Align ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_011781173.1 MVAN_RS20120 5-dehydro-2-deoxygluconokinase
Query= BRENDA::A0A0H2UL04 (309 letters) >NCBI__GCF_000015305.1:WP_011781173.1 Length = 322 Score = 106 bits (264), Expect = 8e-28 Identities = 89/284 (31%), Positives = 125/284 (44%), Gaps = 21/284 (7%) Query: 41 GGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMI 100 GG AN AVAAAR+ I+ VGDD FG +R ++ V P PT + Sbjct: 38 GGSAANVAVAAARLGHRSALISGVGDDPFGRYVRAELARLDVDNRFVATHPEFPTPVTFC 97 Query: 101 QVSDSGENSICISAEANAK-LTAAAIEPDLAAIRDARYLLMQL----ETPLDGILKAAQE 155 ++ + + + +A L E D A+ AR + E P AA Sbjct: 98 EIFPPDDFPLYFYRKPSAPDLQIKPEEIDAEAVHSARLFWATVTGLSEEPSRSAHFAAWG 157 Query: 156 AKTAKTNVILN----------PAPARELPDELLKCVDLITPNETEAEVLTGITVYDDSSA 205 A+ K +L+ PA A E + L V + N E E+ G S+ Sbjct: 158 ARERKPLTVLDLDYRPMFWDSPAAATEQVQKALAHVTVAVGNREECEIAVG-----QSNP 212 Query: 206 QQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGL 265 +AADAL G+E+ I+ G +GV +P V + AGD F G+L GL Sbjct: 213 HKAADALLDLGVELAIVKQGPRGVLGKTRHSSVTVPPNEVDVVNGLGAGDAFGGSLCHGL 272 Query: 266 LQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLAEHS 309 LQ PLE +++A+AA AI R T++PT AEV A LAE + Sbjct: 273 LQGWPLEKTLRYANAAGAIVAGRLECSTAMPTAAEVAA-LAEQT 315 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: 185 Number of extensions: 9 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: 322 Length adjustment: 27 Effective length of query: 282 Effective length of database: 295 Effective search space: 83190 Effective search space used: 83190 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 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