Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_011841936.1 RSPH17029_RS14505 ribokinase
Query= reanno::Smeli:SMc01103 (299 letters) >NCBI__GCF_000015985.1:WP_011841936.1 Length = 284 Score = 153 bits (387), Expect = 4e-42 Identities = 130/306 (42%), Positives = 164/306 (53%), Gaps = 30/306 (9%) Query: 1 MITVFGSINMDLIATTARLPKPGETVAGTDFSTAAGGKGANQALAARRAGASVRMAGAVG 60 M+ GSIN+D + LP PGET+ +S GGKGANQ++AA RAGA V GAVG Sbjct: 1 MLLNLGSINIDHVYRMPHLPAPGETLEAESYSVGLGGKGANQSVAAARAGARVLHVGAVG 60 Query: 61 SDAFAEGALALLKEAGTDLDLTKT-VGE-PTGTAHIIVGGDGENVIVVVASANARVSGDD 118 EG A A +D+T VGE TG A I V + EN IV+ AN + D Sbjct: 61 P----EGRWARDWMAAAGVDVTHVAVGEVATGHAIINVDEEAENTIVIFPGANRTL---D 113 Query: 119 AANVVAQMSA---GDTLMLQLEIPSASVEKALSEAKRRGIRSIINIAPLTPDAAR-LGRM 174 AA V A ++A GDTL+LQ E SA VE A A+R G++ I AP A R + Sbjct: 114 AATVTAALAAAGPGDTLLLQNET-SAQVEAARLAAER-GLKVIYCAAPFEIGAVRAVLPY 171 Query: 175 ADIVIANETEFELLAGKAGIAGAEREEAMNGLHAETRQTVIVTLGAEGVVAIHEGELHRA 234 +++ NE E L KA + GA E AM +VTLGA G + GE + Sbjct: 172 VSLLVMNEGEAAAL--KAAL-GALPEVAM-----------VVTLGARGAEWLVPGEDRLS 217 Query: 235 -KGLTIEPVDTVGAGDTFCGYLAAGLDAGLAFSEALRRAAIAGSLACLKPGAQPSIPLAA 293 + VDTVGAGD F G LAA LDAGL +EA+RRA+ A +L +PGA ++P A Sbjct: 218 VPAFPVTAVDTVGAGDCFTGNLAAALDAGLDPAEAMRRASAAAALQVTRPGAAEAMPTAD 277 Query: 294 EVAARL 299 EV A L Sbjct: 278 EVDAFL 283 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: 211 Number of extensions: 15 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: 284 Length adjustment: 26 Effective length of query: 273 Effective length of database: 258 Effective search space: 70434 Effective search space used: 70434 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 Apr 10 2024. 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