Align 6-phosphofructokinase (EC 2.7.1.11); 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178); 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) (characterized)
to candidate WP_007691604.1 C447_RS05255 sugar kinase
Query= BRENDA::D4GR05 (318 letters) >NCBI__GCF_000336675.1:WP_007691604.1 Length = 314 Score = 203 bits (516), Expect = 5e-57 Identities = 129/306 (42%), Positives = 164/306 (53%), Gaps = 5/306 (1%) Query: 3 AELVTFGETMIRLSPPEGERIETARSLEFRTAGAESNVAVAASRLGCSAAWLSKLPDSPL 62 A+L+ G +++ L+PPE R+ETA AG ESN +AASRLG AAW+SKLP +PL Sbjct: 2 ADLLALGVSVLELTPPEHRRLETAERFAAGVAGPESNTTIAASRLGADAAWVSKLPGNPL 61 Query: 63 GRRVTTELRTHGVEPYVRWDDDARQGAYYIEQGRAPRPTNVIYDRADAAVTTARPDELAV 122 GRRV LR HGVE V W + RQG + E+ PR ++DR +A V + +P +L Sbjct: 62 GRRVAGALRRHGVETAVSWAETGRQGLAFTERAGDPRGGMTLHDR-NAPVASMQPADLPA 120 Query: 123 DIVEDAAAFYTSGITPALSETLRETTGELLQTATEAGTTTAFDLNYRSKLWSPSDARDAC 182 E A+ TSG T LSETL ETT + + TTT L+ R ++ +A Sbjct: 121 TATERASMVLTSGATATLSETLTETTRTVFEECAAGETTTVCSLS-RPRVVESGSVCEAL 179 Query: 183 ESLFPKVDVLVAAERDIRAVLELDGDAPT-LASELAGDFDFETVVVTRGEDGALARHGGT 241 L DVL+ E A +D PT A LA FETVV+ R + GA+ H Sbjct: 180 SPLLAATDVLLTTEAGAAAF--VDRATPTETAHALAAGHGFETVVLVRADLGAVVWHDNR 237 Query: 242 VYEQPVFETDTVDAIGTGDAFVGAFLSRLIAGEPVETALAYGAATAALKRTVHGDLAVVT 301 V + V TD VD G DA G FL+R IAGE + ALA G A AL RTV G + V Sbjct: 238 VDDHDVPATDAVDDRGAFDALCGGFLARRIAGESPDRALAAGVACGALARTVAGPVPTVD 297 Query: 302 PDEVER 307 P VER Sbjct: 298 PAAVER 303 Lambda K H 0.315 0.132 0.378 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: 295 Number of extensions: 12 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: 318 Length of database: 314 Length adjustment: 27 Effective length of query: 291 Effective length of database: 287 Effective search space: 83517 Effective search space used: 83517 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 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