Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_103233526.1 C1634_RS17380 glucokinase
Query= curated2:Q9A6N3 (331 letters) >NCBI__GCF_002899945.2:WP_103233526.1 Length = 349 Score = 117 bits (292), Expect = 6e-31 Identities = 86/295 (29%), Positives = 136/295 (46%), Gaps = 20/295 (6%) Query: 40 YRGEDYGTAEDAIEEYLRKVGVKHPDQAVVAVAGPIDHGQVHMTNLDWRISEDGLRRAGG 99 Y ++Y D ++++++ +++ + +AV GP+ +G+ L W + + R G Sbjct: 54 YATKEYAAFSDILKKFIQDNQLQNVKRLGMAVPGPVLYGKSSPVRLGWNLDVEEYARDFG 113 Query: 100 FRNAKLINDFTAQALAAPRVGPKDLRQIGELPTSGEGDLAILGPGTGFGVAGLVRRHGQE 159 F ++ND A A + DL I G++A+L PG G G AG Sbjct: 114 FEKVDMLNDLEASAYGMALLEDNDLEAIYTSGHLERGNVAVLAPGNGLGEAGYFFDGKYL 173 Query: 160 IPLATEGGHVAFAPVDDVEIEVLRALTRRLDGGRVSVERILSGPGMEDLH---------- 209 P ATEGGH F+P +VE+E + L G VS E +LS G+ +++ Sbjct: 174 RPFATEGGHSEFSPRTNVEVEFYQFLNNIY--GIVSWENVLSKSGLFNIYRFLRDVKRHP 231 Query: 210 ----VDLAAAEGRGVEALTAKQITERAVEGCADSLATVNRFCAILGSTAGDIALTLGARG 265 + A+G VE L K E V C +L T F L A ++ L L A G Sbjct: 232 EPEWLSERLAQGNFVEEL-YKAAVEENVLICKIALDT---FLEFLAREANNLTLKLKATG 287 Query: 266 GVFIAGGIAPRIIDILEKSPFRERFDSKGRLSGFTRSIPTHVILHPHTALIGAAV 320 G+ IAG I I + ++K+ F E+F ++ RS P +++ HTAL G A+ Sbjct: 288 GLLIAGDIPQTIREYIDKAKFYEKFKISDKMEEMLRSTPIYLVKQNHTALNGIAL 342 Lambda K H 0.319 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: 277 Number of extensions: 18 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: 331 Length of database: 349 Length adjustment: 28 Effective length of query: 303 Effective length of database: 321 Effective search space: 97263 Effective search space used: 97263 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 (21.7 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