Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate SMc01564 SMc01564 L-threonine 3-dehydrogenase
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__Smeli:SMc01564 Length = 344 Score = 513 bits (1322), Expect = e-150 Identities = 240/340 (70%), Positives = 282/340 (82%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL K K E G+WM VPVPE+G ND+LI++RK+AICGTDVHI+NWD+W++KTIPVPMV Sbjct: 5 MKALVKTKPEVGLWMERVPVPEIGPNDVLIRVRKSAICGTDVHIWNWDQWAEKTIPVPMV 64 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHE++GEVV +G V +G+RVSGEGHI CG CRNCR GR HLCRNT+GVGVNRPG Sbjct: 65 VGHEFMGEVVEVGPAVSKHHVGERVSGEGHIVCGKCRNCRAGRGHLCRNTLGVGVNRPGS 124 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAE++ +P +N IPD++ D++AAIFDPFGNAVHTALSFDLVGEDVLV+GAGPIGIM A Sbjct: 125 FAEFVCLPEYNVVSIPDDVPDEIAAIFDPFGNAVHTALSFDLVGEDVLVTGAGPIGIMGA 184 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 VAK GAR VVITD+N RL+LARK+GI V+ +KE L DVM +GMTEGFDVGLEMS Sbjct: 185 MVAKRCGARKVVITDINPVRLDLARKLGIDHVVDASKEKLADVMRVIGMTEGFDVGLEMS 244 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 GA PAFR M+D MN+GG+IA+LGI P+ IDW KVIFK L +KGIYGREMFETWYKM A Sbjct: 245 GAAPAFRDMIDKMNNGGKIAILGIAPAGFEIDWNKVIFKMLNLKGIYGREMFETWYKMIA 304 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340 +Q GLDLSPIITHR IDDF+ GF+AMRSG SGKV++ W Sbjct: 305 FVQGGLDLSPIITHRIGIDDFRDGFEAMRSGNSGKVVMDW 344 Lambda K H 0.322 0.140 0.433 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: 525 Number of extensions: 20 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: 341 Length of database: 344 Length adjustment: 29 Effective length of query: 312 Effective length of database: 315 Effective search space: 98280 Effective search space used: 98280 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate SMc01564 SMc01564 (L-threonine 3-dehydrogenase)
to HMM TIGR00692 (tdh: L-threonine 3-dehydrogenase (EC 1.1.1.103))
# 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/TIGR00692.hmm # target sequence database: /tmp/gapView.2486.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00692 [M=340] Accession: TIGR00692 Description: tdh: L-threonine 3-dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-158 511.2 1.8 6.9e-158 511.0 1.8 1.0 1 lcl|FitnessBrowser__Smeli:SMc01564 SMc01564 L-threonine 3-dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc01564 SMc01564 L-threonine 3-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 511.0 1.8 6.9e-158 6.9e-158 1 339 [. 7 343 .. 7 344 .] 0.99 Alignments for each domain: == domain 1 score: 511.0 bits; conditional E-value: 6.9e-158 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeeve 75 al+k+k+e G ++ vpvpe+g+n+vli+v++++icGtdvhi+nwd+wa+k+i+vp+v+Ghe+ Gevv++G+ v+ lcl|FitnessBrowser__Smeli:SMc01564 7 ALVKTKPEVGLWMERVPVPEIGPNDVLIRVRKSAICGTDVHIWNWDQWAEKTIPVPMVVGHEFMGEVVEVGPAVS 81 799************************************************************************ PP TIGR00692 76 gvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGn 150 +vG++vs+e+hivcGkc++cr+G+ h+crnt +vGv+++G fae+v +p n+ +p+d+++e+aai++p+Gn lcl|FitnessBrowser__Smeli:SMc01564 82 KHHVGERVSGEGHIVCGKCRNCRAGRGHLCRNTLGVGVNRPGSFAEFVCLPEYNVVSIPDDVPDEIAAIFDPFGN 156 *************************************************************************** PP TIGR00692 151 avdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvael 225 av+t+l++dl+Ge+vlv+GaGpiG++++ vak +Ga++v+++d n rl+la+k+G+++vv+ ke+l +v+ + lcl|FitnessBrowser__Smeli:SMc01564 157 AVHTALSFDLVGEDVLVTGAGPIGIMGAMVAKRCGARKVVITDINPVRLDLARKLGIDHVVDASKEKLADVMRVI 231 *************************************************************************** PP TIGR00692 226 tsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrl 300 +++eG+dv+le+sGa +a+++++d ++ngG++a+lg+ ++ id++ kvifk l +kGi+Gr++fetwyk+ ++ lcl|FitnessBrowser__Smeli:SMc01564 232 GMTEGFDVGLEMSGAAPAFRDMIDKMNNGGKIAILGIAPAGFEIDWN-KVIFKMLNLKGIYGREMFETWYKMIAF 305 **********************************************9.*************************** PP TIGR00692 301 iqsnkldlapiithkfkldefekgfelmrsGksGkvili 339 +q +ldl+piith+ +d+f++gfe+mrsG+sGkv++ lcl|FitnessBrowser__Smeli:SMc01564 306 VQG-GLDLSPIITHRIGIDDFRDGFEAMRSGNSGKVVMD 343 **8.9********************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (344 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: 00:00:00.01 # Mc/sec: 6.82 // [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