Align glucokinase (EC 2.7.1.2) (characterized)
to candidate SMc03109 SMc03109 hypothetical protein
Query= reanno::SB2B:6937235 (310 letters) >FitnessBrowser__Smeli:SMc03109 Length = 298 Score = 310 bits (794), Expect = 3e-89 Identities = 154/293 (52%), Positives = 196/293 (66%), Gaps = 1/293 (0%) Query: 5 GIDLGGTKIELVTLNEKGEEVFRKRVPTPKD-YRATLEAVAGLVHDSEKETGQVSSVGIG 63 GID GGTK+E++ L+ GE R RVPTP Y + AV LV +E G+ S+GIG Sbjct: 4 GIDWGGTKMEVIALDRDGETRARHRVPTPTSGYEDCIRAVVELVASAESTAGERGSIGIG 63 Query: 64 IPGVVSAVTGRVKNSNAVWLNGQPMDKDLGAMLGREVRIANDANCFAVSESVDGGGAGKT 123 IPG + TG V+NSNAV +NG+P+ +DL A LGREVR+ANDANC AVSE+VDG G Sbjct: 64 IPGSPNPRTGIVRNSNAVLINGKPLGRDLAAALGREVRLANDANCLAVSEAVDGAGKDAG 123 Query: 124 LVFGAILGTGCGAGIAINHKVHGGGNGIGGEWGHNPLPWMTADEFNSTRCFCGNADCIET 183 +VFG I+GTG G G+AI KVH G G+ E GH PLPWMT DE+ RC+CG C++ Sbjct: 124 VVFGVIVGTGHGGGLAIGKKVHAGYQGVAAEIGHYPLPWMTKDEYPGHRCWCGKLGCLDM 183 Query: 184 FVSGTGFVRDFRAHGGEAASGIEIVALMGKGEPLAEAAFGRFIDRLARALAHVINLLDPD 243 + GTG D+R G G +I+ G+P+A +GRF+DRLAR+LA + N++DPD Sbjct: 184 YACGTGLELDYRMTTGTDRRGRDIIEAKRAGDPVAIGVYGRFVDRLARSLALLTNIVDPD 243 Query: 244 VIVLGGGVSNIDEIYEYLPALLPKYVLGGECATKVVKNHHGASSGVRGAAWLW 296 V VLGGG+SN+DEIY LPA + +Y+ G T + K HG SSGVRGAAWLW Sbjct: 244 VFVLGGGMSNVDEIYGELPASITRYLFGDSFETPIRKAVHGDSSGVRGAAWLW 296 Lambda K H 0.318 0.138 0.424 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: 297 Number of extensions: 11 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: 310 Length of database: 298 Length adjustment: 27 Effective length of query: 283 Effective length of database: 271 Effective search space: 76693 Effective search space used: 76693 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 (21.6 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