Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF1854 Psest_1893 glucokinase, proteobacterial type
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__psRCH2:GFF1854 Length = 320 Score = 216 bits (549), Expect = 8e-61 Identities = 135/317 (42%), Positives = 169/317 (53%), Gaps = 7/317 (2%) Query: 5 ALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEE--HKVEVKDG-CI 61 ALVGD+GGTNAR AL I Q + DY S E IR YL E ++ + C+ Sbjct: 4 ALVGDIGGTNARFALW--RDQRIEQIRVLPTADYASPELAIRAYLREVDQPLDALEAVCL 61 Query: 62 AIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGG 121 A A P+ GD TN+ W S + LG L +INDFTA+++ + L I Sbjct: 62 ACAGPVGGDLFRFTNNHWQLSREAFCRELGVKELLLINDFTAMALGMTRLHDGERITVCQ 121 Query: 122 AEPVEGKPIAVYGAGTGLGVAHLVHVDKR-WVSLPGEGGHVDFAPNSEEEAIILEILRAE 180 EP G+P V G GTGLGVA L+ + W +LPGEGGH+ SE EA I L Sbjct: 122 GEPEPGRPRLVIGPGTGLGVAGLLPLSGGGWRALPGEGGHICLPIGSEREAAIWAHLHRS 181 Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240 GHV+AE VLSGPGL+ LYRA D + E P IT+ ALA L FC Sbjct: 182 QGHVNAEAVLSGPGLLTLYRACCALDGQQVEFDSPAAITKAALAGDAY-ATAVLEQFCRW 240 Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300 +GR G+ L LG GGV+I GG+VPRF E F SGF A +KG+ Y +PV+L+ Sbjct: 241 LGRIVGDNVLTLGARGGVYIVGGVVPRFAEMFLRSGFSEALREKGQMSRYFDRLPVWLVT 300 Query: 301 HDNPGLLGSGAHLRQTL 317 PGL G+G L+ L Sbjct: 301 APYPGLEGAGVALQPLL 317 Lambda K H 0.322 0.141 0.426 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: 319 Number of extensions: 22 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: 321 Length of database: 320 Length adjustment: 28 Effective length of query: 293 Effective length of database: 292 Effective search space: 85556 Effective search space used: 85556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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