Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-dehydrogenase
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__Burk376:H281DRAFT_03586 Length = 343 Score = 552 bits (1423), Expect = e-162 Identities = 258/340 (75%), Positives = 299/340 (87%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL+KL+ G+ +TDV VPE+GHND++I+I++TAICGTD+HI+ WD+W+QKTIPVPM Sbjct: 1 MKALAKLERAPGLTLTDVKVPEVGHNDVMIRIKRTAICGTDIHIWKWDDWAQKTIPVPMH 60 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHEYVGE+V +G EV+GF IGDRVSGEGHITCG CRNCR GR HLCRNT+GVGVNR G Sbjct: 61 VGHEYVGEIVEMGAEVRGFSIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNREGA 120 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAEYLVIPAFNAFKIP ISDDLAAIFDPFGNA HTALSF+LVGEDVL++GAGPIGIMA Sbjct: 121 FAEYLVIPAFNAFKIPPEISDDLAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAV 180 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 A+AKHVGARNVVITD+N+YRL LARKMG TRAVNV++E+L DVMA+L M EGFDVGLEMS Sbjct: 181 AIAKHVGARNVVITDINDYRLGLARKMGATRAVNVSRESLRDVMADLHMAEGFDVGLEMS 240 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 G P AF ML+ MNHGG+IA+LGIPP+ +IDW +VIFKGL IKGIYGREMFETWYKM A Sbjct: 241 GVPGAFTGMLEAMNHGGKIALLGIPPAQTAIDWNQVIFKGLEIKGIYGREMFETWYKMVA 300 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340 ++QSGLDLSPI+TH F +DD+Q+ F M SG+SGKVIL W Sbjct: 301 MLQSGLDLSPILTHHFKVDDYQQAFATMLSGESGKVILDW 340 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: 530 Number of extensions: 13 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: 343 Length adjustment: 29 Effective length of query: 312 Effective length of database: 314 Effective search space: 97968 Effective search space used: 97968 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 H281DRAFT_03586 H281DRAFT_03586 (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.14241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-166 538.4 0.5 3.7e-166 538.2 0.5 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 538.2 0.5 3.7e-166 3.7e-166 1 340 [] 3 340 .. 3 340 .. 0.99 Alignments for each domain: == domain 1 score: 538.2 bits; conditional E-value: 3.7e-166 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGe 66 al+k++ + G +lt+v+vpe+g+n+v+i++k+t+icGtd+hi++wd+waqk+i+vp+ +Ghe++Ge lcl|FitnessBrowser__Burk376:H281DRAFT_03586 3 ALAKLERAPGLTLTDVKVPEVGHNDVMIRIKRTAICGTDIHIWKWDDWAQKTIPVPMHVGHEYVGE 68 7999************************************************************** PP TIGR00692 67 vvgiGeevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifk 132 +v++G ev+g+ +Gd+vs+e+hi+cG c++cr+G+ h+crnt++vGv+++G+faey+v+pa+n+fk lcl|FitnessBrowser__Burk376:H281DRAFT_03586 69 IVEMGAEVRGFSIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNREGAFAEYLVIPAFNAFK 134 ****************************************************************** PP TIGR00692 133 npkdidpelaaiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyr 198 +p +i+++laai++p+Gna +t+l+++l+Ge+vl++GaGpiG++ava+ak++Ga++v+++d n+yr lcl|FitnessBrowser__Burk376:H281DRAFT_03586 135 IPPEISDDLAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAVAIAKHVGARNVVITDINDYR 200 ****************************************************************** PP TIGR00692 199 lelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpe 264 l la+k+Gatr+vnv +e l +v+a+l ++eG+dv+le+sG p a++ +l+a+++gG++allg+p+ lcl|FitnessBrowser__Burk376:H281DRAFT_03586 201 LGLARKMGATRAVNVSRESLRDVMADLHMAEGFDVGLEMSGVPGAFTGMLEAMNHGGKIALLGIPP 266 ****************************************************************** PP TIGR00692 265 skvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrs 330 ++ +id++ +vifkgl ikGi+Gr++fetwyk+ +++qs +ldl+pi+th+fk+d+++++f m s lcl|FitnessBrowser__Burk376:H281DRAFT_03586 267 AQTAIDWN-QVIFKGLEIKGIYGREMFETWYKMVAMLQS-GLDLSPILTHHFKVDDYQQAFATMLS 330 *******9.9*****************************.9************************* PP TIGR00692 331 GksGkvilil 340 G+sGkvil + lcl|FitnessBrowser__Burk376:H281DRAFT_03586 331 GESGKVILDW 340 *******965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (343 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: 00:00:00.01 # Mc/sec: 10.14 // [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