Align hexokinase (EC 2.7.1.1) (characterized)
to candidate 17293 b3222 putative NAGC-like transcriptional regulator (VIMSS)
Query= BRENDA::Q5RLG0 (302 letters) >FitnessBrowser__Keio:17293 Length = 291 Score = 140 bits (354), Expect = 3e-38 Identities = 102/296 (34%), Positives = 151/296 (51%), Gaps = 13/296 (4%) Query: 1 MKVVGLDLGGTKIAAGVF--DGKRLLSKVVVPTPKEGGERVAEALAEAAERAEREAGVRG 58 M + +D+GGTK+AA + DG+ + + +PTP + EAL +A Sbjct: 1 MTTLAIDIGGTKLAAALIGADGQ-IRDRRELPTP---ASQTPEALRDALSALVSPLQAHA 56 Query: 59 EAIGLGTPGPLDFRRGVIRFAPNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEHHL 118 + + + + G + + N+ G+ FP+ + LE+ T P NDA AAA AE Sbjct: 57 QRVAIASTGIIRDGSLLALNPHNLGGLLHFPLVKTLEQLTNLPTIAINDAQAAAWAEFQ- 115 Query: 119 GAAQGEESSL-YLTVSTGIGGGVVLGGRVLRGERGQGGELGHLTLLPGGPACGCGLEGCL 177 A G+ + + ++TVSTG+GGGVV G ++L G G G +GH P GP CGCG GC+ Sbjct: 116 -ALDGDITDMVFITVSTGVGGGVVSGCKLLTGPGGLAGHIGHTLADPHGPVCGCGRTGCV 174 Query: 178 EALAAGRALERDATYAFQCPVDTRELFRLFQAGDPKAERLVLQAARYVGIGLASLVKAFD 237 EA+A+GR + A D + +F GD +A++L+ ++AR + +A + D Sbjct: 175 EAIASGRGIAA-AAQGELAGADAKTIFTRAGQGDEQAQQLIHRSARTLARLIADIKATTD 233 Query: 238 PGVVVLGGGVALNAPEGYWEALLEAYRRYLQGWEAPPLRRARLGAEAGLLGAALTA 293 VV+GG V L EGY AL+E Y L A +AGLLGAAL A Sbjct: 234 CQCVVVGGSVGL--AEGYL-ALVETYLAQEPAAFHVDLLAAHYRHDAGLLGAALLA 286 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: 135 Number of extensions: 4 Number of successful extensions: 2 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: 291 Length adjustment: 26 Effective length of query: 276 Effective length of database: 265 Effective search space: 73140 Effective search space used: 73140 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 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