Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_015820817.1 TERTU_RS12910 fructokinase
Query= BRENDA::Q5RLG0 (302 letters) >NCBI__GCF_000023025.1:WP_015820817.1 Length = 296 Score = 105 bits (261), Expect = 2e-27 Identities = 104/317 (32%), Positives = 143/317 (45%), Gaps = 50/317 (15%) Query: 5 GLDLGGTKIAAGVFDGKRLL--SKVVVPTPKEGGERVAEALAEAAERAEREAGVRGEAIG 62 G++ GGTK V G + ++ +P+E +RV + A+G Sbjct: 7 GVEAGGTKFVCAVGTGPSDIHETRFATTSPEETLQRVLAFFSPYKPELA--------ALG 58 Query: 63 LGTPGPLDFRR-----GVIRFAPNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEHH 117 +G GPLD R+ G I P PG Q+ I ++ PV L+ D NAAALAE Sbjct: 59 IGAFGPLDLRQESPTYGFITSTPK-PGWQNTDIAGVIARELQVPVALDTDVNAAALAEGR 117 Query: 118 LGAAQGEESSLYLTVSTGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGP----ACGCGL 173 GAA+G LY+TV TGIGGG+V GGR++ G ELGH LLP P A C Sbjct: 118 WGAARGLSDYLYITVGTGIGGGIVSGGRLVHGL--VHPELGH-CLLPKHPDDTFAGSCPY 174 Query: 174 EG--CLEALAAGRALERDATYAFQCPVDTRELFRLFQAGDPKAERLVLQAARYVGIGLAS 231 G C E LA+G AL A + D L A D + A Y+G+ +A+ Sbjct: 175 HGDRCFEGLASGPAL------AARWGCDPAALPADHHAWDIQ--------AFYMGVAIAN 220 Query: 232 LVKAFDPGVVVLGGGVALNAPEGYWEALLEAYRRYLQGWEAPP---------LRRARLGA 282 V P V+LGGGV A + A YL G+ P + LG+ Sbjct: 221 CVCTLSPQRVILGGGVM--AQSQMLGKVQTATAGYLNGYVRHPAIEENIESYIVLPALGS 278 Query: 283 EAGLLGAALTAYLEVKD 299 +AG+ GA A ++++ Sbjct: 279 QAGVAGALALAGQKIEE 295 Lambda K H 0.319 0.141 0.416 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: 128 Number of extensions: 8 Number of successful extensions: 1 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: 302 Length of database: 296 Length adjustment: 27 Effective length of query: 275 Effective length of database: 269 Effective search space: 73975 Effective search space used: 73975 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 (21.7 bits) S2: 48 (23.1 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