Align L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (characterized)
to candidate WP_085544742.1 B9Y55_RS07460 L-fuculose-phosphate aldolase
Query= BRENDA::C4B4W3 (240 letters) >NCBI__GCF_900177735.1:WP_085544742.1 Length = 217 Score = 107 bits (267), Expect = 2e-28 Identities = 74/219 (33%), Positives = 111/219 (50%), Gaps = 13/219 (5%) Query: 23 REIVSNLHAELPRWQLVVWTAGNVSQRVVVDKEAGPGPEDLFVIKPSGVSYDELTPEAMV 82 RE V +L L T GNVS V ++E G + PSG+ Y ++ PE +V Sbjct: 7 REQVVEYGRKLMEANLTTGTGGNVS---VFNREEG-----YIALSPSGMDYFDVKPEDVV 58 Query: 83 VCNTEGDLIEGTRS-PSSDTAAHAYVYKHMDTVGGIVHTHSTYACAWAALGEEVPCVLTM 141 + +G +E P+++ H +YK IVH HS YA A + LG ++P V M Sbjct: 59 IMTLDGGFVEEDHLVPTTEWGLHLGLYKVRPDASAIVHCHSDYATAVSCLGIDLPAVNYM 118 Query: 142 MADEFGGPVPIGPFAIIGDDSIGRGIVDTLKTSRSPAVLMKNHGPFTIGKDGRDAVKAAV 201 +A G VPI PFA+ G + + + D + AVLM NHG +G+ + A A+ Sbjct: 119 VAVA-GDRVPITPFAVYGTPELAKNVADNIGDYN--AVLMANHGQIALGRSMKAAFTVAL 175 Query: 202 MVEEVSKAAHLARTIGTPQIVPDEAIDALYDRYQNVYGQ 240 VE V++ LA++ G P I+P EAI+ ++ + YGQ Sbjct: 176 NVEYVARLYILAKSAGEPVILPKEAIEGTQRQFAS-YGQ 213 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: 141 Number of extensions: 11 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: 240 Length of database: 217 Length adjustment: 23 Effective length of query: 217 Effective length of database: 194 Effective search space: 42098 Effective search space used: 42098 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