Citrus Sinensis ID: 023907

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-----
Protein Sequence
MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHcccccccccccccccccccEEEEEccHHHHHHHHHHHHHccccccccccHHHccccccEEEEEEEccccccccEEEccccccccccccEEEEEEEccccccccccEEEEEEEEEEccccEEEEEEEEccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccHHHHccccccccccccEEEEEccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHHHccccccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHcccccccccEEEccccccccccccEEEEEEEEccccccccccEEEEEEEEcccccEEEEEEEEccccccEEEEEHHHHcccccccccccccccccccccccHHccccccccEEEEccccccHHHHHHHHHHHHccHHHHHHHHccccccHHHHHHcccccccccccccEEEEEccccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mpvqggigiRRSIDELAATCltydysepprlvhrldrdssgilvmgrtQTSATVLHSIFREktfsaskedndneKRILQRWYWALVVgtprcskgvisaplgkvvvdngksdritvvnndqimSAQHAVTRYqvikpschgytwlklspltgrkhqlRVHCAevlgtpivgdykygwqthrkwkqfhpsdlskdsneeipkektlhfgldlesgsilekqprlhlhckemtlpnvSQAIQKVQLssgcdvskletlklvaplpshmqrswdvlns
Flexible Loop (DISEMBL)
mpvqggigirrSIDELAATCLTydysepprlvhRLDRDSSGILVMGRTQTSATVLHSIfrektfsaskedndnekRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQfhpsdlskdsneeIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLklvaplpshmqrswdvlns
Low Complexity Region (SEG)
MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Disordered region (IsUnstruct)
******IGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFRE**************RILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQF*******************HFGLDLE**SILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVA***************
Disordered Region (DISOPRED)
MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSD************AQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Disordered Region (DISEMBL)
MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Disordered Region (DISPRO)
*PVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	275	2.2.26 [Sep-21-2011]
Q9LT72	477	RNA pseudourine synthase	yes	no	0.978	0.563	0.607	5e-87
Q5XET6	478	RNA pseudourine synthase	no	no	0.989	0.569	0.450	2e-68
Q0J4D4	475	RNA pseudourine synthase	yes	no	0.989	0.572	0.451	6e-68
Q69K07	448	RNA pseudourine synthase	no	no	0.552	0.339	0.557	1e-41
Q28C59	324	RNA pseudouridylate synth	yes	no	0.712	0.604	0.308	9e-23
Q68XB2	303	Ribosomal large subunit p	yes	no	0.610	0.554	0.314	4e-20
Q4QQT0	377	RNA pseudouridylate synth	yes	no	0.810	0.591	0.278	2e-19
Q92IS6	303	Ribosomal large subunit p	yes	no	0.610	0.554	0.309	2e-18
Q9ZDR7	303	Ribosomal large subunit p	yes	no	0.610	0.554	0.304	2e-18
Q96CM3	377	RNA pseudouridylate synth	yes	no	0.752	0.549	0.276	3e-18

>sp|Q9LT72|PUS4_ARATH RNA pseudourine synthase 4, mitochondrial OS=Arabidopsis thaliana GN=At3g19440 PE=2 SV=1

 Score =  320 bits (821), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 167/275 (60%), Positives = 210/275 (76%), Gaps = 6/275 (2%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           + VQGG GI+ SIDELAA+CL +D SE PRLVHRLDRD SG+LV+ RTQT+ATVLHSIFR
Sbjct: 201 LAVQGGSGIKTSIDELAASCLKFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFR 260

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  AS        + L+R Y ALV+G P   +G ISAPL KVVVD+GKS+RITV +N 
Sbjct: 261 EKTTGASAYGVKKNVKSLKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNG 320

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           +++S QHA+T Y+VI+ S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct: 321 ELVSTQHAITEYRVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAH 380

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           +  + F    +S ++N    K+ +  FGLDL+ G +  KQP LHLH K++ LPN+SQ ++
Sbjct: 381 KAREPF----VSSENNPT--KQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLE 434

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
           K+Q+SS  D+S L++LK  APLPSHMQ S+++L S
Sbjct: 435 KMQVSSDSDISDLDSLKFDAPLPSHMQLSFNLLKS 469

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp|Q5XET6|PUS3_ARATH RNA pseudourine synthase 3, mitochondrial OS=Arabidopsis thaliana GN=At1g78910 PE=2 SV=1

 Score =  258 bits (660), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 127/282 (45%), Positives = 191/282 (67%), Gaps = 10/282 (3%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +PV+G + I  S+D LAA  L++   E PRLVHRLDR++SG+LVMGRT+ S   LHS+F 
Sbjct: 197 LPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGLLVMGRTKESIDYLHSVFS 256

Query: 61  E-KTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNN 119
           + K  ++S +  +     + + YWALV+G+P+  +G+ISAPL KV++D+GK+DR+ +   
Sbjct: 257 DYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLDDGKTDRVVLAQG 316

Query: 120 DQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT 179
               ++Q A+T Y+V+ P  +G +W++L P+T RKHQLRVHCAE LGTPIVGDYKYGW  
Sbjct: 317 SGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHCAEALGTPIVGDYKYGWFV 376

Query: 180 HRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAI 239
           H++WKQ    D+   + +  P +     GLD++ GS+L K P LHLHC+EM LPN+++ +
Sbjct: 377 HKRWKQMPQVDIEPTTGK--PYKLRRPEGLDVQKGSVLSKVPLLHLHCREMVLPNIAKFL 434

Query: 240 QKVQ------LSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
             +       L +G  + K + L+ VA +PSHM+ SW++++S
Sbjct: 435 HVMNQQETEPLHTGI-IDKPDLLRFVASMPSHMKISWNLMSS 475

Arabidopsis thaliana (taxid: 3702)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|Q0J4D4|PUS3_ORYSJ RNA pseudourine synthase 3, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0520100 PE=2 SV=1

 Score =  257 bits (657), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 127/281 (45%), Positives = 187/281 (66%), Gaps = 9/281 (3%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +P++G + +  S+D LAA  L+Y   E P+LVHRLDR+SSG+L+ GRT+ S T LH +F 
Sbjct: 195 VPMKGNLPVHNSMDVLAAAALSYGNEEGPKLVHRLDRESSGLLLFGRTKESFTRLHWLFT 254

Query: 61  EKTFSASKED--NDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVN 118
               + +     N   +  +QR YWALV+GTP+  +G+ISAPL KV++D+GK++R+ + +
Sbjct: 255 SVNLAKTNSQVWNAACEAYMQR-YWALVIGTPKEREGIISAPLSKVLLDDGKAERVILAH 313

Query: 119 NDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178
              I  AQ AVT Y+V+ P+ HG +W++L PLTGRKHQLRVHCAE LGTPIVGDYKYGW 
Sbjct: 314 PSGIDGAQEAVTAYRVMGPTIHGCSWIELRPLTGRKHQLRVHCAEALGTPIVGDYKYGWF 373

Query: 179 THRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238
            H++WKQ    D    + E  P +     GL+++ GS+L K P LHLHC+EM +PN+++ 
Sbjct: 374 VHQRWKQNPQPDFEPFTGE--PYKLRRPEGLEIQKGSVLSKVPLLHLHCREMVIPNIAKF 431

Query: 239 IQKV----QLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
           +       +  +     K   L+ +AP+P+HM+ SW++++S
Sbjct: 432 LSSNGEWHENGAPWSKEKPNLLRFIAPMPAHMKISWNIMSS 472

Oryza sativa subsp. japonica (taxid: 39947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|Q69K07|PUS4_ORYSJ RNA pseudourine synthase 4, mitochondrial OS=Oryza sativa subsp. japonica GN=Os09g0103500 PE=2 SV=1

 Score =  170 bits (431), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 87/156 (55%), Positives = 112/156 (71%), Gaps = 4/156 (2%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGG+GI+ SID LA+     + SE PRLVHRLDRD SGILV+GR Q S ++LH+IFR
Sbjct: 194 MPVQGGVGIKNSIDVLASM-FEENSSEAPRLVHRLDRDCSGILVLGRNQLSTSMLHAIFR 252

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  A     D  + +LQR Y ALV+GTPR  KG++SAPL K+++ +GKS+R+T+  + 
Sbjct: 253 EKTADALA---DGTQHVLQRKYVALVIGTPRHPKGLLSAPLAKILLQDGKSERLTIRASS 309

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQ 156
              S Q A+T Y+VI+    GYTWL+L P TGRKHQ
Sbjct: 310 NAASVQDALTEYRVIESCPQGYTWLELFPRTGRKHQ 345

Oryza sativa subsp. japonica (taxid: 39947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|Q28C59|RUSD4_XENTR RNA pseudouridylate synthase domain-containing protein 4 OS=Xenopus tropicalis GN=rpusd4 PE=2 SV=1

 Score =  107 bits (267), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 79/256 (30%), Positives = 119/256 (46%), Gaps = 60/256 (23%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDY---SEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
           +PV GG  + RS+  L      + +   +EP +L HRLDRD++G L++ RT  +A  +  
Sbjct: 67  LPVHGGPTVERSVASLLPALAKHHFGWKAEPLKLCHRLDRDTTGALILARTTEAAERVQQ 126

Query: 58  IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKV------------- 104
             RE              R + R YWAL +GTP   +G++  P+ +              
Sbjct: 127 ALRE--------------REVHRVYWALCLGTPSPREGILDIPIMEKETSGPQKHYKMAL 172

Query: 105 -----VVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRV 159
                V + G  +R+ V       SA  AVTRY+ +  +  G + ++L P+TG KHQLRV
Sbjct: 173 SPRFRVSEEGAVERVRVPR-----SAHEAVTRYRTLG-AASGASLVELHPITGVKHQLRV 226

Query: 160 HCAEVLGTPIVGDYKYG-WQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILE 218
           H A  L  PI+GD+KY  W   R   Q  P  + +     +P+ +TL             
Sbjct: 227 HLALGLNCPILGDHKYSHWG--RLAPQKPPDSVLRALGLTVPQARTLS------------ 272

Query: 219 KQPRLHLHCKEMTLPN 234
               LHLH  ++TLP+
Sbjct: 273 ----LHLHAVQLTLPS 284

Xenopus tropicalis (taxid: 8364)

>sp|Q68XB2|RLUC_RICTY Ribosomal large subunit pseudouridine synthase C OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=rluC PE=3 SV=1

 Score = 98.6 bits (244), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 61/194 (31%), Positives = 109/194 (56%), Gaps = 26/194 (13%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +  QGG  I  SID  A   L Y  ++  +LVHRLD+++SG+L++ +   S+  LH  F+
Sbjct: 107 LATQGGSKINLSIDS-ALKYLNYQGADF-KLVHRLDKETSGLLLIAKNYLSSVKLHDAFK 164

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EK              ++ + Y+A+  G P  + G++ + +GK     G+  +IT +++D
Sbjct: 165 EK--------------LVIKKYFAITYGRPVKNVGIVKSNIGK---SKGRMFKITDIDSD 207

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT- 179
              + + A+T Y+++K   +    ++  P+TGR HQLR+H A++LG PI+GD KYG +  
Sbjct: 208 ---NGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQLRLH-AQLLGCPILGDDKYGNKEV 263

Query: 180 --HRKWKQFHPSDL 191
             + K+   H +++
Sbjct: 264 MPYSKYMFLHANNI 277

Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.

Rickettsia typhi (strain ATCC VR-144 / Wilmington) (taxid: 257363)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

>sp|Q4QQT0|RUSD4_RAT RNA pseudouridylate synthase domain-containing protein 4 OS=Rattus norvegicus GN=Rpusd4 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 127/294 (43%), Gaps = 71/294 (24%)

Query: 1   MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
           +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct: 115 LPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQE 174

Query: 58  IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVV----------- 106
           +FR               R +++ YWA+ V  P  S GV+  P+ +  V           
Sbjct: 175 LFRT--------------RQVEKKYWAITVRVPLPSAGVVDIPIMEKEVAGQQQHHKMTL 220

Query: 107 ------DNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160
                 DNGK  ++    +  +     AVT+YQV+  S      ++L P+TG KHQLRVH
Sbjct: 221 RPSYRMDNGKMVKVRASRDAHV-----AVTQYQVLS-STPSSALVELQPVTGIKHQLRVH 274

Query: 161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQ 220
            A  L  PI+GD+KY       W +  P  LS  + +++        GL       +   
Sbjct: 275 LAFGLDCPILGDHKYS-----DWNRLAPQKLSAGTLKKL--------GLQQSKARYIP-- 319

Query: 221 PRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274
             LHLH +++ LP +               S+ E L L   LP    RS   L 
Sbjct: 320 --LHLHARQLILPALG--------------SRTEELLLACKLPHFFARSLRRLG 357

Rattus norvegicus (taxid: 10116)

>sp|Q92IS6|RLUC_RICCN Ribosomal large subunit pseudouridine synthase C OS=Rickettsia conorii (strain ATCC VR-613 / Malish 7) GN=rluC PE=3 SV=1

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 60/194 (30%), Positives = 108/194 (55%), Gaps = 26/194 (13%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +  QGG  I  SID  A   L Y  ++  +LVHRLD+ +SG+L++ +   S+  LH+ F+
Sbjct: 107 LATQGGTKINLSIDS-ALKYLNYKGADF-KLVHRLDKKTSGLLLIAKNYLSSVKLHNAFK 164

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EK              ++ + Y+A+  G P  + G + + + K     G + +IT ++++
Sbjct: 165 EK--------------LVVKTYFAVTYGKPIKNVGEVRSNIEK---SKGSTPKITDIDSE 207

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT- 179
              + + A+T Y+V+K   +    ++ +P+TGR HQLR+H A++LG PI+GD KYG +  
Sbjct: 208 ---NGKLAITYYKVLKSLDNNLFLIEFTPVTGRMHQLRLH-AKLLGCPILGDDKYGNKEI 263

Query: 180 --HRKWKQFHPSDL 191
             + K+   H +++
Sbjct: 264 MPYSKYMFLHANNI 277

Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.

