Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate GFF836 Psest_0850 glucokinase, proteobacterial type
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__psRCH2:GFF836 Length = 319 Score = 209 bits (533), Expect = 5e-59 Identities = 126/321 (39%), Positives = 173/321 (53%), Gaps = 11/321 (3%) Query: 3 KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV---EVKDG 59 + ALVGD+GGTNAR AL + + + D+ + E + YL + V+ Sbjct: 2 RLALVGDIGGTNARFALW--RDSRLESVRVLAAADFATPEMAVEYYLASLGLAPGSVEAA 59 Query: 60 CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKK--EHLI 117 C+A A P+ G+ TN+ W + ++ L L +INDF A+++ + + + +I Sbjct: 60 CLACAGPVKGEQFTFTNNHWRLTRSDFCGALQMGELLLINDFAAMALGMTRVGEAGRRMI 119 Query: 118 QFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEI 176 G AEP P V G GTGLGVA L+ + W +LPGEGGHVD EA + ++ Sbjct: 120 CAGEAEP--DAPALVIGPGTGLGVAGLLPLGGGSWRALPGEGGHVDLPVADAHEAALWQM 177 Query: 177 LRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSL 236 L A++GHV AE VLSG GL+ LYR + P P ++T ALA L Sbjct: 178 LFAQLGHVRAEDVLSGGGLLLLYRTVCTVAGLAPRLASPAEVTAAALAGDHVAVA-TLEQ 236 Query: 237 FCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPV 296 FCV +GR GN L LG GGV+I GG+VPRF +FF ASGF F KG Y+ D+PV Sbjct: 237 FCVWLGRVAGNNVLTLGARGGVYIVGGVVPRFADFFAASGFARGFTSKGCMSRYLGDVPV 296 Query: 297 YLIVHDNPGLLGSGAHLRQTL 317 +L+ + PGL G+G L Q L Sbjct: 297 WLVTAEFPGLEGAGVALEQAL 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: 329 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: 321 Length of database: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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