Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate 5208906 Shew_1407 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__PV4:5208906 Length = 246 Score = 99.4 bits (246), Expect = 6e-26 Identities = 73/251 (29%), Positives = 119/251 (47%), Gaps = 17/251 (6%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRA--RTAHPQLHAGVADVSDC 69 G ++L++G +GIG AIA+ L+ GA+V IC D +D L DVSD Sbjct: 4 GKKILVTGGGSGIGLAIAKRALNRGASVLICGRDKIKLDNVIKEVDDSNLKMLSLDVSDI 63 Query: 70 AQVDRIIDDARSKLGG-LDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKA 128 + ++ A LGG +D+L+NNAGI ++ + W+R N YFL ++ Sbjct: 64 SSHKDSLEQAVQLLGGEIDILVNNAGIIDGADFLQ-VSEETWDRIYAVNCKGM-YFLSQS 121 Query: 129 VPLLKETSANPGIIAMASVAGRLGYAFRT-PYAASKWAIVGMVKSLAIELGPNNVRVNAI 187 + + +++ + GY T PY SKW +VGM + LA++L P + VN + Sbjct: 122 ICSRWINKGCTNGRRILNISSQGGYVAATYPYRLSKWDVVGMTQGLALKLAPLGILVNGL 181 Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQ 247 PG+V + ++ + +L L+R + ++A +A+FL S + Sbjct: 182 APGIVATDMQKDLVKDDTNA-----------FLPLNPLQRHASPDEIAELAVFLVSDSCS 230 Query: 248 NISGQAISVDG 258 I GQ I DG Sbjct: 231 FIVGQTIVCDG 241 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: 160 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: 246 Length adjustment: 24 Effective length of query: 239 Effective length of database: 222 Effective search space: 53058 Effective search space used: 53058 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