1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	D	R	S	M	P	V	P	D	G	L	A	G	M	R	V	D	T	G	L	A	R	L	L	G	L	S	R	T	A	A	A	A	L	A	E	E	G	A	V	E	L	N	G	V	P	A	G	K	S	D	R	L	V	S	G	A	L	L
Secondary structure
SS confidence
Disorder		?	?	?																																														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	V	R	L	P	E	A	P	A	P	L	Q	N	T	P	I	D	I	E	G	M	T	I	L	Y	S	D	D	D	I	V	A	V	D	K	P	A	A	V	A	A	H	A	S	V	G	W	T	G	P	T	V	L	G	G	L	A	A	A	G
Secondary structure
SS confidence
Disorder								?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	R	I	T	T	S	G	V	H	E	R	Q	G	I	V	H	R	L	D	V	G	T	S	G	V	M	V	V	A	I	S	E	R	A	Y	T	V	L	K	R	A	F	K	Y	R	T	V	D	K	R	Y	H	A	L	V	Q	G	H	P	D
Secondary structure
SS confidence
Disorder				?	?	?	?																																						?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	S	S	G	T	I	D	A	P	I	G	R	H	R	G	H	E	W	K	F	A	I	T	K	N	G	R	H	S	L	T	H	Y	D	T	L	E	A	F	V	A	A	S	L	L	D	V	H	L	E	T	G	R	T	H	Q	I	R	V	H
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	A	A	L	H	H	P	C	C	G	D	L	V	Y	G	A	D	P	K	L	A	K	R	L	G	L	D	R	Q	W	L	H	A	R	S	L	A	F	A	H	P	A	D	G	R	R	V	E	I	V	S	P	Y	P	A	D	L	Q	H	A
Secondary structure
SS confidence
Disorder																				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		L	K	I	L	R	G	E	G
Secondary structure
SS confidence
Disorder							?	?	?
Disorder confidence

Confidence Key High(9)                     Low (0)

? Disordered ( 10%) Alpha helix ( 24%) Beta strand ( 35%) TM helix ( 5%) (View membrane topology prediction)

Rank Aligned region

PDB 2ist chain A Region: 5 - 307 Aligned: 294 Modelled: 303 Confidence: 100.0% Identity: 35% PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: crystal structure of rlud from e. coli Phyre2 PDB 1qyu chain A Region: 74 - 307 Aligned: 230 Modelled: 234 Confidence: 100.0% Identity: 38% PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: structure of the catalytic domain of 23s rrna pseudouridine2 synthase rlud Phyre2 PDB 1v9f chain A Region: 74 - 307 Aligned: 230 Modelled: 234 Confidence: 100.0% Identity: 38% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1v9f chain A Region: 74 - 307 Aligned: 230 Modelled: 234 Confidence: 100.0% Identity: 38% PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: crystal structure of catalytic domain of pseudouridine2 synthase rlud from escherichia coli Phyre2 PDB 1v9k chain A Region: 83 - 305 Aligned: 216 Modelled: 221 Confidence: 100.0% Identity: 33% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 2i82 chain D Region: 71 - 294 Aligned: 213 Modelled: 224 Confidence: 100.0% Identity: 32% PDB header:lyase/rna Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure Phyre2 PDB 5uba chain A Region: 81 - 305 Aligned: 218 Modelled: 225 Confidence: 100.0% Identity: 28% PDB header:rna binding protein Chain: A: PDB Molecule:rna pseudouridylate synthase domain-containing protein 4; PDBTitle: human rna pseudouridylate synthase domain containing 4 Phyre2 PDB 5vbb chain A Region: 75 - 294 Aligned: 200 Modelled: 220 Confidence: 100.0% Identity: 37% PDB header:rna binding protein Chain: A: PDB Molecule:rna pseudouridylate synthase domain-containing protein 1; PDBTitle: human rna pseudouridylate synthase domain containing 1 Phyre2 PDB 1ksk chain A Region: 13 - 256 Aligned: 206 Modelled: 226 Confidence: 100.0% Identity: 17% PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: structure of rsua Phyre2 PDB 1vio chain A Region: 15 - 256 Aligned: 202 Modelled: 216 Confidence: 100.0% Identity: 20% PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridylate synthase Phyre2 PDB 3dh3 chain C Region: 12 - 254 Aligned: 203 Modelled: 219 Confidence: 100.0% Identity: 18% PDB header:isomerase/rna Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of rluf in complex with a 22 nucleotide rna2 substrate Phyre2 PDB 4lgt chain A Region: 15 - 253 Aligned: 209 Modelled: 239 Confidence: 100.0% Identity: 22% PDB header:isomerase/rna Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase b; PDBTitle: crystal structure of the catalytic domain of rlub in complex with a2 21-nucleotide rna substrate Phyre2 PDB 2oml chain A Region: 86 - 256 Aligned: 158 Modelled: 169 Confidence: 100.0% Identity: 16% PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue Phyre2 PDB 2olw chain B Region: 88 - 256 Aligned: 156 Modelled: 169 Confidence: 100.0% Identity: 17% PDB header:isomerase Chain: B: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue Phyre2 PDB 1vio chain A domain 1 Region: 86 - 257 Aligned: 147 Modelled: 172 Confidence: 100.0% Identity: 19% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1ksk chain A domain 4 Region: 88 - 254 Aligned: 144 Modelled: 167 Confidence: 100.0% Identity: 19% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 2gml chain A Region: 87 - 254 Aligned: 141 Modelled: 154 Confidence: 100.0% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of catalytic domain of e.coli rluf Phyre2 PDB 2k6p chain A Region: 15 - 97 Aligned: 82 Modelled: 83 Confidence: 99.5% Identity: 23% PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein hp_1423; PDBTitle: solution structure of hypothetical protein, hp1423 Phyre2 PDB 5z81 chain A Region: 13 - 88 Aligned: 76 Modelled: 76 Confidence: 99.1% Identity: 24% PDB header:chaperone Chain: A: PDB Molecule:heat shock protein 15; PDBTitle: trimeric structure of vibrio cholerae heat shock protein 15 at 2.32 angstrom resolution Phyre2 PDB 3bbn chain D Region: 15 - 117 Aligned: 100 Modelled: 103 Confidence: 99.0% Identity: 14% PDB header:ribosome Chain: D: PDB Molecule:ribosomal protein s4; PDBTitle: homology model for the spinach chloroplast 30s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome. Phyre2 1 c2istA_ 2 c1qyuA_ 3 d1v9fa_ 4 c1v9fA_ 5 d1v9ka_ 6 c2i82D_ 7 c5ubaA_ 8 c5vbbA_ 9 c1kskA_ 10 c1vioA_ 11 c3dh3C_ 12 c4lgtA_ 13 c2omlA_ 14 c2olwB_ 15 d1vioa1 16 d1kska4 17 c2gmlA_ 18 c2k6pA_ 19 c5z81A_ 20 c3bbnD_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108