Align Sugar amine kinase; EC 2.7.1.- (characterized, see rationale)
to candidate N515DRAFT_0916 N515DRAFT_0916 Sugar or nucleoside kinase, ribokinase family
Query= uniprot:Q92VI2 (311 letters) >FitnessBrowser__Dyella79:N515DRAFT_0916 Length = 312 Score = 93.6 bits (231), Expect = 5e-24 Identities = 85/282 (30%), Positives = 128/282 (45%), Gaps = 17/282 (6%) Query: 7 IGNVNVDLILGPAEPWPKPGTEVIVDHDELRVGGCAGNNALAWDSLGVDYVIAANVGNDQ 66 +G VNVDL+L P PG EV+ D + G + A+ LG +G D Sbjct: 12 VGEVNVDLVLKGLHAEPAPGQEVLADDFLMTPGSSSMICAMGLARLGNAVAFHGRLGADA 71 Query: 67 FGTW----LKEAFGERSRNWPVEAVGTTLSVGITHPDGERTFFTTRGHLPLFSFPEVHSM 122 +G++ L++A + + P A+ T ++V ++ P +R+ T G + +V Sbjct: 72 WGSYCLDALRDAGIDVASLQPEAALRTGITVSLSTPR-DRSLVTFSGAIAALRAEDVSDA 130 Query: 123 LDGNRLRGGYALLSGSFLTDALTLAYDALFDWADAHEIAVALDTGW-PLDGWTETNRLRT 181 L G+ +S +L AL LF A + ++LD G+ P W + R Sbjct: 131 LLAG---AGHLHVSSFYLQKALRADIRQLFARARKAGLTLSLDPGFDPEQRWGDDLR--- 184 Query: 182 LGWLKRCHCALFNEVETTTLTGLSDPAEAALSLKGEMPAEAIVVVKRGPHGALAIDRDGG 241 G L+ L NE E LTG + +A +L ++V KRG G A+ DG Sbjct: 185 -GVLEDVDVFLPNEEELRALTGENHVRKALAALDN---GRTLIVAKRGRQGC-AVLHDGK 239 Query: 242 TFSVPAPQVQVVDTIGAGDVFNAGFLAALAAEMPLEACLKTG 283 PA V+ VD+ GAGD F+AGFL A +PL CL+ G Sbjct: 240 LLVAPALAVEAVDSTGAGDSFDAGFLHAWLRGLPLRDCLRWG 281 Lambda K H 0.319 0.137 0.426 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: 211 Number of extensions: 13 Number of successful extensions: 2 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: 311 Length of database: 312 Length adjustment: 27 Effective length of query: 284 Effective length of database: 285 Effective search space: 80940 Effective search space used: 80940 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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