Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate HSERO_RS05485 HSERO_RS05485 phosphoesterase
Query= BRENDA::Q5JI69 (350 letters) >FitnessBrowser__HerbieS:HSERO_RS05485 Length = 345 Score = 145 bits (366), Expect = 2e-39 Identities = 100/317 (31%), Positives = 153/317 (48%), Gaps = 22/317 (6%) Query: 29 PGEVLIKVLATSICGTDLHIYEWNEWAQSRIKPPQIMGHEVAGEVVEVGPGVEDLQVGDY 88 P ++ +KV A ICG+DLH Y + RIK P ++GHEV+G++ EVG V D+ G Sbjct: 25 PQQLKVKVKAGGICGSDLHYYHHGGFGVVRIKEPMVLGHEVSGQIAEVGTAVTDIAPGTR 84 Query: 89 ISVETHIVCGKCYACKHNRYHVCQNTKIFGVDM-----DGVFAHYAIVPAKNAWKNPKDM 143 I++ CG C C+ + + C + + +G M G F I+ A + Sbjct: 85 IAISPSRPCGACKYCQEGKQNHCLDMRFYGSAMRTPHVQGAFRQEIIIERSQAHVVADHV 144 Query: 144 PPEYAALQEPLGNAVDTV-LAGPIAGRSTLITGAGPLGLLGIAVAKASGAYPVIVSEPSE 202 AA+ EPL A+ V AGP+ G+ L+TG GP+G L + A+ +GA V+V++ + Sbjct: 145 SDGEAAMAEPLSVALHAVRRAGPLVGKRVLVTGCGPIGALVVVAARRAGALEVVVTDVAS 204 Query: 203 FRRKLAKKVGADYVVNPFEEDPVKFVMDITDGAGVEVFLEFSGAPKALEQGLKAVTPGGR 262 + A +VGAD +N E P D +V E SG +AL L+A+ P Sbjct: 205 MPLQAALQVGADSAIN-MAETPAALKAYAADKGTFDVLFEASGNERALVGALEALRPQAI 263 Query: 263 VSLLGL-----FPREVTIDFNNLIIFKALEVHGITGRHLWETWYTVSSLIQSGKLNLDPI 317 + +GL FP NL++ K LE G H E + L+ +++ P+ Sbjct: 264 IVQVGLGGDIQFPA-------NLLVGKELEWRGAFRFH--EEFAMAVELMNRKLVDVKPL 314 Query: 318 ITHKYKGFDKFEEAFEL 334 IT Y + EAFE+ Sbjct: 315 ITATYP-IAQAVEAFEI 330 Lambda K H 0.319 0.139 0.423 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: 280 Number of extensions: 9 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: 350 Length of database: 345 Length adjustment: 29 Effective length of query: 321 Effective length of database: 316 Effective search space: 101436 Effective search space used: 101436 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 (21.7 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