Rickettsia conorii (strain ATCC VR-613 / Malish 7) (taxid: 272944)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

>sp|Q9ZDR7|RLUC_RICPR Ribosomal large subunit pseudouridine synthase C OS=Rickettsia prowazekii (strain Madrid E) GN=rluC PE=3 SV=1

 Score = 92.8 bits (229), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/194 (30%), Positives = 104/194 (53%), Gaps = 26/194 (13%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +  QGG  I  SID  A   L Y  ++  +LVHRLD+++SG+L++ +   S+  LH+ F+
Sbjct: 107 LATQGGSKINLSIDS-ALKYLNYQGADF-KLVHRLDKETSGLLLIAKNYLSSVKLHNAFK 164

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EK              ++ + Y+A+  G P  + G + + +GK         R++ + N 
Sbjct: 165 EK--------------LVIKKYFAITYGRPVKNVGTVKSNIGK------SKRRLSKIANI 204

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT- 179
                + A+T Y+++K   +    ++  P+TGR HQLR+H A++LG PI+GD KYG +  
Sbjct: 205 DSDDGKLAITYYKLLKSLNNNLFLIEFMPVTGRMHQLRLH-AQLLGCPILGDDKYGNKEI 263

Query: 180 --HRKWKQFHPSDL 191
             + K+   H +++
Sbjct: 264 MPYSKYMFLHANNI 277

Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.

Rickettsia prowazekii (strain Madrid E) (taxid: 272947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

>sp|Q96CM3|RUSD4_HUMAN RNA pseudouridylate synthase domain-containing protein 4 OS=Homo sapiens GN=RPUSD4 PE=2 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/264 (27%), Positives = 122/264 (46%), Gaps = 57/264 (21%)

Query: 1   MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
           +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct: 115 LPVHGGPGVQLCITDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWDKDMAHQVQE 174

Query: 58  IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGK-------------- 103
           +FR               R + + YWA+ V  P  S GV+  P+ +              
Sbjct: 175 LFRT--------------RQVVKKYWAITVHVPMPSAGVVDIPIVEKEAQGQQQHHKMTL 220

Query: 104 ---VVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH 160
                +D+GK  ++    N Q+     AVT+YQV+  S      ++L P+TG KHQLRVH
Sbjct: 221 SPSYRMDDGKMVKVRRSRNAQV-----AVTQYQVLS-STLSSALVELQPITGIKHQLRVH 274

Query: 161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQ 220
            +  L  PI+GD+KY       W +  P  LS  + +++        GL+      +   
Sbjct: 275 LSFGLDCPILGDHKYS-----DWNRLAPQKLSVGTLKKL--------GLEQSKARYIP-- 319

Query: 221 PRLHLHCKEMTLPNVSQAIQKVQL 244
             LHLH +++ LP +    +++ L
Sbjct: 320 --LHLHARQLILPALGSGKEELNL 341

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	275
225428918	476	PREDICTED: RNA pseudourine synthase 4, m	1.0	0.577	0.76	1e-123
255555275	536	ribosomal pseudouridine synthase, putati	0.996	0.511	0.730	1e-114
224105621	324	predicted protein [Populus trichocarpa]	0.989	0.839	0.721	1e-113
356495831	427	PREDICTED: RNA pseudourine synthase 4, m	0.989	0.637	0.689	1e-106
358343831	430	RNA pseudourine synthase [Medicago trunc	0.996	0.637	0.682	1e-104
449438639	466	PREDICTED: RNA pseudourine synthase 4, m	0.970	0.572	0.653	1e-101
449526979	471	PREDICTED: RNA pseudourine synthase 4, m	0.967	0.564	0.652	1e-100
297830600	477	pseudouridine synthase family protein [A	0.978	0.563	0.618	5e-87
15230381	477	RNA pseudourine synthase 4 [Arabidopsis	0.978	0.563	0.607	3e-85
357154257	465	PREDICTED: RNA pseudourine synthase 4, m	0.974	0.576	0.572	9e-82

>gi|225428918|ref|XP_002282614.1| PREDICTED: RNA pseudourine synthase 4, mitochondrial [Vitis vinifera] gi|296090438|emb|CBI40257.3| unnamed protein product [Vitis vinifera]

 Score =  446 bits (1148), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 209/275 (76%), Positives = 242/275 (88%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +PVQGGIGI+RS+DELAAT L YD SEPPRLVHRLDRDSSGIL+MGRTQTSAT+LHSIFR
Sbjct: 202 LPVQGGIGIKRSLDELAATYLRYDCSEPPRLVHRLDRDSSGILIMGRTQTSATILHSIFR 261

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKTF AS  D D +KRILQR YWALV+G+PR  +G+ISAPLGKVVVD+GKS+RIT+V+N 
Sbjct: 262 EKTFGASNNDIDTKKRILQRRYWALVIGSPRRPRGLISAPLGKVVVDDGKSERITIVDNV 321

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           Q MS+QHA+T Y+VIK SCHGYTWL+LSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct: 322 QTMSSQHAITEYRVIKSSCHGYTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAH 381

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           RKWKQ   S++ K+ +E +   KT  FGLDLESGSIL+KQP LHLHCK+M LPNVS A+Q
Sbjct: 382 RKWKQLFQSNIEKNLDENLSNRKTHPFGLDLESGSILDKQPHLHLHCKQMVLPNVSLALQ 441

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
            +QLS+ CD+S+LE+L+ VAPLPSHMQRSWD+LNS
Sbjct: 442 NLQLSAECDLSELESLEFVAPLPSHMQRSWDILNS 476

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555275|ref|XP_002518674.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223542055|gb|EEF43599.1| ribosomal pseudouridine synthase, putative [Ricinus communis]

 Score =  417 bits (1071), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 201/275 (73%), Positives = 231/275 (84%), Gaps = 1/275 (0%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGGIGI+ S DELAA+CL+YDYSEPPRLVHRLDRDSSGILVMGRTQTS  VLHS+FR
Sbjct: 263 MPVQGGIGIKSSFDELAASCLSYDYSEPPRLVHRLDRDSSGILVMGRTQTSTMVLHSVFR 322

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKTF+AS  D    +RILQR YWALV+G+PR  KG+ISAPLGKVVVD+GKSDRITVV N 
Sbjct: 323 EKTFAASNHDIGERRRILQRKYWALVIGSPRRQKGIISAPLGKVVVDDGKSDRITVVENA 382

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           +  S QHAVT+Y+V++ S HGY WL+LSP+TGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct: 383 ESTSFQHAVTQYRVME-SSHGYAWLELSPITGRKHQLRVHCAEVLGTPIVGDYKYGWQVH 441

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           RKWKQ    +L K SNE    +K L FG+DLESGSI EK PRLHLHCK+M LP+VSQA++
Sbjct: 442 RKWKQLPFPNLEKISNENALCKKILPFGIDLESGSISEKHPRLHLHCKQMVLPDVSQALR 501

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
            VQ SS  D S L++++L APLPS+MQRSWD+LNS
Sbjct: 502 GVQTSSNYDFSDLKSIELDAPLPSYMQRSWDILNS 536

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105621|ref|XP_002313876.1| predicted protein [Populus trichocarpa] gi|222850284|gb|EEE87831.1| predicted protein [Populus trichocarpa]

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 197/273 (72%), Positives = 233/273 (85%), Gaps = 1/273 (0%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGGIGI+RS+DEL+A+C + DYSEPPRLVHRLDRD SGILVMGRTQTSATVLH+IFR
Sbjct: 53  MPVQGGIGIKRSLDELSASCFSSDYSEPPRLVHRLDRDCSGILVMGRTQTSATVLHAIFR 112

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT +AS +D  N++RILQR YWALV+G+PR  KG+ISAPLGKVVVDNGKSDRITVV N 
Sbjct: 113 EKTLAASNDDVGNKRRILQRKYWALVIGSPRRPKGLISAPLGKVVVDNGKSDRITVVENS 172

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           Q +S+QHAVT+Y+VI+ S HG+TWL+LSPLTGRKHQLRVHCAEVLGTPIVGDYKY WQ H
Sbjct: 173 QNLSSQHAVTQYRVIE-SSHGFTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYAWQAH 231

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           R WKQ   S++  +SN++   EK L F LDL+SGSI EK PRLHLHCK+M LP+VS+A+Q
Sbjct: 232 RNWKQLQWSNIEDNSNDKSLSEKILPFALDLDSGSISEKHPRLHLHCKQMVLPDVSKALQ 291

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVL 273
            VQLSS  D S+L +LK  APLP +M++SWD+L
Sbjct: 292 DVQLSSDYDFSQLASLKFDAPLPPYMKKSWDIL 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356495831|ref|XP_003516775.1| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Glycine max]

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 189/274 (68%), Positives = 221/274 (80%), Gaps = 2/274 (0%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGGI I+RS+D +AA  L Y YS+PPRLVHRLDRD SGILVMGRT TS TVLHSIFR
Sbjct: 155 MPVQGGINIKRSLDAVAAASLNYGYSQPPRLVHRLDRDCSGILVMGRTHTSTTVLHSIFR 214

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  AS +D   EKRILQR YWALV+G PR  KG+++A LGKVVVDNG+SDRIT+V+N 
Sbjct: 215 EKTSRAS-DDIGKEKRILQRRYWALVLGCPRRPKGLVTASLGKVVVDNGRSDRITIVDNS 273

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
            +MS+QHA+T Y+VI  S  GYTWL+L+PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct: 274 TLMSSQHAITEYRVIASSSQGYTWLELTPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAH 333

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           RKW  F   ++ +DS EE+  E+ L FGL+L  GSI E  PRLHLHCK+M LPN+SQA+Q
Sbjct: 334 RKWGHFDLPNV-EDSREELLNEEKLPFGLNLNKGSISENHPRLHLHCKQMVLPNISQALQ 392

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274
            VQ +S CD+S +E L+LVA LP +MQRSWDV N
Sbjct: 393 NVQSASSCDLSLVEELELVADLPPYMQRSWDVTN 426

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358343831|ref|XP_003635999.1| RNA pseudourine synthase [Medicago truncatula] gi|355501934|gb|AES83137.1| RNA pseudourine synthase [Medicago truncatula]

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 189/277 (68%), Positives = 225/277 (81%), Gaps = 3/277 (1%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGGI I+ S+D +AA  L YDYS+PPRLVHRLDRD SGILVMGRT+TS  +LHSIFR
Sbjct: 155 MPVQGGINIKLSLDAVAAQSLNYDYSQPPRLVHRLDRDCSGILVMGRTKTSTALLHSIFR 214

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  AS E+ND EK ILQR YWALV+G PR S GV++APLGKVVVDNGKSDRIT+V+N 
Sbjct: 215 EKTSRASNEENDTEKIILQRRYWALVLGCPRRSGGVVNAPLGKVVVDNGKSDRITIVDNS 274

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
            ++S+QHAVT Y+VI  S HG+TWL+LSPLTGRKHQLRVHCAEVLGTPIVGDYKYG Q H
Sbjct: 275 ALLSSQHAVTEYRVISSSSHGFTWLELSPLTGRKHQLRVHCAEVLGTPIVGDYKYGRQAH 334

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           +KW QF  S+L +DS EE  KE+ L FGL+L  GSI +K PRLHLHCK++ LPN+SQA+Q
Sbjct: 335 KKWGQFDFSNL-EDSTEEHLKEEALPFGLNLNKGSISDKHPRLHLHCKQIVLPNISQALQ 393

Query: 241 KVQ--LSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
            VQ    S  D+S +E+L+L A LP +M++SW+V NS
Sbjct: 394 NVQSVSDSSYDLSAVESLELEADLPPYMKKSWEVTNS 430

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438639|ref|XP_004137095.1| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Cucumis sativus]

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 181/277 (65%), Positives = 226/277 (81%), Gaps = 10/277 (3%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +PVQGGIG++RS+DELAA+CL+Y YSEPPRLVHRLDRDSSGIL+MGRT TS ++LHS+FR
Sbjct: 198 LPVQGGIGVKRSLDELAASCLSYGYSEPPRLVHRLDRDSSGILIMGRTSTSTSLLHSVFR 257

Query: 61  EKTFSASKEDN--DNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVN 118
           EKTF ASK  N  D+EK+IL + YWALV+G+PR SKG+I+APLGK+V+D+G+S++I V++
Sbjct: 258 EKTFEASKHANHVDSEKKILLKRYWALVIGSPRRSKGLITAPLGKIVLDDGRSEQIMVID 317

Query: 119 NDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178
           N + M  Q A+T+Y+VIK S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ
Sbjct: 318 NAEPMPFQQAITQYKVIK-SHHGYTWLELCPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 376

Query: 179 THRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238
            H+ WK F  S+  K+      K++ L FGLD ESGSI E  PRLHLHCK++TLP+VS A
Sbjct: 377 AHKNWKPFC-SNFHKNQG----KKQFLPFGLDFESGSIAENNPRLHLHCKQLTLPDVSFA 431

Query: 239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
           +    L   C  S+LE L+L APLPS+MQ+SWD++NS
Sbjct: 432 LHNDSLDRDC--SRLECLELDAPLPSYMQKSWDIINS 466

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449526979|ref|XP_004170490.1| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Cucumis sativus]

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 180/276 (65%), Positives = 225/276 (81%), Gaps = 10/276 (3%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           +PVQGGIG++RS+DELAA+CL+Y YSEPPRLVHRLDRDSSGIL+MGRT TS ++LHS+FR
Sbjct: 203 LPVQGGIGVKRSLDELAASCLSYGYSEPPRLVHRLDRDSSGILIMGRTSTSTSLLHSVFR 262

Query: 61  EKTFSASKEDN--DNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVN 118
           EKTF ASK  N  D+EK+IL + YWALV+G+PR SKG+I+APLGK+V+D+G+S++I V++
Sbjct: 263 EKTFEASKHANHVDSEKKILLKRYWALVIGSPRRSKGLITAPLGKIVLDDGRSEQIMVID 322

