Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate Pf6N2E2_2118 Trehalose synthase (EC 5.4.99.16)
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2118 Length = 1114 Score = 226 bits (576), Expect = 4e-63 Identities = 167/560 (29%), Positives = 250/560 (44%), Gaps = 109/560 (19%) Query: 5 PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNG 64 P W+++ VIYQ++ KS+ D+ G GD G+I+ LDY+ LGV+ IWL PFY SP+ D+G Sbjct: 14 PLWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIEKLDYIADLGVNTIWLLPFYPSPRRDDG 73 Query: 65 YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE--SP 122 YD+A Y + YGT+ D + +A R +R+I ++V NHTS QH WF+ A + S Sbjct: 74 YDIAEYRGVSADYGTMADARRFIAEAHKRNLRVITELVINHTSDQHPWFQRARKAKPGSK 133 Query: 123 YRQFYIWRDGEPETPPNNWRSKF---GGSAWRWHAESEQYYLHLFAPEQADLNWENPAVR 179 R FY+W D + + + R F S W W + QY+ H F Q DLN++NP V Sbjct: 134 ARDFYVWSDDDHKY--DGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVI 191 Query: 180 AELKKVCEFWADRGVDGLRLDVV-NLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNR 238 + V +W D G+DGLRLD + LI +D E+L P H+ L + Sbjct: 192 KAVLSVMRYWLDMGIDGLRLDAIPYLIERDGTNNENL-----------PETHDVLKLIRA 240 Query: 239 DV---FTPRGLMTVGEMSSTSLEHCQRY------AALTGSELSMTFNFHHLKVDYPGGEK 289 ++ + R L+ E Q Y + G E M F+F + Y Sbjct: 241 EIDANYPDRMLLAEANQWP---EDTQLYFGDVDAQGMNGDECHMAFHFPLMPRMY----- 292 Query: 290 WTLAKPDFVALKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEY---------- 339 LA+ D + + R + N W A+F NHD+ + E +Y Sbjct: 293 MALAQEDRFPITDILRQTPEIPANCQW-AIFLRNHDELTLEMVTDKERDYLWNYYAADRR 351 Query: 340 -RV----------------PAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDV 382 R+ ++L +L M GTP +Y G+EIGM + Sbjct: 352 ARINLGIRRRLAPLVERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD------------ 399 Query: 383 ESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQWSNGDNAGFTAGE-------PWIG 435 N++ RD RTPMQWS N GF+ + P + Sbjct: 400 ---NIYL------------------GDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMD 438 Query: 436 LGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWK 495 YQ +NVE D S+ ++++A+RKQ G + L P++ + Y RE+ Sbjct: 439 PQYGYQSVNVETQAGDPHSLLNWTRRMLAVRKQSKAFGRGTLKMLSPSNRRILAYTREYT 498 Query: 496 G-----QTLLVIANLSREIQ 510 G + +L +AN+SR Q Sbjct: 499 GPDGKHEIILCVANVSRSAQ 518 Lambda K H 0.320 0.136 0.448 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: 1623 Number of extensions: 82 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 1114 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1073 Effective search space: 547230 Effective search space used: 547230 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 (21.8 bits) S2: 55 (25.8 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