Align Fructokinase; D-fructose kinase; Manno(fructo)kinase; EC 2.7.1.4 (characterized)
to candidate 6937023 Sama_1197 putative ROK-family protein (RefSeq)
Query= SwissProt::P23917 (302 letters) >FitnessBrowser__SB2B:6937023 Length = 335 Score = 158 bits (399), Expect = 2e-43 Identities = 105/315 (33%), Positives = 156/315 (49%), Gaps = 25/315 (7%) Query: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQ---- 56 M G+D+GGTK + D+ + R ++PTP DY Q ++ + ++ A++ Q Sbjct: 1 MHYGLDIGGTKIALALFDDSMACVERWQIPTPVADYGQFLDEVCAQIERADELAQQHSGV 60 Query: 57 --------RGTVGMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANC 108 +G+VG+ +PG I G V ++N LNG+ ++L+ RL R V L ND C Sbjct: 61 TVQPAEVSKGSVGIALPGVILS-DGTVLSSNVPCLNGRTVAQELTVRLGRPVALGNDCRC 119 Query: 109 LAVSEAVDGAAAGAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDEL 168 A+SE + GA G + V VI+GTG G GV + + +G + AGE+GH LP + Sbjct: 120 FALSEVLLGAGVGFERVLGVILGTGLGGGVCISQKLILGAHCLAGEFGHIGLP----ASV 175 Query: 169 RYREEVP---CYCGKQGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAEL-- 223 + ++P C CG GC ET++SGTG Y+ G A + L + AE Sbjct: 176 IIKHQLPLFECGCGLTGCAETYVSGTGLGRLYQHFGGTA---DTYVWLADYRSGKAEAIS 232 Query: 224 ALRRYELRLAKSLAHVVNILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRK 283 Y L LA + LDPD +V GGG+S V + + + +F R Sbjct: 233 TFDAYMDALGSVLAGQILSLDPDCLVFGGGISEVKEIIAALPDATARHLFASAKLPEFRV 292 Query: 284 AKHGDSSGVRGAAWL 298 A+ G +SGVRGAA L Sbjct: 293 AEFGAASGVRGAALL 307 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: 356 Number of extensions: 16 Number of successful extensions: 4 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: 335 Length adjustment: 27 Effective length of query: 275 Effective length of database: 308 Effective search space: 84700 Effective search space used: 84700 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