Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate Ga0059261_1580 Ga0059261_1580 Glycosidases
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__Korea:Ga0059261_1580 Length = 541 Score = 319 bits (818), Expect = 2e-91 Identities = 193/535 (36%), Positives = 277/535 (51%), Gaps = 49/535 (9%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 WW+ VIYQIYP+SF D+ G G GDL GV A LD++ LG DAIWL+PF+ SP D GYD Sbjct: 16 WWRGAVIYQIYPRSFADSNGDGIGDLPGVAAHLDHVAALGADAIWLSPFFTSPMRDFGYD 75 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQS-LNKESPYRQ 125 +A+Y +DP +GT+ADFDA++ +A A G+++++D V +HTS +HEWF++S ++++ Sbjct: 76 IADYCGVDPVFGTLADFDAVIEKAHALGLKVIIDQVYSHTSDQHEWFKESRSSRDNAKAD 135 Query: 126 FYIWRDGEPD-ALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELKK 184 +Y+W D + D + P NW+S FGG AW W A GQYYLH F EQ DLN NP V+ Sbjct: 136 WYVWADAKADGSPPTNWQSVFGGPAWTWDARRGQYYLHNFLSEQPDLNLHNPQVQNAALA 195 Query: 185 VCEFWADRGVDGLRLDVVNLISKDQTF----PCDLDGDGRR---------FYTDGPRVHE 231 FW DRGVDG R+D +N D F P G R + P + Sbjct: 196 AARFWLDRGVDGFRVDAINFAMHDPEFRDNPPAPYTGTPRTRPFDFQQHLYNQSHPDIVR 255 Query: 232 FLQEMSRDVFTPRNLMTVGEMSSTSLEHCQQYAALDG-RELSMTFNFHHLKVDYPGGEKW 290 FL+ + TV E+ + E + +A G + L+ + F D+ K Sbjct: 256 FLERHRELTDSYGGRFTVAEVGGPTPE-AEMHAFTQGQKRLNSAYGF-----DFLYANKL 309 Query: 291 TLARPDYVALKALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMV 350 T A +K W H W + + NHD PR +SR+ D E+R A M ++ Sbjct: 310 TPA-----LVKKAVETWPD-THGTGWPSWAFENHDAPRALSRWVD-AEHRDAFAAMKMLL 362 Query: 351 LHGMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSR 410 L ++G ++QGEE+G+T + Q Q P+ + + SR Sbjct: 363 LMCLRGNAILFQGEELGLTQVEIA-----------------YDQLQDPEAIANWPLTLSR 405 Query: 411 DNSRTPMPWHA-GENGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQLITLRKTL 469 D RTPMPW A EN GF+ G PW+ LG ++ + V+ +A S+ + LI LR Sbjct: 406 DGVRTPMPWKADAENLGFTAGRPWLPLGPDHGALAVDRQIAQNGSLLNLTRGLIALRAAN 465 Query: 470 PLLTWGDYEDLLPEHPSLWCYRRQWQGQTLVVAANLSRELQAWQPAEAPGEWKMI 524 P L G E +L +L + R GQ L A NL + AW PA+ P ++++ Sbjct: 466 PALRAGAME-VLAADEALLVFTRIADGQALTCAFNLGKTPLAWHPAQ-PDRFRLL 518 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: 995 Number of extensions: 58 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: 541 Length adjustment: 35 Effective length of query: 516 Effective length of database: 506 Effective search space: 261096 Effective search space used: 261096 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