Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate Echvi_3892 Echvi_3892 Transcriptional regulator/sugar kinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Cola:Echvi_3892 Length = 412 Score = 141 bits (356), Expect = 2e-38 Identities = 80/257 (31%), Positives = 140/257 (54%), Gaps = 3/257 (1%) Query: 52 LQRMGISVKDVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDA 111 +Q GI + + ++G+ +PG+ D+ G+ L + K L + D +++ENDA Sbjct: 143 MQESGIPNEKIIAIGMSMPGLVDSVNGV--NHTYLKFGKKSLVENFEARFDRKVFIENDA 200 Query: 112 NVAALAEATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNG-I 170 LAE F + + + I +G G+G G I+DGK+Y G FA E H I ++ I Sbjct: 201 RAMTLAEFKFSQDQKYNNVLGIFVGWGIGLGIIIDGKLYRGGAGFAGEFSHSPIFESREI 260 Query: 171 RCNCGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDE 230 C CGK GC E AS TA++R ++A +++ ++++ + A EGI ++DAA D+ Sbjct: 261 SCTCGKKGCLEAVASGTAMVRMAEEAIEKDSDSILSRMARERGEGIDPSLIVDAALAGDQ 320 Query: 231 EALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELP 290 A+ I + L GI +I L +P++II+GG VA A +L+ P+++ + + K Sbjct: 321 RAITILSDVGLDLGRGISILIQLLNPDLIIVGGSVAEAQQYLITPIQQALNIFSMAKSRE 380 Query: 291 YADIRKAELGNDAGIIG 307 +++ +LG + G++G Sbjct: 381 KSELTLYKLGKEVGLLG 397 Score = 23.9 bits (50), Expect = 0.007 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 1/53 (1%) Query: 141 SGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCF-ETYASATALIRE 192 S F++ IY ++ E G I N + KIG F ETY + + E Sbjct: 99 SKFVVRAAIYDSSNQAVTETGTFKITLNNEKSTFDKIGDFMETYMQESGIPNE 151 Lambda K H 0.318 0.140 0.397 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: 357 Number of extensions: 25 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 312 Length of database: 412 Length adjustment: 29 Effective length of query: 283 Effective length of database: 383 Effective search space: 108389 Effective search space used: 108389 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 (21.7 bits) S2: 49 (23.5 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