Query: 119 NDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178
           N + M  Q A+T+Y+VIK S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ
Sbjct: 323 NAEPMPFQQAITQYKVIK-SHHGYTWLELCPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 381

Query: 179 THRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238
            H+ WK F  S+  K+      K++ L FGLD ESGSI E  PRLHLHCK++TLP+VS A
Sbjct: 382 AHKNWKPFC-SNFHKNQG----KKQFLPFGLDFESGSIAENSPRLHLHCKQLTLPDVSFA 436

Query: 239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN 274
           +    L   C  S+LE L+L APLPS+MQ+SWD++N
Sbjct: 437 LHNDSLDRDC--SRLECLELDAPLPSYMQKSWDIIN 470

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830600|ref|XP_002883182.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297329022|gb|EFH59441.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  327 bits (837), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 170/275 (61%), Positives = 208/275 (75%), Gaps = 6/275 (2%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           + VQGG GI+ SIDELAATCLT+D SE PRLVHRLDRD SG+LV+ RTQT+ATVLHSIFR
Sbjct: 201 LAVQGGSGIKTSIDELAATCLTFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFR 260

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  AS        + L+R Y ALV+G PR  KG ISAPL KVVVD+GKSDRITV +N 
Sbjct: 261 EKTCGASAYGVKKNIKSLKRKYMALVIGCPRRQKGQISAPLRKVVVDDGKSDRITVNDNG 320

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           +++S QHA+T Y+VI+ S HGYTWL+L PLTGRKHQLRVHCAEVLGTPI+GDYKYGWQ H
Sbjct: 321 ELVSTQHAITEYKVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPILGDYKYGWQAH 380

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           +  + F  S+ +       P      FGLDL+ G +  KQP LHLH K++ LPN+SQ ++
Sbjct: 381 KAREPFVSSETTPTKPSSSP------FGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLE 434

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
           K+Q+SS  D+S L++LK  APLPSHMQ S+++L S
Sbjct: 435 KMQVSSDSDISDLDSLKFDAPLPSHMQLSFNLLKS 469

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15230381|ref|NP_188575.1| RNA pseudourine synthase 4 [Arabidopsis thaliana] gi|75274073|sp|Q9LT72.1|PUS4_ARATH RecName: Full=RNA pseudourine synthase 4, mitochondrial; AltName: Full=RNA pseudouridylate synthase 4; AltName: Full=RNA-uridine isomerase 4; Flags: Precursor gi|11994467|dbj|BAB02469.1| unnamed protein product [Arabidopsis thaliana] gi|110737723|dbj|BAF00800.1| hypothetical protein [Arabidopsis thaliana] gi|134031916|gb|ABO45695.1| At3g19440 [Arabidopsis thaliana] gi|332642719|gb|AEE76240.1| RNA pseudourine synthase 4 [Arabidopsis thaliana]

 Score =  320 bits (821), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 167/275 (60%), Positives = 210/275 (76%), Gaps = 6/275 (2%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           + VQGG GI+ SIDELAA+CL +D SE PRLVHRLDRD SG+LV+ RTQT+ATVLHSIFR
Sbjct: 201 LAVQGGSGIKTSIDELAASCLKFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFR 260

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  AS        + L+R Y ALV+G P   +G ISAPL KVVVD+GKS+RITV +N 
Sbjct: 261 EKTTGASAYGVKKNVKSLKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNG 320

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
           +++S QHA+T Y+VI+ S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct: 321 ELVSTQHAITEYRVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAH 380

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           +  + F    +S ++N    K+ +  FGLDL+ G +  KQP LHLH K++ LPN+SQ ++
Sbjct: 381 KAREPF----VSSENNPT--KQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLE 434

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
           K+Q+SS  D+S L++LK  APLPSHMQ S+++L S
Sbjct: 435 KMQVSSDSDISDLDSLKFDAPLPSHMQLSFNLLKS 469

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357154257|ref|XP_003576723.1| PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Brachypodium distachyon]

 Score =  309 bits (791), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 158/276 (57%), Positives = 198/276 (71%), Gaps = 8/276 (2%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
           MPVQGG+GI+ SID LA      + SE PRLVHRLDRD SG+LV+GRTQ SA++LH+IFR
Sbjct: 194 MPVQGGVGIKNSIDVLAPM-FEENSSEAPRLVHRLDRDCSGVLVLGRTQLSASILHAIFR 252

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           EKT  A     D  +++LQR Y ALV+GTPR SKG++SAPL KV++ +GKS+R+TV    
Sbjct: 253 EKTADALA---DGTQQVLQRKYVALVIGTPRHSKGLLSAPLAKVLLQDGKSERLTVKAGP 309

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
              S Q A+T Y+VI+    G+TWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYG Q H
Sbjct: 310 NTTSVQDALTEYRVIESCPQGFTWLELFPLTGRKHQLRVHCAEVLGTPIVGDYKYGRQAH 369

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
           + W    P    +   EE+ K++ L FGL L  GS++E+QP+LHLHCK+M LP++S A+Q
Sbjct: 370 QNWS---PLPAPQAIEEELLKKRRLPFGLVLGGGSVVEEQPQLHLHCKQMVLPDISAAVQ 426

Query: 241 KVQLSSGC-DVSKLETLKLVAPLPSHMQRSWDVLNS 275
            +Q      D S LE L  VAPLP HM+ SW+VL S
Sbjct: 427 GLQSEDADRDFSDLEKLSFVAPLPQHMRLSWEVLKS 462

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	275
TAIR|locus:2090689	477	AT3G19440 [Arabidopsis thalian	0.978	0.563	0.607	1e-84
TAIR|locus:2037593	478	AT1G78910 [Arabidopsis thalian	0.989	0.569	0.453	2e-65
DICTYBASE|DDB_G0285543	718	DDB_G0285543 [Dictyostelium di	0.421	0.161	0.447	5.7e-32
TIGR_CMR|SPO_0516	347	SPO_0516 "ribosomal large subu	0.581	0.461	0.375	1.9e-26
RGD|1311268	377	Rpusd4 "RNA pseudouridylate sy	0.763	0.557	0.293	4.1e-20
UNIPROTKB|E1BYI6	354	RPUSD4 "Uncharacterized protei	0.701	0.545	0.301	1.7e-19
MGI|MGI:1919239	377	Rpusd4 "RNA pseudouridylate sy	0.763	0.557	0.285	2.1e-19
UNIPROTKB|F1S6H1	376	LOC100737111 "Uncharacterized	0.756	0.553	0.296	6.4e-18
UNIPROTKB|F6XEH2	378	RPUSD4 "Uncharacterized protei	0.756	0.550	0.28	4.2e-16
UNIPROTKB|Q5E9Z1	377	RPUSD4 "RNA pseudouridylate sy	0.763	0.557	0.297	5.3e-16

TAIR|locus:2090689 AT3G19440 [Arabidopsis thaliana (taxid:3702)]

 Score = 848 (303.6 bits), Expect = 1.0e-84, P = 1.0e-84
 Identities = 167/275 (60%), Positives = 210/275 (76%)

Query:     1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
             + VQGG GI+ SIDELAA+CL +D SE PRLVHRLDRD SG+LV+ RTQT+ATVLHSIFR
Sbjct:   201 LAVQGGSGIKTSIDELAASCLKFDKSESPRLVHRLDRDCSGLLVLARTQTAATVLHSIFR 260

Query:    61 EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
             EKT  AS        + L+R Y ALV+G P   +G ISAPL KVVVD+GKS+RITV +N 
Sbjct:   261 EKTTGASAYGVKKNVKSLKRKYMALVIGCPPRQRGQISAPLRKVVVDDGKSERITVNDNG 320

Query:   121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
             +++S QHA+T Y+VI+ S HGYTWL+L PLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ H
Sbjct:   321 ELVSTQHAITEYRVIESSPHGYTWLELRPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQAH 380

Query:   181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
             +  + F    +S ++N    K+ +  FGLDL+ G +  KQP LHLH K++ LPN+SQ ++
Sbjct:   381 KAREPF----VSSENNPT--KQSSSPFGLDLDGGDVSSKQPHLHLHSKQIDLPNISQLLE 434

Query:   241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
             K+Q+SS  D+S L++LK  APLPSHMQ S+++L S
Sbjct:   435 KMQVSSDSDISDLDSLKFDAPLPSHMQLSFNLLKS 469

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS

GO:0019243 "methylglyoxal catabolic process to D-lactate" evidence=RCA

TAIR|locus:2037593 AT1G78910 [Arabidopsis thaliana (taxid:3702)]

 Score = 666 (239.5 bits), Expect = 2.0e-65, P = 2.0e-65
 Identities = 128/282 (45%), Positives = 193/282 (68%)

Query:     1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
             +PV+G + I  S+D LAA  L++   E PRLVHRLDR++SG+LVMGRT+ S   LHS+F 
Sbjct:   197 LPVKGNVPIHNSMDALAAAALSFGNDEGPRLVHRLDRETSGLLVMGRTKESIDYLHSVFS 256

Query:    61 E-KTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNN 119
             + K  ++S +  +     + + YWALV+G+P+  +G+ISAPL KV++D+GK+DR+ +   
Sbjct:   257 DYKGRNSSCKAWNKACEAMYQQYWALVIGSPKEKEGLISAPLSKVLLDDGKTDRVVLAQG 316

Query:   120 DQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT 179
                 ++Q A+T Y+V+ P  +G +W++L P+T RKHQLRVHCAE LGTPIVGDYKYGW  
Sbjct:   317 SGFEASQDAITEYKVLGPKINGCSWVELRPITSRKHQLRVHCAEALGTPIVGDYKYGWFV 376

Query:   180 HRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAI 239
             H++WKQ    D+   + +  P +     GLD++ GS+L K P LHLHC+EM LPN+++ +
Sbjct:   377 HKRWKQMPQVDIEPTTGK--PYKLRRPEGLDVQKGSVLSKVPLLHLHCREMVLPNIAKFL 434

Query:   240 -----QKVQ-LSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
                  Q+ + L +G  + K + L+ VA +PSHM+ SW++++S
Sbjct:   435 HVMNQQETEPLHTGI-IDKPDLLRFVASMPSHMKISWNLMSS 475

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0009451 "RNA modification" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS

DICTYBASE|DDB_G0285543 DDB_G0285543 [Dictyostelium discoideum (taxid:44689)]

 Score = 240 (89.5 bits), Expect = 5.7e-32, Sum P(2) = 5.7e-32
 Identities = 55/123 (44%), Positives = 77/123 (62%)

Query:    58 IFREK-TFSASK---EDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDR 113
             +FREK  F+ +K   E+N+N  + +++ YWAL+  TP   +G I APL KVVV   +   
Sbjct:   535 LFREKEVFNNNKNKDEENENYSKGIKKTYWALLGSTPTPKEGRIRAPLKKVVVGGFEKVV 594

Query:   114 ITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDY 173
              T+   D    A+ A+T Y+V++ S   + ++ L P TGR HQLRVHCA VL TPI+GD 
Sbjct:   595 PTLTTGD---GAKIAITEYKVLESSLTKHCFISLWPETGRTHQLRVHCASVLNTPIIGDP 651

Query:   174 KYG 176
             KYG
Sbjct:   652 KYG 654

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

TIGR_CMR|SPO_0516 SPO_0516 "ribosomal large subunit pseudouridine synthase C" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 255 (94.8 bits), Expect = 1.9e-26, Sum P(2) = 1.9e-26
 Identities = 68/181 (37%), Positives = 98/181 (54%)

Query:     1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
             + VQGG G  R +D L+   L +   E PRLVHRLD+D+SG+LV+ RT+ +A  L + FR
Sbjct:   109 LAVQGGSGQTRHVDGLSEA-LRFGNDENPRLVHRLDKDTSGVLVLARTREAAARLTAAFR 167

Query:    61 EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDN--GKSDRITVVN 118
              +          N ++I    YWALV G P    G I   L K       G+ +++ VV+
Sbjct:   168 HR----------NTRKI----YWALVAGVPTPYLGEIKTGLVKAGGHGARGEGEKMNVVH 213

Query:   119 NDQIMS---AQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 175
               ++ +   A+ A T Y  +       +W+ + P+TGR HQLR H A + G PI+GD KY
Sbjct:   214 LSELDATPGAKRAHTYYATLYRVAGRASWVAMEPVTGRTHQLRAHMAGI-GHPIIGDGKY 272

Query:   176 G 176
             G
Sbjct:   273 G 273

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

RGD|1311268 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Rattus norvegicus (taxid:10116)]

 Score = 216 (81.1 bits), Expect = 4.1e-20, Sum P(2) = 4.1e-20
 Identities = 73/249 (29%), Positives = 123/249 (49%)

Query:     1 MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct:   115 LPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQE 174

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPL-GKVVVDNGKSDRITV 116
             +FR +           EK+     YWA+ V  P  S GV+  P+  K V    +  ++T+
Sbjct:   175 LFRTRQV---------EKK-----YWAITVRVPLPSAGVVDIPIMEKEVAGQQQHHKMTL 220

Query:   117 -----VNNDQIMSAQ-----H-AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVL 165
                  ++N +++  +     H AVT+YQV+  S      ++L P+TG KHQLRVH A  L
Sbjct:   221 RPSYRMDNGKMVKVRASRDAHVAVTQYQVLS-STPSSALVELQPVTGIKHQLRVHLAFGL 279

Query:   166 GTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI--PKEKTLHFGLDLESGSILEKQPRL 223
               PI+GD+KY       W +  P  LS  + +++   + K  +  L L +  ++   P L
Sbjct:   280 DCPILGDHKYS-----DWNRLAPQKLSAGTLKKLGLQQSKARYIPLHLHARQLI--LPAL 332

Query:   224 HLHCKEMTL 232
                 +E+ L
Sbjct:   333 GSRTEELLL 341

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0009982 "pseudouridine synthase activity" evidence=IEA

UNIPROTKB|E1BYI6 RPUSD4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 233 (87.1 bits), Expect = 1.7e-19, P = 1.7e-19
 Identities = 70/232 (30%), Positives = 125/232 (53%)

