Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 6935882 Sama_0097 L-threonine 3-dehydrogenase (RefSeq)
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__SB2B:6935882 Length = 341 Score = 632 bits (1630), Expect = 0.0 Identities = 302/341 (88%), Positives = 320/341 (93%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL+KLK EEGIWM D P PE+GHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV Sbjct: 1 MKALAKLKPEEGIWMVDAPKPEMGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHEYVGEVVGIGQEV+GFKIGDRVSGEGHITCGHCRNCR GRTHLCRNT GVGVNR G Sbjct: 61 VGHEYVGEVVGIGQEVRGFKIGDRVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNREGS 120 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAEYLVIPAFNAFKIPD+ISDDLAAIFDPFGNAVHTALSFDLVGEDVL++GAGPIGIMAA Sbjct: 121 FAEYLVIPAFNAFKIPDDISDDLAAIFDPFGNAVHTALSFDLVGEDVLITGAGPIGIMAA 180 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 AV +HVGAR+VVITDVNEYRLELARKMG TRAVNVAKENL DVM +LGMTEGFDVGLEMS Sbjct: 181 AVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAKENLKDVMKDLGMTEGFDVGLEMS 240 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 G P AF MLDTMNHGG+IAMLGIP +M+IDW+KVIFKGL IKGIYGREMFETWYKMA+ Sbjct: 241 GVPAAFHAMLDTMNHGGKIAMLGIPGGEMAIDWSKVIFKGLIIKGIYGREMFETWYKMAS 300 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341 L+QSGLDLSPI+TH F +DDFQ+GFDAMRSGQSGKVILSWD Sbjct: 301 LLQSGLDLSPIVTHHFKVDDFQQGFDAMRSGQSGKVILSWD 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: 591 Number of extensions: 17 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 6935882 Sama_0097 (L-threonine 3-dehydrogenase (RefSeq))
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.908284.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-183 594.6 1.3 2.9e-183 594.5 1.3 1.0 1 FitnessBrowser__SB2B:6935882 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6935882 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 594.5 1.3 2.9e-183 2.9e-183 1 340 [] 3 340 .. 3 340 .. 1.00 Alignments for each domain: == domain 1 score: 594.5 bits; conditional E-value: 2.9e-183 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGeevegvkvGd 81 al+k+k+eeG+++++ p pe+g+n++lik+++t+icGtdvhiynwdew+qk+i+vp+v+Ghe++GevvgiG+ev+g+k+Gd FitnessBrowser__SB2B:6935882 3 ALAKLKPEEGIWMVDAPKPEMGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMVVGHEYVGEVVGIGQEVRGFKIGD 83 799****************************************************************************** PP TIGR00692 82 yvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqeplGnavdtvlesdlaG 162 +vs+e+hi+cG+c++cr+G++h+crnt++vGv+++G faey+v+pa+n+fk+p+di+++laai++p+Gnav+t+l++dl+G FitnessBrowser__SB2B:6935882 84 RVSGEGHITCGHCRNCRAGRTHLCRNTTGVGVNREGSFAEYLVIPAFNAFKIPDDISDDLAAIFDPFGNAVHTALSFDLVG 164 ********************************************************************************* PP TIGR00692 163 esvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlelsGapka 243 e+vl++GaGpiG++a+av +++Ga++v+++d+neyrlela+k+Gatr+vnvake+l +v+ +l+++eG+dv+le+sG p a FitnessBrowser__SB2B:6935882 165 EDVLITGAGPIGIMAAAVCRHVGARHVVITDVNEYRLELARKMGATRAVNVAKENLKDVMKDLGMTEGFDVGLEMSGVPAA 245 ********************************************************************************* PP TIGR00692 244 leqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkfkldefekg 324 ++ +ld++++gG++a+lg+p ++++id++ kvifkgl+ikGi+Gr++fetwyk++ l+qs +ldl+pi+th+fk+d+f++g FitnessBrowser__SB2B:6935882 246 FHAMLDTMNHGGKIAMLGIPGGEMAIDWS-KVIFKGLIIKGIYGREMFETWYKMASLLQS-GLDLSPIVTHHFKVDDFQQG 324 ****************************9.******************************.9******************* PP TIGR00692 325 felmrsGksGkvilil 340 f++mrsG+sGkvil++ FitnessBrowser__SB2B:6935882 325 FDAMRSGQSGKVILSW 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.16 // [ok]
This GapMind analysis is from Apr 09 2024. 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