Align Ribokinase; RK; EC 2.7.1.15 (uncharacterized)
to candidate SMc03138 SMc03138 sugar kinase
Query= curated2:P36945 (293 letters) >FitnessBrowser__Smeli:SMc03138 Length = 270 Score = 61.6 bits (148), Expect = 2e-14 Identities = 75/258 (29%), Positives = 102/258 (39%), Gaps = 24/258 (9%) Query: 34 QTVPGGKGANQAVAAARLGAQVFMVGKVGDDHYGTAILNNLKANGVRTDYMEPVTHTESG 93 Q+ GG N AV ARLG F G VG D G + L ANGV D++ + Sbjct: 23 QSYVGGNAINVAVQLARLGHGSFYFGAVGRDSDGAQVRRLLLANGVNVDHLLARDTNTAY 82 Query: 94 TAHIVLAEGDNSIV-----VVKGANDDITPAYALNALEQIE---KVDMVLIQQEIPEETV 145 T V GD V G D L ++ + D L+++ + V Sbjct: 83 TDIDVTPAGDRIFVHEDFGACAGYRPDAGEIELLKTMDHVHIGWLDDGGLLRRALSAAGV 142 Query: 146 DEVCKYCHSHDIPIILNPAPARPLKQETIDHATYLTPNEHEASILFPELTISEALALYPA 205 S D+ + A A L+ + + A + + E E S E E LA Sbjct: 143 SV------SQDVSV---NAAAADLEVDGLSIA-FGSAGEDETSA---ERLTGEFLARGAR 189 Query: 206 KLFITEGKQGVRYSAGSKEVLIPSFPVEPVDTTGAGDTFNAAFAVALAEGKDIEAALRFA 265 +T G G S G++ VE VDTTGAGD+F A F A EG+ + A L A Sbjct: 190 LAVVTRGALGSLASDGAEVASAGIRAVEVVDTTGAGDSFIAGFIAARLEGRALAACLE-A 248 Query: 266 NRAASLSVCSFGAQGGMP 283 R + C+ GG P Sbjct: 249 GRDLAADTCTH--VGGFP 264 Lambda K H 0.315 0.132 0.376 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: 172 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 293 Length of database: 270 Length adjustment: 26 Effective length of query: 267 Effective length of database: 244 Effective search space: 65148 Effective search space used: 65148 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: 47 (22.7 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