Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate AZOBR_RS11685 AZOBR_RS11685 hypothetical protein
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__azobra:AZOBR_RS11685 Length = 299 Score = 126 bits (317), Expect = 6e-34 Identities = 92/273 (33%), Positives = 134/273 (49%), Gaps = 28/273 (10%) Query: 1 MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60 MRIGVDLGGT IA L+ DG A T RGY + +A L +R G + Sbjct: 1 MRIGVDLGGTKIAATLLAPDGTERARHRADTP--RGYAETLQALAGAVAALEERAG---R 55 Query: 61 DVKSMGIGVPGVADNEKGIVIRAVNLFWTKV-PLAKEIRKYIDLPIYMENDANVAALAEA 119 ++G+ +PG+ D G V RAVNL W P A ++ + +D P+ + NDAN L+EA Sbjct: 56 RDATVGLCLPGIVDAAAGTV-RAVNLPWLDGRPFAADLARALDRPVRIANDANAFVLSEA 114 Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGH----MVIGDNG--IRCN 173 GA G+ I LGTGVG G + D +I GA+ A E GH + ++G + C Sbjct: 115 MDGAAAGAPLVFGIILGTGVGGGIVADRRILPGANALAGEWGHNPLPWRVTEDGPPVPCG 174 Query: 174 CGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEAL 233 CG+ GC ET L R + + G E +T + A+ D A Sbjct: 175 CGREGCIETLLCGAGLAR-------------LHLWRTG--ETLTPPEIAARAQSGDAPAR 219 Query: 234 KIFEEYVKYLAVGIVNIINLFDPEVIILGGGVA 266 + + LA + ++NL DP+V+++GGG++ Sbjct: 220 ATLDRHADALARALAAVVNLLDPDVVVVGGGLS 252 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: 249 Number of extensions: 14 Number of successful extensions: 4 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: 299 Length adjustment: 27 Effective length of query: 285 Effective length of database: 272 Effective search space: 77520 Effective search space used: 77520 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