Align L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (characterized)
to candidate WP_013011378.1 DACET_RS10645 fuculose phosphate aldolase
Query= reanno::Cola:Echvi_0503 (234 letters) >NCBI__GCF_000025725.1:WP_013011378.1 Length = 214 Score = 85.1 bits (209), Expect = 1e-21 Identities = 60/196 (30%), Positives = 93/196 (47%), Gaps = 20/196 (10%) Query: 5 LELKRECYEANMQLPALDLVVYTFGNVSAVDRKEGVFAIKPSGVAYEALTPEDIVICDFD 64 L+ ++ E +L +L T GN+S +R E + A+ PSGV Y T EDIVI D D Sbjct: 4 LKERKLLVEYGKKLVTTNLTSGTGGNLSIYNRDENLVAVTPSGVDYMKTTVEDIVITDID 63 Query: 65 AKIVEGEMRPSSDTKTHAYLYKEWENIGGIVHTHSLYGVSWAQAQMDVPIFGTTHADHLT 124 +VEG+ RP+S+ H LYK+ ++ +VHTHS+Y + A M++P + Sbjct: 64 GNVVEGDNRPTSELSFHLSLYKDRADVCAVVHTHSVYATTVACLGMELPAVHYM-VGYSG 122 Query: 125 KDIPCAPPM---ADELIEGDYEHMTGKQILDCFAEKGLDYEEVEMILVGSHGPFTWGKTA 181 +P AP + EL E EH+ G +L+ +HG T Sbjct: 123 SKVPLAPYCTFGSPELAESIIEHIGG----------------YNAVLLANHGLVTVSGNM 166 Query: 182 AKAVYNSKVLEEVAKM 197 A ++ +E VA++ Sbjct: 167 PTAFAAAEEIEFVARI 182 Lambda K H 0.318 0.135 0.412 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: 149 Number of extensions: 4 Number of successful extensions: 1 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: 234 Length of database: 214 Length adjustment: 22 Effective length of query: 212 Effective length of database: 192 Effective search space: 40704 Effective search space used: 40704 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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