Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_011649737.1 RL_RS26925 ribokinase
Query= reanno::pseudo5_N2C3_1:AO356_00950 (304 letters) >NCBI__GCF_000009265.1:WP_011649737.1 Length = 297 Score = 142 bits (359), Expect = 7e-39 Identities = 92/300 (30%), Positives = 150/300 (50%), Gaps = 9/300 (3%) Query: 4 KVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGCVG 63 + ++G++ +D LP G +++G + + GGKG NQAV AR G ++V VG Sbjct: 2 RAYIVGNVAIDETIAVSELPVTGASILGNAGGSDLGGKGTNQAVVMARCGVSTTLVAPVG 61 Query: 64 DDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEVLD 123 DA + +R L E + + + +E SS V++I +NAIV + +L+ + Sbjct: 62 KDARADTIRHYLADEPLRSELIEMEDASSDVSIIFRLPGGENAIVTTTESAQSLSLSDVR 121 Query: 124 GVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACIDYLI 183 + S D++I Q + D T L+ RA+G + NP+P + +D + ID Sbjct: 122 RILSTAGSGDLMILQGNLSDRTTRDILEHARAIGMVTAFNPSPV-RSYFSDLWDLIDIAF 180 Query: 184 PNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPAPRV 243 N+ EA L+G T AA +L++ G ++++TLG G N PA Sbjct: 181 LNKGEAQALTG------TTGRDAAEYLLSRGLREIVLTLGGDGATLVNRHDSIEVPAQVC 234 Query: 244 KAVDTTAAGDTFVGGFAAALACGKSEVD--AIRFGQVAAALSVTRAGAQPSIPTLLEVQA 301 + VDTT AGDTF+ A+ A +D AI AAA++V+R G + + PT+ E++A Sbjct: 235 EVVDTTGAGDTFMAAALASCALRGQRLDRLAIEHAVAAAAITVSRHGTRKAFPTISELEA 294 Lambda K H 0.318 0.133 0.377 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: 198 Number of extensions: 7 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: 304 Length of database: 297 Length adjustment: 27 Effective length of query: 277 Effective length of database: 270 Effective search space: 74790 Effective search space used: 74790 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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