Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase
Query= BRENDA::P07913 (341 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase Length = 344 Score = 476 bits (1224), Expect = e-139 Identities = 221/340 (65%), Positives = 267/340 (78%), Gaps = 1/340 (0%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL K E+GIWM +VPVPE+G N++LIK+ KTAICGTD+HIY WDEWSQ+TI + Sbjct: 5 MKALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIKPGLT 64 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 +GHE+VG +V IG V G+K+GDRVS EGHI CGHCRNCR GR HLC NT+G+GVNR G Sbjct: 65 IGHEFVGRIVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVNRNGA 124 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 FAEY+ +PA N + IPD I +LAA FDP+GNA H AL FDL+GEDVL++GAGPIGI+AA Sbjct: 125 FAEYMTMPASNLWPIPDQIPSELAAFFDPYGNAAHCALEFDLIGEDVLITGAGPIGIIAA 184 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 +AKHVGARNVV+TDVN+YRL+LA MG TR VNVA ++L DV+ +L + EGFDVGLEMS Sbjct: 185 GIAKHVGARNVVVTDVNDYRLKLAADMGATRVVNVANQSLRDVVKDLHI-EGFDVGLEMS 243 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 G P AF MLD M HGG+IA+LGI P IDW KVIFKGL ++GIYGR M+ETWYKM Sbjct: 244 GNPRAFNDMLDCMYHGGKIALLGIMPRGAGIDWDKVIFKGLTLQGIYGRRMYETWYKMTQ 303 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340 ++ SG L ++TH+ IDDFQKGFD M +G GKV+ SW Sbjct: 304 MVLSGFPLQKVLTHQIHIDDFQKGFDLMDAGHCGKVVCSW 343 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: 481 Number of extensions: 12 Number of successful extensions: 2 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 N515DRAFT_0039 N515DRAFT_0039 (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.21621.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-154 499.0 0.3 3.5e-154 498.8 0.3 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 N515DRAFT_0039 L-threonine 3-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 498.8 0.3 3.5e-154 3.5e-154 1 340 [] 7 343 .. 7 343 .. 0.99 Alignments for each domain: == domain 1 score: 498.8 bits; conditional E-value: 3.5e-154 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGe 66 al+k+ +e+G+++ evpvpe+g+nevlik+++t+icGtd+hiy+wdew+q++ik+ +Ghe++G lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 7 ALVKRLPEQGIWMEEVPVPEVGPNEVLIKMEKTAICGTDLHIYKWDEWSQRTIKPGLTIGHEFVGR 72 79999************************************************************* PP TIGR00692 67 vvgiGeevegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifk 132 +v+iG++v g kvGd+vsae+hivcG+c++cr+G++h+c nt+++Gv+++G+faey+ +pa+n++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 73 IVDIGPGVTGYKVGDRVSAEGHIVCGHCRNCRAGRQHLCPNTVGIGVNRNGAFAEYMTMPASNLWP 138 ****************************************************************** PP TIGR00692 133 npkdidpelaaiqeplGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyr 198 +p++i+ elaa ++p+Gna + +le+dl Ge+vl++GaGpiG++a+ +ak++Ga++v+v+d+n+yr lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 139 IPDQIPSELAAFFDPYGNAAHCALEFDLIGEDVLITGAGPIGIIAAGIAKHVGARNVVVTDVNDYR 204 ****************************************************************** PP TIGR00692 199 lelakkvGatrvvnvakedlvkvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpe 264 l+la +Gatrvvnva++ l +vv +l eG+dv+le+sG+p+a++++ld + +gG++allg+ + lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 205 LKLAADMGATRVVNVANQSLRDVVKDLH-IEGFDVGLEMSGNPRAFNDMLDCMYHGGKIALLGIMP 269 **************************96.69*********************************** PP TIGR00692 265 skvtidltnkvifkgltikGitGrklfetwykvsrliqsnkldlapiithkfkldefekgfelmrs 330 id+ kvifkglt++Gi+Gr+++etwyk+++++ s ++ l+ ++th+ ++d+f+kgf+lm + lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 270 RGAGIDWD-KVIFKGLTLQGIYGRRMYETWYKMTQMVLS-GFPLQKVLTHQIHIDDFQKGFDLMDA 333 *******9.******************************.89************************ PP TIGR00692 331 GksGkvilil 340 G++Gkv+ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0039 334 GHCGKVVCSW 343 ******9876 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.27 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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