Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate Pf1N1B4_600 Glucokinase (EC 2.7.1.2)
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 Length = 319 Score = 203 bits (516), Expect = 5e-57 Identities = 124/321 (38%), Positives = 176/321 (54%), Gaps = 11/321 (3%) Query: 3 KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKV---EVKDG 59 K ALVGD+GGTNAR AL + ++ + + D+ S E I +YL + + Sbjct: 2 KLALVGDIGGTNARFALWK--NQQLESVQVLATADHASPEEAIALYLSGLGLAPGSIGSV 59 Query: 60 CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLK--KEHLI 117 C+++A P++GD TN+ W S K L L ++NDF+A+++ + L+ + ++ Sbjct: 60 CLSVAGPVSGDEFKFTNNHWRLSRQGFCKTLQVDQLLLVNDFSAMALGMTRLQPGEFRVV 119 Query: 118 QFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEI 176 G EP+ +P V G GTGLGV L+ + + R+ LPGEGGHVD +S E + + Sbjct: 120 CEGTPEPL--RPAVVIGPGTGLGVGTLLDLGEGRFAPLPGEGGHVDLPLSSPRETQLWQH 177 Query: 177 LRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSL 236 + EIGHVSAE LSG GL +YRAI D P P+ IT+ LA L Sbjct: 178 IFNEIGHVSAETALSGSGLPRVYRAICAVDGHTPVLDTPEAITKAGLAGDPI-ALEVLEQ 236 Query: 237 FCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPV 296 FC +GR GN L G GGV+I GG++PRF +FF SGF F DKG +Y IPV Sbjct: 237 FCCWLGRVAGNNVLTTGARGGVYIVGGVIPRFADFFIESGFARCFADKGCMSDYFKGIPV 296 Query: 297 YLIVHDNPGLLGSGAHLRQTL 317 +L+ GL+G+G L Q++ Sbjct: 297 WLVTAPYSGLVGAGVALEQSI 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: 330 Number of extensions: 22 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