Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_157093474.1 AYX06_RS19760 ribokinase
Query= reanno::Smeli:SMc01103 (299 letters) >NCBI__GCF_001580365.1:WP_157093474.1 Length = 393 Score = 157 bits (396), Expect = 5e-43 Identities = 116/287 (40%), Positives = 139/287 (48%), Gaps = 26/287 (9%) Query: 2 ITVFGSINMDLIATTARLPKPGETVAGTDFSTAAGGKGANQALAARRAGASVRMAGAVGS 61 +TV GSIN+DL A RLP PGETV G D GGKGANQA+AA R RM GAVG Sbjct: 109 LTVVGSINVDLTAVCERLPAPGETVIGADLQRQPGGKGANQAVAAARLAGRARMIGAVGD 168 Query: 62 DAFAEGALALLKEAGTDLDLTKTVGEPTGTAHIIVGGDGENVIVVVASANARVSGDDAAN 121 D L L AG D + V PTGTA I V GEN I V A ANA VS +D + Sbjct: 169 DPDGGLLLRHLAAAGVDTTGVRRVPAPTGTALITVDRHGENQITVCAGANAEVSLEDVS- 227 Query: 122 VVAQMSAGDTLMLQLEIPSASVEKALSEAKRRGIRSIINIAPLTPDAARLGRMADIVIAN 181 + D ++ QLEI ++ A+R +N AP P A L D+VI N Sbjct: 228 ----FAPEDVVLCQLEI---ELDTVCETARRTPGFFALNAAPARPLPAELVERCDLVIVN 280 Query: 182 ETEFELLAGKAGIAGAEREEAMNGLHAETRQTVIVTLGAEG-VVAIHEGELHRAKGLTIE 240 ETE+ A +A AE V VT GA+G + H ++ A + Sbjct: 281 ETEY---ARIPELADAE--------------LVAVTYGAQGSALYAHGRQIASAPAHEVA 323 Query: 241 PVDTVGAGDTFCGYLAAGLDAGLAFSEALRRAAIAGSLACLKPGAQP 287 V TVGAGD FC L L AGL ALR A G+ A +QP Sbjct: 324 VVSTVGAGDAFCAALVLALAAGLDHETALRAANAVGAHAVGDASSQP 370 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: 327 Number of extensions: 17 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: 299 Length of database: 393 Length adjustment: 29 Effective length of query: 270 Effective length of database: 364 Effective search space: 98280 Effective search space used: 98280 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: 49 (23.5 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