Align Glucose kinase (characterized, see rationale)
to candidate WP_057506803.1 ABB28_RS00795 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >NCBI__GCF_001431535.1:WP_057506803.1 Length = 341 Score = 249 bits (635), Expect = 9e-71 Identities = 150/319 (47%), Positives = 197/319 (61%), Gaps = 8/319 (2%) Query: 15 PETFVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAP 74 P+ + ADVGGT RLA S+ + +R+YRCA YP LA I+A F A + P Sbjct: 25 PDAQIVADVGGTFARLAW---SHGGAHAPRIDGFRRYRCAQYPSLAAILADFAATATPQP 81 Query: 75 VRRGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGN 134 V+A AG L+ ++ ANLPW ++ + RQQ G+++L L+NDFEAVA A ++ + Sbjct: 82 AA-AVVAIAGL-LQGDTLVNANLPWPVSVDATRQQAGLRSLQLINDFEAVALAIPHVRSD 139 Query: 135 QVMQLSGPAQGAPG-PALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLEVAL 193 ++ L G A A PALVLGPGTGLGAAL +G V L +E GH+AL+A + LE+ + Sbjct: 140 ALVALHGSADPATAWPALVLGPGTGLGAALRFADGARPV-LASEVGHSALSAGTALELDV 198 Query: 194 LQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLAHEA 253 L+ L + HV E LSG GLL LY L LR A A A+ AAA GDD LA E Sbjct: 199 LRLLLQRWDHVDNERVLSGTGLLNLYQCLCQLRGASAHCDDTEALLAAAHRGDDPLARET 258 Query: 254 LQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQ 313 + FCG++GS VGD+ + +G R+ VYLAGG IA F+ S F AR L+KG L L+Q Sbjct: 259 VDVFCGWLGSFVGDLAITFGARA-VYLAGGVSAHIAPFLPDSPFVARFLNKGVLGSVLQQ 317 Query: 314 VPVRIVEHGQLGVIGAASW 332 VPV VEHG+LGV+GAA+W Sbjct: 318 VPVWRVEHGELGVLGAAAW 336 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: 241 Number of extensions: 13 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: 338 Length of database: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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 24 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