Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate BPHYT_RS16050 BPHYT_RS16050 iditol 2-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__BFirm:BPHYT_RS16050 Length = 365 Score = 164 bits (414), Expect = 4e-45 Identities = 119/356 (33%), Positives = 182/356 (51%), Gaps = 20/356 (5%) Query: 3 EKMVAIMKTKP-EYGAELVEVDVPKPGPGEVLIKILATSICGTDLHIYEWNE--WAQTR- 58 + M AI+ P +Y E +V P+ G E++I+I A IC +D + + W Sbjct: 11 QNMTAIVCHAPKDYRVE--QVSKPRAGAHELVIRIAACGICASDCKCHSGAKMFWGGPSP 68 Query: 59 -IRPPQIMGHEVAGEVVEVGPGVE---GIEVGDYVSVETHIVCGKCYACKRGQYHVCQNT 114 ++ P I GHE G V E+G G G+++GD V E + CGKC CK GQY +C+ Sbjct: 69 WVKAPVIPGHEFFGFVEEIGEGAADHFGVKMGDRVIAEQIVPCGKCRYCKSGQYWMCEVH 128 Query: 115 KIFGVD---TDGVFAEYA-VVPAQNVWKNPKNIPPEYATLQEPLGNAVDTVLAGPIA-GK 169 IFG DG AEY + P V K P I E A + EPL A+ TV G + Sbjct: 129 NIFGFQREVADGGMAEYMRIPPTAIVHKIPDGISLEDAAIIEPLACAIHTVNRGEVQLDD 188 Query: 170 SVLITGAGPLGLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVM 229 V+I GAGPLGL+ +A ++V + E R LA++ GAD INP ++D + + Sbjct: 189 VVVIAGAGPLGLMMTQIAHLKTPKKLVVIDLVEERLALAREYGADVTINPKQDDALAIIH 248 Query: 230 DITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVY 289 +TDG G DV++E +GAP + QG+ + GR +F ++D++ + K L V Sbjct: 249 SLTDGYGCDVYIETTGAPIGVNQGMDLIRKLGRFVEFSVFGADTTLDWSVIGDRKELDV- 307 Query: 290 GITGRHLWETWYTVS-RLLQSGKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVV 344 G HL Y ++ LL G + I+TH + ++++EA ++ + + KV+ Sbjct: 308 --RGAHLGPYCYPIAIDLLARGLVTSKGIVTHGF-SLEEWDEAIKIANSLDSIKVL 360 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: 332 Number of extensions: 22 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: 348 Length of database: 365 Length adjustment: 29 Effective length of query: 319 Effective length of database: 336 Effective search space: 107184 Effective search space used: 107184 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 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