Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate N515DRAFT_3391 N515DRAFT_3391 Glycosidase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Dyella79:N515DRAFT_3391 Length = 526 Score = 226 bits (576), Expect = 2e-63 Identities = 167/508 (32%), Positives = 230/508 (45%), Gaps = 80/508 (15%) Query: 10 NGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYDVAN 69 +GV Y+I+ +++ DT G G GDL GVTA+LDYLQ LGV IWL P SP +GYDV + Sbjct: 43 SGVWYEIFVRAWYDTNGDGIGDLNGVTAKLDYLQSLGVSGIWLMPINPSPTY-HGYDVTD 101 Query: 70 YTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQSLNKESPYRQFYIW 129 Y I+P YG+MADF+ LV+EA RGI +++D+V+NH+S +H WF+ +L+ S YR +Y W Sbjct: 102 YEGINPQYGSMADFEKLVSEAHKRGIEVIIDLVINHSSDQHPWFKSALDPHSQYRHWYTW 161 Query: 130 RDGEPDALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELKKVCEFW 189 + D S G A WHA+ Q+YL F DLN++ PAVR E+ + +FW Sbjct: 162 AGKDTDL---KAISAVDGPA--WHANGKQHYLGDFTGAMPDLNYDEPAVRREMIAIGKFW 216 Query: 190 ADRGVDGLRLDVVNLISKDQTFPCDLDGDGRRFYTDGPRVHEFLQEMSRDVFTPRNLMTV 249 +G DG RLD I D R+ + L+++ DV+ V Sbjct: 217 LSKGADGFRLDAARHIYDDLKSDNGQPAVIRKNAQWWSEFRQGLRQVRPDVY------LV 270 Query: 250 GEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKWTLARPDYVA--LKALFRHW 307 GE+S+ Y G D+P E+ + A L AL Sbjct: 271 GEVSARQPGELAPYLPALGSVF-----------DFPLAEQLIASAKQEQAGKLPALLTES 319 Query: 308 QQGMHNRAW----NALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMVLHGMQGTPYIYQG 363 H A +A F NHDQ R++S+ G + + TAA ML + G PYIY G Sbjct: 320 YAAFHAAAGDDYADAPFLSNHDQERVLSQLGGDLHHMRTAAAMLLT----LPGRPYIYYG 375 Query: 364 EEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSRDNSRTPMPWHAGE 423 EEIGM G+ PDE N R PM W Sbjct: 376 EEIGML-------------------------GRKPDE-----------NLREPMRWQR-- 397 Query: 424 NGGFSDGEPWIGLGDNYQ-----EINVEAALADPDSVFYTYQQLITLRKTLPLLTWGDYE 478 + P Y +++V+A PDS+ Y+ LI R +P L G Sbjct: 398 ----TPAAPGDSRWKTYSVKQGGDVSVQAERDQPDSLLNLYRTLIHWRVEVPALRDGALR 453 Query: 479 DLLPEHPSLWCYRRQWQGQTLVVAANLS 506 + P+L Y R +V NLS Sbjct: 454 VIATGKPALVAYERATADSRALVVHNLS 481 Lambda K H 0.320 0.136 0.446 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: 932 Number of extensions: 50 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: 551 Length of database: 526 Length adjustment: 35 Effective length of query: 516 Effective length of database: 491 Effective search space: 253356 Effective search space used: 253356 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: 52 (24.6 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