Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate N515DRAFT_2652 N515DRAFT_2652 glucokinase
Query= curated2:Q55855 (355 letters) >FitnessBrowser__Dyella79:N515DRAFT_2652 Length = 355 Score = 120 bits (302), Expect = 4e-32 Identities = 105/344 (30%), Positives = 158/344 (45%), Gaps = 37/344 (10%) Query: 8 FLAGDIGGTKTILALVTINESSPGLARPVTLFEQTYSSPAFPDLVPMVQQFRQEAAFVLG 67 FLA DIGGT L LV P L +++ P L +V+ F E Sbjct: 33 FLAADIGGTHARLGLVAAQPEGA----PRVLAYRSFRCADHPHLDDIVRMFCAELD-ARP 87 Query: 68 NPISVAKACFAIAGPVIDNTCRLTNLDWHLSGDRLAQELAIAQVDLINDFAAVGYGILGL 127 + +A A + AG V++ NL W L LA EL + +V +NDF A+ + I + Sbjct: 88 RELVLASAGYLHAGVVVNR-----NLAWPLVPATLAHELRLERVRFLNDFEALAHAIAYV 142 Query: 128 GSEDLTVLQAA--PVDPSGAIAILGAGTGLGQCYVIPQGQGRYRVFASEGAHGDFAPRSP 185 L+ A P G IA++G GTGLG P R V A+E A R Sbjct: 143 DEHSSVSLKTAFAPDAGKGPIAVIGPGTGLGAAVWFPGEPPR--VIATEAGQIQLAARGG 200 Query: 186 LEWQLLEYLKKKYSLGRISIERVVSGMGIAMIYEFLRHQYPERESAQFSKLYQTWNREKD 245 LE ++L+ + S E V+SG G+ +Y L Y S Sbjct: 201 LEREVLDRIAP--SDCHTPYEAVLSGPGLHRLYAALCAVYDRYPSC-------------- 244 Query: 246 QETKTVDLAAAVSQAALEGTDVLADQAMELFLGAYGAEAGNLALKLLPRGGLYVAGGIAP 305 + D+ AA E D +A +A+++F G G+ AG+LA+ GG+Y+AGG Sbjct: 245 --AEPADVVAAA-----EAGDEVAYEAVQMFGGWMGSFAGDLAMLYGATGGVYLAGGFLS 297 Query: 306 KIIPLLEKGSFMQGFSDKGRMQSLMGTIPVQVVLNAKVGLIGAA 349 +I+ LL G ++ F DKG M+ + +P++VV + ++G++GAA Sbjct: 298 RIVDLLRCGPLVERFLDKGVMRPFLHKVPIRVVDHGQLGVVGAA 341 Lambda K H 0.320 0.137 0.399 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: 285 Number of extensions: 14 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: 355 Length of database: 355 Length adjustment: 29 Effective length of query: 326 Effective length of database: 326 Effective search space: 106276 Effective search space used: 106276 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