Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_008630241.1 C943_RS16815 ROK family protein
Query= curated2:Q9KCZ4 (330 letters) >NCBI__GCF_000330725.2:WP_008630241.1 Length = 412 Score = 151 bits (381), Expect = 3e-41 Identities = 89/266 (33%), Positives = 137/266 (51%), Gaps = 8/266 (3%) Query: 60 HKSKSDL-----IGIGLGAPGFIEMDTGFIYHAVNIGWRDFPLKDKLEEETKLPVIVDND 114 HK KS L I +G+ PG I+ G + + G + L + E V ++ND Sbjct: 142 HKEKSGLDNEKVIAVGISMPGLIDSINGVNHTYLKFGKKS--LVENFESRLGRKVFLEND 199 Query: 115 ANIAALGEMWKGAGDGAKNMLLITLGTGVGGGIVANGNILHGVNGMAGEIGHITVIPEGG 174 A L E G D KN+L I +G G+G GI+ +G I G +G AGE H + Sbjct: 200 ARAMTLAEFKFGHNDNYKNVLGIFIGWGIGLGILIDGKIYQGASGFAGEFSHSPIFDSSD 259 Query: 175 APCNCGKTGCLETVASATGIARIATEGVTEHKESQLA-LDYDKHGVLTAKDVFSAADASD 233 C+CGK GCLE+VAS T I R+A + + +S LA + D + + V AA A D Sbjct: 260 ITCSCGKKGCLESVASGTAIVRMARQAIATDSDSILARMTRDNNDEIEPYLVVDAALAGD 319 Query: 234 AFALSVVDHIAYYLGFAIANLANALNPEKIVIGGGVSKAGDTLLKPIKQHFEAYALPRVA 293 A++++ + LG I+ L LNPE I+IGG V++A L+ PI+Q Y++ + Sbjct: 320 QRAITILSEVGLDLGRGISILIQLLNPELIIIGGSVAEAKQYLITPIQQALNIYSMAKAR 379 Query: 294 DGAEFRIATLGNDAGVIGGGWLVKQQ 319 + + + LG + G++GG +V ++ Sbjct: 380 ENTQLTLYKLGKEVGLLGGVAVVNEK 405 Lambda K H 0.316 0.137 0.405 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: 279 Number of extensions: 15 Number of successful extensions: 2 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: 330 Length of database: 412 Length adjustment: 30 Effective length of query: 300 Effective length of database: 382 Effective search space: 114600 Effective search space used: 114600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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