Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS23680 BWI76_RS23680 ribokinase
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__Koxy:BWI76_RS23680 Length = 313 Score = 199 bits (505), Expect = 9e-56 Identities = 127/296 (42%), Positives = 168/296 (56%), Gaps = 2/296 (0%) Query: 6 KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVG 65 K+ V GS N D V +V FP PGE+L GGKGANQA AA + A+V +I +G Sbjct: 4 KVCVFGSFNFDMVARVERFPVPGESLVACGSMTSAGGKGANQATAALKAGANVHYIGKIG 63 Query: 66 DDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVS-DSGENSICISAEANAKLTAAA 124 +D+FG R K G N + + + PTG A+I V+ + EN I + AN ++ Sbjct: 64 NDTFGHFARRHLKGVGFNAVTLLVAEDIPTGNALIYVAGNDAENMIAVDPGANMTVSDDE 123 Query: 125 IEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLI 184 I + AI A +L+QLE L I + AK A V+LNPAP + + + L VDL+ Sbjct: 124 IAGCVPAIGCADVVLVQLENNLSAIERVVDAAKAAGAFVVLNPAPWQPVDNAFLSKVDLL 183 Query: 185 TPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFV 244 TPN TEA ++TG V ++A +AADALH +G VIITLG+KG LS+ G IP F Sbjct: 184 TPNATEAGLMTGCQVDSLAAAAEAADALHAQGARNVIITLGAKGALLSEQGVKSPIPCFP 243 Query: 245 VKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAE 300 DTT AGD FNGAL L PL +A +FA A AA+SV + GA +S+P E Sbjct: 244 SHPRDTTGAGDAFNGALAARLACGEPLHTAARFAAAYAAVSVEKQGA-SSLPDYEE 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: 220 Number of extensions: 12 Number of successful extensions: 2 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: 313 Length adjustment: 27 Effective length of query: 282 Effective length of database: 286 Effective search space: 80652 Effective search space used: 80652 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