Align glucokinase (EC 2.7.1.2) (characterized)
to candidate SMc02880 SMc02880 hypothetical protein
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__Smeli:SMc02880 Length = 303 Score = 144 bits (363), Expect = 2e-39 Identities = 102/295 (34%), Positives = 148/295 (50%), Gaps = 10/295 (3%) Query: 7 DLGGTKIELVALGEDGSELFR-KRIATP-REYQGTLNAVVTLVNEAEATLGTQGSLGIGI 64 D+GG+ I+ A+ +F R ATP ++ + A+ ++++EA G + I I Sbjct: 6 DIGGSAIK-GAITHSPERIFPLPRRATPLTDFGRFVEAMESVLDEAG---GLPERVAISI 61 Query: 65 PGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAAGKRV 124 GVI P T +K AN I+G L +L A L+ V +ANDA+CFA++EA GA G R+ Sbjct: 62 TGVIDPETRRIKCANIPCIDGRELVAELEAALHLPVVIANDADCFALAEAGVGAGRGHRI 121 Query: 125 VFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNP----LPWMRPDEFNTTECFCGNKDC 180 VFGAILGTG G GL DGR+ G GEWGH P P C CG C Sbjct: 122 VFGAILGTGVGGGLVIDGRLINADGGFAGEWGHGPAVAAAAGHPPIAIPAFPCGCGQSRC 181 Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240 ++T G R G A + +I+ G+ A D ++D ++ LA VIN+ Sbjct: 182 VDTVGGARGLERLHETVHGKALSSHDIIEGWQNGNAEAARTIDVFVDLVSSPLALVINIT 241 Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWL 295 + +GGG+SN +A+ A + + ++ R R VV+ G+ GAA L Sbjct: 242 GATIVPVGGGLSNAEALLAEIDRAVRARILRRFDRPLVVRGECRVEPGLIGAALL 296 Lambda K H 0.320 0.139 0.429 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: 291 Number of extensions: 19 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: 299 Length of database: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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