Query:     1 MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+ R + +A  +  
Sbjct:   104 LPVHGGPGVKNCIADVLPILAKMLVNMKAEPLHLCHRLDKETTGVMVLARNKEAADRIRL 163

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSD-RITV 116
             +F  KT            R +++ YWA+ VG+P  ++G++  P+ +  V + +   ++T+
Sbjct:   164 LF--KT------------RQVEKIYWAISVGSPDPAEGIVEIPMVEREVQSHQPHFKMTL 209

Query:   117 VNNDQIM-------------SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAE 163
               N ++              +A+ AVT+Y+V+  S    + L+L P+TG KHQLRVH A 
Sbjct:   210 APNYRMSPEDGKVLKIRKNRNAESAVTQYRVLASSS-ACSLLELQPITGVKHQLRVHLAY 268

Query:   164 VLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNE--EIPKEKTLHFGLDLES 213
              LG PI+GD+KY   +H  W +  P  L + + +  ++ + K+ H  L L +
Sbjct:   269 GLGCPILGDHKY---SH--WSKLAPQKLPEITLKRLKLQQSKSRHLPLHLHA 315

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

MGI|MGI:1919239 Rpusd4 "RNA pseudouridylate synthase domain containing 4" [Mus musculus (taxid:10090)]

 Score = 210 (79.0 bits), Expect = 2.1e-19, Sum P(2) = 2.1e-19
 Identities = 71/249 (28%), Positives = 123/249 (49%)

Query:     1 MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct:   115 LPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKDMAHQVQE 174

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSD-RITV 116
             +FR +           EK+     YWA+ V  P  S GV+  P+ +  V   +   ++T+
Sbjct:   175 LFRTRQV---------EKK-----YWAITVRVPLPSAGVVDIPIKEKEVQGPQQHHKMTL 220

Query:   117 -----VNNDQIMSAQ-----H-AVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVL 165
                  ++N +++  +     H AVT+YQV+  S      ++L P+TG KHQLRVH +  L
Sbjct:   221 SPSYRLDNGKMVKVRASRDAHVAVTQYQVLS-SASSSALVELQPVTGIKHQLRVHLSFGL 279

Query:   166 GTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI--PKEKTLHFGLDLESGSILEKQPRL 223
               PI+GD+KY       W +  P  LS  + +++   + K  +  L L +  ++   P L
Sbjct:   280 DCPILGDHKYS-----DWTRLAPQKLSAGTLKKLGLQQSKARYIPLHLHARQLI--LPAL 332

Query:   224 HLHCKEMTL 232
                 +E+ L
Sbjct:   333 GSRTEELLL 341

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0009451 "RNA modification" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

UNIPROTKB|F1S6H1 LOC100737111 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 221 (82.9 bits), Expect = 6.4e-18, P = 6.4e-18
 Identities = 74/250 (29%), Positives = 124/250 (49%)

Query:     1 MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct:   114 LPVHGGPGVQLCISDVLPILAKILHGHKAEPLHLCHRLDKETTGVMVLAWEKEVAHQVQE 173

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPL-GKVVVDNGKSDRITV 116
             +FR  T   +K+            YWA+ V  P  S GV+  P+  K V    +  ++T+
Sbjct:   174 LFR--TRQVAKK------------YWAITVRVPVPSAGVVDIPIIEKEVQGQQQHHKMTL 219

Query:   117 -----VNNDQIM------SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVL 165
                  ++N +++      +A  AVT+YQV+  +      L+L P+TG KHQLRVH +  L
Sbjct:   220 CPSYRMDNGKMVRVRTSRNAHLAVTQYQVLSSTLSS-ALLELQPVTGIKHQLRVHLSFGL 278

Query:   166 GTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI--PKEKTLHFGLDLESGSIL-----E 218
               PI+GD+KY       W +  P  LS    +++  P+ K  H  L L +  ++      
Sbjct:   279 DCPILGDHKYS-----DWNRLAPQKLSVGVLKKLGLPQSKARHIPLHLHARQLILPALQS 333

Query:   219 KQPRLHLHCK 228
             ++  L+L CK
Sbjct:   334 RKEELNLVCK 343

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

UNIPROTKB|F6XEH2 RPUSD4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 205 (77.2 bits), Expect = 4.2e-16, P = 4.2e-16
 Identities = 70/250 (28%), Positives = 122/250 (48%)

Query:     1 MPVQGGIGIRRSIDE---LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I +   + A  L    +EP  L HRLD++++G++V+   +  A  +  
Sbjct:   116 LPVHGGPGVQLCISDVLPILAKMLHGHKAEPLHLCHRLDKETTGVMVLAWEKEVAHQVQE 175

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSD-RITV 116
              FR  T   +K+            YWA+ V  P  S GV+  P+ +  V   +   ++T+
Sbjct:   176 FFR--TRQVAKK------------YWAITVRVPVPSAGVVDIPITEKAVQGQQQHYKMTL 221

Query:   117 -----VNNDQIM------SAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVL 165
                  ++N +++      +A  AVT+Y V+  +      ++L P+TG KHQLRVH +  L
Sbjct:   222 SPDYRMDNGKMVRVRSNRNAHIAVTQYHVLSSTLSS-ALVELQPITGIKHQLRVHLSFGL 280

Query:   166 GTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTL--HFGLDLESGSIL-----E 218
               PI+GD+KY       W +  P  LS  + +++  ++T   H  L L +  ++      
Sbjct:   281 NCPILGDHKYS-----DWNKLAPQKLSLGTLKKLGLQQTKARHLPLHLHARQLILPALGS 335

Query:   219 KQPRLHLHCK 228
             ++  L L CK
Sbjct:   336 RKEELSLVCK 345

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

UNIPROTKB|Q5E9Z1 RPUSD4 "RNA pseudouridylate synthase domain-containing protein 4" [Bos taurus (taxid:9913)]

 Score = 204 (76.9 bits), Expect = 5.3e-16, P = 5.3e-16
 Identities = 74/249 (29%), Positives = 117/249 (46%)

Query:     1 MPVQGGIGIRRSIDELA---ATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHS 57
             +PV GG G++  I ++    A  L    ++P  L HRLD++++G++V+   +  A  +  
Sbjct:   115 LPVHGGPGVKLCISDVLPVLAKILHGPKAKPLHLCHRLDKETTGVMVLAWEKEVAHQVQE 174

Query:    58 IFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPL------G-----KVVV 106
             +FR  T   +K+            YWA+ V  P    GV+  P+      G     K+ +
Sbjct:   175 LFR--TRQVTKK------------YWAITVRVPVPEAGVVDIPIVEKEAQGQQHHHKMTL 220

Query:   107 DNG-KSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVL 165
                 + D   +V      +AQ AVT+YQV+  S      L+L P+TG KHQLRVH +  L
Sbjct:   221 SPSYRMDDGKMVRVRSSRNAQLAVTQYQVLSSSLSA-ALLELQPITGIKHQLRVHMSFGL 279

Query:   166 GTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEI--PKEKTLHFGLDLESGSILEKQPRL 223
               PI+GD+KY       W +  P  LS    +++   + K  H  L L +  +    P L
Sbjct:   280 DCPILGDHKYS-----DWNRLAPQKLSAGILKKLGLQQSKARHLPLHLHACQLT--LPAL 332

Query:   224 HLHCKEMTL 232
                 +E+TL
Sbjct:   333 QPQKEELTL 341

GO:0005739 "mitochondrion" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.4.99	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.IX.2366.1	hypothetical protein (324 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.V.1916.1	annotation not avaliable (149 aa)			•						0.476
	fgenesh4_pg.C_scaffold_18203000001	Predicted protein (261 aa)			•				•		0.442

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	275
cd02869	185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	5e-42
COG0564	289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	2e-39
TIGR00005	299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	2e-33
pfam00849	149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	2e-22
PRK11025	317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	1e-17
cd02563	223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	6e-16
cd02557	213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	1e-15
PRK11112	257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	1e-13
cd02550	154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	9e-13
PRK10158	219	PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy	4e-12
TIGR01621	217	TIGR01621, RluA-like, pseudouridine synthase Rlu f	1e-09
PRK11180	325	PRK11180, rluD, 23S rRNA pseudouridine synthase D;	2e-09
cd02558	246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	4e-08

>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family

 Score =  142 bits (359), Expect = 5e-42
 Identities = 58/178 (32%), Positives = 83/178 (46%), Gaps = 25/178 (14%)

Query: 1   MPVQGGIGIRRSIDE--LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSI 58
           +PV  G G         L    L       P LVHRLD+D+SG+L++ + + +A  L   
Sbjct: 10  LPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQ 69

Query: 59  FREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVN 118
           F+E+           +K      Y ALV G P   +G I APLG+          ++   
Sbjct: 70  FKERKV---------KKT-----YLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS--- 112

Query: 119 NDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
                  + A+T Y+V++      T ++L   TGR HQ+RVH A  +G PIVGD KYG
Sbjct: 113 ----EDGKPAITHYKVLERFG-NVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYG 164

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 185

>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

 Score =  138 bits (350), Expect = 2e-39
 Identities = 64/235 (27%), Positives = 99/235 (42%), Gaps = 57/235 (24%)

Query: 1   MPVQGGIGIRRSIDELAATCL-TYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIF 59
           + V  G G       + A      D  E P +VHRLD+D+SG+L++ + + +A  L   F
Sbjct: 96  LVVHPG-GGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQF 154

Query: 60  REKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNN 119
           +++               +++ Y ALV G     +G I AP+G+   +  K     V   
Sbjct: 155 KQRK--------------VKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKK--MAVVKEG 198

Query: 120 DQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQT 179
                 + A+T Y+V++     YT ++L P TGR HQ+RVH A  LG PIVGD  YG   
Sbjct: 199 S----GKPAITHYEVLERFGDNYTLVELKPETGRTHQIRVHLAH-LGHPIVGDPLYG--- 250

Query: 180 HRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPN 234
                                K+K+   GL            R  LH  +++  +
Sbjct: 251 --------------------GKDKSAGAGLK-----------RQALHAYKLSFTH 274

Length = 289

>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family

 Score =  122 bits (309), Expect = 2e-33
 Identities = 63/259 (24%), Positives = 104/259 (40%), Gaps = 66/259 (25%)

Query: 16  LAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEK 75
           L A C      E   +VHRLDRD+SG++V+ +T  +   L    + +T            
Sbjct: 107 LLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT------------ 154

Query: 76  RILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVI 135
             + + Y ALV G      G + APLG+V  + G    + V  + +    + AVT ++V+
Sbjct: 155 --VTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGL---MAVHPSSE---GKPAVTHFRVL 206

Query: 136 KPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDS 195
           +   +  + ++    TGR HQ+RVH    LG P+ GD  YG       K    ++L+   
Sbjct: 207 ERFGN-ASLVECELETGRTHQIRVHLQY-LGHPLAGDPLYG------NKPVPGNNLNGLL 258

Query: 196 NEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQKVQLSSGCDVSKLET 255
           N +                       R  LH         +  +  +  ++G      E 
Sbjct: 259 NFD-----------------------RQALH---------AYELGFIHPATG------EI 280

Query: 256 LKLVAPLPSHMQRSWDVLN 274
           L+  APLP+ +    + L 
Sbjct: 281 LEFEAPLPADLVLLLEALR 299

In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine [Protein synthesis, tRNA and rRNA base modification]. Length = 299

>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase

 Score = 90.2 bits (224), Expect = 2e-22
 Identities = 47/164 (28%), Positives = 72/164 (43%), Gaps = 27/164 (16%)

Query: 1   MPVQGGIGIRRSIDELAATCLT-YDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIF 59
           +PV            L A  L           VHRLDR++SG+L++ +   +A  L+ +F
Sbjct: 10  VPVHPTDPSDL--LSLTALLLVAELGKFRLYPVHRLDRNTSGLLLLAKDGEAANKLNKLF 67

Query: 60  REKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNN 119
            E+           EK      Y ALV G     +G I AP+ K        D+      
Sbjct: 68  PERKV---------EKE-----YLALVDGPEE-EEGTIKAPIKK--------DKAVGFRK 104

Query: 120 DQIMSAQHAVTRYQVIK-PSCHGYTWLKLSPLTGRKHQLRVHCA 162
            + +  + AVT  +V++  S   Y+ ++L  +TGRKHQ+R H A
Sbjct: 105 KEELDGKLAVTHLRVLRSGSKEKYSLVELELVTGRKHQIRAHLA 148

Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA. Length = 149

>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional

 Score = 80.5 bits (199), Expect = 1e-17
 Identities = 52/146 (35%), Positives = 79/146 (54%), Gaps = 22/146 (15%)

Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           LVHRLDRD+SG+L++ + +++   LH   REK               +Q+ Y ALV G  
Sbjct: 139 LVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQKDYLALVRGQW 184

Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
           +    V+ APL K ++ +G  +RI  V+ +   S     TR++V +      T ++ SP+
Sbjct: 185 QSHVKVVQAPLLKNILQSG--ERIVRVSQEGKPSE----TRFKVEERYAFA-TLVRASPV 237

Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH  +  G PI  D +YG
Sbjct: 238 TGRTHQIRVH-TQYAGHPIAFDDRYG 262

Length = 317

>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C

 Score = 74.3 bits (183), Expect = 6e-16
 Identities = 46/155 (29%), Positives = 66/155 (42%), Gaps = 32/155 (20%)

Query: 32  VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
           VHRLDR +SG+L+   +   A  L   F E                + + Y A+V G   
Sbjct: 49  VHRLDRPTSGVLLFALSSEVARKLGEQFTEHR--------------VHKTYLAVVRGYVP 94

Query: 92  CSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRY---QVIKPSCHG------- 141
            S G I  PL +      + D++         + Q A T Y    V +            
Sbjct: 95  ES-GTIDYPLSE------ELDKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSR 147

Query: 142 YTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
           Y+ ++L+P TGRKHQLR H A  +  PI+GD  +G
Sbjct: 148 YSLVELTPHTGRKHQLRRHLAH-IRHPIIGDTTHG 181

Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved. Length = 223

>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2

 Score = 73.4 bits (181), Expect = 1e-15
 Identities = 40/152 (26%), Positives = 64/152 (42%), Gaps = 23/152 (15%)

Query: 26  SEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWAL 85
               R  HRLDR +SG+L+  +T  +A+ L    R +               +++ Y A 
Sbjct: 57  LTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSRE--------------VKKEYLAR 102

Query: 86  VVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCH-GYTW 144
           V G     + V+  P+G V    G  + +           + A T ++ +  +     + 
Sbjct: 103 VKGEFPDGEVVVDQPIGLVSPKGGLRNDVDEK-------GKDARTIFKRLSYNGDLNTSV 155

Query: 145 LKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
           +   P+TGR HQ+RVH    LG PIV D  Y 
Sbjct: 156 VLCKPITGRTHQIRVHLQY-LGHPIVNDPIYN 186

Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs. Length = 213

>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional

 Score = 68.5 bits (168), Expect = 1e-13
 Identities = 50/155 (32%), Positives = 73/155 (47%), Gaps = 32/155 (20%)

Query: 32  VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
            HRLDR +SG+L+M  +   A +L   F              E+  +Q+ Y A+V G   
Sbjct: 50  AHRLDRPTSGVLLMALSSEVARLLAQQF--------------EQHQIQKTYHAIVRGWLM 95

Query: 92  CSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIK----PSCHG------ 141
             + V+  PL + +      D+I      +  + Q AVT Y+ +     P   G      
Sbjct: 96  -EEAVLDYPLKEEL------DKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTR 148

Query: 142 YTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
           Y+ ++L P TGRKHQLR H A  L  PI+GD K+G
Sbjct: 149 YSLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHG 182

Length = 257

>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family

 Score = 64.3 bits (157), Expect = 9e-13
 Identities = 36/144 (25%), Positives = 54/144 (37%), Gaps = 31/144 (21%)

Query: 29  PRL--VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86
           PR+    RLD+D+SG+L++         L    RE                +++ Y   V
Sbjct: 33  PRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRRE----------------IEKEYLVTV 76

Query: 87  VGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLK 146
            G               +               D+      AVT+ +VI     G   L+
Sbjct: 77  RGEL---------DEEGIEDLATVRRGRLSGLVDE--GVPLAVTKVRVIGEH-GGTGRLR 124

Query: 147 LSPLTGRKHQLRVHCAEVLGTPIV 170
           L+  TGR HQ+R HCA V G P++
Sbjct: 125 LTLKTGRTHQIRRHCAAV-GFPVL 147

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 154

>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional

 Score = 63.9 bits (155), Expect = 4e-12
 Identities = 48/153 (31%), Positives = 68/153 (44%), Gaps = 40/153 (26%)

Query: 32  VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
           VHRLD  +SG++V+  T+ +   L   FRE              R  ++ Y A V G P 
Sbjct: 60  VHRLDMATSGVIVVALTKAAERELKRQFRE--------------REPKKQYVARVWGHPS 105

Query: 92  CSKGVISAPL---------GKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGY 142
            ++G++  PL          KV  + GK                 A T Y+V++ +    
Sbjct: 106 PAEGLVDLPLICDWPNRPKQKVCYETGKP----------------AQTEYEVVEYAADNT 149

Query: 143 TWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 175
             + L P+TGR HQLRVH    LG PI+GD  Y
Sbjct: 150 ARVVLKPITGRSHQLRVHML-ALGHPILGDRFY 181

Length = 219

>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621

 Score = 56.8 bits (137), Expect = 1e-09
 Identities = 44/147 (29%), Positives = 67/147 (45%), Gaps = 27/147 (18%)

Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           LVHRLD+ +SGIL++     SA+ L   F ++               +++ Y AL    P
Sbjct: 46  LVHRLDKMTSGILLLALNAESASELSQGFAKRK--------------IEKTYLALSSKKP 91

Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCH-GYTWLKLSP 149
           +  +G+I   + K    + K       + +       A+TR+     S   G     L P
Sbjct: 92  KKKQGLICGDMEKSRRGSWKLVN----SQENP-----AITRFFSA--SAATGLRLFILKP 140

Query: 150 LTGRKHQLRVHCAEVLGTPIVGDYKYG 176
            TG+ HQLRV   + LG+PI+GD  YG
Sbjct: 141 HTGKTHQLRV-AMKSLGSPILGDPLYG 166

This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity [Protein synthesis, tRNA and rRNA base modification]. Length = 217

>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional

 Score = 57.0 bits (138), Expect = 2e-09
 Identities = 47/162 (29%), Positives = 74/162 (45%), Gaps = 47/162 (29%)

Query: 27  EPPR--LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWA 84
           + PR  +VHRLD+D++G++V+ +T  + T L                  +KR + R Y A
Sbjct: 128 DVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVE--------------ALQKREITREYEA 173

Query: 85  LVVGTPRCSKGVISAPLGK--------VVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIK 136
           + +G    + G +  P+ +         V   GK                 AVT Y++++
Sbjct: 174 VAIGH-MTAGGTVDEPISRHPTKRTHMAVHPMGK----------------PAVTHYRIME 216

Query: 137 PSCH--GYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
              H   +T L+L   TGR HQ+RVH A  +  P+VGD  YG
Sbjct: 217 ---HFRVHTRLRLRLETGRTHQIRVHMAH-ITHPLVGDQVYG 254

Length = 325

>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family

 Score = 52.3 bits (126), Expect = 4e-08
 Identities = 39/151 (25%), Positives = 60/151 (39%), Gaps = 38/151 (25%)

Query: 32  VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
            HRLDR ++G+++  +   +     ++F  +    SK             Y A+    P 
Sbjct: 86  AHRLDRLTAGLVLFSKRPETRGAYQTLFARRE--VSKT------------YEAVAPYVP- 130

Query: 92  CSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQ------HAVTRYQVIKPSCHGYTWL 145
                 +      V       R  +V       A+      +A TR +++     G   L
Sbjct: 131 ------ALTFPLTV-------RSRIVKGRGFFQAREVEGEPNAETRIELLAR--RGGWGL 175

Query: 146 -KLSPLTGRKHQLRVHCAEVLGTPIVGDYKY 175
            +LSP TG+ HQLRVH A  LG PI+ D  Y
Sbjct: 176 YRLSPHTGKTHQLRVHMAA-LGVPILNDPFY 205

This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA. Length = 246

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	100.0
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	100.0
PRK11112	257	tRNA pseudouridine synthase C; Provisional	100.0
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	100.0
TIGR01621	217	RluA-like pseudouridine synthase Rlu family protei	100.0
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	100.0
cd02563	223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	100.0
PRK10158	219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	100.0
cd02558	246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	100.0
cd02557	213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	100.0
cd02869	185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	100.0
KOG1919	371	consensus RNA pseudouridylate synthases [RNA proce	99.97
cd02550	154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.96
PF00849	164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.95
cd02553	167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.94
cd02556	167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.94
TIGR00093	128	pseudouridine synthase. This model identifies pane	99.94
cd02870	146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.93
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	99.92
cd02566	168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.91
cd02555	177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.89
PRK11394	217	23S rRNA pseudouridine synthase E; Provisional	99.88
cd02554	164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.8
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	99.8
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	99.75
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.68
cd02868	226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	98.08
cd01291	87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	96.57
cd02572	182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	92.7
cd00506	210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	91.27
PRK00989	230	truB tRNA pseudouridine synthase B; Provisional	90.69
TIGR00431	209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	89.09
PRK00020	244	truB tRNA pseudouridine synthase B; Provisional	88.12
PF01509	149	TruB_N: TruB family pseudouridylate synthase (N te	87.16
PRK04099	273	truB tRNA pseudouridine synthase B; Provisional	87.15
cd02573	277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	85.78
PRK02193	279	truB tRNA pseudouridine synthase B; Provisional	85.65
PRK02484	294	truB tRNA pseudouridine synthase B; Provisional	84.4
PRK14123	305	tRNA pseudouridine synthase B; Provisional	84.04
PRK14124	308	tRNA pseudouridine synthase B; Provisional	84.0
PRK03287	298	truB tRNA pseudouridine synthase B; Provisional	83.84
PRK14846	345	truB tRNA pseudouridine synthase B; Provisional	83.22
PRK00130	290	truB tRNA pseudouridine synthase B; Provisional	82.97
PRK05389	305	truB tRNA pseudouridine synthase B; Provisional	82.25
PRK04270	300	H/ACA RNA-protein complex component Cbf5p; Reviewe	82.23
PRK01851	303	truB tRNA pseudouridine synthase B; Provisional	80.47

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=100.00  E-value=5.3e-45  Score=333.82  Aligned_cols=204  Identities=32%  Similarity=0.479  Sum_probs=160.9

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+...++.+.+..+.  .....+++|||||++||||||||+|..+++.|+.+|+++.              +.|
T Consensus       111 l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~--------------v~K  174 (317)
T PRK11025        111 TAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQK  174 (317)
T ss_pred             CcCcCCCCCCccHHHHHHHhc--cCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCC--------------ccE
Confidence            689988776555544443221  2234578999999999999999999999999999999877              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++...|.|+.||.+.....+.  .+....    ..++.|.|.|++++.. .++|||+|+|.||||||||+|
T Consensus       175 ~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~--~~~~~~----~~gk~a~T~~~~l~~~-~~~sLv~~~~~TGRtHQIRvh  247 (317)
T PRK11025        175 DYLALVRGQWQSHVKVVQAPLLKNILQSGE--RIVRVS----QEGKPSETRFKVEERY-AFATLVRASPVTGRTHQIRVH  247 (317)
T ss_pred             EEEEEEeCcccCCCceEecccccCcccCCc--eEEecC----CCCccceEEEEEeEEc-CCcEEEEEEeCCCCHHHHHHH
Confidence            999999999988889999998764322211  111111    2478999999999987 789999999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907          161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ  240 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~  240 (275)
                      ||+ +||||+||.+||....               +..+.     ..           ...+++|||++|.|++|     
T Consensus       248 la~-lG~PIlGD~~Yg~~~~---------------~~~~~-----~~-----------~~~r~~LHa~~l~f~~P-----  290 (317)
T PRK11025        248 TQY-AGHPIAFDDRYGDREF---------------DQQLT-----GT-----------GLNRLFLHAAALKFTHP-----  290 (317)
T ss_pred             HHH-CCCCEECCcccCCccc---------------chhhh-----cc-----------CCcchhhhcCcceeeCC-----
Confidence            997 9999999999996421               00000     00           13578999999999998     


Q ss_pred             hhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                .+++.+.|.||+|++|..+++.|.
T Consensus       291 ----------~~~~~~~~~aplP~~~~~~l~~l~  314 (317)
T PRK11025        291 ----------GTGEVMRIEAPLDEQLKRCLQKLR  314 (317)
T ss_pred             ----------CCCCeEEEEcCCCHHHHHHHHHHh
Confidence                      578999999999999999998775

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.9e-45  Score=328.88  Aligned_cols=191  Identities=35%  Similarity=0.560  Sum_probs=153.3

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCC--CCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDY--SEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~--~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||||.+...  ..++..++....  .+.+++||||||+||||||||||..++..|+.+|++++              +
T Consensus        96 l~vhp~~~~~~--~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~--------------v  159 (289)
T COG0564          96 LVVHPGGGHHE--GTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRK--------------V  159 (289)
T ss_pred             CcCcCCCCCcc--HhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCc--------------C
Confidence            68999855433  333332332211  67899999999999999999999999999999999977              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCc-EEEEEEEeCcCchhHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHG-YTWLKLSPLTGRKHQL  157 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~-~slv~~~~~TGR~HQI  157 (275)
                      .|+|+|+|.|.++..+|.|+.|+.+.....   ..+.+.....   +++|+|.|++++.. .. +|+++|+|.|||||||
T Consensus       160 ~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~---~~~~v~~~~~---gk~A~T~~~~l~~~-~~~~tlv~~~~~TGRTHQI  232 (289)
T COG0564         160 KKTYLALVRGHLPEDEGTIDAPIGRDPKNR---KKMAVVKEGS---GKPAITHYEVLERF-GDNYTLVELKPETGRTHQI  232 (289)
T ss_pred             cEEEEEEEECcccCCCCEEeeeeecCCcCC---ceEEEeccCC---CCceEEEEEehhcc-CCceEEEEEEeCCCCHhHH
Confidence            999999999999988899999998854222   2233333221   79999999999998 45 7999999999999999


Q ss_pred             HHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCch
Q 023907          158 RVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQ  237 (275)
Q Consensus       158 R~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~  237 (275)
                      |+||++ +||||+||++||.... .                                 ......+++|||+.|.|+||  
T Consensus       233 RVHl~~-lghPI~GD~~Yg~~~~-~---------------------------------~~~~~~r~~LHA~~l~f~hp--  275 (289)
T COG0564         233 RVHLAH-LGHPIVGDPLYGGKDK-S---------------------------------AGAGLKRQALHAYKLSFTHP--  275 (289)
T ss_pred             HHHHHH-CCCCeeCCcccCCchh-h---------------------------------cccCcchhhhhhceeEccCC--
Confidence            999996 9999999999997520 0                                 00014689999999999998  


Q ss_pred             hhhhhhccCCCCCCCCccEEEEcCCch
Q 023907          238 AIQKVQLSSGCDVSKLETLKLVAPLPS  264 (275)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~aplP~  264 (275)
                                   .+++.+.|.||+|.
T Consensus       276 -------------~t~~~~~~~a~~p~  289 (289)
T COG0564         276 -------------LTGEELEFEAPLPE  289 (289)
T ss_pred             -------------CCCCEEEEecCCCC
Confidence                         47899999999984

>PRK11112 tRNA pseudouridine synthase C; Provisional

Probab=100.00  E-value=8.7e-44  Score=316.84  Aligned_cols=206  Identities=30%  Similarity=0.383  Sum_probs=153.3

