Align ribokinase (EC 2.7.1.15) (characterized)
to candidate Ga0059261_0568 Ga0059261_0568 Sugar kinases, ribokinase family
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__Korea:Ga0059261_0568 Length = 315 Score = 209 bits (531), Expect = 9e-59 Identities = 130/303 (42%), Positives = 176/303 (58%), Gaps = 14/303 (4%) Query: 6 KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQ-ADVGFIACV 64 +++V GS N D V++ P P PGET+ G + V+PGGKGANQAVAAAR AD + + Sbjct: 9 RVLVAGSANVDFVVRAPHIPAPGETVLGGDLSVVPGGKGANQAVAAARAGGADTAMLLAL 68 Query: 65 GDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAA 124 GDD + +S + G++ V+ PTG A+I VSD EN+I ++ AN +L Sbjct: 69 GDDPSAGVLEDSLRAAGVSLHVVRASR--PTGAALITVSDGAENAITVAQGANGELAPE- 125 Query: 125 IEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLI 184 L ++ +LL+QLETP+ ++ A+ A+ A V+LN APA+ LP ELL VDL+ Sbjct: 126 ---HLPSLEGVSWLLLQLETPIASVIAYARAARVAGVGVMLNAAPAQPLPAELLALVDLL 182 Query: 185 TPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFV 244 NE E +TG S A++ A G+ ++TLG +G + +G F Sbjct: 183 VVNEEELAAITG---KQGSIAERVART----GVATTVVTLGERGCCAADHGTLISQAAFS 235 Query: 245 VKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAF 304 V ATDTTAAGDTF G L L L A++ A AAAA+S TR GAQTSIPT AEV AF Sbjct: 236 VAATDTTAAGDTFCGVLGAALAGGTDLLGALRRAAAAAALSATRAGAQTSIPTAAEVAAF 295 Query: 305 LAE 307 LA+ Sbjct: 296 LAD 298 Lambda K H 0.316 0.132 0.373 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: 237 Number of extensions: 10 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: 309 Length of database: 315 Length adjustment: 27 Effective length of query: 282 Effective length of database: 288 Effective search space: 81216 Effective search space used: 81216 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