Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate Echvi_3894 Echvi_3894 Transcriptional regulator/sugar kinase
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__Cola:Echvi_3894 Length = 291 Score = 129 bits (325), Expect = 6e-35 Identities = 98/315 (31%), Positives = 150/315 (47%), Gaps = 50/315 (15%) Query: 3 IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62 +G+D+GGT+I G+++ DG++I PT + E I IA+ ++ Sbjct: 8 LGLDIGGTSINAGIMK-DGELIEKREIPTPSQEPQEVILSTIADFIASYFSH------EI 60 Query: 63 KSMGIGVPGVADNEKGIVIRAVNL-FWTKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121 +GIG+PG+ D EKGIV N+ + KV L + + ++ P+Y+ NDAN AL E F Sbjct: 61 DGIGIGIPGLVDAEKGIVYNLENIPAFNKVALKDYLERTLEKPVYINNDANCFALGEYKF 120 Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFE 181 G + V ITLGTG+G+G I +G++Y G A E G + D+ FE Sbjct: 121 GGANKHRHMVGITLGTGIGTGVITNGELYPGFLCGAGEWGGVPYLDSN----------FE 170 Query: 182 TYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEYVK 241 Y S+ KF + TAK + A + D+EALK+F EY Sbjct: 171 NYCSS--------------------KFFR-KLHHTTAKKLAAKAAEGDQEALKLFYEYGT 209 Query: 242 YLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRK----- 296 ++ I I+ + PE I++GG + A + K LK+ V + PY+ I Sbjct: 210 HIGNLIKYILFTYAPEAIVIGGSIRKAFPYFSKGLKETV------ETFPYSSISDNLTIY 263 Query: 297 AELGNDAGIIGAAIL 311 +D+ I+GAA L Sbjct: 264 TSSFDDSAIMGAAAL 278 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: 289 Number of extensions: 20 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: 291 Length adjustment: 27 Effective length of query: 285 Effective length of database: 264 Effective search space: 75240 Effective search space used: 75240 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