Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate 8500137 DvMF_0900 Glucokinase (RefSeq)
Query= curated2:B2J224 (341 letters) >FitnessBrowser__Miya:8500137 Length = 365 Score = 100 bits (248), Expect = 8e-26 Identities = 107/386 (27%), Positives = 156/386 (40%), Gaps = 79/386 (20%) Query: 4 LLAGDIGGTKTILQLVETSDSQGLHT---------IYQESYHSADFPDLVPIVQQFLIKA 54 +LA DIGGT + L E H + + +A F DL+ A Sbjct: 3 VLAADIGGTNSRFALYEAGGLARGHVPRPQDRLCAVRLPTAGTASFADLLRRAA-----A 57 Query: 55 NTP----IPEKACFAIAGPIVKNTAKLT--NLAWFLDTE----RLQQELGIPHIYLINDF 104 P P A+AGP V+ + T N+ W +D + R +P + LINDF Sbjct: 58 EEPGLFTSPALLVLAVAGP-VRGGRRCTPPNIPWAVDLDEPALRAPGMPPLPPVLLINDF 116 Query: 105 AAVGYGI------------------SGLQKQD-------LHPLQV--GKPQPETPIGIIG 137 A Y G + D L+ L V G P P+ PI ++G Sbjct: 117 VAQAYACLRPAAPDGPVAPVAPVAPDGPDEPDGPVVPDMLNMLDVLDGHPVPDAPIAVVG 176 Query: 138 AGTGLGQGFLIK---QGNNYQVFPSEGGHADFAPRNEIEFQLLKYLLDKHDIQRISVERV 194 AGTGLG+ L+ G +V PSEGGHA F +E E ++ H +++ + V Sbjct: 177 AGTGLGKCLLLPASGDGMPPRVLPSEGGHALFPFTDEREMAFAAFVR-AHTGRQVIGDLV 235 Query: 195 VSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDPGAAIGTAALEKRDRL 254 VSG G+ ++ F GQ + + A + T A L Sbjct: 236 VSGPGLRLLHAF----------------------HTGQWLEPAEVAARLATGAPGADSDL 273 Query: 255 S-EQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLIQNSGFLLNFTQKGRMR 313 + Q L F YG + L+ L GG++I+GG+A L+ + F F Q Sbjct: 274 ALPQVLSWFARFYGRACRDYVLETLALGGVFISGGVAAATPALVTHPAFAEAFRQSDTHA 333 Query: 314 PLLEEIPVYIILNPQVGLIGAALCAA 339 LL +PV ++ +P GL+GAAL A Sbjct: 334 DLLRAVPVRLVRSPDAGLLGAALYGA 359 Lambda K H 0.320 0.140 0.408 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: 306 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 341 Length of database: 365 Length adjustment: 29 Effective length of query: 312 Effective length of database: 336 Effective search space: 104832 Effective search space used: 104832 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 Apr 09 2024. 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