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.........++. ++.......+++|||||++||||||||||+.+++.|+++|+++.              |.|
T Consensus        20 l~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~--------------v~K   84 (257)
T PRK11112         20 WLVHRSWLDRHETVFVMQ-TVRDQIGQHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQ--------------IQK   84 (257)
T ss_pred             CeecCCCCCCCchHHHHH-HHHHHhCCCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCC--------------cce
Confidence            578876422221111222 33323344688999999999999999999999999999999977              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec----------CCcEEEEEEEeC
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS----------CHGYTWLKLSPL  150 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~----------~~~~slv~~~~~  150 (275)
                      +|+|+|.|.++ .++.++.|+.......   .. ....  ....++.|.|.|+++...          ..++|||+|+|.
T Consensus        85 ~Y~Alv~G~~~-~~~~i~~~l~~~~~~~---~~-~~~~--~~~~~k~a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~  157 (257)
T PRK11112         85 TYHAIVRGWLM-EEAVLDYPLKEELDKI---AD-KFAR--EDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK  157 (257)
T ss_pred             EEEEEEEeEeC-CCCeEeeeeeeccccc---ce-eecc--cCCCCeEeEEEEEEEEEecccccccccCCCCeEEEEEEcC
Confidence            99999999886 4578998886531111   01 1111  112478999999999763          135899999999


Q ss_pred             cCchhHHHHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCccccccccccccccee
Q 023907          151 TGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEM  230 (275)
Q Consensus       151 TGR~HQIR~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l  230 (275)
                      ||||||||+|||+ +||||+||.+||.....               ..+.    ..++           ..+++|||++|
T Consensus       158 TGRtHQIRvhla~-lG~PIvGD~~Yg~~~~~---------------~~~~----~~~~-----------~~rl~LHA~~L  206 (257)
T PRK11112        158 TGRKHQLRRHMAH-LRHPIIGDTKHGDLRQN---------------RSLA----EHFG-----------CSRLMLHASEL  206 (257)
T ss_pred             CCChHHHHHHHHH-cCCCEeCCcccCCcccc---------------hhhh----hccC-----------CcchhHhhCcc
Confidence            9999999999996 99999999999964210               0000    0011           35799999999


Q ss_pred             eccCCchhhhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          231 TLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       231 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                      .|+||               .+++.+.|.||+|++|+.+++.|+
T Consensus       207 ~F~hP---------------~t~e~~~~~a~~p~~~~~~~~~~~  235 (257)
T PRK11112        207 SLTHP---------------FTGEPLTITAGLDETWQQLLSQFG  235 (257)
T ss_pred             CccCC---------------CCCCEEEEEcCCCHHHHHHHHHcC
Confidence            99998               588999999999999999998774

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=100.00  E-value=9e-43  Score=320.16  Aligned_cols=210  Identities=28%  Similarity=0.410  Sum_probs=158.8

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhc-CCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTY-DYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~-~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++.+. ..++.+.+..++.. .....+++|||||++||||||||||..++..|+++|.++.              +
T Consensus       102 l~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~--------------v  167 (325)
T PRK11180        102 LVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKRE--------------I  167 (325)
T ss_pred             CeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCC--------------c
Confidence            578876543 34565555444432 2234688999999999999999999999999999999876              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|+|.|.++ .+|.++.+|....   .....+.+.     ..++.|.|.|+++... .++|+|+|+|.||||||||
T Consensus       168 ~K~Y~A~v~G~~~-~~~~i~~~l~~~~---~~~~~~~~~-----~~gk~a~T~~~~l~~~-~~~slv~~~~~TGRtHQIR  237 (325)
T PRK11180        168 TREYEAVAIGHMT-AGGTVDEPISRHP---TKRTHMAVH-----PMGKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIR  237 (325)
T ss_pred             ceEEEEEEecCCC-CCCEEECceecCC---CcCcEEEeC-----CCCcEEeEEEEEeEEc-CCeEEEEEEeCCCCHHHHH
Confidence            9999999999986 4678999986532   111112121     2378999999999987 6889999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +|||+ +||||+||.+||+.....          +.....+...              .....+++|||++|.|+||   
T Consensus       238 vhla~-lG~PI~GD~~Yg~~~~~~----------~~~~~~~~~~--------------~~~~~r~~Lha~~l~f~hP---  289 (325)
T PRK11180        238 VHMAH-ITHPLVGDQVYGGRPRPP----------KGASEEFIST--------------LRKFDRQALHATMLRLYHP---  289 (325)
T ss_pred             HHHHh-CCCCEeCccccCCCcccc----------cccchhhhhh--------------ccccchhhhhcceeEeeCC---
Confidence            99997 999999999999653100          0000000000              0013579999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                  .+++.+.|.||+|++|..+++.|+
T Consensus       290 ------------~~~~~~~~~a~~p~~~~~~~~~l~  313 (325)
T PRK11180        290 ------------ITGIEMEWHAPLPQDMVELIEALR  313 (325)
T ss_pred             ------------CCCCeEEEECCChHHHHHHHHHhh
Confidence                        478999999999999999998775

>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621

Probab=100.00  E-value=2e-42  Score=300.92  Aligned_cols=184  Identities=30%  Similarity=0.433  Sum_probs=147.0

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+. .++.+.+...   .....+++|||||++|||+||||+|+++++.|+++|.++.              +.|
T Consensus        20 l~v~~~~~~-~~l~~~l~~~---~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~--------------v~K   81 (217)
T TIGR01621        20 ISVHKDDGE-TGLLQEVATQ---LGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRK--------------IEK   81 (217)
T ss_pred             CeECCCCCc-ChHHHHHHHh---cCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCC--------------ccE
Confidence            578876543 3444443322   2245789999999999999999999999999999999977              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++..+|.|+.++....  .+.   ..+...    .++.|.|.|+++... +++++++|+|.|||+||||+|
T Consensus        82 ~YlAlV~g~~~~~~~~i~~~~~~~~--~~~---~~~~~~----~~k~a~t~~~~~~~~-~~~slv~~~~~TGR~HQIRvh  151 (217)
T TIGR01621        82 TYLALSSKKPKKKQGLICGDMEKSR--RGS---WKLVNS----QENPAITRFFSASAA-TGLRLFILKPHTGKTHQLRVA  151 (217)
T ss_pred             EEEEEEeccccCCCCEEeCCcccCC--CCC---EEEeCC----CCCceeEEEEEEEEc-CCeEEEEEEeCCCCHHHHHHH
Confidence            9999999999888899998886421  221   122221    368899999999887 689999999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907          161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ  240 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~  240 (275)
                      ||+ +||||+||.+||....                                       ..+++|||++|.|++      
T Consensus       152 la~-lG~PIlGD~~Yg~~~~---------------------------------------~~~~~Lha~~l~f~~------  185 (217)
T TIGR01621       152 MKS-LGSPILGDPLYGTTDE---------------------------------------SDRGYLHAFALRFDY------  185 (217)
T ss_pred             HHH-CCCceeCCcccCCCCC---------------------------------------ccCceeeeeEeEEEE------
Confidence            997 9999999999996320                                       236899999999997      


Q ss_pred             hhhccCCCCCCCCccEEEEcCCchHHHHHH
Q 023907          241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSW  270 (275)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~  270 (275)
                                 +++.+.|.|| |++|..++
T Consensus       186 -----------~~~~~~~~~~-~~~~~~~~  203 (217)
T TIGR01621       186 -----------QNEVIQWLCD-PRQFQKWH  203 (217)
T ss_pred             -----------CCeEEEEEEC-cHHHHHHH
Confidence                       3689999999 77675543

This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=100.00  E-value=2.5e-42  Score=313.85  Aligned_cols=208  Identities=30%  Similarity=0.404  Sum_probs=160.6

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhc-CCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTY-DYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~-~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++.+. ..++.+++..++.. .....+++|||||++||||||||+|..+++.++++|.++.              +
T Consensus        90 ~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~--------------v  155 (299)
T TIGR00005        90 LVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT--------------V  155 (299)
T ss_pred             CeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCC--------------c
Confidence            577876543 34566665544321 1225789999999999999999999999999999999876              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|+|.|.++...|.|+.||.......+   ...+...   .++++|.|.|+++... .++|+++|+|.|||+||||
T Consensus       156 ~K~Y~a~v~g~~~~~~~~i~~~l~~~~~~~~---~~~~~~~---~~~k~a~t~~~~l~~~-~~~slv~~~l~tGR~HQIR  228 (299)
T TIGR00005       156 TKEYVALVHGQFDSGGGTVDAPLGRVPNNRG---LMAVHPS---SEGKPAVTHFRVLERF-GNASLVECELETGRTHQIR  228 (299)
T ss_pred             ceEEEEEEeccccCCCCEEeCceecCCCCCc---eEEEecC---CCCCeeeEEEEEeEEc-CCeEEEEEEeCCCChHHHH
Confidence            9999999999998888999999876422111   1122221   1478999999999886 6889999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +|||+ +||||+||.+||+....  ...        .+.                   .....+++|||++|.|++|   
T Consensus       229 ~hla~-lG~pI~gD~~Yg~~~~~--~~~--------~~~-------------------~~~~~r~~Lha~~l~f~~p---  275 (299)
T TIGR00005       229 VHLQY-LGHPLAGDPLYGNKPVP--GNN--------LNG-------------------LLNFDRQALHAYELGFIHP---  275 (299)
T ss_pred             HHHHH-CCCcEeCccccCCcccc--ccc--------ccc-------------------ccCCcchhhccCeeeccCC---
Confidence            99997 99999999999974310  000        000                   0013579999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                  .+++.+.|.||+|++|..++..|+
T Consensus       276 ------------~~~~~~~~~a~~p~~~~~~~~~~~  299 (299)
T TIGR00005       276 ------------ATGEILEFEAPLPADLVLLLEALR  299 (299)
T ss_pred             ------------CCCCEEEEEcCChHHHHHHHHhhC
Confidence                        478999999999999999987763

modifies uracil-65 in transfer RNAs to pseudouridine.

>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi)

Probab=100.00  E-value=1.9e-42  Score=302.33  Aligned_cols=195  Identities=29%  Similarity=0.382  Sum_probs=145.2

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+.......++. .+.......+++|||||++||||||||+|+.+++.|+++|+++.              ++|
T Consensus        19 ~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~--------------v~K   83 (223)
T cd02563          19 LLVHRSELDRHETRFALQ-TLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHR--------------VHK   83 (223)
T ss_pred             CeEcCCCCCCCCcHHHHH-HHHHHcCCCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCc--------------eeE
Confidence            578876533222122222 23323345788999999999999999999999999999999977              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec----------CCcEEEEEEEeC
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS----------CHGYTWLKLSPL  150 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~----------~~~~slv~~~~~  150 (275)
                      +|+|+|.|.++. +|.|+.++......   .....+...   ..++.|.|.|+++...          ..++|||+|+|.
T Consensus        84 ~Y~alv~G~~~~-~~~i~~~l~~~~~~---~~~~~~~~~---~~~~~a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~  156 (223)
T cd02563          84 TYLAVVRGYVPE-SGTIDYPLSEELDK---LADKFASDD---KAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPH  156 (223)
T ss_pred             EEEEEEECccCC-CCeEEEeeeeCCCc---cceEEeecC---CCCceeEEEEEEeeecccccccccCCCCCeEEEEEEeC
Confidence            999999999876 78999988663211   111112111   2468899999999752          135899999999


Q ss_pred             cCchhHHHHHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCccccccccccccccee
Q 023907          151 TGRKHQLRVHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEM  230 (275)
Q Consensus       151 TGR~HQIR~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l  230 (275)
                      |||+||||+|||+ +||||+||.+||+....               ..+.+    .+           ...+++|||++|
T Consensus       157 TGR~HQIRvhla~-lG~PIvGD~~Yg~~~~~---------------~~~~~----~~-----------~~~rl~Lha~~L  205 (223)
T cd02563         157 TGRKHQLRRHLAH-IRHPIIGDTTHGDGRHN---------------RFFRE----HF-----------GCHRLLLAATRL  205 (223)
T ss_pred             CCCHHHHHHHHHH-cCCCeeCCcccCCcccC---------------hhHHh----hc-----------CCccceeecCee
Confidence            9999999999997 99999999999965310               00000    01           135799999999


Q ss_pred             eccCCchhhhhhhccCCCCCCCCccEEEEcCCc
Q 023907          231 TLPNVSQAIQKVQLSSGCDVSKLETLKLVAPLP  263 (275)
Q Consensus       231 ~f~~~~~~~~~~~~~~~~~~~~~~~~~~~aplP  263 (275)
                      .|++|               .+++.+.|+||+|
T Consensus       206 ~F~hP---------------~t~~~~~~~a~~~  223 (223)
T cd02563         206 EFTHP---------------VTGERLLIEAPLD  223 (223)
T ss_pred             EeeCC---------------CCCCeEEEEccCC
Confidence            99998               5899999999997

No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional

Probab=100.00  E-value=8e-42  Score=297.56  Aligned_cols=185  Identities=30%  Similarity=0.417  Sum_probs=145.5

