Align shikimate kinase (EC 2.7.1.71) (characterized)
to candidate WP_085771497.1 B1812_RS10205 3-dehydroquinate synthase
Query= reanno::Caulo:CCNA_03103 (200 letters) >NCBI__GCF_002117405.1:WP_085771497.1 Length = 591 Score = 167 bits (423), Expect = 4e-46 Identities = 97/197 (49%), Positives = 120/197 (60%), Gaps = 4/197 (2%) Query: 1 MTETDQTPDTAPEAAPEVAPIVSDDLAPLRAKTIVLVGLMGVGKSSVGRRLANVLGLPFR 60 MT + T A P A I A L IVL+G+MG GKSS+G++LA LGL F Sbjct: 1 MTTSPCAETTIAPADPRPAAI----RALLEDNCIVLIGMMGSGKSSIGQKLAQRLGLKFI 56 Query: 61 DADNEVEAAAGRSISEIFAELGEPAFRDGERRVIARLLDEPPHVLATGGGAFVNAETRAL 120 DAD E+ AAG SI EIFA+ GE FRDGERRV+ RLL+ P VLATGGGAF++ TR Sbjct: 57 DADVEIATAAGMSIPEIFAKFGEGYFRDGERRVLYRLLNGGPMVLATGGGAFLDPRTRRR 116 Query: 121 INEKAVSVWLKADVELLARRVSRKDNRPLVRGKDPVKVLTELAEARYPAYAEAQVHVETG 180 I E+ VS+W AD + L RRV RK +RPL++ +DP L L + R P YA A + V + Sbjct: 117 IAERGVSIWFDADHDTLLRRVRRKSDRPLLQTEDPSATLRRLMDERNPVYATADLKVVSH 176 Query: 181 DTPHMVAVEAILTALRQ 197 D PH VE L L + Sbjct: 177 DVPHEAMVEQTLALLAE 193 Lambda K H 0.316 0.132 0.369 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: 278 Number of extensions: 15 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: 200 Length of database: 591 Length adjustment: 28 Effective length of query: 172 Effective length of database: 563 Effective search space: 96836 Effective search space used: 96836 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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