Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate H281DRAFT_03703 H281DRAFT_03703 NADP-dependent 3-hydroxy acid dehydrogenase YdfG
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Burk376:H281DRAFT_03703 Length = 257 Score = 137 bits (345), Expect = 2e-37 Identities = 80/249 (32%), Positives = 125/249 (50%), Gaps = 2/249 (0%) Query: 9 PYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSD 68 P G +++GG +GIG +A A L AGA+V + + LA R+K D Sbjct: 7 PLAGQHAVVTGGGSGIGAAIAEALLHAGARVTLMGRNSERLAAQREKCRAWGDVACITVD 66 Query: 69 AAQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHA 128 Q E+V K E G +D+L+NNAG A WQ +++NLT + Sbjct: 67 VTQEESVAKAFNE-AGAVDILINNAGQA-QAAPFTHTDMTLWQRMLDVNLTGVFLGTRAV 124 Query: 129 VPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLP 188 +P + E HG ++++AS AG++GYA+ Y A K ++GL +SLA E+ + VNA+ P Sbjct: 125 LPGMLERRHGRIVNVASTAGQIGYAYVAAYCAAKHGVIGLTRSLALEVATKGVTVNAVCP 184 Query: 189 GIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNV 248 G E + ++ + E + R+ L R V+ E VA L+LC P + + Sbjct: 185 GYTETELLHASLQQITSKTSRTEEQARESLLRSNPQHRFVSPEQVANAVLWLCQPGSDAI 244 Query: 249 TGQAISVDG 257 TGQ++S+ G Sbjct: 245 TGQSVSISG 253 Lambda K H 0.318 0.133 0.383 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: 166 Number of extensions: 5 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: 262 Length of database: 257 Length adjustment: 24 Effective length of query: 238 Effective length of database: 233 Effective search space: 55454 Effective search space used: 55454 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 (21.7 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