Align Trehalase; Alpha,alpha-trehalase; Alpha,alpha-trehalose glucohydrolase; EC 3.2.1.28 (characterized)
to candidate GFF1902 PS417_09685 glucoamylase
Query= SwissProt::P71741 (680 letters) >FitnessBrowser__WCS417:GFF1902 Length = 608 Score = 363 bits (931), Expect = e-104 Identities = 226/616 (36%), Positives = 324/616 (52%), Gaps = 47/616 (7%) Query: 53 PIADYAFLSDWETTCLISPAGSVEWLCVPRPDSPSVFGAILDR-SAGHFRLGPYGVSVPS 111 PI + + D + L++ GS+++ C P DSPS+F ++LD AG F+L P +P+ Sbjct: 11 PIDAHGIIGDMRSAALVNDKGSIDFFCWPEFDSPSIFCSLLDSPDAGIFQLTP---DLPN 67 Query: 112 ARR---YLPGSLIMETTWQTHTGWLIVRDALVMGKWHDIERRSRTHRRTPMDWDAEHILL 168 ARR YLP + +++T W + + + D L + + D D +L+ Sbjct: 68 ARREQIYLPDTNVLQTRWLSDEAVVEITDLLAISE----------------DVDDLPLLI 111 Query: 169 RTVRCVSGTVELMMSCEPAFDYHRLGATWEYSAEAYGEAIARANTEPDAHPTLRLTTNLR 228 R VR VSG ++ + C DY R T + G A + P LRL+ + Sbjct: 112 RRVRVVSGKADIHLRCAVRHDYAR---TPTQATRDDGTVCFSA----EGQPGLRLSGSYP 164 Query: 229 IGLEGREARARTRMKEGDDVFVALSWTKHPPPQTYDEAADK------MWQTTECWRQWIN 282 + ++ A A + + + L + DE D + T WR WI Sbjct: 165 LQIKDGAAVASFTLGQEEGAEFVLGGQE-------DERVDSRCTDLALAHTLTFWRGWIA 217 Query: 283 IGNFPDHPWRAYLQRSALTLKGLTYSPTGALLAASTTSLPETPRGERNWDYRYAWIRDST 342 N+ WR + RSAL LK LT GA++AA+T LPETP GERNWDYRY WIRD++ Sbjct: 218 QSNYRGR-WREMVNRSALALKLLTSRKHGAIIAAATFGLPETPGGERNWDYRYTWIRDAS 276 Query: 343 FALWGLYTLGLDREADDFFAFIADVSGANNNERHPLQVMYGVGGERSLVEAELHHLSGYD 402 F ++ LG EA+ + ++ N+ + ++YG+ G + L EAEL H +G+ Sbjct: 277 FTVYAFMRLGFVEEANAYMRWLKGRVSDCCNQPTKINILYGIDGRQELPEAELDHFAGHG 336 Query: 403 HARPVRIGNGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPVLKRQVEEAIKHWREPD 462 A+PVRIGN A++Q Q DI+G ++D+ YL K E + W ++ + W D Sbjct: 337 GAKPVRIGNEAFDQIQLDIYGELMDAVYLVNKYGEAISHEGWKHTVEVADQVCEIWNTKD 396 Query: 463 RGIWEVRGEPQHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKADILEH-GV 521 GIWE+RGE HF S++MCWVALDR +LA ++ + +W I ADI + Sbjct: 397 VGIWEMRGEQHHFLHSRLMCWVALDRAIRLASKRSLPAPFARWDQTRQAIYADIWSNFWN 456 Query: 522 DSRGVFTQRYGDEALDASLLLVVLTRFLPPDDPRVRNTVLAIADELTEDGLVLRYRVHET 581 + RG F Q G ALD S+LL+ L RF+ DPR +T+ AI L DG+V RYR ++ Sbjct: 457 EERGHFVQHTGTTALDGSMLLMPLVRFVAATDPRWLSTLEAIQKSLVRDGMVYRYRNDDS 516 Query: 582 D-DGLSGEEGTFTICSFWLVSALVEIGEVGRAKRLCERLLSFASPLLLYAEEIEPRSGRH 640 DGL G EG F CSFW V L G+V +A E+LL +A+PL LYAEE + RH Sbjct: 517 QIDGLQGTEGAFAACSFWYVECLARAGQVEKAHLEFEQLLRYANPLGLYAEEFD-NQARH 575 Query: 641 LGNFPQAFTHLALINA 656 LGN PQA +HLALI+A Sbjct: 576 LGNTPQALSHLALISA 591 Lambda K H 0.319 0.134 0.425 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: 1196 Number of extensions: 65 Number of successful extensions: 7 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: 680 Length of database: 608 Length adjustment: 38 Effective length of query: 642 Effective length of database: 570 Effective search space: 365940 Effective search space used: 365940 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: 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