Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate WP_011033702.1 MM_RS09140 mevalonate kinase
Query= curated2:Q7U1L7 (363 letters) >NCBI__GCF_000007065.1:WP_011033702.1 Length = 301 Score = 66.6 bits (161), Expect = 8e-16 Identities = 86/337 (25%), Positives = 138/337 (40%), Gaps = 54/337 (16%) Query: 3 VSYGAPGRVNLIGEHTDYNLGFALPIALPRRTVVTFTPEHTGAITARSDRADGSARIPLD 62 VS APG++ L GEH A+ A+ RT V E +IT +S G + + Sbjct: 2 VSCSAPGKIYLFGEHAVVYGETAIACAVELRTRV--RAELNDSITIQSQ--IGRTGLDFE 57 Query: 63 TTPGQVTGWAAYAAGAIWALRGAGHPVPGGAMSITSDVEIGSGLSSSAALIGAVLGAVGA 122 P Y + I +R P+ G +++ SD+ +GSGL SSAA+ A +GA+ Sbjct: 58 KHP--------YVSAVIEKMR-KSIPINGVFLTVDSDIPVGSGLGSSAAVTIASIGALNE 108 Query: 123 ATGTRIDRLERARLAQRAENDYVGAPTGLLDHLAALFGAPKTALLIDFRDITVRPVAFDP 182 G + E A+L E GA + D + FG T I R P Sbjct: 109 LFGFGLSLQEIAKLGHEIEIKVQGAASP-TDTYVSTFGGVVT--------IPERRKLKTP 159 Query: 183 DACDVVLLLMDSRARHRHAGGEYALRRASCERAAADLGVSSLRAVQDRGLAALGAIADPI 242 D C +V+ G+ + ++ E A V LR + + +P+ Sbjct: 160 D-CGIVI-------------GDTGVFSSTKELVA---NVRQLR-------ESYPDLIEPL 195 Query: 243 DARRARHVLTENQRVLDFAAALADSDFTAAGQLLTASHESMREDFAITTERIDLIAESAV 302 + Q VL D+ + G+L+ ++ + + + + + SA Sbjct: 196 MTSIGKISRIGEQLVL-------SGDYASIGRLMNV-NQGLLDALGVNILELSQLIYSAR 247 Query: 303 RAGALGARMTGGGFGGAVIALVPADRARDVADTVRRA 339 AGA GA++TG G GG ++AL ++ VA+ V A Sbjct: 248 AAGAFGAKITGAGGGGCMVALTAPEKCNQVAEAVAGA 284 Lambda K H 0.320 0.134 0.390 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: 178 Number of extensions: 4 Number of successful extensions: 1 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: 363 Length of database: 301 Length adjustment: 28 Effective length of query: 335 Effective length of database: 273 Effective search space: 91455 Effective search space used: 91455 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 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