Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate N515DRAFT_3220 N515DRAFT_3220 ribokinase
Query= reanno::Smeli:SMc01103 (299 letters) >FitnessBrowser__Dyella79:N515DRAFT_3220 Length = 309 Score = 187 bits (474), Expect = 3e-52 Identities = 118/290 (40%), Positives = 152/290 (52%), Gaps = 13/290 (4%) Query: 2 ITVFGSINMDLIATTARLPKPGETVAGTDFSTAAGGKGANQALAARRAG-ASVRMAGAVG 60 + V GS N+D + A +P PGETV G F+T GGKGANQA+A RAG A RM A+G Sbjct: 5 VLVAGSANLDFVVRAAHVPAPGETVLGRGFATFPGGKGANQAVACARAGGAPTRMLLALG 64 Query: 61 SDAFAEGALALLKEAGTDLDLTKTVGEPTGTAHIIVGGDGENVIVVVASANARVSGDDAA 120 DA A A L+ AG LD + GE +G A + + DGEN I V ANA + D Sbjct: 65 DDAHAAPIEASLRAAGVGLDAVRMRGESSGVAFVCLADDGENAITVAPGANAALRPDH-- 122 Query: 121 NVVAQMSAGDTLMLQLEIPSASVEKALSEAKRRGIRSIINIAPLTPDAARLGRMADIVIA 180 + ++ L+LQLE P +V+ A R GI +N AP L ++I Sbjct: 123 --LPPLAGVSHLLLQLETPLPTVKAWARVACRAGIHVALNAAPAQALPRSLLDDCQLLIV 180 Query: 181 NETEFELLAGKAGIAGAEREEAMNGLHAETRQTVIVTLGAEGVVAIHEGELHRAKGLTIE 240 NE E + G+ I GL A V+VTLGA G A + G ++ Sbjct: 181 NEGELAAITGEHDITA--------GLDALDVAAVVVTLGARGCCARVGSQYLLQPGFAVD 232 Query: 241 PVDTVGAGDTFCGYLAAGLDAGLAFSEALRRAAIAGSLACLKPGAQPSIP 290 +DT GAGDTFCG L AGL GLA+ ALRRA+ A +LAC + GAQ +P Sbjct: 233 AIDTTGAGDTFCGVLVAGLSLGLAYPAALRRASAASALACTRLGAQAGVP 282 Lambda K H 0.315 0.131 0.356 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: 253 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: 299 Length of database: 309 Length adjustment: 27 Effective length of query: 272 Effective length of database: 282 Effective search space: 76704 Effective search space used: 76704 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: 48 (23.1 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