Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor
Query= BRENDA::Q8R8N4 (312 letters) >FitnessBrowser__SynE:Synpcc7942_2111 Length = 302 Score = 159 bits (403), Expect = 6e-44 Identities = 104/315 (33%), Positives = 157/315 (49%), Gaps = 35/315 (11%) Query: 3 IGVDLGGTNIAVGLVEEDGK----IIATGSRPTKPERGYEAIARDIAELSFELLQRMGIS 58 IGVDLGGT + +G +G+ + P+ P A+ I +L + Sbjct: 8 IGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVRAALVEAIRQLDPQA------- 60 Query: 59 VKDVKSMGIGVPGVADNEKGIVIRAVNLF-WTKVPLAKEIRKYIDLPIYMENDANVAALA 117 + ++GIG PG AD + A+NL WT+VPLA + + P+ + NDAN A L Sbjct: 61 --EALAIGIGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLG 118 Query: 118 EATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKI 177 E G GRG + ++ +TLGTGVG +L+G+++ G A E+G + + G CN G Sbjct: 119 EVWLGGGRGYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELGLITLDPAGPHCNSGNQ 178 Query: 178 GCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFE 237 G E YAS A+ R G K++ D A Q D EA+ ++ Sbjct: 179 GSLEQYASIGAVQRR---------------------FGCDPKDLGDRASQGDPEAIAAWQ 217 Query: 238 EYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKA 297 +Y + LA G+ +++ + PEVIILGGG++ + F L L +E+ +L I A Sbjct: 218 DYGRTLAAGLASLVYVLTPEVIILGGGISGSAAFFLPALTEELHRRVLPTSREDLQIAIA 277 Query: 298 ELGNDAGIIGAAILS 312 LGN+AG +GAA L+ Sbjct: 278 ALGNEAGRVGAAKLA 292 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: 265 Number of extensions: 13 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: 302 Length adjustment: 27 Effective length of query: 285 Effective length of database: 275 Effective search space: 78375 Effective search space used: 78375 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