Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_012385786.1 BIND_RS14455 carbohydrate kinase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3036 (314 letters) >NCBI__GCF_000019845.1:WP_012385786.1 Length = 322 Score = 236 bits (603), Expect = 4e-67 Identities = 132/314 (42%), Positives = 193/314 (61%), Gaps = 7/314 (2%) Query: 1 MYLVCGEALFDFF-SENDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALLAGLSTDY 59 M LVCGEAL DFF SE A GL ++ A+ GGSPFNVA+ L RLG A+ GLS+D+ Sbjct: 1 MILVCGEALIDFFVSETPAGGLKTE----AVLGGSPFNVAIALARLGEQASFCGGLSSDH 56 Query: 60 LGRRLLQVLQDEGVCLDYLLEFAAPTTLAMVAVGANGSPQYSFRGEGCADRQL-QAEHLP 118 G L L E V L Y + TTL++VA + G P Y+F GEG ADRQ+ +A+ Sbjct: 57 FGSLLTARLVREHVDLTYSVRSDCLTTLSIVATDSAGHPTYAFHGEGKADRQVTEADLSA 116 Query: 119 TLGPEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIDLWRKRVA 178 L +++ + GS++L V P++D LAL RRE+ +R+ISLDPN+R PD+ WR+R Sbjct: 117 PLRDDIKAITFGSYTLAVTPVSDAYLALARREASRRVISLDPNLRPTVTPDMAAWRRRFN 176 Query: 179 TLVELADLIKVSDEDLHLLY-PDQDPAQVIEGWLQHRCQLVFLTRGGEGATVFSRAHGSW 237 + +AD++K S+ED+ + Y + D A + E WL+ LV +TRG +GA F ++ Sbjct: 177 DFLAIADIVKASEEDIAIAYGAEADIADIAESWLKAGAALVLITRGPDGAIGFLKSGERV 236 Query: 238 SAPACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGVKQLGREQIDRMLKFAVRAAALT 297 + P S+ + DTVGAGDTF AAL+ L Q + ++ L E + R + +AV A+++T Sbjct: 237 TVPGRSITVVDTVGAGDTFHAALLADLGRQGMLHKSKLRDLNTEGLRRTMHYAVAASSIT 296 Query: 298 CSKTGPDLPYRKQL 311 C++ G DLP +++ Sbjct: 297 CTRQGADLPTHEEV 310 Lambda K H 0.321 0.138 0.410 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: 244 Number of extensions: 12 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: 314 Length of database: 322 Length adjustment: 27 Effective length of query: 287 Effective length of database: 295 Effective search space: 84665 Effective search space used: 84665 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 (21.9 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