Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_110207115.1 DNK54_RS11370 ribokinase
Query= reanno::acidovorax_3H11:Ac3H11_3034 (350 letters) >NCBI__GCF_003194585.1:WP_110207115.1 Length = 310 Score = 46.6 bits (109), Expect = 9e-10 Identities = 82/276 (29%), Positives = 108/276 (39%), Gaps = 53/276 (19%) Query: 78 RGLHDAGVALAAPTPVRAPSAL--------ALAALDAEG-KASYSFYRDGVADRQVTAAA 128 +G + A A A VR A+ ALA L AE S GVA T A Sbjct: 41 KGANAAVAAARAGAEVRYVGAVGADDLGTGALAELVAENIDVSGVVVEPGVA----TGTA 96 Query: 129 LTAACSALPELQVVATGCLALVAQDAALYLPWLAAQRAAGRMVVVDANLRL----SAVDD 184 L A VA G A+V+ ++ + LA R V+V + + +AV+ Sbjct: 97 LIVVDHAGENQIAVAAGANAVVSPESVRQV--LARSRGWATCVLVSTEIPMDAVVAAVET 154 Query: 185 ADAYR-------ANVMAALQHAHLIKVSD----------DDLEALAIPGANALERAHFLQ 227 A AY A V A L A L+ +S D AL P +LE Sbjct: 155 ARAYDLPCVLNPAPVAAGL--AGLVSMSPVLTPNQGELRDLCRALGEPDETSLEAMASAV 212 Query: 228 QQTQAQWLALTLGPNGAWLLQRDGLAVHAREEAPITVVDTVGAGDCFLAGLITAWLAGPE 287 + +A+TLG +G + DG H VVDT GAGD F G++ A LA E Sbjct: 213 AHSSKAAVAVTLGADGVMVADPDGSTCHIPAAPVAEVVDTTGAGDTF-NGVLAAALASGE 271 Query: 288 -------RGEDALAL-------RAGGLTAPVTEARL 309 RG A ++ RAG TA V +A L Sbjct: 272 TISGAVRRGVAAASISVGSAGARAGMPTAEVIDAAL 307 Lambda K H 0.320 0.133 0.392 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: 250 Number of extensions: 13 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: 350 Length of database: 310 Length adjustment: 28 Effective length of query: 322 Effective length of database: 282 Effective search space: 90804 Effective search space used: 90804 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