Align Glucose kinase (characterized, see rationale)
to candidate 8500137 DvMF_0900 Glucokinase (RefSeq)
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Miya:8500137 Length = 365 Score = 84.0 bits (206), Expect = 6e-21 Identities = 100/355 (28%), Positives = 138/355 (38%), Gaps = 46/355 (12%) Query: 19 VAADVGGTHVRLAL-----ACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAE---L 70 +AAD+GGT+ R AL + PR P L + A A+++ AE L Sbjct: 4 LAADIGGTNSRFALYEAGGLARGHVPR-PQDRLCAVRLPTAGTASFADLLRRAAAEEPGL 62 Query: 71 SCAPVRRGVIASAGYALEDGRVITANLPWVL-APEQIRQQLGMQALH---LVNDFEAVAY 126 +P V+A AG R N+PW + E + GM L L+NDF A AY Sbjct: 63 FTSPALL-VLAVAGPVRGGRRCTPPNIPWAVDLDEPALRAPGMPPLPPVLLINDFVAQAY 121 Query: 127 AANYMTGNQ------------------------VMQLSGPAQGAP---GPALVLGPGTGL 159 A ++ + G P P V+G GTGL Sbjct: 122 ACLRPAAPDGPVAPVAPVAPDGPDEPDGPVVPDMLNMLDVLDGHPVPDAPIAVVGAGTGL 181 Query: 160 GAALWIPNGGNSV---VLPTEAGHAALAAASDLEVALLQELR-RTRTHVATEHFLSGPGL 215 G L +P G+ + VLP+E GHA + E+A +R T V + +SGPGL Sbjct: 182 GKCLLLPASGDGMPPRVLPSEGGHALFPFTDEREMAFAAFVRAHTGRQVIGDLVVSGPGL 241 Query: 216 LTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEALQTFCGFMGSVVGDMMLLYGVR 275 L+ PA A A T A A D+ + L F F G D +L Sbjct: 242 RLLHAFHTGQWLEPAEVAARLA-TGAPGADSDLALPQVLSWFARFYGRACRDYVLETLAL 300 Query: 276 SGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVPVRIVEHGQLGVIGAA 330 GV+++GG + FA L VPVR+V G++GAA Sbjct: 301 GGVFISGGVAAATPALVTHPAFAEAFRQSDTHADLLRAVPVRLVRSPDAGLLGAA 355 Lambda K H 0.321 0.136 0.407 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: 290 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 338 Length of database: 365 Length adjustment: 29 Effective length of query: 309 Effective length of database: 336 Effective search space: 103824 Effective search space used: 103824 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 (21.9 bits) S2: 49 (23.5 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