Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate 3608216 Dshi_1621 PfkB domain protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_20835 (305 letters) >FitnessBrowser__Dino:3608216 Length = 316 Score = 71.6 bits (174), Expect = 2e-17 Identities = 77/258 (29%), Positives = 118/258 (45%), Gaps = 12/258 (4%) Query: 38 SGGKGANQAVASARLGAQVSMIGCVGDDAYGEQLRAALLAEQIDCQAL-TSVEGSSGVAL 96 +GG G N + A A LG Q S+ GE++R L E I L +VE +++ Sbjct: 37 AGGGGVNVSRAIAFLGGQ-SLAALALGGGPGERVRQLLRVEGIPVHDLGVAVETRQNLSV 95 Query: 97 IVVDDNSQNAIVIVAGANGQLTPGMVAGFDAVLA-AADVIICQLEVPMHT----VGYVLK 151 I D +Q ++ + LA A D+I+ +P + + Sbjct: 96 IARDTGAQYRFIMPGQTWTDVDVDRSCEALCKLARAGDLIVPSGSLPPGVGPGDLVALTN 155 Query: 152 RGRELGKTVILNPAPATSPLPADWYSSIDYLIPNE-SEASALSGLPVDSLESAELAASRL 210 R LG ++L+ + A A + +++ + EA +L+G +D++ L Sbjct: 156 RLAVLGVRIVLDTSGAALQAFATGRAKTLHVLRMDLEEAQSLAGRDLDTVADVAQFGREL 215 Query: 211 IAAGAGK-VIITLGPQGSLF--ANGQSCEHFPAPKVKSVDTTAAGDTFVGGFAAALAAGK 267 + AGA K VI+ G +GS+ + GQ H PKV V T AGD+FV GF ALA G Sbjct: 216 VDAGAAKSVIVAKGAEGSILVTSRGQGW-HVRPPKVNVVSKTGAGDSFVAGFTLALAQGS 274 Query: 268 SEVEAIRFGQVAAALSVT 285 S++EA G AAA +VT Sbjct: 275 SDLEATVRGVGAAASAVT 292 Lambda K H 0.315 0.130 0.363 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: 222 Number of extensions: 11 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: 305 Length of database: 316 Length adjustment: 27 Effective length of query: 278 Effective length of database: 289 Effective search space: 80342 Effective search space used: 80342 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 17 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