Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate 3608297 Dshi_1700 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__Dino:3608297 Length = 251 Score = 250 bits (639), Expect = 2e-71 Identities = 132/252 (52%), Positives = 173/252 (68%), Gaps = 2/252 (0%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADI 60 M +++ +V+G ASGLG AT + L GA V ++D +A A E G A F D+ Sbjct: 1 MQVSDHAILVTGGASGLGEATVRHLRAKGAAVAVLDRDATRGHQLAAESG--ALFFETDV 58 Query: 61 SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFN 120 +D+ +A+++V AA +A G + V CAG+ + K LG++GPHGL +F + I++NL+G+FN Sbjct: 59 TDDVSAEASVTAAATALGRITACVTCAGVATSAKTLGREGPHGLDAFQRTIDINLVGTFN 118 Query: 121 LLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELA 180 + RLAAA MA A D G RGVI+ TASIAA+DGQ GQAAYAASK + L+LP AR+LA Sbjct: 119 IARLAAAEMARNAPDADGARGVIVTTASIAAFDGQKGQAAYAASKAGVTGLSLPMARDLA 178 Query: 181 RFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLN 240 R GIRVM+IAPGIF TPM+ G+ +E+ +LAA V FP RLG P EYA L I+E LN Sbjct: 179 REGIRVMSIAPGIFRTPMLIGLGEEIMEALAADVTFPKRLGDPVEYARLVAFILECGYLN 238 Query: 241 GEVIRLDGALRM 252 G IRLDGALRM Sbjct: 239 GTTIRLDGALRM 250 Lambda K H 0.318 0.131 0.358 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: 152 Number of extensions: 3 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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: 46 (22.3 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