Align ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_083763540.1 AMB_RS16380 carbohydrate kinase family protein
Query= BRENDA::Q8NQR0 (307 letters) >NCBI__GCF_000009985.1:WP_083763540.1 Length = 311 Score = 111 bits (277), Expect = 2e-29 Identities = 90/297 (30%), Positives = 135/297 (45%), Gaps = 18/297 (6%) Query: 9 IVVVGSINADLTAKVQRHPEPGETLLGSGGTVSAGGKGANQAVAAAQLGAKVTMIGAVGT 68 IVV+GS+ D ++ G L G+ GG GAN A+A G +V+++ AVGT Sbjct: 26 IVVLGSVARDEVIRLDHRLREGAHLQGAPPLARLGGGGANTAIALTHAGHEVSLVAAVGT 85 Query: 69 DQMAGEALTHLRQSGADMSAIATVDGPTGLAIITVSDDGENTIIVIPGANASVTAEFVDK 128 D +A E L L + G D+ + + GP+ +++ + +GE TI+ + A S + Sbjct: 86 DPLADELLAELARHGVDIGPVTRISGPSTHSLVLLDPEGERTIVNLTRARESRPPR---R 142 Query: 129 HSQLIENAGIVLLQGEIPADGFERAVDLSQGRVVINLAPVVPVGHDQLRRADPLLVNEHE 188 L + V G++ D L ++ + P+ D L A +LV H Sbjct: 143 LLDLAADCVYVRSNGQVLEDLLREKAALCP--IIAQIRPL----EDGLLPAQ-VLVGSH- 194 Query: 189 GALVLDMLGTPATTSDPQSLVTELLEQGFTSVVMTLGAEGA-LVGTPGQLTAIPTPKIQA 247 G L D+L P + L ++L VV+T G EGA G G+ P ++ Sbjct: 195 GDLDADLLSNPLEAG--RQLAGDILRW----VVITHGEEGAEAFGVDGRRLRATAPDVEV 248 Query: 248 VDTTGSGDAFAGALVAKLSEGAGLIEAATFAARVGAYAATRPGAQASYPTLTTDLPS 304 VDTTG+GDAFA L L+ G + A A GA TRPG+ T+ L S Sbjct: 249 VDTTGAGDAFAAGLAHALALGLDMERALPLAVGWGAAKVTRPGSFLDRETVREILKS 305 Lambda K H 0.312 0.130 0.357 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: 256 Number of extensions: 12 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: 307 Length of database: 311 Length adjustment: 27 Effective length of query: 280 Effective length of database: 284 Effective search space: 79520 Effective search space used: 79520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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