Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate RR42_RS22860 RR42_RS22860 l-threonine 3-dehydrogenase
Query= BRENDA::P07913 (341 letters) >FitnessBrowser__Cup4G11:RR42_RS22860 Length = 351 Score = 559 bits (1441), Expect = e-164 Identities = 263/340 (77%), Positives = 300/340 (88%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL+KL+ G+ +TDVP PE+GHND++I+IR+TAICGTD+HI+ WDEW+Q TIPVPM Sbjct: 1 MKALAKLERAPGLTLTDVPEPEVGHNDVMIRIRQTAICGTDIHIWKWDEWAQNTIPVPMQ 60 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHEYVGE+V IGQEV+G IGDRVSGEGHITCG CRNCR GR HLCRN++GVGVNR G Sbjct: 61 VGHEYVGEIVAIGQEVRGLAIGDRVSGEGHITCGFCRNCRAGRRHLCRNSVGVGVNRAGA 120 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAEYLVIPAFNAF+IPD+I D++AAIFDPFGNA HTALSF+LVGEDVL++GAGPIGIMAA Sbjct: 121 FAEYLVIPAFNAFRIPDDIPDEIAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAA 180 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 A+A+HVGARNVVITDVNEYRL LARKMG TRAVNV ENL DV AEL MTEGFDVG+EMS Sbjct: 181 AIARHVGARNVVITDVNEYRLALARKMGATRAVNVQHENLKDVAAELHMTEGFDVGMEMS 240 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 G P AF TML+ MNHGG+IAMLGIPPS M+IDW +VIFKGL IKGIYGREMFETWYKM A Sbjct: 241 GVPTAFATMLEHMNHGGKIAMLGIPPSKMAIDWNQVIFKGLEIKGIYGREMFETWYKMVA 300 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340 ++QSGLDL+P+ITHRF + DF+ GF AM SG SGKV+L W Sbjct: 301 MLQSGLDLTPMITHRFRVGDFEAGFAAMLSGNSGKVVLDW 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: 502 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: 341 Length of database: 351 Length adjustment: 29 Effective length of query: 312 Effective length of database: 322 Effective search space: 100464 Effective search space used: 100464 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 RR42_RS22860 RR42_RS22860 (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.15698.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-166 538.6 0.7 3.2e-166 538.4 0.7 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS22860 RR42_RS22860 l-threonine 3-dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS22860 RR42_RS22860 l-threonine 3-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 538.4 0.7 3.2e-166 3.2e-166 1 340 [] 3 340 .. 3 340 .. 0.99 Alignments for each domain: == domain 1 score: 538.4 bits; conditional E-value: 3.2e-166 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvg 69 al+k++ + G +lt+vp pe+g+n+v+i++++t+icGtd+hi++wdewaq++i+vp+ +Ghe++Ge+v lcl|FitnessBrowser__Cup4G11:RR42_RS22860 3 ALAKLERAPGLTLTDVPEPEVGHNDVMIRIRQTAICGTDIHIWKWDEWAQNTIPVPMQVGHEYVGEIVA 71 7999***************************************************************** PP TIGR00692 70 iGeevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdid 138 iG+ev+g+ +Gd+vs+e+hi+cG c++cr+G+ h+crn+++vGv++aG+faey+v+pa+n+f++p+di+ lcl|FitnessBrowser__Cup4G11:RR42_RS22860 72 IGQEVRGLAIGDRVSGEGHITCGFCRNCRAGRRHLCRNSVGVGVNRAGAFAEYLVIPAFNAFRIPDDIP 140 ********************************************************************* PP TIGR00692 139 pelaaiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGa 207 +e+aai++p+Gna +t+l+++l+Ge+vl++GaGpiG++a+a+a+++Ga++v+++d+neyrl la+k+Ga lcl|FitnessBrowser__Cup4G11:RR42_RS22860 141 DEIAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAAAIARHVGARNVVITDVNEYRLALARKMGA 209 ********************************************************************* PP TIGR00692 208 trvvnvakedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvi 276 tr+vnv++e+l +v ael ++eG+dv++e+sG p+a++++l+ +++gG++a+lg+p+sk++id++ +vi lcl|FitnessBrowser__Cup4G11:RR42_RS22860 210 TRAVNVQHENLKDVAAELHMTEGFDVGMEMSGVPTAFATMLEHMNHGGKIAMLGIPPSKMAIDWN-QVI 277 ****************************************************************9.9** PP TIGR00692 277 fkgltikGitGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340 fkgl ikGi+Gr++fetwyk+ +++qs +ldl+p+ith+f++ +fe gf +m sG+sGkv+l + lcl|FitnessBrowser__Cup4G11:RR42_RS22860 278 FKGLEIKGIYGREMFETWYKMVAMLQS-GLDLTPMITHRFRVGDFEAGFAAMLSGNSGKVVLDW 340 ***************************.9********************************965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (351 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: 00:00:00.01 # Mc/sec: 6.69 // [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