Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate CCNA_01001 CCNA_01001 ribokinase
Query= reanno::Smeli:SMc01103 (299 letters) >FitnessBrowser__Caulo:CCNA_01001 Length = 303 Score = 202 bits (515), Expect = 6e-57 Identities = 124/301 (41%), Positives = 161/301 (53%), Gaps = 5/301 (1%) Query: 2 ITVFGSINMDLIATTARLPKPGETVAGTDFSTAAGGKGANQALAARRAGASVRMAGAVGS 61 + V GSIN+D +A LP+PGETVAG GGKGANQA+AA R G + R+ GAVG Sbjct: 3 VFVLGSINLDAVARVDDLPRPGETVAGLSLELFLGGKGANQAVAAARMGVATRLMGAVGG 62 Query: 62 DAFAEGALALLKEAGTDL-DLTKTVGEPTGTAHIIVGGDGENVIVVVASANARVSGDDAA 120 D G A L G + D+ + G PTG AH+ V EN+IVV A ANA V+ A Sbjct: 63 DDSGAGLKAKLAGYGVQVGDVVELPGVPTGQAHVWVANSAENMIVVTAGANAMVTPQQVA 122 Query: 121 NVVAQMSAGDTLMLQLEIPSASVEKALSEAKRRGIRSIINIAPLTPDAARLGRMADIVIA 180 + L+ QLE P+ ++E +G I+N AP P A L + DI+I Sbjct: 123 --ATTIEGQRVLLCQLETPATAIETLFRAGSAKGALRILNAAPALPQGAALFPLTDILIV 180 Query: 181 NETEFELLA--GKAGIAGAEREEAMNGLHAETRQTVIVTLGAEGVVAIHEGELHRAKGLT 238 N+TE A + + E A L + QT+IVTLGA G + E +G Sbjct: 181 NQTELATYAKLDREPVKLEEVSVAARKLMSRPDQTIIVTLGAAGAAVVRRDEAFLVEGKK 240 Query: 239 IEPVDTVGAGDTFCGYLAAGLDAGLAFSEALRRAAIAGSLACLKPGAQPSIPLAAEVAAR 298 ++ VDTVGAGD FCG LAA L AG+ +EA+ A A +L+ K GA PS+P EV A Sbjct: 241 VKAVDTVGAGDCFCGALAATLAAGMDLAEAVETANAAAALSVQKAGAAPSMPNRREVEAF 300 Query: 299 L 299 L Sbjct: 301 L 301 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: 241 Number of extensions: 14 Number of successful extensions: 5 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: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 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