Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_106713900.1 CU102_RS25640 L-threonine 3-dehydrogenase
Query= BRENDA::P07913 (341 letters) >NCBI__GCF_003010955.1:WP_106713900.1 Length = 345 Score = 515 bits (1327), Expect = e-151 Identities = 246/341 (72%), Positives = 281/341 (82%) Query: 1 MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60 MKAL K KAE GIWM VPVPE G ND+LI+++K+AICGTDVHIYNWD+W+Q TIPVPMV Sbjct: 5 MKALVKAKAEPGIWMERVPVPEPGPNDVLIRVKKSAICGTDVHIYNWDKWAQATIPVPMV 64 Query: 61 VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120 VGHE+ GE+ IG V +K+G RVSGEGHI CG CRNCR GR HLCRNT+GVGV+RPG Sbjct: 65 VGHEFSGEIAEIGSAVTKYKVGQRVSGEGHIVCGTCRNCRAGRGHLCRNTLGVGVHRPGS 124 Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180 F EY+ IP N IPD+++D++AAIFDPFGNAVHTALSFDLVGEDVLV+GAGPIGIM A Sbjct: 125 FGEYVCIPEANVVPIPDDVADEIAAIFDPFGNAVHTALSFDLVGEDVLVTGAGPIGIMGA 184 Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240 VAK GAR VVITD+N RL LARK+GI V+ + +NL DVM E+GMTEGFDVGLEMS Sbjct: 185 LVAKRSGARKVVITDINPARLALARKLGIDYVVDASSQNLTDVMREIGMTEGFDVGLEMS 244 Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300 GA PAFR M+D MN+GG+IA+LGI P+ IDW KVIFK L +KGIYGREMFETWYKM A Sbjct: 245 GAAPAFRDMIDKMNNGGKIAILGIAPTGFEIDWNKVIFKMLNLKGIYGREMFETWYKMIA 304 Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSWD 341 +Q GLDLS IITHR SIDDFQ GFDAMRSG SGKV+LSW+ Sbjct: 305 FVQGGLDLSQIITHRLSIDDFQAGFDAMRSGSSGKVVLSWN 345 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: 534 Number of extensions: 21 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: 345 Length adjustment: 29 Effective length of query: 312 Effective length of database: 316 Effective search space: 98592 Effective search space used: 98592 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 WP_106713900.1 CU102_RS25640 (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.2456229.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-157 508.1 0.9 5.9e-157 507.9 0.9 1.0 1 NCBI__GCF_003010955.1:WP_106713900.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106713900.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 507.9 0.9 5.9e-157 5.9e-157 1 340 [] 7 344 .. 7 344 .. 1.00 Alignments for each domain: == domain 1 score: 507.9 bits; conditional E-value: 5.9e-157 TIGR00692 1 almkkkaeeGavltevpvpelgknevlikvkatsicGtdvhiynwdewaqkrikvpqvlGhevaGevvgiGee 73 al+k kae G+++ vpvpe+g+n+vli+vk+++icGtdvhiynwd+waq +i+vp+v+Ghe++Ge+ +iG NCBI__GCF_003010955.1:WP_106713900.1 7 ALVKAKAEPGIWMERVPVPEPGPNDVLIRVKKSAICGTDVHIYNWDKWAQATIPVPMVVGHEFSGEIAEIGSA 79 799********************************************************************** PP TIGR00692 74 vegvkvGdyvsaethivcGkcvacrrGkshvcrntkivGvdtaGvfaeyvvvpadnifknpkdidpelaaiqe 146 v kvG++vs+e+hivcG c++cr+G+ h+crnt +vGv+++G f eyv +p n+ +p+d+ +e+aai++ NCBI__GCF_003010955.1:WP_106713900.1 80 VTKYKVGQRVSGEGHIVCGTCRNCRAGRGHLCRNTLGVGVHRPGSFGEYVCIPEANVVPIPDDVADEIAAIFD 152 ************************************************************************* PP TIGR00692 147 plGnavdtvlesdlaGesvlvsGaGpiGllavavakaaGasqvivsdkneyrlelakkvGatrvvnvakedlv 219 p+Gnav+t+l++dl+Ge+vlv+GaGpiG++++ vak +Ga++v+++d n rl la+k+G+++vv+ ++l+ NCBI__GCF_003010955.1:WP_106713900.1 153 PFGNAVHTALSFDLVGEDVLVTGAGPIGIMGALVAKRSGARKVVITDINPARLALARKLGIDYVVDASSQNLT 225 ************************************************************************* PP TIGR00692 220 kvvaeltsgeGvdvvlelsGapkaleqgldavangGrvallglpeskvtidltnkvifkgltikGitGrklfe 292 +v+ e++++eG+dv+le+sGa +a+++++d ++ngG++a+lg+ ++ id++ kvifk l +kGi+Gr++fe NCBI__GCF_003010955.1:WP_106713900.1 226 DVMREIGMTEGFDVGLEMSGAAPAFRDMIDKMNNGGKIAILGIAPTGFEIDWN-KVIFKMLNLKGIYGREMFE 297 ****************************************************9.******************* PP TIGR00692 293 twykvsrliqsnkldlapiithkfkldefekgfelmrsGksGkvilil 340 twyk+ +++q +ldl+ iith+ ++d+f+ gf++mrsG sGkv+l++ NCBI__GCF_003010955.1:WP_106713900.1 298 TWYKMIAFVQG-GLDLSQIITHRLSIDDFQAGFDAMRSGSSGKVVLSW 344 **********8.9*********************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (345 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: 17.54 // [ok]
This GapMind analysis is from Sep 24 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