Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate HSERO_RS17235 HSERO_RS17235 3-ketoacyl-ACP reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__HerbieS:HSERO_RS17235 Length = 261 Score = 245 bits (626), Expect = 6e-70 Identities = 129/255 (50%), Positives = 184/255 (72%), Gaps = 8/255 (3%) Query: 14 RVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIA----DVSKQ 69 +V V+AGA GIGLAI AF+EA A V+ICDV++ + A +RF HA ++ DVS + Sbjct: 9 KVIVTAGAQGIGLAITAAFVEAGAHVHICDVSEDFLASARARFG--HAPVSYSRTDVSSE 66 Query: 70 AQVDQIIDD-ARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKA 128 +VD + D A+R G LDVL+NNAGIAGPT VEE+ + W+ T++ NL F R+A Sbjct: 67 REVDAMFADLAQRWSGRLDVLINNAGIAGPTSPVEEVALSDWDQTLAVNLTGPFLCTRRA 126 Query: 129 VPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAIL 188 VP+LK+ A I+ +SSVAGRLG+ RTPY+++K+ ++GL ++ A ELGPS++RVNA+L Sbjct: 127 VPLLKKNGGGA-IVNISSVAGRLGFALRTPYSASKYGVIGLTETWAIELGPSHIRVNAVL 185 Query: 189 PGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSN 248 PG+VEG R +R+++A+A A GI MR+ L ++SLR+MVT +DIA +FL SPAG++ Sbjct: 186 PGIVEGARQERIVAAKAAAYGIGHEEMRQRLLSRVSLRKMVTAEDIANQVIFLCSPAGAS 245 Query: 249 VTGQAISVDGNVEYL 263 ++GQ++SV GNVE L Sbjct: 246 ISGQSLSVCGNVEVL 260 Lambda K H 0.318 0.134 0.375 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: 169 Number of extensions: 7 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: 261 Length adjustment: 25 Effective length of query: 238 Effective length of database: 236 Effective search space: 56168 Effective search space used: 56168 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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