Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate WP_041936476.1 RL_RS21760 ROK family protein
Query= SwissProt::P23917 (302 letters) >NCBI__GCF_000009265.1:WP_041936476.1 Length = 304 Score = 125 bits (313), Expect = 2e-33 Identities = 92/308 (29%), Positives = 142/308 (46%), Gaps = 22/308 (7%) Query: 1 MRIGIDLGGT---------KTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAE 51 M I D+GG+ +T+++ LG R PTPRDD+ +ET+ D+ Sbjct: 1 MIISFDIGGSAIKGGIARSETDILPLG---------RRPTPRDDFAAFVETLR---DIIA 48 Query: 52 QATGQRGTVGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAV 111 + Q + + I G + P T + AN ++ + DL A L V +ANDA+C A+ Sbjct: 49 ETGEQPSRIVLSIAGVVDPDTQRLICANIPCIHDRTLAADLEAELGLPVLIANDADCFAM 108 Query: 112 SEAVDGAAAGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNP-LPWMDEDELRY 170 +EA GA G + VF I+GTG G G+ +GR G AGEWGH P + D Sbjct: 109 AEAGLGAGRGHRIVFGAILGTGVGGGLVADGRLVNEAGGFAGEWGHGPIIASAAGDPPVA 168 Query: 171 REEVPCYCGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYEL 230 C CG++GC++T G ++ L L EII + A + Y Sbjct: 169 IPAYACGCGQRGCVDTVGGARGLERLHKTLHDLDLASEEIIGQWRHGEEKATRTIDVYVD 228 Query: 231 RLAKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSS 290 +A LA +NI ++ +GGG+SNV+ L + ++ + V +++ Sbjct: 229 LVASPLALAINITGATIVPVGGGLSNVEPLLAELDHAVRARILRKFDRPLVVRSECRIEP 288 Query: 291 GVRGAAWL 298 G+ GAA L Sbjct: 289 GLIGAALL 296 Lambda K H 0.318 0.137 0.418 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: 297 Number of extensions: 17 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: 302 Length of database: 304 Length adjustment: 27 Effective length of query: 275 Effective length of database: 277 Effective search space: 76175 Effective search space used: 76175 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