Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate Ga0059261_3694 Ga0059261_3694 threonine ammonia-lyase, medium form
Query= reanno::Korea:Ga0059261_3694 (420 letters) >FitnessBrowser__Korea:Ga0059261_3694 Length = 420 Score = 806 bits (2082), Expect = 0.0 Identities = 420/420 (100%), Positives = 420/420 (100%) Query: 1 MVYGPPMATQAATAAQPLPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFE 60 MVYGPPMATQAATAAQPLPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFE Sbjct: 1 MVYGPPMATQAATAAQPLPVTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFE 60 Query: 61 NLQFTAAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKST 120 NLQFTAAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKST Sbjct: 61 NLQFTAAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKST 120 Query: 121 PTVKVMQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEM 180 PTVKVMQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEM Sbjct: 121 PTVKVMQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEM 180 Query: 181 LADAPAIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGG 240 LADAPAIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGG Sbjct: 181 LADAPAIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTGAHEPIGG 240 Query: 241 DTLAEGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAA 300 DTLAEGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAA Sbjct: 241 DTLAEGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAA 300 Query: 301 LMTQPERFRGKTVGVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVAR 360 LMTQPERFRGKTVGVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVAR Sbjct: 301 LMTQPERFRGKTVGVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVAR 360 Query: 361 IFQEQTVNILELSHQRIFTNLPAKGLSLDVECETRDRAHLERLISALQEAGYEVRLIELA 420 IFQEQTVNILELSHQRIFTNLPAKGLSLDVECETRDRAHLERLISALQEAGYEVRLIELA Sbjct: 361 IFQEQTVNILELSHQRIFTNLPAKGLSLDVECETRDRAHLERLISALQEAGYEVRLIELA 420 Lambda K H 0.319 0.135 0.374 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: 706 Number of extensions: 15 Number of successful extensions: 1 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: 420 Length of database: 420 Length adjustment: 32 Effective length of query: 388 Effective length of database: 388 Effective search space: 150544 Effective search space used: 150544 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate Ga0059261_3694 Ga0059261_3694 (threonine ammonia-lyase, medium form)
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (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/TIGR01127.hmm # target sequence database: /tmp/gapView.30586.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01127 [M=380] Accession: TIGR01127 Description: ilvA_1Cterm: threonine ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-131 423.9 0.0 3.2e-131 423.7 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3694 Ga0059261_3694 threonine ammonia Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3694 Ga0059261_3694 threonine ammonia-lyase, medium form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.7 0.0 3.2e-131 3.2e-131 1 379 [. 39 415 .. 39 416 .. 0.98 Alignments for each domain: == domain 1 score: 423.7 bits; conditional E-value: 3.2e-131 TIGR01127 1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakv 69 tp +s+tlsd+tga vylk enlq t ++k rGaln + +l + + +Gv+aasaGnhaqG a+ ++ lcl|FitnessBrowser__Korea:Ga0059261_3694 39 TPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTLLQLDDAARAKGVIAASAGNHAQGLAYHGNR 107 78889**************************************************************** PP TIGR01127 70 fgikakivmPesaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtl 138 gi+ +ivmP+s+p kv +t+s Ga +iL+G++fDeay++a++l++ +g++fvh+fdD+ +iaGqGt+ lcl|FitnessBrowser__Korea:Ga0059261_3694 108 LGIPVTIVMPKSTPTVKVMQTESHGATIILEGETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTV 176 ********************************************************************* PP TIGR01127 139 gleiledlpdvdtvivPvGGGGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvkti 207 le+l+d p +dt+ivP+GGGGLisG +++k + v+Gv+ae ps+ + + +++ +t+ lcl|FitnessBrowser__Korea:Ga0059261_3694 177 FLEMLADAPAIDTLIVPIGGGGLISGALTVAKAADKPIEVVGVQAELFPSMFNRFTG--AHEPIGGDTL 243 *****************************************************9975..4567789*** PP TIGR01127 208 aDGiavkkpgdltfeivkelvDevvavdeeeiakaillLlerakivaegaGavgvaavleekvdvkgkk 276 a+Giavk+pg lt +iv+ lvDe++ v+e ++ +a+ lLl+ +k+v+egaGa+g+aa++ + gk+ lcl|FitnessBrowser__Korea:Ga0059261_3694 244 AEGIAVKEPGGLTAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRGKT 312 ************************************************************9999***** PP TIGR01127 277 vavvvsGGnidlnllekiiekgLvksgrkvkietvlkDkPGaLkklleviaekranivkiehdrlskei 345 v+v+++GGnid++ll +++ ++L++sgr+++++ l+D+PGaL++++ + +e+ ni++++h+r+ +++ lcl|FitnessBrowser__Korea:Ga0059261_3694 313 VGVILTGGNIDTRLLANVLLRDLARSGRLARLRIRLQDRPGALYQVARIFQEQTVNILELSHQRIFTNL 381 ********************************************************************* PP TIGR01127 346 algaakvelelevkgkehleellktlrdkgyevk 379 + ++ +e e++++ hle+l + l++ gyev+ lcl|FitnessBrowser__Korea:Ga0059261_3694 382 PAKGLSLDVECETRDRAHLERLISALQEAGYEVR 415 *******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (380 nodes) Target sequences: 1 (420 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: 7.60 // [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