Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS14585 BWI76_RS14585 ribokinase
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__Koxy:BWI76_RS14585 Length = 290 Score = 126 bits (316), Expect = 7e-34 Identities = 93/306 (30%), Positives = 138/306 (45%), Gaps = 29/306 (9%) Query: 6 KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVG 65 ++ V G++ D +P P+ G ++HG GGKGANQA+ AR + IA G Sbjct: 2 RVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILARCGIETRLIAATG 61 Query: 66 DDSFGINIRESFKLDGINTAGVKLQP----NCPTGIAMIQVSDSGENSICISAEANAKLT 121 +DS G+ IR+ K + + L P N + ++I S G+N+I + A Sbjct: 62 NDSNGVWIRQQIKNEPLT-----LLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFR 116 Query: 122 AAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCV 181 I P +A LL Q LD Q AK+ + NP+P L + Sbjct: 117 LDDIIPHIADAVAGDILLQQGNFSLDKTRALFQYAKSRSMTTVFNPSPVNPEFCHLWPLI 176 Query: 182 DLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIP 241 D+ NE+EAE+L G++ ++IT G+ G WL Q G+ + P Sbjct: 177 DIAVVNESEAELLQPY------------------GVKSLVITQGAAGAWLVQEGQRRFCP 218 Query: 242 GFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHA--AAAISVTRFGAQTSIPTRA 299 +A DTT AGDTF ++ L A+ AHA AAAI+V+R G ++ P Sbjct: 219 AVPAEALDTTGAGDTFLAVMLASALLRDVAPDALALAHASRAAAITVSRRGTLSAFPGSH 278 Query: 300 EVEAFL 305 E+ A L Sbjct: 279 ELAALL 284 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: 173 Number of extensions: 10 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: 309 Length of database: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 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