Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate CA265_RS18205 CA265_RS18205 hypothetical protein
Query= reanno::Cola:Echvi_2804 (295 letters) >FitnessBrowser__Pedo557:CA265_RS18205 Length = 293 Score = 219 bits (557), Expect = 8e-62 Identities = 113/284 (39%), Positives = 168/284 (59%), Gaps = 1/284 (0%) Query: 1 MNKKAVIFGEMLWDCFPDKQLPGGAPMNVALHLQHLGITTTFISKIGSDSLGADLLSFVQ 60 M K + GE+LWD FP+ + GG+ MNVAL+L I ++FIS +G D G +L +F+ Sbjct: 1 MQNKVITIGEILWDVFPEGKKAGGSSMNVALNLHKQSIESSFISAVGDDENGKELFNFLA 60 Query: 61 KNGLNGDFVQRDTAHETSRVVVDNSDKENIKYEIVKPVAWDFMEWNTAIQEKVDEADVFV 120 N D +Q ++ TS VVV + Y I +PVAWD ++ V +AD V Sbjct: 61 SNHFATDLIQVNSELPTSTVVVQLDENHQATYTIKQPVAWDDIKITDENIAAVKQADALV 120 Query: 121 FGSLAARSSQSQNTLFRLLETSTLKVLDINLRPPHYSTKVLERLLKNTDVLKINEDELEI 180 + SL RS QS+ + +LLE + K+ DINLR P Y+ +++ LL D+LKINEDE+ Sbjct: 121 YCSLTCRSEQSKKAILKLLENAKTKIFDINLRAPFYTRELIAELLTKADILKINEDEILW 180 Query: 181 LIEMSALDKN-EEKALSAIVDRYELQLVCMTKGSAGAIIYDGREFYRHPGYQVDVEDTVG 239 + E L N +E+ L + ++ ++++C+T G GA + + ++H GY+V V DTVG Sbjct: 181 VKESFGLSGNTDEQLLKQLSSQFNIEIICLTLGDKGACVLKDGKLFKHAGYKVQVADTVG 240 Query: 240 SGDAFLSGFISQYLKGNHPNKILDFACALGALVATQKGGTPRYD 283 +GDAFL+ FI+ YL+G LD AC +GA VA+Q G P Y+ Sbjct: 241 AGDAFLATFIACYLQGYPMETTLDNACKVGAFVASQAGANPEYN 284 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: 240 Number of extensions: 6 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: 295 Length of database: 293 Length adjustment: 26 Effective length of query: 269 Effective length of database: 267 Effective search space: 71823 Effective search space used: 71823 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 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