Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate WP_009563598.1 RSPH17029_RS17955 SDR family oxidoreductase
Query= metacyc::MONOMER-20835 (262 letters) >NCBI__GCF_000015985.1:WP_009563598.1 Length = 240 Score = 134 bits (338), Expect = 1e-36 Identities = 82/248 (33%), Positives = 124/248 (50%), Gaps = 22/248 (8%) Query: 12 GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATRADVSDAAQ 71 G VL++GGA+GIG +A +E GA+ +CD++ + G VA DV+D A Sbjct: 8 GKVVLVTGGASGIGRSVAEVCVELGARTAICDLAPG------EAPEGQVALNCDVTDPAA 61 Query: 72 IEAVFKVQREHLGGLDVLVNNAGIAGPT--GGIDAISDAEWQATININLTAQYRFAHHAV 129 +E F RE G +D +VN AG+ P G I A+SD W I +NLT + AV Sbjct: 62 VERAFAAAREAFGRVDAVVNCAGVWRPRSDGPITAVSDETWDRIIAVNLTGTFNVCREAV 121 Query: 130 PMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPG 189 +++ HG ++ IASV G+ Y+A+K ++ L ++LA E G +IRVN + PG Sbjct: 122 RVMEAQGHGSIVTIASVVAITGWEKLNAYSASKGGVLSLSRALAIECGPKNIRVNCICPG 181 Query: 190 IVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVT 249 ++E P + V+ V + + R+ D+A A FLCS + T Sbjct: 182 VIETPMTEKVLAYSQPDV--------------LPIGRLGHPRDIAHTAAFLCSDRSGFTT 227 Query: 250 GQAISVDG 257 + VDG Sbjct: 228 AATVVVDG 235 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: 167 Number of extensions: 8 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: 262 Length of database: 240 Length adjustment: 24 Effective length of query: 238 Effective length of database: 216 Effective search space: 51408 Effective search space used: 51408 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 2024. 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