Align glucokinase (EC 2.7.1.2) (characterized)
to candidate GFF3638 PGA1_262p00420 Transcriptional regulator/sugar kinase
Query= BRENDA::P0A4E1 (317 letters) >FitnessBrowser__Phaeo:GFF3638 Length = 404 Score = 142 bits (358), Expect = 1e-38 Identities = 95/315 (30%), Positives = 157/315 (49%), Gaps = 24/315 (7%) Query: 6 GVDIGGTKIAAGVVDEEGNILSTHKVPT---PTTPEAIVDAIASAVE-----GARVGHEI 57 G+ + I + D EG L +H++P +PE++ + I A++ G +I Sbjct: 91 GLKLSHHAITTLITDFEGTELISHEMPLRGGQMSPESLCEKIVEALDQSCAKGGLTRTQI 150 Query: 58 VAVGIGAAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFG 117 VGIG AG ++ +R+ +Y++ +++ R L +++ + +PV ++NDAN A E+ FG Sbjct: 151 SGVGIGMAGVMDAERNFIYWSSSLNVRNIDLGSALKSHLSMPVFIDNDANLVAKAEHLFG 210 Query: 118 GGKGHRNVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQ 177 G N + +T+ G+G GI+I N++ RG G AEFGHI++ +G LC CG +GC E Sbjct: 211 EGDTRSNFVVVTVEHGVGMGIVIDNQIYRGARGCGAEFGHIKVQLEGALCQCGQRGCLEA 270 Query: 178 YASGRALVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELA 237 Y AL+R A + ER + L +L A +G +A Sbjct: 271 YVGDYALLREANITSGV--ERHKDLASL-------------YAAVAEGDMMAQSILDRAG 315 Query: 238 RWAGAGLADLASLFDPSAFIVGGGLSDEGDLVLDPIRKSYKRWLVGGNWRPVADVIAAQL 297 R GLA++ ++FDP ++ G G L D + + +RW+V + P+ +V Sbjct: 316 RMFAMGLANIVNIFDPQMIVLAGAQLAFGYLSSDKVVEEMRRWVVQVD-GPLPEVRVHGW 374 Query: 298 GNKAGLVGAADLARE 312 GN+ GAA A E Sbjct: 375 GNQMWAKGAAAYAIE 389 Lambda K H 0.318 0.139 0.426 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: 308 Number of extensions: 19 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: 317 Length of database: 404 Length adjustment: 29 Effective length of query: 288 Effective length of database: 375 Effective search space: 108000 Effective search space used: 108000 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 (21.7 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