Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate WP_086510996.1 BZY95_RS16175 sugar kinase
Query= BRENDA::Q97U29 (313 letters) >NCBI__GCF_002151265.1:WP_086510996.1 Length = 334 Score = 130 bits (327), Expect = 4e-35 Identities = 91/310 (29%), Positives = 154/310 (49%), Gaps = 14/310 (4%) Query: 3 DVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFG 62 +++ GE + F + PG L V +F++ +AG++ N I + R ++RVG D FG Sbjct: 15 EILTFGEAMTLFVADAPGHLAEVEHFQRRIAGADTNVAIGLARLGFHVGWLSRVGADSFG 74 Query: 63 KNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDIN 122 I A+G++ H+ VD + TG+ F +R + Y+R+GSA S LSP+D Sbjct: 75 TFIRHTLEAEGLNCRHLGVDPDHPTGLLFKERALG-GADPRVEYFRRGSAASHLSPKDAA 133 Query: 123 ENYVRNSRLVHSTGITLAISDNAKE----AVIKAFELAKSRSLDTNIRPKLWSSLEKAKE 178 E R +H+TGI A+S +A++ + +A ++ S S D N+RP LW S + ++ Sbjct: 134 EVDFTALRHLHATGIPPALSPSARDLSRHMLAQARQVGASISFDPNLRPSLWKSEAEMRD 193 Query: 179 TILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDN 238 T+ ++ D ++ + ++L P+ Y E G ++ KLG +G+ Y+ + Sbjct: 194 TLNALAALSD--WVLPGLAEGRLLTGQNTPEAIADFYLERGASAVIIKLGPEGSF-YRGS 250 Query: 239 VKAFKDAYKVP------VEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVR 292 + + + VP V D GAGD A VS L G+ ++ G +L + V Sbjct: 251 LGGKLETFSVPGFAVDEVVDTVGAGDGFAVGAVSALLDGRSPWEAVRRGNLIGSLAVQVV 310 Query: 293 GDNELTPTLE 302 GD E P+ E Sbjct: 311 GDMEGLPSRE 320 Lambda K H 0.317 0.136 0.383 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: 233 Number of extensions: 12 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: 313 Length of database: 334 Length adjustment: 28 Effective length of query: 285 Effective length of database: 306 Effective search space: 87210 Effective search space used: 87210 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