Q ss_pred             CCccCCCC--CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIG--IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~--~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++..  ...++.+.+...+     ..+++|||||++||||||||+|.++++.|+++|+++.              +
T Consensus        32 l~~~~~~~~~~~~sl~~~l~~~~-----~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~--------------v   92 (219)
T PRK10158         32 LLSVPGRLEEHKDSVMTRIQRDY-----PQAESVHRLDMATSGVIVVALTKAAERELKRQFRERE--------------P   92 (219)
T ss_pred             CcEeCCCCCccchhHHHHHHHhC-----CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhCC--------------c
Confidence            57887653  2334444443221     2578999999999999999999999999999999876              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|+|.|.++..++.++.|+.....   ......+..    .+++.+.|.|++++......++|+|+|+|||+||||
T Consensus        93 ~K~Yla~v~G~~~~~~~~i~~~i~~~~~---~~~~~~~~~----~~gk~a~t~~~~l~~~~~~~sll~~~~~TGRtHQIR  165 (219)
T PRK10158         93 KKQYVARVWGHPSPAEGLVDLPLICDWP---NRPKQKVCY----ETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLR  165 (219)
T ss_pred             cEEEEEEEecccCCCCcEEecceecCCC---CCceEEecC----CCCceeeEEEEEEEEcCCCCEEEEEEeCCCCHHHHH
Confidence            9999999999998888999999865321   111122221    236899999999998634458999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +||++ +||||+||.+||.....               .                     ..++++|||++|.|++|   
T Consensus       166 ~hla~-lG~PIvGD~~Yg~~~~~---------------~---------------------~~~r~~Lha~~l~f~~P---  205 (219)
T PRK10158        166 VHMLA-LGHPILGDRFYASPEAR---------------A---------------------MAPRLLLHAEMLTITHP---  205 (219)
T ss_pred             HHHHH-CCCcEECCcccCCcccc---------------c---------------------cccchhhhhCccCccCC---
Confidence            99996 99999999999964210               0                     03469999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLP  263 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP  263 (275)
                                  .+++.++|.||.|
T Consensus       206 ------------~~~~~~~~~a~~~  218 (219)
T PRK10158        206 ------------AYGNSMTFKAPAD  218 (219)
T ss_pred             ------------CCCCeEEEEeCCC
Confidence                        4789999999986

>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family

Probab=100.00  E-value=6.7e-41  Score=296.48  Aligned_cols=187  Identities=22%  Similarity=0.288  Sum_probs=140.9

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      |+||++.+. ..++.+.+...+   ....+++|||||++|||+||||||+++++.++.+|+++.              ++
T Consensus        57 l~~~~~~~~~~~t~~~~l~~~~---~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~--------------v~  119 (246)
T cd02558          57 LPVTPRGRYVTETLLVRLRRQT---GNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARRE--------------VS  119 (246)
T ss_pred             CccCCCCcchhhhHHHHHHHHh---CCCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCC--------------cc
Confidence            678876443 234444433222   234678999999999999999999999999999999876              99


Q ss_pred             eEEEEEEecccCCCcc-EEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           80 RWYWALVVGTPRCSKG-VISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        80 K~Y~alv~G~~~~~~g-~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      |+|+|+|.|.++...+ .++.++...   .+ .......     .+++.|.|.|++++.. .++|+++|+|.|||+||||
T Consensus       120 K~YlA~v~G~~~~~~~~~~~~~i~~~---~~-~~~~~~~-----~~~~~a~T~~~~l~~~-~~~slv~~~l~TGRtHQIR  189 (246)
T cd02558         120 KTYEAVAPYVPALTFPLTVRSRIVKG---RG-FFQAREV-----EGEPNAETRIELLARR-GGWGLYRLSPHTGKTHQLR  189 (246)
T ss_pred             EEEEEEEecCCCCCCCcceecccccc---CC-cceeecc-----CCCCCceEEEEEEEec-CCeEEEEEEeCCCCHHHHH
Confidence            9999999998865443 355555432   11 1111111     2357899999999886 6899999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +|||+ +||||+||.+||......             ..                 .   ...+++|||++|.|+||   
T Consensus       190 vhla~-lG~PIvGD~~Yg~~~~~~-------------~~-----------------~---~~~~~~Lha~~l~f~hP---  232 (246)
T cd02558         190 VHMAA-LGVPILNDPFYPVLLDKD-------------PD-----------------D---FSRPLQLLAKELEFTDP---  232 (246)
T ss_pred             HHHHH-CCCcccCCccCCCCCccc-------------cc-----------------c---cccCchhhhcccCccCC---
Confidence            99996 999999999999642100             00                 0   01348999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLP  263 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP  263 (275)
                                  .+++.+.|.||+|
T Consensus       233 ------------~t~~~~~~~~~~~  245 (246)
T cd02558         233 ------------LTGRPRRFESGRS  245 (246)
T ss_pred             ------------CCCCEEEEecCCC
Confidence                        5889999999998

This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like

Probab=100.00  E-value=3.5e-40  Score=286.15  Aligned_cols=177  Identities=27%  Similarity=0.352  Sum_probs=142.8

Q ss_pred             CCccCCCC-CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGIG-IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~~-~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      |+||++.. ...++.+++...+   ....+++|||||++||||||||+|+++++.|+++|+++.              ++
T Consensus        34 l~~~~~~~~~~~sl~~~l~~~~---~~~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~--------------v~   96 (213)
T cd02557          34 IPVHPTGRYRYNTVTEILKSEY---GLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSRE--------------VK   96 (213)
T ss_pred             CcCCCCCCCCcChHHHHHHHHc---CCCCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCC--------------cc
Confidence            57786543 3456666665322   124688999999999999999999999999999999876              99


Q ss_pred             eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecC-CcEEEEEEEeCcCchhHHH
Q 023907           80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSC-HGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~-~~~slv~~~~~TGR~HQIR  158 (275)
                      |+|+|+|.|.++...+.++.||.......+    +....   ...++.|.|.|+++.... .++++|+|+|.|||+||||
T Consensus        97 K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~----~~~~~---~~~~~~a~t~~~~~~~~~~~~~slv~v~~~TGR~HQIR  169 (213)
T cd02557          97 KEYLARVKGEFPDGEVVVDQPIGLVSPKGG----LRNDV---DEKGKDARTIFKRLSYNGDLNTSVVLCKPITGRTHQIR  169 (213)
T ss_pred             EEEEEEEeCcCCCCCeEEecceeccCcCCc----eeecc---CCCCceeeEEEEEEEEcCCCCeEEEEEEeCCCCHHHHH
Confidence            999999999998888999999876432221    11111   124688999999998862 2789999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +|||+ +||||+||.+||..                                           +++|||++|.|+     
T Consensus       170 ~hla~-lG~PIlGD~~Yg~~-------------------------------------------~l~Lha~~l~f~-----  200 (213)
T cd02557         170 VHLQY-LGHPIVNDPIYNNL-------------------------------------------GIYLHALRYEGP-----  200 (213)
T ss_pred             HHHHH-CCCCCcCccccCCc-------------------------------------------ChhhhhccCcCc-----
Confidence            99996 99999999999951                                           379999999984     


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCchHH
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLPSHM  266 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f  266 (275)
                                      .+.|.||+|.||
T Consensus       201 ----------------~~~~~~~~p~~~  212 (213)
T cd02557         201 ----------------DWSYETELPDWA  212 (213)
T ss_pred             ----------------cEEEEeCCCccc
Confidence                            688999999987

This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.

>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family

Probab=100.00  E-value=2.2e-36  Score=255.75  Aligned_cols=156  Identities=38%  Similarity=0.595  Sum_probs=121.3

Q ss_pred             CCccCCCCC-cCcHHHHHHH-HhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGI-RRSIDELAAT-CLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~-~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      ++||++... ..++.+++.. .........+++|||||++|||+||||+|+++++.|.++|+++.              +
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~--------------~   75 (185)
T cd02869          10 LPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERK--------------V   75 (185)
T ss_pred             CeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCc--------------e
Confidence            467765443 3444544321 12233456799999999999999999999999999999998866              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|+|.|.++...+.++.++....   ..........    .+++.+.|+|+++... .++++++|+|.|||+||||
T Consensus        76 ~K~Y~a~v~g~~~~~~~~~~~~~~~~~---~~~~~~~~~~----~~~~~~~t~~~~l~~~-~~~s~~~~~l~tGR~HQIR  147 (185)
T cd02869          76 KKTYLALVDGKPPEDEGTIDAPLGRKK---RKKRARVVVS----EDGKPAITHYKVLERF-GNVTLVELQLETGRTHQIR  147 (185)
T ss_pred             eEEEEEEEeCCCCCCccEEecccccCC---ccCceEEEEC----CCCeEEEEEEEEEEEc-CCcEEEEEEeCcCCccHHH
Confidence            999999999999988888888775420   0011111111    2368899999999886 6889999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCc
Q 023907          159 VHCAEVLGTPIVGDYKYGWQT  179 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~  179 (275)
                      +||++ +||||+||.+||...
T Consensus       148 ~hl~~-~G~pIvGD~~Yg~~~  167 (185)
T cd02869         148 VHLAS-IGHPIVGDPKYGGKA  167 (185)
T ss_pred             HHHHH-CCCCEeCccccCCcc
Confidence            99997 999999999999754

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.

>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]

Probab=99.97  E-value=1.7e-29  Score=232.53  Aligned_cols=155  Identities=34%  Similarity=0.500  Sum_probs=121.2

Q ss_pred             CCccC-CCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQG-GIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~-g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      ||||+ |.-..+++..++...   ...+.+++|||||+.|||+||||+++.++..+++.|++++              +.
T Consensus       124 ipVhp~g~~~~n~i~~~l~~~---~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~--------------~~  186 (371)
T KOG1919|consen  124 IPVHPTGRYRENTITKILAAL---HKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRT--------------VK  186 (371)
T ss_pred             CceeccCccccccchHHHHHh---ccccccccccccCccccceEEEEechhHhHHHHHHHhccc--------------ce
Confidence            68994 444455555554422   3567799999999999999999999999999999999977              99


Q ss_pred             eEE-EEEEecccC-CCccEEeccceeeeccCCceeeEEEecCCC--CCCCcceEEEEEEeeecCCcEEEEEEEeCcCchh
Q 023907           80 RWY-WALVVGTPR-CSKGVISAPLGKVVVDNGKSDRITVVNNDQ--IMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKH  155 (275)
Q Consensus        80 K~Y-~alv~G~~~-~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~--~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~H  155 (275)
                      |.| .|-|.|.++ .....+..++.....    ..++.+.....  ...++.|.|.|+++... ++.++|+|.|+|||||
T Consensus       187 k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~----~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~-~~ss~V~~~PlTGRtH  261 (371)
T KOG1919|consen  187 KEYVVARVEGPFPVVGEVEIKEPIGEEER----PLRMGLNAVGVRDEVAAKDAKTLFKVLSYD-GGSSLVECRPLTGRTH  261 (371)
T ss_pred             eEEEEEEEeccCCCCceEEeCCCcccccc----ccceEeeecccccccccccceeEEEEcccC-CceEEEEeeccCCcHH
Confidence            999 688999887 444556666654321    11222222211  13479999999999998 8999999999999999


Q ss_pred             HHHHHHHhcCCCceeCCCCCCCC
Q 023907          156 QLRVHCAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       156 QIR~hla~~lG~PIvGD~~Yg~~  178 (275)
                      |||+||+. +|+||+||.+|+..
T Consensus       262 QIRvHlq~-lG~PI~gD~~Y~~~  283 (371)
T KOG1919|consen  262 QIRVHLQY-LGHPIAGDPKYGNH  283 (371)
T ss_pred             HHHHHHHH-hCCCcCCCcccccc
Confidence            99999996 99999999999763

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family

Probab=99.96  E-value=3.3e-29  Score=206.81  Aligned_cols=137  Identities=24%  Similarity=0.316  Sum_probs=103.3

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      ++||++.+. ..++.+.+    .......+++|||||++||||||||+|+++++.|+++  ++.              +.
T Consensus        10 ~~~~~~~~~~~~~~~~~l----~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~--------------v~   69 (154)
T cd02550          10 LVCHPTDRDRDPTVVVRL----DKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RRE--------------IE   69 (154)
T ss_pred             CEEecCCCCCCCcHHHhh----hcccCCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hcc--------------Cc
Confidence            467766543 23443332    2233467899999999999999999999999999998  433              99


Q ss_pred             eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHH
Q 023907           80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRV  159 (275)
Q Consensus        80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~  159 (275)
                      |+|+|+|.|.+++ ++.+..++..    .+.. .. +..    .+++.+.|.|++++.. .++++++|+|.|||+||||+
T Consensus        70 K~Y~a~v~g~~~~-~~~~~~~~~~----~~~~-~~-~~~----~~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~  137 (154)
T cd02550          70 KEYLVTVRGELDE-EGIEDLATVR----RGRL-SG-LVD----EGVPLAVTKVRVIGEH-GGTGRLRLTLKTGRTHQIRR  137 (154)
T ss_pred             EEEEEEEEeecCc-chheeccccc----cCcc-ee-EEc----CCCcccceEEEEEEec-CCcEEEEEEEcCCCcHHHHH
Confidence            9999999999864 4556665543    1111 11 111    2367889999999876 67899999999999999999


Q ss_pred             HHHhcCCCcee
Q 023907          160 HCAEVLGTPIV  170 (275)
Q Consensus       160 hla~~lG~PIv  170 (275)
                      |||+ +||||.
T Consensus       138 hla~-~G~pI~  147 (154)
T cd02550         138 HCAA-VGFPVL  147 (154)
T ss_pred             HHHH-cCCcEE
Confidence            9997 999997

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.

