Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 203742 SO4673 threonine 3-dehydrogenase (NCBI ptt file)
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__MR1:203742 Length = 341 Score = 624 bits (1608), Expect = 0.0 Identities = 299/341 (87%), Positives = 319/341 (93%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKALSKLKAE+GIW+ D P PE+GHNDLLIKI+KTAICGTD+HIYNWDEWSQKTIPVPMV Sbjct: 1 MKALSKLKAEKGIWLVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMV 60 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHEYVGEVV IGQEV+GF IGDRVSGEGHITCGHCRNCR GRTHLCRNT GVGVNR G Sbjct: 61 VGHEYVGEVVDIGQEVRGFNIGDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNREGS 120 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAEYLVIPAFNAFKIPD+ISDDLA+IFDPFGNAVHTALSFDLVGEDVL++GAGPIGIMAA Sbjct: 121 FAEYLVIPAFNAFKIPDDISDDLASIFDPFGNAVHTALSFDLVGEDVLITGAGPIGIMAA 180 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 AV +HVGAR+VVITDVNEYRLELARKMG TRAVNVA+ENL DVM ELGMTEGFDVGLEMS Sbjct: 181 AVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAQENLKDVMKELGMTEGFDVGLEMS 240 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 G P AFR MLDTMNHGG+IAMLGIP +M+IDW+KVIFKGL IKGIYGREMFETWYKMA+ Sbjct: 241 GVPSAFRAMLDTMNHGGKIAMLGIPGGEMAIDWSKVIFKGLVIKGIYGREMFETWYKMAS 300 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341 LIQSGLD+SPIITH + IDDFQKGFDAM SGQSGKVILSWD Sbjct: 301 LIQSGLDISPIITHHYKIDDFQKGFDAMGSGQSGKVILSWD 341 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: 586 Number of extensions: 18 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: 341 Length adjustment: 29 Effective length of query: 312 Effective length of database: 312 Effective search space: 97344 Effective search space used: 97344 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 203742 SO4673 (threonine 3-dehydrogenase (NCBI ptt file))
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.16946.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-182 589.4 1.6 1.1e-181 589.3 1.6 1.0 1 lcl|FitnessBrowser__MR1:203742 SO4673 threonine 3-dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:203742 SO4673 threonine 3-dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 589.3 1.6 1.1e-181 1.1e-181 1 340 [] 3 340 .. 3 340 .. 1.00 Alignments for each domain: == domain 1 score: 589.3 bits; conditional E-value: 1.1e-181 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeevegvkv 79 al+k+kae G++l++ p pe+g+n++lik+k+t+icGtd+hiynwdew+qk+i+vp+v+Ghe++Gevv+iG+ev+g+++ lcl|FitnessBrowser__MR1:203742 3 ALSKLKAEKGIWLVDAPKPEMGHNDLLIKIKKTAICGTDMHIYNWDEWSQKTIPVPMVVGHEYVGEVVDIGQEVRGFNI 81 89***************************************************************************** PP TIGR00692 80 GdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGnavdtvles 158 Gd+vs+e+hi+cG+c++cr+G++h+crnt +vGv+++G faey+v+pa+n+fk+p+di+++la+i++p+Gnav+t+l++ lcl|FitnessBrowser__MR1:203742 82 GDRVSGEGHITCGHCRNCRAGRTHLCRNTSGVGVNREGSFAEYLVIPAFNAFKIPDDISDDLASIFDPFGNAVHTALSF 160 ******************************************************************************* PP TIGR00692 159 dlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlel 237 dl+Ge+vl++GaGpiG++a+av +++Ga++v+++d+neyrlela+k+Gatr+vnva+e+l +v+ el+++eG+dv+le+ lcl|FitnessBrowser__MR1:203742 161 DLVGEDVLITGAGPIGIMAAAVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAQENLKDVMKELGMTEGFDVGLEM 239 ******************************************************************************* PP TIGR00692 238 sGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkf 316 sG p+a++ +ld++++gG++a+lg+p ++++id++ kvifkgl+ikGi+Gr++fetwyk++ liqs +ld++piith++ lcl|FitnessBrowser__MR1:203742 240 SGVPSAFRAMLDTMNHGGKIAMLGIPGGEMAIDWS-KVIFKGLVIKGIYGREMFETWYKMASLIQS-GLDISPIITHHY 316 **********************************9.******************************.9*********** PP TIGR00692 317 kldefekgfelmrsGksGkvilil 340 k+d+f+kgf++m sG+sGkvil++ lcl|FitnessBrowser__MR1:203742 317 KIDDFQKGFDAMGSGQSGKVILSW 340 **********************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (341 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: 11.55 // [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