Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_086510996.1 BZY95_RS16175 sugar kinase
Query= BRENDA::P37829 (319 letters) >NCBI__GCF_002151265.1:WP_086510996.1 Length = 334 Score = 94.7 bits (234), Expect = 3e-24 Identities = 92/322 (28%), Positives = 138/322 (42%), Gaps = 29/322 (9%) Query: 13 IVSFGEMLIDFVPTVSGVSLAEAPGFLKAPGGAPANVAIAVTRLGGKSAFVGKLGDDEFG 72 I++FGE + FV G LAE F + GA NVAI + RLG ++ ++G D FG Sbjct: 16 ILTFGEAMTLFVADAPG-HLAEVEHFQRRIAGADTNVAIGLARLGFHVGWLSRVGADSFG 74 Query: 73 HMLAGILKTNGVQADGINFDKGARTALAFVTLRADG--EREFMFYRNPSADMLLTPDELN 130 + L+ G+ + D T L F G R F R +A L D Sbjct: 75 TFIRHTLEAEGLNCRHLGVDPDHPTGLLFKERALGGADPRVEYFRRGSAASHLSPKDAAE 134 Query: 131 LDLIRSAKVFHYGSISLIVEPCRSAHLKAMEVAKEAGALLSYDPNLRLPLWSSEAEARKA 190 +D + G + R + A++ GA +S+DPNLR LW SEAE R Sbjct: 135 VDFTALRHLHATGIPPALSPSARDLSRHMLAQARQVGASISFDPNLRPSLWKSEAEMRDT 194 Query: 191 IK----VSD------VELEFLTGSDKIDDESAMSLWHPNLKLLLVTLGEKGCNYYTKKFH 240 + +SD E LTG + + + L +++ LG +G ++Y Sbjct: 195 LNALAALSDWVLPGLAEGRLLTGQNTPEAIADFYL-ERGASAVIIKLGPEG-SFYRGSLG 252 Query: 241 G-----SVGGFHV-KTVDTTGAGDSFVGALLTKIVDDQAILEDEARLKEVLRFSCACGAI 294 G SV GF V + VDT GAGD F ++ ++D ++ E +R G++ Sbjct: 253 GKLETFSVPGFAVDEVVDTVGAGDGFAVGAVSALLDGRSPW-------EAVRRGNLIGSL 305 Query: 295 TTTKKGAIPALPTESEALTLLK 316 G + LP+ E LT L+ Sbjct: 306 AVQVVGDMEGLPSR-EQLTALE 326 Lambda K H 0.318 0.135 0.388 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: 272 Number of extensions: 11 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: 319 Length of database: 334 Length adjustment: 28 Effective length of query: 291 Effective length of database: 306 Effective search space: 89046 Effective search space used: 89046 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