Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate WP_003468267.1 J416_RS08060 erythritol/L-threitol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >NCBI__GCF_000359605.1:WP_003468267.1 Length = 358 Score = 177 bits (450), Expect = 3e-49 Identities = 116/336 (34%), Positives = 181/336 (53%), Gaps = 19/336 (5%) Query: 1 MSEKMVAIMKTKPE-YGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNE--WA-- 55 + E M A++ PE Y E EV+ P GPGE++IK+ A ICG+DL +Y + WA Sbjct: 4 LPETMKAVVCHGPEDYRVE--EVNTPTAGPGEIVIKVKACGICGSDLKVYHGADMYWAGD 61 Query: 56 QTRIRPPQIMGHEVAGEVVEVGPGV---EGIEVGDYVSVETHIVCGKCYACKRGQYHVCQ 112 ++ P I GHE GEV E+G G +++GD ++ + CG C C G+Y +CQ Sbjct: 62 DPWLKAPVIPGHEFYGEVAELGEGAAETHDLQIGDRITTDQINPCGNCMYCNSGKYWMCQ 121 Query: 113 NTKIFGVD---TDGVFAEYAVV-PAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIAG 168 ++G +G AEY P ++K P+ + A+L EP+ AV V I Sbjct: 122 VHNMYGFQREVAEGAMAEYMKFSPQSKIYKVPEGVNDYEASLLEPMACAVHAVQRATIEF 181 Query: 169 KS-VLITGAGPLGLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKE 227 + V++ GAG LGL I + K ++V + ++ R LAKK GAD +NP +EDV+++ Sbjct: 182 EDFVVMAGAGTLGLCMIQLIKLKTPKTLVVLDANDRRLELAKKYGADICMNPTKEDVIQK 241 Query: 228 VMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALT 287 V D+T+G G DV++E +G PK + QGL+ V GR +F + + D++ + K L Sbjct: 242 VKDLTNGYGCDVYIEATGNPKGVTQGLEMVRKLGRYVEFSVFGKETTTDWSVIGDKKEL- 300 Query: 288 VYGITGRHLWETWYTVS-RLLQSGKLNIDPIITHKY 322 I G HL Y ++ L + G ++ + I+TH + Sbjct: 301 --DIRGSHLGPYTYPIAIDLFERGLVSAEGIVTHTF 334 Lambda K H 0.318 0.138 0.417 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: 310 Number of extensions: 15 Number of successful extensions: 3 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: 348 Length of database: 358 Length adjustment: 29 Effective length of query: 319 Effective length of database: 329 Effective search space: 104951 Effective search space used: 104951 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
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