Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate 3607850 Dshi_1258 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Dino:3607850 Length = 247 Score = 106 bits (265), Expect = 4e-28 Identities = 73/245 (29%), Positives = 121/245 (49%), Gaps = 16/245 (6%) Query: 16 LISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAG--VADVSDCAQVD 73 LI+G A GIG A A+A GA + + D+ D + A +L + D+ D A V Sbjct: 8 LITGGAQGIGYACAEALAAEGARIILADIQ----DSVQEAAARLGGAGYLCDMGDAAAVG 63 Query: 74 RIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAVPLLK 133 + D ++ G + L+NNAGIA P G D D A ++R + NL F ++A + Sbjct: 64 ALFDRIEAEHGAVTYLVNNAGIAAP-GDFLDYDLATFDRVLDINLRGVFVATQRAGRSMV 122 Query: 134 ETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILPGVVE 193 ++ M+S+ ++ Y ASK ++ + K A+ L P+ +RVNA+ PG ++ Sbjct: 123 AHGIKGAVVNMSSINAQVAIPSIPAYCASKGGLMQLTKVAALALAPHGIRVNAVGPGSID 182 Query: 194 GERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQNISGQA 253 E M V +A E++ + L + L+R+ T ++A + FL S ++G+ Sbjct: 183 TEMMAGV-NANPEAMNM--------VLSRTPLKRVGTAQEIANVVAFLCSDKASYVTGET 233 Query: 254 ISVDG 258 I VDG Sbjct: 234 IYVDG 238 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: 158 Number of extensions: 12 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: 247 Length adjustment: 24 Effective length of query: 239 Effective length of database: 223 Effective search space: 53297 Effective search space used: 53297 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