Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate AO356_05215 AO356_05215 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05215 Length = 318 Score = 207 bits (526), Expect = 4e-58 Identities = 125/318 (39%), Positives = 171/318 (53%), Gaps = 7/318 (2%) Query: 3 KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVE---VKDG 59 K ALVGD+GGTNAR AL + + + DY E I+VYL ++ + Sbjct: 2 KLALVGDIGGTNARFALWK--DHTLENIQVLATADYACPEDAIQVYLGGLGLKPGAIGSV 59 Query: 60 CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF 119 C+++A P++GD TN+ W S K L L ++NDF+A+++ + L+ + Sbjct: 60 CLSVAGPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVV 119 Query: 120 GGAEPVEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEILR 178 P +P V G GTGLGV L+ + + R+ +LPGEGGHVD +S E + + + Sbjct: 120 CEGTPEPMRPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIY 179 Query: 179 AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFC 238 EIGHVSAE LSG GL +YRAI D +P P+ IT LA L FC Sbjct: 180 NEIGHVSAETALSGSGLPRVYRAICAVDGHVPVLDTPESITAAGLAGDPI-ALEVLEQFC 238 Query: 239 VIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYL 298 +GR GN L LG GGV+I GG+VPRF +FF SGF F DKG +Y IPV+L Sbjct: 239 RWLGRVAGNNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWL 298 Query: 299 IVHDNPGLLGSGAHLRQT 316 + GL+G+G L Q+ Sbjct: 299 VTAPYSGLMGAGVALEQS 316 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: 356 Number of extensions: 19 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: 318 Length adjustment: 28 Effective length of query: 293 Effective length of database: 290 Effective search space: 84970 Effective search space used: 84970 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