Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate N515DRAFT_0393 N515DRAFT_0393 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__Dyella79:N515DRAFT_0393 Length = 333 Score = 191 bits (485), Expect = 2e-53 Identities = 118/313 (37%), Positives = 168/313 (53%), Gaps = 8/313 (2%) Query: 3 KYALVGDVGGTNARLALCDIA-----SGEISQAKTYSGLDYPSLEAVIRVYLEEHKVE-V 56 K L DVGGT+AR+ L D A SG ++ + Y+G D+P L ++ +L H V Sbjct: 14 KLVLAADVGGTHARIGLVDAAAPAGASGVLAYER-YAGADWPGLAEILADFLARHPGHAV 72 Query: 57 KDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHL 116 + IA+A + + N W +AE+++ L L+++NDF A++ A L + Sbjct: 73 DEAAIAVAGYVRDGELVAENLRWPVRLAELRERLRLRRLQVVNDFEALAFATQYLGADDS 132 Query: 117 IQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEI 176 + A P P+AV G GTGLG A LV LP EGGHV AP SE E +L++ Sbjct: 133 LAVIDA-PAAAGPVAVVGPGTGLGCALLVPDGNGVTVLPSEGGHVALAPGSEREMALLQL 191 Query: 177 LRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSL 236 L +V VLSGPGLVNLYRAI + D + +P+ I+ AL L Sbjct: 192 LSRGRDYVHTGHVLSGPGLVNLYRAIGELDGLSAVHAQPEQISAAALDGGDALALDTLHT 251 Query: 237 FCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPV 296 FC ++G F G+LA+ GGVF+AGGI+P+ EF S FR F +KG ++++ +PV Sbjct: 252 FCAMLGGFVGDLAVLFKASGGVFLAGGILPQLREFLPYSAFRERFFNKGVMRDFLAGVPV 311 Query: 297 YLIVHDNPGLLGS 309 LI H G+LG+ Sbjct: 312 RLIEHGRLGVLGA 324 Lambda K H 0.322 0.141 0.426 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: 340 Number of extensions: 21 Number of successful extensions: 4 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: 321 Length of database: 333 Length adjustment: 28 Effective length of query: 293 Effective length of database: 305 Effective search space: 89365 Effective search space used: 89365 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: 48 (23.1 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