Align ribokinase (EC 2.7.1.15) (characterized)
to candidate N515DRAFT_2221 N515DRAFT_2221 2-dehydro-3-deoxygluconokinase
Query= BRENDA::A0A0H2UL04 (309 letters) >FitnessBrowser__Dyella79:N515DRAFT_2221 Length = 311 Score = 108 bits (270), Expect = 2e-28 Identities = 88/275 (32%), Positives = 130/275 (47%), Gaps = 22/275 (8%) Query: 41 GGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMI 100 GG +N +AAAR A V +I+ GDD FG +R+ ++ +G+ + V+ P PTG+ + Sbjct: 31 GGDTSNFCIAAARQGASVDYISATGDDRFGQGLRDLWQAEGVGHSHVRTDPQAPTGVYFV 90 Query: 101 QVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYL------LMQLETPLDGILKAAQ 154 SG + + A + A A P AI AR L L + D L+A Sbjct: 91 SHDASGHHFDYLRAGSAASRYVPAYLPG-QAIASARALHLSGISLAISQDACDAGLEAMA 149 Query: 155 EAKTA------KTNVILNPAP---ARELPDELLKCVDLITPNETEAEVLTGITVYDDSSA 205 +A+ A TN+ L P AR + E L+ DL P+ + V D Sbjct: 150 QARAAGVMVSFDTNLRLRLWPLARARAVMREALRLCDLCLPSWDDITA-----VLDCHEP 204 Query: 206 QQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGL 265 D L GIE+V + +G++G +++ +P V A D T AGD F GA V L Sbjct: 205 DAILDTLLDCGIELVALKMGARGCYVATPESRILVPPHAVDAVDATGAGDCFGGAFVARL 264 Query: 266 LQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAE 300 + +A ++A+ AAA+S T +GA SIP RAE Sbjct: 265 VAGDDAVAAARYANVAAALSTTGYGAIASIP-RAE 298 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: 4 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: 311 Length adjustment: 27 Effective length of query: 282 Effective length of database: 284 Effective search space: 80088 Effective search space used: 80088 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