Align Glucose kinase (characterized, see rationale)
to candidate GFF4431 PS417_22685 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__WCS417:GFF4431 Length = 318 Score = 139 bits (351), Expect = 7e-38 Identities = 104/314 (33%), Positives = 146/314 (46%), Gaps = 12/314 (3%) Query: 19 VAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAE--LSCAPVR 76 + D+GGT+ R AL + + R + AD+ + + + E L + Sbjct: 5 LVGDIGGTNARFALWRDQE-------LHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIG 57 Query: 77 RGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQV 136 ++ AG D T N W L+ + L + L LVNDF A+A + ++ Sbjct: 58 AVCLSVAGPVSGDEFKFTNN-HWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEF 116 Query: 137 MQLSGPAQGAPGPALVLGPGTGLGAALWIPNG-GNSVVLPTEAGHAALAAASDLEVALLQ 195 + PA+V+GPGTGLG + G G LP E GH L +S E L Q Sbjct: 117 RVVCEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQ 176 Query: 196 ELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEALQ 255 + HV+ E LSG GL LY A+ + V TP A+TAA LAGD V A E L Sbjct: 177 HIYTEIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPV-AMEVLD 235 Query: 256 TFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVP 315 F ++G V G+ +L G R GVY+ GG +P+ ADF S FA DKG + + +P Sbjct: 236 QFSIWLGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIP 295 Query: 316 VRIVEHGQLGVIGA 329 V +V G+ GA Sbjct: 296 VWLVTAPYSGLTGA 309 Lambda K H 0.321 0.136 0.407 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: 228 Number of extensions: 16 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: 338 Length of database: 318 Length adjustment: 28 Effective length of query: 310 Effective length of database: 290 Effective search space: 89900 Effective search space used: 89900 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: 49 (23.5 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