Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_058859757.1 AS188_RS05785 carbohydrate kinase
Query= reanno::pseudo3_N2E3:AO353_25910 (314 letters) >NCBI__GCF_001482365.1:WP_058859757.1 Length = 309 Score = 173 bits (438), Expect = 5e-48 Identities = 116/316 (36%), Positives = 159/316 (50%), Gaps = 15/316 (4%) Query: 1 MYLVCGEALFDFFSENAASSQASTVNYKAIAGGSPFNVAVGLRRLGVDSALFAGLSTDYL 60 M V GEAL D S+ +A AGGSP NVAVGL RLG + D Sbjct: 1 MLTVIGEALVDVVSKQGQEPRAH-------AGGSPMNVAVGLARLGHEVQFLGRYGGDEH 53 Query: 61 GRRLQQVLADEGVRADYLLDFDAPTTLAMVAVGANGSPHYSFRGEGCADRQLTLAHLPEL 120 G R+Q L D GVR + D PT++A + +G+ Y FR + + L L L Sbjct: 54 GTRVQAHLRDNGVRLPFEPD-TRPTSVAEAVIDDDGAATYDFRLDWSLE--LDDDRLERL 110 Query: 121 SDEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIELWRSRIAEL 180 LH+GS +++P A + V G+ ++S DPN R + PD R+R EL Sbjct: 111 LAGTELLHVGSIGAMLEPGASRVRRAVELAHGRAVVSYDPNCRPSIIPDSSAARARAEEL 170 Query: 181 MKYADLIKVSDEDLSLLYPGREPQSVIDSWLEHRCQLVFLTRGGQGATVFSRRHG--SWS 238 + AD++K SDEDL LYP R + +WL +LV +TRG G +R G Sbjct: 171 VALADVVKASDEDLLWLYPHRSVEETAAAWLRAGARLVVVTRGPMGPWARTRATGPRGVE 230 Query: 239 APASKVVIADTVGAGDTFQAALITWLTEQQLDSVDGLQR---LSREQIDAMLRFAISAAA 295 PA++ + DTVGAGD+F AA + WL + +R L Q++ +LRFA +AAA Sbjct: 231 VPAARAEVVDTVGAGDSFMAATLGWLADHGYTGATARERIDDLDAGQVEDLLRFAAAAAA 290 Query: 296 LTCSKTGPDLPYRHQL 311 +T S+ G DLP R L Sbjct: 291 VTVSRAGADLPRREDL 306 Lambda K H 0.320 0.136 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: 255 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: 314 Length of database: 309 Length adjustment: 27 Effective length of query: 287 Effective length of database: 282 Effective search space: 80934 Effective search space used: 80934 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: 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