Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate SMc02041 SMc02041 short chain dehydrogenase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Smeli:SMc02041 Length = 254 Score = 136 bits (343), Expect = 4e-37 Identities = 96/258 (37%), Positives = 129/258 (50%), Gaps = 16/258 (6%) Query: 3 TIDLLRPTPGLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAG 62 + D L G V+++GAA GIG A+A+AF A V + D D A D A + A Sbjct: 6 SFDDLLDFSGKTVVVTGAATGIGRAVAEAFATKRARVALLDRDAAVSDVAVSLGTGHIAH 65 Query: 63 VADVSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQF 122 VADV+D V+R + G +D+LINNAGI GP E AEW+RT+ NL F Sbjct: 66 VADVTDEQGVERAVKSVTEAFGRIDILINNAGI-GPLAPAESYPTAEWDRTLAVNLKGAF 124 Query: 123 YFLRKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNV 182 R P + E + I+ MAS A +G Y ASK I+GM +A+E GP V Sbjct: 125 LMARAIAPGMLEQGSG-RIVNMASQAAIIGIEGHVAYCASKAGIIGMTNCMALEWGPRGV 183 Query: 183 RVNAILPGVVEGERMDRVISARAESLGI-GFDQMKGEYLQ-KISLRRMVTVHDVAAMALF 240 VNA+ P VVE E LG+ G+ KGE + I RR ++AA L+ Sbjct: 184 TVNAVSPTVVETE------------LGLTGWAGEKGERARAAIPTRRFAKPWEIAASVLY 231 Query: 241 LASPAGQNISGQAISVDG 258 LA A ++G + +DG Sbjct: 232 LAGGAAAMVNGANLMIDG 249 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: 174 Number of extensions: 13 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: 263 Length of database: 254 Length adjustment: 24 Effective length of query: 239 Effective length of database: 230 Effective search space: 54970 Effective search space used: 54970 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: 47 (22.7 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