Align glucokinase (EC 2.7.1.2) (characterized)
to candidate CA265_RS11300 CA265_RS11300 sugar kinase
Query= BRENDA::Q8RDE9 (315 letters) >FitnessBrowser__Pedo557:CA265_RS11300 Length = 313 Score = 166 bits (419), Expect = 9e-46 Identities = 101/313 (32%), Positives = 163/313 (52%), Gaps = 18/313 (5%) Query: 2 KKFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLE 61 + + G+D+GG+ + G+V++NG I+ SI + K +I I E+I+ K Sbjct: 3 QSYAIGIDVGGSSLKCGVVNQNGEILYSIIVSLKNAKTQGAIIALIVEAIHTCAKKF--- 59 Query: 62 MSNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIG 121 + + G+GIG PG + K I+ NLP + + + EIL + + ++NDAN +G Sbjct: 60 KNPILGVGIGFPGIIYNNK-IIAGADNLPGFKQLALGEILQEVTRYNIVMDNDANLMGLG 118 Query: 122 EHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNY 181 E +G+ + + V++TV TGIGG V+I+ KLY G + E+GH + +G C CG Sbjct: 119 EMTYGAAKDCSDVVFLTVGTGIGGAVMIDNKLYGGFRNRGTELGHIVVQHNGLACACGGR 178 Query: 182 GCFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKE 241 GC EAYAS TA+ + I E E+ +++ E +E+A E +E Sbjct: 179 GCLEAYASVTALLNH-----YQSIHPNPPE-----EIDGKYMVEKYLAREEYAVEAMESH 228 Query: 242 AFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKA--LKPNAEVCEVVKA 299 YL GI + + ++P+KI IGGG+S ++ ++ A + P E+ VV A Sbjct: 229 FDYLATGIISFVNVFSPQKIVIGGGISESGAFYVREIERRIKTLAVPIAPGNEL--VVAA 286 Query: 300 QLGENIGVLGAAA 312 +LG G+LG AA Sbjct: 287 RLGNKAGLLGCAA 299 Lambda K H 0.316 0.138 0.398 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: 270 Number of extensions: 15 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: 315 Length of database: 313 Length adjustment: 27 Effective length of query: 288 Effective length of database: 286 Effective search space: 82368 Effective search space used: 82368 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: 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