Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__SynE:Synpcc7942_2111 Length = 302 Score = 96.7 bits (239), Expect = 6e-25 Identities = 84/260 (32%), Positives = 111/260 (42%), Gaps = 28/260 (10%) Query: 3 IGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGT--V 60 IG+DLGGT ++ G+ +PTP + A LV+ Q Q + Sbjct: 8 IGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVR--AALVEAIRQLDPQAEALAI 65 Query: 61 GMGIPGSISPYTGVVKNA-NSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAA 119 G+G PG V + A N P L A LQR V LANDANC + E G Sbjct: 66 GIGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEVWLGGG 125 Query: 120 AGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCG 179 G + + +GTG G + NG +G GTA E G L +D C G Sbjct: 126 RGYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELG---LITLDP------AGPHCNSG 176 Query: 180 KQGCIETFIS----GTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKS 235 QG +E + S F D + L A +G DP A A + Y LA Sbjct: 177 NQGSLEQYASIGAVQRRFGCDPKDLGDRASQG----------DPEAIAAWQDYGRTLAAG 226 Query: 236 LAHVVNILDPDVIVLGGGMS 255 LA +V +L P+VI+LGGG+S Sbjct: 227 LASLVYVLTPEVIILGGGIS 246 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: 298 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 302 Length of database: 302 Length adjustment: 27 Effective length of query: 275 Effective length of database: 275 Effective search space: 75625 Effective search space used: 75625 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