Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 3610773 Dshi_4159 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= BRENDA::Q5JI69 (350 letters) >FitnessBrowser__Dino:3610773 Length = 350 Score = 181 bits (458), Expect = 3e-50 Identities = 120/346 (34%), Positives = 173/346 (50%), Gaps = 19/346 (5%) Query: 9 MKTKPAYGAELV---EVDVPKPGPGEVLIKVLATSICGTDLHIY--------EWNEWAQS 57 MK +GA+ + +VD P PG GEV IKV T ICG+DLH + + S Sbjct: 1 MKAARWHGAKDIRVEDVDEPTPGAGEVKIKVAWTGICGSDLHEFLAGPIFVPVGEDHPLS 60 Query: 58 RIKPPQIMGHEVAGEVVEVGPGVEDLQVGDYISVETHIVCGKCYACKHNRYHVCQNTKIF 117 K P MGHE GE+ E+G GV DL VGD +++E CG C AC+ RY++C+ Sbjct: 61 HDKAPITMGHEYCGEITELGDGVTDLSVGDRVAIEPIFACGTCAACRDGRYNLCEKLGFV 120 Query: 118 GVD-MDGVFAHYAIVPAKNAWKNPKDMPPEYAALQEPLGNAVDTVLAGPI-AGRSTLITG 175 G+ G FA Y++VPA+ + P+ + E AL EP A+ V AG + G Sbjct: 121 GLSGGHGGFAAYSVVPARMLHRMPEGLSMEQGALVEPAAVALHAVRVSAFKAGDRAAVFG 180 Query: 176 AGPLGLLGIAVAKASGAYPVIVSEPSEFRRKLAKKVGADYVVNPFEEDPVKFVMDITDGA 235 AGP+GLL + + +GA ++V EPSE RR A ++GA V+P ED V V G Sbjct: 181 AGPIGLLVVESLRIAGASKIVVVEPSETRRAKAMELGATTAVDPGAEDAVAAVQAACPG- 239 Query: 236 GVEVFLEFSGAPKALEQGLKAVTPGGRVSLLGLFPREVTIDFNNLIIFKALEVHGITGRH 295 GVEV E +G P L Q + A G ++ ++ E + N ++ L+ I G Sbjct: 240 GVEVAFEVTGVPAVLAQAIDATRYEGETLVVSIWETEASFQPNTVV----LKERNIKGTI 295 Query: 296 LWETWY-TVSSLIQSGKLNLDPIITHKYKGFDKFEEAFELMRAGKT 340 + Y V L+Q G + ++T + D + FE + A K+ Sbjct: 296 AYRNVYPAVMDLMQQGYFQAERLVTRRIGLDDIVRDGFEALVAEKS 341 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: 294 Number of extensions: 14 Number of successful extensions: 5 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: 350 Length adjustment: 29 Effective length of query: 321 Effective length of database: 321 Effective search space: 103041 Effective search space used: 103041 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