Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate BWI76_RS11225 BWI76_RS11225 N-acetylglucosamine kinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Koxy:BWI76_RS11225 Length = 303 Score = 122 bits (307), Expect = 8e-33 Identities = 97/330 (29%), Positives = 155/330 (46%), Gaps = 50/330 (15%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 M G D+GG+ IA+G+ ++ + + R P+ YEA + + L E QR G Sbjct: 1 MYYGFDIGGSKIALGIFDK-ARRLQWEKRVATPKESYEAFLQAVEALVQEADQRFGCQ-- 57 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLP------IYMENDANVA 114 S+GIG+PG+ + E G L+ VP A R DL + ++NDAN Sbjct: 58 --GSVGIGIPGMPETEDG------TLYAANVPAASGRRLRADLSERLGRDVRLDNDANCF 109 Query: 115 ALAEATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGI---- 170 AL+EA + + LGTGVG G +L+GK +G + E GH+ + + + Sbjct: 110 ALSEAWDDEFTQYPLVMGLILGTGVGGGLVLNGKSITGHRYITGEFGHIRLPVDALEVVG 169 Query: 171 ------RCNCGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDA 224 RC CG++GC E Y S R L F + +T+ ++ Sbjct: 170 RDFPLTRCGCGQLGCIENYLSG------------RGFAWLYQHFYQ---QSLTSPEIVAL 214 Query: 225 AKQYDEEALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENI 284 +Q D +A + E Y+ LAV + NI+ + DP++++LGGG++N + + +A+ + Sbjct: 215 WQQGDAKAREHVERYLDLLAVCLGNILTIVDPDLLVLGGGLSN-----FTAITEGLAQRL 269 Query: 285 LFKELPYAD---IRKAELGNDAGIIGAAIL 311 LP A I +A G+ G+ GAA L Sbjct: 270 PRHLLPVASVPRIERARHGDAGGMRGAAFL 299 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: 296 Number of extensions: 18 Number of successful extensions: 5 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: 303 Length adjustment: 27 Effective length of query: 285 Effective length of database: 276 Effective search space: 78660 Effective search space used: 78660 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: 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