTGNNFDEASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVM 199 + G+ FD+ AAA + G + PFD + + GQ ++A EI +QL G + DHV+ Sbjct: 119 HLVGDYFDDTLAAAQKWCADEGGHFLSPFDDDDVIEGQSSIAVEIEAQL---GAAPDHVI 175 Query: 200 VPVGGGGLLAGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAV 259 +PVGGGG+ +GV + D R + EP+G A ++AAL G P+ L+ VD FVDGAAV Sbjct: 176 LPVGGGGMSSGVARWFGD---RVHCLFAEPSGGACLRAALAAGHPVALDHVDTFVDGAAV 232 Query: 260 KRVGDLNYTIVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLKEM-SF 318 RVG + ++ K ++S E +CT +L++ EG++ EPAGAL+I L+++ S+ Sbjct: 233 GRVGARPFEVL-KQVPLPDVLSIAEDRICTTILEMLNVEGVVLEPAGALAIEALRDVRSW 291 Query: 319 APGSVVVCIISGGNNDVLRYAEIAERSLVHRGLKHYFLVNFPQKPGQLRHFLEDILGPDD 378 G VVC+ SGGN D R E+ ER+ + GLK YFL+ PQ+PG L+ FL ILGP+D Sbjct: 292 IRGKTVVCLTSGGNFDFERLPEVKERAQRYMGLKKYFLLRLPQRPGALKEFL-GILGPED 350 Query: 379 DITLFEYLKRNNRETGTALVGIHLSEASGLDSLLERME 416 DI FEY+K++ R G+ L+GI L R++ Sbjct: 351 DIARFEYMKKSARNFGSVLIGIETKRPENFADLYARLD 388 Lambda K H 0.316 0.133 0.373 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: 432 Number of extensions: 24 Number of successful extensions: 6 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: 436 Length of database: 408 Length adjustment: 32 Effective length of query: 404 Effective length of database: 376 Effective search space: 151904 Effective search space used: 151904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate GFF3437 PGA1_c34900 (threonine dehydratase biosynthetic)
to HMM TIGR02079 (ilvA: threonine dehydratase (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/TIGR02079.hmm # target sequence database: /tmp/gapView.14161.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02079 [M=410] Accession: TIGR02079 Description: THD1: threonine dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-160 520.1 0.0 2.1e-160 519.9 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3437 PGA1_c34900 threonine dehydratas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3437 PGA1_c34900 threonine dehydratase biosynthetic # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 519.9 0.0 2.1e-160 2.1e-160 4 410 .] 9 408 .] 6 408 .] 0.97 Alignments for each domain: == domain 1 score: 519.9 bits; conditional E-value: 2.1e-160 TIGR02079 4 ekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvcasaGnhaqGv 79 +a++ ++ ++ tPlq+++ lse+++aeiylkredl+ vrsyk+rGa+n++++ + +vcasaGnhaqGv lcl|FitnessBrowser__Phaeo:GFF3437 9 RAAEQAMRAIFPATPLQRSALLSERFGAEIYLKREDLSPVRSYKIRGAFNAMRKQ---LEQSLFVCASAGNHAQGV 81 579999*********************************************9543...345679************ PP TIGR02079 80 ayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfddkdiieGqg 155 ay cr+lg +g++fmPvttP+qk++k+++fGg+ +e+ lvGd fd++ aaa+k +++eg +++ Pfdd+d+ieGq+ lcl|FitnessBrowser__Phaeo:GFF3437 82 AYMCRELGKRGVIFMPVTTPQQKIQKTRMFGGDSVEIHLVGDYFDDTLAAAQKWCADEGGHFLSPFDDDDVIEGQS 157 **************************************************************************** PP TIGR02079 156 tvaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkagevvtldkidkfvdG 231 ++avei ql + +d v++pvGGGG++sGv+ ++ +++ + ++ eP+G ++l+a+l+ag++v ld++d fvdG lcl|FitnessBrowser__Phaeo:GFF3437 158 SIAVEIEAQLGAA-PDHVILPVGGGGMSSGVARWFGDRV---HCLFAEPSGGACLRAALAAGHPVALDHVDTFVDG 229 ***********97.*********************9887...589******************************* PP TIGR02079 232 aavkrvGdlnfkalkkvvd.evtlveegavcstildlynkegivaePaGalsiaaleelseeikgktvvcvvsGgn 306 aav rvG f++lk+v +v + e+++c+til+++n eg+v+ePaGal+i al +++ i+gktvvc+ sGgn lcl|FitnessBrowser__Phaeo:GFF3437 230 AAVGRVGARPFEVLKQVPLpDVLSIAEDRICTTILEMLNVEGVVLEPAGALAIEALRDVRSWIRGKTVVCLTSGGN 305 *****************998******************************************************** PP TIGR02079 307 ndierleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksnretGevliGielsdkedf 382 +d+erl+e+ker+ +y Glk+yfl+++pqr+Gal+efl +lGP+ddi++fey+kks+r++G+vliGie++ e+f lcl|FitnessBrowser__Phaeo:GFF3437 306 FDFERLPEVKERAQRYMGLKKYFLLRLPQRPGALKEFLG-ILGPEDDIARFEYMKKSARNFGSVLIGIETKRPENF 380 **************************************9.************************************ PP TIGR02079 383 eGllerlkaadieyeainenetlyellv 410 + l +rl+aa+ y++i+ +etl ++++ lcl|FitnessBrowser__Phaeo:GFF3437 381 ADLYARLDAAGFAYTDITSDETLAQFVI 408 **********************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (410 nodes) Target sequences: 1 (408 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: 00:00:00.01 # Mc/sec: 8.60 // [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