Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate GFF3717 Psest_3786 Glycosidases
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__psRCH2:GFF3717 Length = 539 Score = 198 bits (503), Expect = 5e-55 Identities = 164/546 (30%), Positives = 251/546 (45%), Gaps = 106/546 (19%) Query: 5 PHWWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNG 64 P W++N IYQI P F+D+ G G GDLRG+T RLDY++ LG A+WL PFY SP D G Sbjct: 3 PLWYRNAAIYQIDPTLFRDSNGDGCGDLRGITERLDYIRGLGCTAVWLMPFYQSPFEDAG 62 Query: 65 YDVANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQS-LNKESPY 123 YD++++ +D +G +AD AL+ +A+ G+ +++++V+ HTS +H+WF+++ ++ SPY Sbjct: 63 YDISDHLQVDERFGDLADIVALLEKAEELGLHVIIELVVQHTSIQHKWFQEARRDRNSPY 122 Query: 124 RQFYIWRDGEPDALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELK 183 R +YIW D EPD + W W ++GQYY HLF + DL+ NP V E++ Sbjct: 123 RDYYIWAD-EPDDFMEPIFPTVEDSIWTWDEEAGQYYRHLFYKHEPDLDLTNPRVIHEIE 181 Query: 184 KVCEFWADRGVDGLRLD-VVNLISKDQTFPCDLDGDGRRFYTDGPRVHEFLQEMSRDVFT 242 ++ FW GV G R+D V+++ + G+ + Y +L E RD T Sbjct: 182 RIMSFWLRLGVSGFRIDAAVHMVRQAG------GGELEKGY--------WLLEHMRDFVT 227 Query: 243 PRNLMTV--GEMSSTSLEHCQQYAALDGRELSMTFNF---HHLKVDYPGGEKWTLARPDY 297 R TV GE+ T + +Y + +++ +F +HL + + L R Sbjct: 228 MRRPETVLLGEI-DTDPDKYVEYFGDEADRVTLLLDFWTNNHLFLSLARQQAEPLVR--- 283 Query: 298 VALKALFRHWQQGMHNRAWNALFWCNHDQ------------------------------- 326 AL + Q + + AL+ NHD+ Sbjct: 284 -ALNS-----QPLPPSHSQYALWIRNHDELSLDRLEEDERNEVMDTFAPDENMRAYNRGI 337 Query: 327 PRIVSRFGDEGEYRVTAAKMLAMVLHGMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHN 386 R ++ D E R+ A L L + GTP I GEEIGM + D++ Sbjct: 338 RRRLAPMLDGDERRIAATHAL---LFSLPGTPIIRYGEEIGMGD----------DLDR-- 382 Query: 387 MFIERAAQGQSPDELLAILASKSRDNSRTPMPWHAGENGGFS--DGE---PWIGLGD-NY 440 E LA+ RTPM W N GFS GE P I G Y Sbjct: 383 ------------PERLAV---------RTPMQWSNEPNAGFSCTKGELAAPVIDEGPFTY 421 Query: 441 QEINVEAALADPDSVFYTYQQLITLRKTLPLLTWGDYEDLLPEHPSLWCYRRQWQGQTLV 500 ++INV A DS+ +I R L + G + P+++ R G T++ Sbjct: 422 EKINVFAQTLRSDSLMARTGNMIRTRIGLREIGIGKRTTVEVNDPAVFAIRHD-NGSTVL 480 Query: 501 VAANLS 506 + NL+ Sbjct: 481 MLVNLA 486 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: 885 Number of extensions: 43 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: 3 Length of query: 551 Length of database: 539 Length adjustment: 35 Effective length of query: 516 Effective length of database: 504 Effective search space: 260064 Effective search space used: 260064 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