Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate H281DRAFT_06109 H281DRAFT_06109 3-oxoacyl-[acyl-carrier protein] reductase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Burk376:H281DRAFT_06109 Length = 252 Score = 123 bits (308), Expect = 4e-33 Identities = 86/243 (35%), Positives = 129/243 (53%), Gaps = 19/243 (7%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAI----DRARTAHPQLHAGVADVS 67 G R +++GAA+GIGAAIA A+ GA + + D++ A + D R ++ VADV Sbjct: 9 GRRAVVTGAASGIGAAIALAYAQAGARLVLADLNEARLAAHADACRANGVEVQTIVADVG 68 Query: 68 DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127 D I+D + GG+D+L+NNAG+ DL W+ + +L S F R+ Sbjct: 69 DETGAHGIVDRCIAAYGGIDILVNNAGMLTQARCT-DLTTQMWDDMLRVDLRSVFLCSRR 127 Query: 128 AVPLLKETSANPG-IIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNA 186 A+P + T+ G II +AS G G A T YAA+K ++G KSLA+E P+NV VNA Sbjct: 128 ALPSM--TAQRWGRIINVASQLGIKGGAELTHYAAAKAGVIGFTKSLALEAAPDNVLVNA 185 Query: 187 ILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246 I PG +E +D + ++ E+ +++ LRR +VA A+ LAS G Sbjct: 186 IAPGPIETPLVDGISASWKEAKS-----------KELPLRRFGRADEVAPTAVLLASDPG 234 Query: 247 QNI 249 N+ Sbjct: 235 GNL 237 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: 181 Number of extensions: 11 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: 252 Length adjustment: 24 Effective length of query: 239 Effective length of database: 228 Effective search space: 54492 Effective search space used: 54492 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