Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate RR42_RS13550 RR42_RS13550 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS13550 Length = 266 Score = 131 bits (329), Expect = 2e-35 Identities = 86/266 (32%), Positives = 130/266 (48%), Gaps = 15/266 (5%) Query: 1 MSVLQRLQPYPGLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTV 60 M+ L LQ G L++GG GIG +A L GA V + + LA D V Sbjct: 1 MNTLLSLQ---GRHALVTGGGRGIGAAIARRLLSHGASVTLLGRDAATLAATADTLAEAV 57 Query: 61 AT-------RADVSDAAQIEAVFKVQREHLGGLDVLVNNAGIA--GPTGGIDAISDAEWQ 111 + AD+S A + A F G +D+L+NNAG A P G D A WQ Sbjct: 58 VSPAMLCTVAADISQADSVAAAFADAAGKAGPIDLLINNAGQARSAPFGKTDL---ALWQ 114 Query: 112 ATININLTAQYRFAHHAVPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKS 171 + + +NLT + A+P + + G ++++AS AG +GY + + Y A K ++GL ++ Sbjct: 115 SMLEVNLTGTFLCTQAALPHMLANGWGRIINVASTAGLVGYGYVSAYCAAKHGVIGLTRA 174 Query: 172 LASELGESDIRVNALLPGIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAE 231 LA E S + VNA+ PG E + + + G EA+ R E R+V + Sbjct: 175 LALETASSGVTVNAVCPGYTETDIVRDAVANIVRKTGRTEAQARAELAKGNPQGRLVQPD 234 Query: 232 DVAAMALFLCSPAARNVTGQAISVDG 257 +VA +LC P+A +TGQ+I+V G Sbjct: 235 EVADAVAWLCQPSASAITGQSIAVAG 260 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: 164 Number of extensions: 8 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: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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