Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_008629480.1 C943_RS15180 carbohydrate kinase
Query= reanno::Cola:Echvi_2804 (295 letters) >NCBI__GCF_000330725.2:WP_008629480.1 Length = 295 Score = 322 bits (825), Expect = 6e-93 Identities = 154/287 (53%), Positives = 195/287 (67%) Query: 1 MNKKAVIFGEMLWDCFPDKQLPGGAPMNVALHLQHLGITTTFISKIGSDSLGADLLSFVQ 60 M+KK + FGEMLWDCFPDK++PGGAPMNVALHL LG+ IS++G D G L F+ Sbjct: 1 MSKKVICFGEMLWDCFPDKEIPGGAPMNVALHLHQLGLEVGMISRVGDDERGRKFLDFIS 60 Query: 61 KNGLNGDFVQRDTAHETSRVVVDNSDKENIKYEIVKPVAWDFMEWNTAIQEKVDEADVFV 120 G D VQ D H T V+V N D ENIKY IV PVAWD++E N V AD + Sbjct: 61 GYGFPTDLVQIDHIHPTGNVIVHNEDPENIKYTIVSPVAWDYIEMNEQNIHAVQSADALI 120 Query: 121 FGSLAARSSQSQNTLFRLLETSTLKVLDINLRPPHYSTKVLERLLKNTDVLKINEDELEI 180 FGSLA R++QS +TL+ LL TL + DINLR P Y + +E LL TD+LKINEDELEI Sbjct: 121 FGSLAVRNTQSWDTLYHLLHQPTLNIFDINLRAPFYDFEKIELLLGYTDILKINEDELEI 180 Query: 181 LIEMSALDKNEEKALSAIVDRYELQLVCMTKGSAGAIIYDGREFYRHPGYQVDVEDTVGS 240 + + L + + + +Q+VC+T GS GA+IY+ + ++HPGY+V VEDTVG+ Sbjct: 181 VADYFNLKNDINTVCDMLTTHFPIQMVCVTLGSKGAMIYENGKVFKHPGYKVTVEDTVGA 240 Query: 241 GDAFLSGFISQYLKGNHPNKILDFACALGALVATQKGGTPRYDTDQI 287 GDAFL GF+ YL+G P +ILDFACA+GA VAT+KGGTPRY D+I Sbjct: 241 GDAFLGGFVKSYLEGKKPEEILDFACAIGAFVATKKGGTPRYQVDEI 287 Lambda K H 0.317 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: 308 Number of extensions: 12 Number of successful extensions: 1 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: 295 Length of database: 295 Length adjustment: 26 Effective length of query: 269 Effective length of database: 269 Effective search space: 72361 Effective search space used: 72361 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