Align trehalose-6-phosphate hydrolase (TreC) (EC 3.2.1.93) (characterized)
to candidate AO353_22940 AO353_22940 alpha-amylase
Query= CAZy::AAC77196.1 (551 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22940 Length = 1113 Score = 226 bits (577), Expect = 3e-63 Identities = 167/556 (30%), Positives = 251/556 (45%), Gaps = 103/556 (18%) Query: 5 PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNG 64 P W+++ VIYQ++ KS+ D+ G GD G+I LDY+ +LGV+ IWL PFY SP+ D+G Sbjct: 14 PLWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIAELGVNTIWLLPFYPSPRRDDG 73 Query: 65 YDVANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREALNKE--SP 122 YD+A Y + YGTL D + +A +RG+R+I ++V NHTS QH WF+ A + S Sbjct: 74 YDIAEYRGVHRDYGTLTDAKRFIAEAHNRGLRVITELVINHTSDQHPWFQRARKAKPGSA 133 Query: 123 YRQFYIWRDGEPETPPNNWRSKF---GGSAWRWHAESEQYYLHLFAPEQADLNWENPAVR 179 R FY+W D + + + R F S W W + QY+ H F Q DLN++NP V Sbjct: 134 ARDFYVWSDDDQKY--DGTRIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQVM 191 Query: 180 AELKKVCEFWADRGVDGLRLDVV-NLISKDPRFPEDLDGDGRRFYTDGPRAHEFLHEMNR 238 + V +W D G+DGLRLD + LI +D E+L P H L ++ Sbjct: 192 KAVLSVMRYWLDLGIDGLRLDAIPYLIERDGTNNENL-----------PETHAVLKQIRA 240 Query: 239 DV---FTPRGLMTVGEM--SSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLA 293 ++ + R L+ T L + G E M F+F + Y LA Sbjct: 241 EIDAHYPDRMLLAEANQWPEDTQLYFGDVHGD-NGDECHMAFHFPLMPRMY-----MALA 294 Query: 294 KPDFVALKTLFRHWQQGMHNVAWNALFWCNHDQPRIVSRFGDEGEY-----------RV- 341 + D + + R + N W A+F NHD+ + E +Y R+ Sbjct: 295 QEDRFPITDILRQTPEIPANCQW-AIFLRNHDELTLEMVTDKERDYLWNYYAADRRARIN 353 Query: 342 ---------------PAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFTRITDYRDVESLN 386 ++L +L M GTP +Y G+EIGM + N Sbjct: 354 LGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD---------------N 398 Query: 387 MFAELRNDGRDADELLAILASKSRDNSRTPMQWSNGDNAGFTAGE-------PWIGLGDN 439 ++ RD RTPMQWS N GF+ + P + Sbjct: 399 IYL------------------GDRDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPLYG 440 Query: 440 YQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQDLLPNSPVLWCYRREWKG--- 496 Y +NVE D S+ ++++A+RKQ G+ + L P++ + Y RE+ G Sbjct: 441 YLSVNVETQAGDPHSLLNWTRRMLAIRKQSKAFGRGSLKMLSPSNRRILAYTREYTGDDG 500 Query: 497 --QTLLVIANLSREIQ 510 + +L +AN+SR Q Sbjct: 501 KHEIILCVANVSRSAQ 516 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: 1614 Number of extensions: 94 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: 1113 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1072 Effective search space: 546720 Effective search space used: 546720 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