Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate GFF1301 PGA1_c13170 sorbitol dehydrogenase PolS
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Phaeo:GFF1301 Length = 257 Score = 142 bits (357), Expect = 9e-39 Identities = 94/251 (37%), Positives = 130/251 (51%), Gaps = 8/251 (3%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAGVA----DVS 67 G R LI+GAA GIGAA A+A+ + GA V I D+D A RA Q+ A DV+ Sbjct: 6 GKRALITGAARGIGAAFAEAYANEGARVVIADIDTA---RAEATAAQIGAAAIAVELDVT 62 Query: 68 DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127 D A +DR + GGLD+LINNA + VE A ++RT N++ + ++ Sbjct: 63 DQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREA-YQRTFDINVSGTLFMMQA 121 Query: 128 AVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAI 187 A + II MAS AGR G + Y A+K A++ + +S + L + + VNAI Sbjct: 122 AAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNAI 181 Query: 188 LPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAGQ 247 PGVV+GE D V + A+ G Q K E Q + RM T D+ MA+FLAS Sbjct: 182 APGVVDGEHWDGVDAFFAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASEDAD 241 Query: 248 NISGQAISVDG 258 + Q +VDG Sbjct: 242 YVVAQTYNVDG 252 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: 5 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 239 Effective length of database: 233 Effective search space: 55687 Effective search space used: 55687 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