Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate GFF4171 PS417_21365 sugar kinase
Query= reanno::Koxy:BWI76_RS00290 (309 letters) >FitnessBrowser__WCS417:GFF4171 Length = 305 Score = 118 bits (295), Expect = 2e-31 Identities = 97/313 (30%), Positives = 145/313 (46%), Gaps = 21/313 (6%) Query: 6 KLVVLGSINADHILNLDAFPTPGETVTGHHYQVAFGGKGANQAVAAGRSGANISFIACTG 65 +L+ G + D ++ LD P G V GG G N AA R+G + ++ G Sbjct: 3 RLLHTGQVIVDLVMALDTLPATGGDVLAQSASFEAGG-GFNVMAAARRNGLPVVYLGRHG 61 Query: 66 DDDIGERVRRQLESDNIDVAPVRAVAGESTGVALIFVNAEGENTIGIHAGANAALCVAQV 125 + G+ R ++++ I++A + A AG+ TG+ + A E T H GA L + Sbjct: 62 NGRFGDLARAAMQAEGIEMA-LAASAGKDTGLCVSLTEATTERTFISHIGAEGELNAEDL 120 Query: 126 DAEKERI-----ASAQALLMQLES-PLESVLAAAKIAHQNQTSVILNPAPARELPDE--- 176 ++ S +LL+++++ PL L +A + V+ +P P + PD Sbjct: 121 ARVVPQLDDYVYVSGYSLLLEVKAQPLIDWL----LALPREIVVVFDPGPLVKAPDSALM 176 Query: 177 --LLTLVDIITPNETEAEKLTGVRVENDEDAAKAAKVLHDKGIGTVIITLGSRGVWASSE 234 LL +DI T N EA TG D AA H +++ G G W Sbjct: 177 RTLLPRIDIWTSNGPEALAFTGAL---DIAAALPELSQHLPAETLLVVRDGPNGCWVGRT 233 Query: 235 GNGRRVPGFKVQAVDTIAAGDTFNGALVTALLEGRELAEAIRFAHAAAAIAVTRKGAQPS 294 G+ VPGFKV AVD+ AGD G + L +G + AEA R A+AAAA+AVTR G S Sbjct: 234 GSVEHVPGFKVLAVDSNGAGDAHAGVFIAGLAKGLKPAEAARRANAAAALAVTRWGPATS 293 Query: 295 VPWRKEIDEFLRQ 307 P E+D L + Sbjct: 294 -PGTAEVDALLTE 305 Lambda K H 0.315 0.131 0.366 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: 16 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: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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 (21.5 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