Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate 8500137 DvMF_0900 Glucokinase (RefSeq)
Query= curated2:Q7P1R6 (348 letters) >FitnessBrowser__Miya:8500137 Length = 365 Score = 108 bits (271), Expect = 2e-28 Identities = 113/363 (31%), Positives = 149/363 (41%), Gaps = 65/363 (17%) Query: 12 LLGDVGGSNARFALETAPGVIEDILTLSNERY-----PTLEDA-LRDYLAQVGARRV--- 62 L D+GG+N+RFAL A G+ + +R PT A D L + A Sbjct: 4 LAADIGGTNSRFALYEAGGLARGHVPRPQDRLCAVRLPTAGTASFADLLRRAAAEEPGLF 63 Query: 63 ---AHAAIGIANPLNGDLVRMT--NCHWSFSI-EATRRALGLSTL---LLLNDFTALALA 113 A + +A P+ G R T N W+ + E RA G+ L LL+NDF A A A Sbjct: 64 TSPALLVLAVAGPVRGGR-RCTPPNIPWAVDLDEPALRAPGMPPLPPVLLINDFVAQAYA 122 Query: 114 L--PRLPRRELAQVG-------------------------GGAPRPDAPLALIGPGTGLG 146 P P +A V G P PDAP+A++G GTGLG Sbjct: 123 CLRPAAPDGPVAPVAPVAPDGPDEPDGPVVPDMLNMLDVLDGHPVPDAPIAVVGAGTGLG 182 Query: 147 VSALVPHAGGW---RALAGEGGHTSFAPANEREIGIWRYASARFG-HVSHERLLSGSGLS 202 L+P +G R L EGGH F +ERE+ + A G V + ++SG GL Sbjct: 183 KCLLLPASGDGMPPRVLPSEGGHALFPFTDEREMAFAAFVRAHTGRQVIGDLVVSGPGLR 242 Query: 203 LLHRALCALDGAEEAG--LAPAEVSARGLSGA-----DARCREALEIFCALLGSAAGNLA 255 LLH A G L PAEV+AR +GA D + L F G A + Sbjct: 243 LLH--------AFHTGQWLEPAEVAARLATGAPGADSDLALPQVLSWFARFYGRACRDYV 294 Query: 256 LTLGARGGVYIGGGIVPRLSGFFEQSPFRRRFEDKGRMSAYLADIPVYLITSAYPALPGV 315 L A GGV+I GG+ F F + L +PV L+ S L G Sbjct: 295 LETLALGGVFISGGVAAATPALVTHPAFAEAFRQSDTHADLLRAVPVRLVRSPDAGLLGA 354 Query: 316 AAH 318 A + Sbjct: 355 ALY 357 Lambda K H 0.320 0.138 0.420 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: 407 Number of extensions: 24 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: 348 Length of database: 365 Length adjustment: 29 Effective length of query: 319 Effective length of database: 336 Effective search space: 107184 Effective search space used: 107184 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: 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