Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_110207115.1 DNK54_RS11370 ribokinase
Query= reanno::pseudo5_N2C3_1:AO356_00950 (304 letters) >NCBI__GCF_003194585.1:WP_110207115.1 Length = 310 Score = 187 bits (476), Expect = 2e-52 Identities = 132/309 (42%), Positives = 172/309 (55%), Gaps = 12/309 (3%) Query: 1 MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60 M +VVV+G+LN+DLV + PRLP GET++G GGKGAN AVAAAR GA+V VG Sbjct: 1 MTPRVVVVGALNVDLVVKVPRLPGPGETVVGPEVQRHGGGKGANAAVAAARAGAEVRYVG 60 Query: 61 CVGDDAYGEQLRGALLAEGIDCQAVRVEQG-SSGVALIVVDDNSQNAIVIVAGANGALTA 119 VG D G L+AE ID V VE G ++G ALIVVD +N I + AGAN ++ Sbjct: 61 AVGADDLGTGALAELVAENIDVSGVVVEPGVATGTALIVVDHAGENQIAVAAGANAVVSP 120 Query: 120 EVLDGVDDVLQS----ADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADW 175 E V VL A ++ E+P V A++ RA +LNPAP + L A Sbjct: 121 E---SVRQVLARSRGWATCVLVSTEIPMDAVVAAVETARAYDLPCVLNPAPVAAGL-AGL 176 Query: 176 YACIDYLIPNESEAAVLSGLAVDSLETA-EAAAAHLIAAGAGKVIVTLGAQGLMFAN-GA 233 + L PN+ E L + ET+ EA A+ + + V VTLGA G+M A+ Sbjct: 177 VSMSPVLTPNQGELRDLCRALGEPDETSLEAMASAVAHSSKAAVAVTLGADGVMVADPDG 236 Query: 234 SFEHFP-APRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPS 292 S H P AP + VDTT AGDTF G AAALA G++ A+R G AA++SV AGA+ Sbjct: 237 STCHIPAAPVAEVVDTTGAGDTFNGVLAAALASGETISGAVRRGVAAASISVGSAGARAG 296 Query: 293 IPTLLEVQA 301 +PT + A Sbjct: 297 MPTAEVIDA 305 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: 316 Number of extensions: 16 Number of successful extensions: 5 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: 310 Length adjustment: 27 Effective length of query: 277 Effective length of database: 283 Effective search space: 78391 Effective search space used: 78391 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