Align Glucose kinase (characterized, see rationale)
to candidate Ac3H11_2067 Glucokinase (EC 2.7.1.2)
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2067 Length = 325 Score = 166 bits (421), Expect = 6e-46 Identities = 111/315 (35%), Positives = 159/315 (50%), Gaps = 11/315 (3%) Query: 21 ADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAELSCAPVRRGVI 80 AD+GGT++RLA P VL CA +P + +AA+ E+ R Sbjct: 8 ADIGGTNIRLAWQASPTGPLNDTRVLP-----CAQFPTVDAALAAYLQEVGVPTPREAAF 62 Query: 81 ASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANYMTGNQVMQLS 140 A D +T N W + +R+ G + L ++NDF A+A A +T Q+ + Sbjct: 63 GIANPVTGDAIRMT-NHSWSFSQRAVREAFGFERLVVINDFTALALALPLLTPEQLRPVG 121 Query: 141 GPAQGAPGPAL-VLGPGTGLGAA-LWIPNGGN-SVVLPTEAGHAALAAASDLEVALLQEL 197 G A PG A+ +LGPGTGLG + L P G + V L E GH LAA + E +L L Sbjct: 122 GGA-AVPGAAIALLGPGTGLGVSGLVFPPGSHLGVPLSGEGGHVTLAAQTQREFDVLAIL 180 Query: 198 RRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAA-VTAAALAGDDVLAHEALQT 256 + HV+ E + G GL+ LY AL L + AA VT AL +D LA EAL+ Sbjct: 181 QERYGHVSAERAVCGAGLVDLYHALRRLAQRGGKEISSAAQVTELALQANDPLALEALEL 240 Query: 257 FCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPALEQVPV 316 FCGF+GSV G++ L G R GV++ GG +P++ + +S F AR KG + L +P Sbjct: 241 FCGFLGSVAGNLALTLGARGGVFIGGGMVPRLGAWFDQSPFRARFESKGRFQSYLAGIPC 300 Query: 317 RIVEHGQLGVIGAAS 331 +++ G + AS Sbjct: 301 WVIDPGATPALHGAS 315 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: 239 Number of extensions: 13 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: 325 Length adjustment: 28 Effective length of query: 310 Effective length of database: 297 Effective search space: 92070 Effective search space used: 92070 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