Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 14532 b0394 possible NAGC-like transcriptional regulator (VIMSS)
Query= reanno::SB2B:6938110 (299 letters) >FitnessBrowser__Keio:14532 Length = 302 Score = 379 bits (974), Expect = e-110 Identities = 181/299 (60%), Positives = 225/299 (75%), Gaps = 4/299 (1%) Query: 2 MRMGVDLGGTKIELVALGEDGSELFRKRIATPRE-YQGTLNAVVTLVNEAEATLGTQGSL 60 MR+G+DLGGTK E++ALG+ G +L+R R+ TPR+ Y+ T+ + TLV+ AE G +G++ Sbjct: 1 MRIGIDLGGTKTEVIALGDAGEQLYRHRLPTPRDDYRQTIETIATLVDMAEQATGQRGTV 60 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 G+GIPG ISPYTG+VKNANSTW+NG P D+DL A L REVR+ANDANC AVSEAVDGAAA Sbjct: 61 GMGIPGSISPYTGVVKNANSTWLNGQPFDKDLSARLQREVRLANDANCLAVSEAVDGAAA 120 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTE---CFCGN 177 G + VF I+GTGCGAG+AF+GR H GGNG GEWGHNPLPWM DE E C+CG Sbjct: 121 GAQTVFAVIIGTGCGAGVAFNGRAHIGGNGTAGEWGHNPLPWMDEDELRYREEVPCYCGK 180 Query: 178 KDCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVI 237 + CIETF+SGTGF D+R G A G+EI+ LV+ D +A L RY RLA+SLAHV+ Sbjct: 181 QGCIETFISGTGFAMDYRRLSGHALKGSEIIRLVEESDPVAELALRRYELRLAKSLAHVV 240 Query: 238 NMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296 N+LDPD IVLGGGMSNV +Y + ++ ++V G EC TPV + +G SSGVRGAAWLW Sbjct: 241 NILDPDVIVLGGGMSNVDRLYQTVGQLIKQFVFGGECETPVRKAKHGDSSGVRGAAWLW 299 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: 347 Number of extensions: 18 Number of successful extensions: 3 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: 302 Length adjustment: 27 Effective length of query: 272 Effective length of database: 275 Effective search space: 74800 Effective search space used: 74800 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