Align Glucose kinase (characterized, see rationale)
to candidate N515DRAFT_2652 N515DRAFT_2652 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Dyella79:N515DRAFT_2652 Length = 355 Score = 263 bits (672), Expect = 5e-75 Identities = 154/320 (48%), Positives = 194/320 (60%), Gaps = 10/320 (3%) Query: 18 FVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRR 77 F+AAD+GGTH RL L P VL YR +RCAD+P L +I+ F AEL P R Sbjct: 33 FLAADIGGTHARLGLVAAQ--PEGAPRVLAYRSFRCADHPHLDDIVRMFCAELDARP-RE 89 Query: 78 GVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVM 137 V+ASAGY L G V+ NL W L P + +L ++ + +NDFEA+A+A Y+ + + Sbjct: 90 LVLASAGY-LHAGVVVNRNLAWPLVPATLAHELRLERVRFLNDFEALAHAIAYVDEHSSV 148 Query: 138 QLS---GPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVALL 194 L P G GP V+GPGTGLGAA+W P G V+ TEAG LAA LE +L Sbjct: 149 SLKTAFAPDAGK-GPIAVIGPGTGLGAAVWFP-GEPPRVIATEAGQIQLAARGGLEREVL 206 Query: 195 QELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEAL 254 + + H E LSGPGL LY AL + D A PA V AAA AGD+V A+EA+ Sbjct: 207 DRIAPSDCHTPYEAVLSGPGLHRLYAALCAVYDRYPSCAEPADVVAAAEAGDEV-AYEAV 265 Query: 255 QTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQV 314 Q F G+MGS GD+ +LYG GVYLAGGFL +I D + R LDKG +RP L +V Sbjct: 266 QMFGGWMGSFAGDLAMLYGATGGVYLAGGFLSRIVDLLRCGPLVERFLDKGVMRPFLHKV 325 Query: 315 PVRIVEHGQLGVIGAASWFL 334 P+R+V+HGQLGV+GAASW L Sbjct: 326 PIRVVDHGQLGVVGAASWHL 345 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: 284 Number of extensions: 13 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: 338 Length of database: 355 Length adjustment: 29 Effective length of query: 309 Effective length of database: 326 Effective search space: 100734 Effective search space used: 100734 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