Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate GFF4500 PS417_23035 PTS mannose transporter subunit IIC
Query= BRENDA::P37349 (472 letters) >FitnessBrowser__WCS417:GFF4500 Length = 838 Score = 107 bits (267), Expect = 2e-27 Identities = 106/348 (30%), Positives = 141/348 (40%), Gaps = 26/348 (7%) Query: 134 QLGLPSSDTEISDTCPAYDEEAR----SLAVVIKNRNGLHVRPASRLVYTLSTFNADMLL 189 + G P S A DEE S + + N NGLH RPA+ FNA + L Sbjct: 142 ETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAAKGFNASIYL 201 Query: 190 EKNGKCVTPESINQIALLQVRYNDTLRLIAKGPEAEEALIAFRQLAEDNFGETE-EVAPP 248 K + +S+ I LQ DTL++ A G +AE A+ A L + GE VA P Sbjct: 202 HKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEP 261 Query: 249 T--------LRPVPPVSGKAFYYQPVLCTVQAKSTLTVEEEQDRLRQAIDFTLLDLMTLT 300 LR V G AF VQ V EQ A + L L Sbjct: 262 VATQSSATLLRGVCASPGSAFGQ-----VVQVTDPELVITEQGT-GGATERAALTRGLLA 315 Query: 301 AKAEASGLDDIAA------IFSGHHTLLDDPELLAAASELLQHEHCTAEYAWQQVLKELS 354 A L D AA IF H LL+DP LL A LL E +A +AW Sbjct: 316 ANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLG-EGKSAAFAWNSATLATV 374 Query: 355 QQYQQLDDEYLQARYIDVDDLLHRTLVHLTQTKEELPQFNSPTILLAENIYPSTVLQLDP 414 +Q L + + R D+ D+ R L + ++ IL+AE + PS LD Sbjct: 375 TLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDT 434 Query: 415 AVVKGICLSAGSPVSHSALIARELGIGWICQQGEKLYAIQPEETLTLD 462 V G AG SH A++AR LG+ IC ++ A+ + + LD Sbjct: 435 RKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLD 482 Lambda K H 0.316 0.132 0.368 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: 766 Number of extensions: 29 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: 472 Length of database: 838 Length adjustment: 38 Effective length of query: 434 Effective length of database: 800 Effective search space: 347200 Effective search space used: 347200 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: 54 (25.4 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