Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_014265891.1 ACIX8_RS13435 ROK family protein
Query= BRENDA::Q5RLG0 (302 letters) >NCBI__GCF_000178955.2:WP_014265891.1 Length = 337 Score = 169 bits (429), Expect = 6e-47 Identities = 119/329 (36%), Positives = 167/329 (50%), Gaps = 40/329 (12%) Query: 4 VGLDLGGTKIA-AGVFDGKRLLSKVVVPTP-KEGGERVAEALAEAAER-AEREAGVRGEA 60 +G+DLGGT + A DG L ++VPT EG +RV + EA A ++ G R A Sbjct: 7 IGVDLGGTNLRIASYTDGTDFLDTILVPTRLAEGRDRVVRDMCEAINALAIKDYGNRRLA 66 Query: 61 -IGLGTPGPLDFRRGVIRFAPNIPGVQDFPIRRILEEATGRPVFLENDANAAALAEHHLG 119 +G+GTPGPL+ G++R PN+PG F +R+ +E GRPV +E+DAN AALAE G Sbjct: 67 GVGIGTPGPLELPEGILRNPPNLPGWDGFDLRQAVESTLGRPVEIESDANIAALAEFKFG 126 Query: 120 A--AQGEESSLYLTVSTGIGGGVVLGGRVLRGERGQGGELGHLTLLP-GGPACGCGLEGC 176 A A +S LT+ TG+G G++LG + G G GGE GH+ + GG CGCG GC Sbjct: 127 AGRAHNVKSLCMLTLGTGVGNGLILGKHIWHGSTGMGGEGGHIVVQDIGGAPCGCGGYGC 186 Query: 177 LEALAAGRALERDATYAF--QCPVDTRELFRLFQAGDPKAERLVLQAARYVGIGLASLVK 234 LE A+ A+ R A P + E+ L AG+ + ++ + + IGL L+ Sbjct: 187 LEQYASAPAIVRMAGELMGPAAPSTSEEIAHLAMAGNQQCLQVFERVGHALAIGLTGLIN 246 Query: 235 AFDPGVVVLGGGVA----------------------LNAPEGYWEALLEAYRRYLQGWEA 272 + + ++GGGV L AP+ LE ++ Y+ G Sbjct: 247 TLNLPLYLIGGGVCEAWDLFAPAMFRELPVRSYVYRLTAPDVLQPEHLERHKTYILG--- 303 Query: 273 PPLRRARLGAEAGLLGAALTAYLEVKDGS 301 A+LG AGLLGA L L K GS Sbjct: 304 -----AQLGPSAGLLGACLLP-LHQKSGS 326 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: 180 Number of extensions: 8 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: 337 Length adjustment: 28 Effective length of query: 274 Effective length of database: 309 Effective search space: 84666 Effective search space used: 84666 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