Align L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (characterized)
to candidate WP_058932579.1 AU252_RS22365 L-ribulose-5-phosphate 4-epimerase
Query= BRENDA::C4B4W3 (240 letters) >NCBI__GCF_001484605.1:WP_058932579.1 Length = 234 Score = 292 bits (747), Expect = 5e-84 Identities = 150/231 (64%), Positives = 173/231 (74%), Gaps = 17/231 (7%) Query: 19 VARTREIVSNLHAELPRWQLVVWTAGNVSQRVVVDKEAGPGPEDLFVIKPSGVSYDELTP 78 +AR R V LHAEL R+ LVVWTAGNVS RV PG DL VIKPSGVSY++LTP Sbjct: 12 IARIRREVCALHAELTRYGLVVWTAGNVSARV-------PG-RDLMVIKPSGVSYEDLTP 63 Query: 79 EAMVVCNTEGDLIEGTR---------SPSSDTAAHAYVYKHMDTVGGIVHTHSTYACAWA 129 E MVV + G ++G SPSSDTAAHAYVY+HM VGG+VHTHSTYA AWA Sbjct: 64 EQMVVTDLYGVAVDGDADGEWGNPPLSPSSDTAAHAYVYRHMPDVGGVVHTHSTYATAWA 123 Query: 130 ALGEEVPCVLTMMADEFGGPVPIGPFAIIGDDSIGRGIVDTLKTSRSPAVLMKNHGPFTI 189 A GE +PCVLTMM DEFGG +P+GPFA+IGDDSIG+GIV+TLK S SPAVLM+NHGPFTI Sbjct: 124 ARGESIPCVLTMMGDEFGGSIPVGPFALIGDDSIGQGIVETLKNSTSPAVLMQNHGPFTI 183 Query: 190 GKDGRDAVKAAVMVEEVSKAAHLARTIGTPQIVPDEAIDALYDRYQNVYGQ 240 GKD R AVKAAVM EEV++ H++R +G P + ID+LY RYQNVYGQ Sbjct: 184 GKDARSAVKAAVMCEEVARTVHISRQLGEPITIDQGHIDSLYARYQNVYGQ 234 Lambda K H 0.316 0.132 0.392 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: 246 Number of extensions: 9 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: 240 Length of database: 234 Length adjustment: 23 Effective length of query: 217 Effective length of database: 211 Effective search space: 45787 Effective search space used: 45787 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 (21.6 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