Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate 18274 b4249 predicted oxidoreductase with NAD(P)-binding Rossmann-fold domain (NCBI)
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Keio:18274 Length = 237 Score = 97.4 bits (241), Expect = 2e-25 Identities = 76/250 (30%), Positives = 112/250 (44%), Gaps = 31/250 (12%) Query: 7 GKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKL-----------D 55 GKT LI +GIG A F +GA V T AG A++L D Sbjct: 6 GKTVLILGGSRGIGAAIVRRFVTDGANVRFT------YAGSKDAAKRLAQETGATAVFTD 59 Query: 56 VRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLP 115 D A+ + + GA+D+L AG G LE + +D D F +N+ A Y Sbjct: 60 SADRDAVIDVVRKSGALDILVVNAGIGVFGEALELNADDIDRLFKINIHAPYHASVEAAR 119 Query: 116 AMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPG 175 M + GG I+ + S V AY+ASK+A+ G+ + +A DF RG+ N + PG Sbjct: 120 QMPE--GGRILIIGSVNGDRMPVAGMAAYAASKSALQGMARGLARDFGPRGITINVVQPG 177 Query: 176 TVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTT 235 + + + A G D + + + R G+PEE+A + +L E+SF T Sbjct: 178 PIDTDA--------NPANGPMRDMLHSLMAIK----RHGQPEEVAGMVAWLAGPEASFVT 225 Query: 236 GHAHVIDGGW 245 G H IDG + Sbjct: 226 GAMHTIDGAF 235 Lambda K H 0.320 0.133 0.381 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: 134 Number of extensions: 6 Number of successful extensions: 4 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: 247 Length of database: 237 Length adjustment: 23 Effective length of query: 224 Effective length of database: 214 Effective search space: 47936 Effective search space used: 47936 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 (21.8 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