Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_044409634.1 NA59_RS06230 hypothetical protein
Query= reanno::SB2B:6938110 (299 letters) >NCBI__GCF_000934765.1:WP_044409634.1 Length = 302 Score = 281 bits (718), Expect = 2e-80 Identities = 144/299 (48%), Positives = 190/299 (63%), Gaps = 4/299 (1%) Query: 1 MMRMGVDLGGTKIELVALGEDGSELFRKRIATPR-EYQGTLNAVVTLVNEAE--ATLGTQ 57 M+R+G+DLGGTKIE+VA+ G L R R+ATP+ +Y TL A+ LV +A+ L + Sbjct: 1 MVRLGIDLGGTKIEIVAINPMGDVLLRTRVATPQGDYLATLQAIAGLVEQAQNQLALSYK 60 Query: 58 GSLGIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDG 117 S+G+GIPG IS TG VKNANS W+ G L DL LL R + +ANDANCFA++EA G Sbjct: 61 PSIGVGIPGAISAKTGRVKNANSIWLIGEDLKGDLENLLLRPICIANDANCFALAEASQG 120 Query: 118 AAAGKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGN 177 AA G + VFG I+GTGCG GL F+G + EG NGI GEWGHNPLPW + C+CG Sbjct: 121 AAFGAKSVFGVIIGTGCGGGLVFNGEIVEGANGIAGEWGHNPLPW-NSQYMSNQACYCGK 179 Query: 178 KDCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVI 237 +DCIETF+SG G + F+ +I+ + D+ A + + Y D LA+ LA VI Sbjct: 180 QDCIETFLSGPGLAKRFKEVTARHLTAQQIVEQMRQADQQAIDIMNAYYDWLAKGLASVI 239 Query: 238 NMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296 N+ DP+ +VLGGG+S + +Y +P K+V E T + L G S+GV GAAWLW Sbjct: 240 NVFDPEVVVLGGGLSQIHELYDEVPKRWSKWVFSDEVVTQLKAPLLGDSAGVIGAAWLW 298 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: 269 Number of extensions: 8 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 24 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