Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate 3608608 Dshi_2001 ROK family protein (RefSeq)
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Dino:3608608 Length = 414 Score = 148 bits (373), Expect = 3e-40 Identities = 94/311 (30%), Positives = 149/311 (47%), Gaps = 8/311 (2%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPER-GYEAIARDIAELSFELLQRMGISVKD 61 +G+ L V L + G +AT R ++P R EA+ ++A L E+L + Sbjct: 99 LGLRLSDEMHTVSLSDFSGTELATAHRASQPGRYAVEALLTEMATLIDEVLAAAALPRDR 158 Query: 62 VKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121 V ++G+G+PG +E G V + L L I LP ++ENDANV LAE F Sbjct: 159 VAALGVGLPGAVHHETGRVAWSPILAGQDHALQAIIEDRFGLPAHLENDANVLTLAELWF 218 Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFE 181 GAGR + +T+ GVG G +L+ +++ GA E+GH + +G C CG+ GC E Sbjct: 219 GAGRAMQDFAVVTIEQGVGMGLVLNNRLFRGAQGLGLELGHTKVQLDGALCRCGQRGCLE 278 Query: 182 TYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVK 241 Y + AL+RE A R+P + +++ D AK + A IF+ + Sbjct: 279 AYLADYALVREASTALDRDPR-------SAQTAAAMLESLFDQAKAGNGAAKAIFQRAGR 331 Query: 242 YLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAELGN 301 +L++G+ N++ LFDPE+IIL G + + E+ L P + + G+ Sbjct: 332 FLSLGLANVVQLFDPELIILSGARMRYDYLYAEEVLAEMQRMTLHPATPRSRVEIHAWGD 391 Query: 302 DAGIIGAAILS 312 GA L+ Sbjct: 392 QVWARGATALA 402 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: 277 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: 312 Length of database: 414 Length adjustment: 29 Effective length of query: 283 Effective length of database: 385 Effective search space: 108955 Effective search space used: 108955 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