Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate 7026544 Shewana3_3687 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__ANA3:7026544 Length = 243 Score = 87.4 bits (215), Expect = 3e-22 Identities = 72/238 (30%), Positives = 118/238 (49%), Gaps = 20/238 (8%) Query: 6 LLRPTPGLRVLISGAAAGIGAAIAQAFLDVGANVYICD--VDPAAIDRARTAHPQLHAGV 63 + +PT L V+I+GA++GIGAAIA+ F G + + V+P +A L GV Sbjct: 1 MTKPTQPL-VVITGASSGIGAAIAKQFSAAGHPLLLLARRVEPM---QALELPNSLAIGV 56 Query: 64 ADVSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFY 123 DV+D + I+ A ++ G + LINNAG+ G ++ DP EW R + N+ Sbjct: 57 -DVTDTDAIKAAINQAEAQFGPVGCLINNAGVM-LLGQIDTQDPNEWSRMLNINVMGVLN 114 Query: 124 FLRKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVR 183 + + +K II ++SVAGR + Y A+K+A+ + +++ E+ ++VR Sbjct: 115 GIHAVLAGMKARKTGT-IINISSVAGRKTFPNHAAYCATKFAVHALTENIREEVAMDDVR 173 Query: 184 VNAILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQ-KISLRRMVTVHDVAAMALF 240 + I PG VE E + D +K Y K+ + ++ +VAA ALF Sbjct: 174 LITIAPGAVETELLSHTTD----------DAIKAGYQDWKVQMGGVIAPENVAAAALF 221 Lambda K H 0.320 0.136 0.391 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: 132 Number of extensions: 5 Number of successful extensions: 3 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: 263 Length of database: 243 Length adjustment: 24 Effective length of query: 239 Effective length of database: 219 Effective search space: 52341 Effective search space used: 52341 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