Align glucokinase; EC 2.7.1.2 (characterized)
to candidate Echvi_3420 Echvi_3420 Transcriptional regulator/sugar kinase
Query= CharProtDB::CH_014478 (324 letters) >FitnessBrowser__Cola:Echvi_3420 Length = 280 Score = 100 bits (250), Expect = 3e-26 Identities = 76/302 (25%), Positives = 132/302 (43%), Gaps = 50/302 (16%) Query: 9 VGVDLGGTTIKMAFINHYGEIIHKWEINTDVSEQGRKIPTDIAKAIDKKLNDLGE----- 63 +G+DLGGT +++ E N + Q + T+ ++ L L E Sbjct: 3 IGIDLGGTKVQIGL-----------EKNGTIVRQQKAFLTE-KDNLEASLAQLKEFIRPF 50 Query: 64 VKSRLVGIGIGAPGPVNFANGSIEVAVNL-GWEKFPIKDILEVETSLPVVVDNDANIAAI 122 + + GIGIG P V+ A G + N+ WEK +KDILE E ++PV+V+ND N + Sbjct: 51 ISEAVSGIGIGVPSVVDTAQGIVYNVTNIPAWEKVHLKDILEEEFNIPVMVNNDVNCFVL 110 Query: 123 GEMWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCG 182 GE G G + ++ + +GTG+G G++ + ++ G N AGEIG + + + Sbjct: 111 GEHRFGLGKNFQHIVGLCIGTGLGAGLVLDNQLYMGHNCGAGEIGLVPYLDQN------- 163 Query: 183 KTGCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHV 242 +E AS + T+ F AA + D A+ Sbjct: 164 ----IEYYASGNFFTAIH---------------------DTTALQAFHAATAGDHDALQQ 198 Query: 243 VDKVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELA 302 ++ H G A+ + +PE I++GG +S+A ++ F +P + ++ Sbjct: 199 WEEFGLHFGKAMLAAMYTYDPEAIIIGGSISKAYPFFSQALQKTLAEFIYPESFKRLKIL 258 Query: 303 IA 304 I+ Sbjct: 259 IS 260 Lambda K H 0.316 0.137 0.404 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: 240 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 324 Length of database: 280 Length adjustment: 27 Effective length of query: 297 Effective length of database: 253 Effective search space: 75141 Effective search space used: 75141 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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