>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family

Probab=99.95  E-value=4e-27  Score=195.41  Aligned_cols=144  Identities=35%  Similarity=0.517  Sum_probs=103.7

Q ss_pred             CCccCCCC-CcCcHHHHHHH-HhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIG-IRRSIDELAAT-CLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~-~~~sl~~l~~~-~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |++|+..+ ........... .........+++|||||++||||||||+|+++++.|+++|..+.              +
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~--------------~   76 (164)
T PF00849_consen   11 VPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRK--------------V   76 (164)
T ss_dssp             SBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTC--------------S
T ss_pred             CeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCC--------------C
Confidence            46666552 22233333332 33445677899999999999999999999999999999999866              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec--------CCcEEEEEEEeC
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS--------CHGYTWLKLSPL  150 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~--------~~~~slv~~~~~  150 (275)
                      +|+|+|+|.|.+....+.++.++............. ..    ...++.+.|.|+++...        ..+.++++|+|.
T Consensus        77 ~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~t~~~~l~~~~~~~~~~~~~~~s~v~~~l~  151 (164)
T PF00849_consen   77 EKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKD-PP----GRDGKPAITRYRVLRSGSRTPSKDENAGCSLVECELI  151 (164)
T ss_dssp             EEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCE-EE----TTTSBTSEEEEEEEEEETT---EECCSSEEEEEEEES
T ss_pred             cEEEEEeEcccccccceeeeccccccccccccceee-ee----cccccccceeeeeeccccccccccccCCCEEEEEEEC
Confidence            999999999877788899999987632112111111 11    12478899999999875        357899999999


Q ss_pred             cCchhHHHHHHHh
Q 023907          151 TGRKHQLRVHCAE  163 (275)
Q Consensus       151 TGR~HQIR~hla~  163 (275)
                      |||+||||+|||+
T Consensus       152 tGr~HQIR~hla~  164 (164)
T PF00849_consen  152 TGRTHQIRVHLAH  164 (164)
T ss_dssp             S-STTHHHHHHHH
T ss_pred             cCCCHHHHHHhcC
Confidence            9999999999984

This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like

Probab=99.94  E-value=1.2e-27  Score=200.16  Aligned_cols=136  Identities=18%  Similarity=0.181  Sum_probs=96.6

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.....++.+++..++   ....+++|||||++||||||||+|..+++.+...  .+              .++|
T Consensus        11 ~~~~~~~~~~~tl~~~l~~~~---~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~--------------~i~K   71 (167)
T cd02553          11 VVCATKDPHHPTVIDLLPEPD---RRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSP--KK--------------HVPK   71 (167)
T ss_pred             CEeCCCCCCCCcHHHHhhhhc---ccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhCC--cC--------------CCce
Confidence            467766665667766665433   2346899999999999999999999988877653  32              3999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++....  ....      .+    +.. .+.    .+...+.+++++     .++++|+|.|||+||||+|
T Consensus        72 ~Y~a~V~G~~~~~~~--~~~~------~~----~~~-~~~----~~~~~~~~~~~~-----~sll~v~l~tGR~HQIR~h  129 (167)
T cd02553          72 TYEVTLAGPLTEDDI--EAFA------EG----VLL-HDG----YPTKPAKLEILS-----PTTVRLTITEGKYHQVKRM  129 (167)
T ss_pred             EEEEEEccCCCHHHH--HHHH------CC----eEE-cCC----CEeeeeEEEEeC-----CcEEEEEEEeCCCHHHHHH
Confidence            999999998865432  1111      11    111 110    122334555553     2899999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCC
Q 023907          161 CAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~  178 (275)
                      ||+ +||||++|..++-.
T Consensus       130 la~-lG~pI~~~~R~~~g  146 (167)
T cd02553         130 FAA-VGNKVVALHRIRIG  146 (167)
T ss_pred             HHH-cCCeEEEEEEEEEC
Confidence            997 99999999887643

This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.

>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like

Probab=99.94  E-value=1.1e-26  Score=194.36  Aligned_cols=131  Identities=17%  Similarity=0.205  Sum_probs=96.2

Q ss_pred             CCccCCC-CCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGI-GIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~-~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      +++|+.. ....++.+++..+    ....+++|||||++||||||||+|+++++.|..  .++.              +.
T Consensus        11 ~~~~~~~~~~~~tl~~~l~~~----~~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~--------------i~   70 (167)
T cd02556          11 LICTRKDPKGRPTVFDLLPKL----GIPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNE--------------IE   70 (167)
T ss_pred             cEECccCCCCCccHHHhhhhh----ccCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCC--------------CC
Confidence            3566532 2345555554422    235678999999999999999999999999975  3433              99


Q ss_pred             eEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHH
Q 023907           80 RWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRV  159 (275)
Q Consensus        80 K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~  159 (275)
                      |+|+|+|.|.++...  +.. +     ..|    +..      .+++.+.|.|+++... .++++++|+|.|||+||||+
T Consensus        71 K~Y~a~V~g~~~~~~--~~~-~-----~~g----v~~------~~~~~~~~~~~~~~~~-~~~sll~v~l~tGR~HQIR~  131 (167)
T cd02556          71 REYAVRVFGQVTDEQ--LKS-L-----KKG----VEL------EDGFAGFKSIQLEGGE-GKNSWYRVTLREGRNREVRR  131 (167)
T ss_pred             eEEEEEECccCCHHH--HHH-H-----HcC----CEE------CCCcCcceEEEEEecC-CCcEEEEEEEEeCCCHHHHH
Confidence            999999999886543  110 0     111    111      1256788999999765 56799999999999999999


Q ss_pred             HHHhcCCCceeC
Q 023907          160 HCAEVLGTPIVG  171 (275)
Q Consensus       160 hla~~lG~PIvG  171 (275)
                      ||++ +||||+-
T Consensus       132 ~~a~-~G~pV~~  142 (167)
T cd02556         132 LWEA-FGLQVSR  142 (167)
T ss_pred             HHHH-cCCeEeE
Confidence            9997 9999985

This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.

>TIGR00093 pseudouridine synthase

Probab=99.94  E-value=5.4e-27  Score=187.90  Aligned_cols=111  Identities=23%  Similarity=0.356  Sum_probs=86.9

Q ss_pred             cccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeeeccCCce
Q 023907           32 VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKS  111 (275)
Q Consensus        32 vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~  111 (275)
                      |||||++||||||||+|+++++.|.+  .++              .+.|+|+|+|.|.++...  ++ ++.     .+  
T Consensus         1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~--------------~i~K~Y~a~v~g~~~~~~--~~-~~~-----~g--   54 (128)
T TIGR00093         1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGH--------------HCEKTYLVTVEGPVTDED--LE-ALR-----KG--   54 (128)
T ss_pred             CCCCCCCCEEEEEEEeCHHHHHHHhC--CCC--------------CCCeEEEEEECCCCCHHH--HH-HHh-----CC--
Confidence            79999999999999999999999987  233              399999999999886532  11 111     11  


Q ss_pred             eeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCCCC
Q 023907          112 DRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       112 ~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg~~  178 (275)
                        +.. .     +++.+.+.|+++... .+.++++|+|.|||+||||+||++ +||||+||..+.-.
T Consensus        55 --~~~-~-----~~~~~~~~~~~l~~~-~~~~~l~~~l~tGR~HQIR~~~~~-lG~pI~g~~R~~~g  111 (128)
T TIGR00093        55 --VQL-E-----DGPTKPAKLEVITEP-GFPTWLRITLSEGRNRQVRRMFAA-VGFPVLRLHRVRIG  111 (128)
T ss_pred             --eEE-C-----CcEEeeeEEEEEccC-CCceEEEEEEeCCCCHHHHHHHHH-cCCeEeEEEEEEEC
Confidence              111 1     135567888988765 557899999999999999999997 99999999988543

This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.

>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA

Probab=99.93  E-value=3.7e-27  Score=192.95  Aligned_cols=110  Identities=23%  Similarity=0.312  Sum_probs=87.3

Q ss_pred             CCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeee
Q 023907           26 SEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVV  105 (275)
Q Consensus        26 ~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~  105 (275)
                      ...+++|||||++|||+||||+|+++++.|...  ++.              +.|+|+|+|.|.+.....  ...     
T Consensus        31 ~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~--~~~--------------i~K~Y~a~v~g~~~~~~~--~~~-----   87 (146)
T cd02870          31 GERLFPVGRLDYDTEGLLLLTNDGELANRLTHP--RYG--------------VEKTYLVKVRGVPSEEEL--RRL-----   87 (146)
T ss_pred             CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhCc--cCC--------------CCeEEEEEECCCCCHHHH--HHH-----
Confidence            456899999999999999999999999998763  323              999999999998864331  110     


Q ss_pred             ccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeC
Q 023907          106 VDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVG  171 (275)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvG  171 (275)
                       ..+    +. .     .+++.+.|+|++++.. .++++++|+|.|||+||||+||++ +|+||+.
T Consensus        88 -~~~----~~-~-----~~~~~~~t~~~~l~~~-~~~sll~~~l~tGR~HQIR~hla~-~G~pI~~  140 (146)
T cd02870          88 -RAG----VE-L-----DDGKTAPAKVKVLSRD-PKNTLLEVTLHEGRNRQVRRMFEA-VGHPVLR  140 (146)
T ss_pred             -HCC----eE-e-----CCceEcceEEEEeccC-CCCcEEEEEEEeCCcHHHHHHHHH-cCCcCCe
Confidence             011    11 1     1257789999999876 578999999999999999999997 9999973

The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=99.92  E-value=7.5e-26  Score=198.78  Aligned_cols=133  Identities=16%  Similarity=0.140  Sum_probs=93.4

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||+......++.+++    .......+++|||||++||||||||+|+.++..|..  ..+              .+.|
T Consensus        71 ~~~~~~~~~~~tl~~~l----~~~~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~--------------~i~K  130 (232)
T PRK10839         71 YVCSTDDPDHPTVLYFL----DEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRH--------------HCEK  130 (232)
T ss_pred             eEecccCCCCCeEEEec----ccccccCceecCCCCCCceeEEEEecCHHHHHHHhC--CCC--------------CCCe
Confidence            45676543333433332    222234688999999999999999999999888875  333              3999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|.+.+.+.....  .. +     ..+      +..     .++.|.|.|.+++.. + .++++|+|.||||||||+|
T Consensus       131 ~Y~a~i~~~i~~~~~--~~-~-----~~~------~~~-----~g~~a~t~~~~~~~~-~-~sll~~~l~tGRtHQIR~h  189 (232)
T PRK10839        131 TYLVTLESPVADDTA--EQ-F-----AKG------VQL-----HNEKDLTKPAVLEVI-T-PTQVRLTISEGRYHQVKRM  189 (232)
T ss_pred             EEEEEECCCCCHHHH--HH-H-----HCC------eEE-----CCCcccccccEEEEe-c-CCEEEEEEEcCcCHHHHHH
Confidence            999987776543210  00 0     011      111     256788999999875 3 3899999999999999999


Q ss_pred             HHhcCCCceeCCCCC
Q 023907          161 CAEVLGTPIVGDYKY  175 (275)
Q Consensus       161 la~~lG~PIvGD~~Y  175 (275)
                      |++ +||||+|=...
T Consensus       190 ~~~-~G~pi~gl~R~  203 (232)
T PRK10839        190 FAA-VGNHVVELHRE  203 (232)
T ss_pred             HHH-cCCeEeeEEEE
Confidence            997 99999986543

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE

Probab=99.91  E-value=1.2e-24  Score=182.15  Aligned_cols=145  Identities=17%  Similarity=0.193  Sum_probs=92.3

Q ss_pred             CCccCCCC--CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIG--IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~--~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      +++|++..  ...++.+.+.       ...+++|||||++||||||||+|+.+++.|.+...                .+
T Consensus        10 ~~~~~~~~~~~~~~l~~~l~-------~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~~~----------------~v   66 (168)
T cd02566          10 VLSQFTDESEKHKTLKDYID-------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSF----------------KH   66 (168)
T ss_pred             CEEecCCCcCCCccHHHHcC-------cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCCCC----------------CC
Confidence            45675432  3345544432       14678999999999999999999998888766522                29


Q ss_pred             ceEEEEEEecccCCCccE-EeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeec-CCcEEEEEEEeCcCchhH
Q 023907           79 QRWYWALVVGTPRCSKGV-ISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS-CHGYTWLKLSPLTGRKHQ  156 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~-i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~-~~~~slv~~~~~TGR~HQ  156 (275)
                      +|+|+|+|.|.++..... +...+.   .+++......+....   ......|.|.++... ....++++|+|.|||+||
T Consensus        67 ~K~Y~a~v~g~~~~~~~~~l~~g~~---~~~~~~~~~~v~~~~---~~~~~~~~~~~~~~~~~~~~sll~v~l~tGR~HQ  140 (168)
T cd02566          67 PKTYYVQVEGVPTEDALEQLRNGVE---LGDGLTLPAKVEKVD---EPPWLWEREPPIRFRKNIPTSWIEITICEGKNRQ  140 (168)
T ss_pred             CEEEEEEECCcCCHHHHHHHhCCcE---ECCeEecceEEEEec---ccccccccccccccccCCCccEEEEEEecCccHH
Confidence            999999999998643210 000010   011111111111110   112344555556532 135689999999999999


Q ss_pred             HHHHHHhcCCCceeCCCCC
Q 023907          157 LRVHCAEVLGTPIVGDYKY  175 (275)
Q Consensus       157 IR~hla~~lG~PIvGD~~Y  175 (275)
                      ||+||++ +||||+.....
T Consensus       141 IR~~la~-lG~pV~~L~R~  158 (168)
T cd02566         141 VRRMTAA-VGFPTLRLIRV  158 (168)
T ss_pred             HHHHHHH-cCCeEeEEEEE
Confidence            9999997 99999976654

This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.

>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family

Probab=99.89  E-value=1.4e-23  Score=176.96  Aligned_cols=108  Identities=19%  Similarity=0.258  Sum_probs=81.5

Q ss_pred             CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccE--Eeccceee
Q 023907           27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGV--ISAPLGKV  104 (275)
Q Consensus        27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~--i~~~l~~~  104 (275)
                      .++++|||||++||||||||+|+.+++.|.+++..                +.|+|+|+|.|.+++. +.  +...+.  
T Consensus        45 ~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~----------------i~K~Y~v~v~g~~~~~-~l~~l~~g~~--  105 (177)
T cd02555          45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASR----------------LEQEYLVEVRGELTAG-GLERLNHGLT--  105 (177)
T ss_pred             CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcC----------------CCEEEEEEEcccCCHH-HHHHHhcCcc--
Confidence            46889999999999999999999999999987543                9999999999988653 21  111110  


Q ss_pred             eccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCC
Q 023907          105 VVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG  176 (275)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg  176 (275)
                                 + .+.   ..+.+.+.+       .+.++++++|.|||+||||+||++ +||||+|+....
T Consensus       106 -----------~-~~~---~~~~~~~~~-------~~~~~l~i~l~tGr~hQIR~~~~~-~G~pV~~L~R~~  154 (177)
T cd02555         106 -----------Y-DGR---ELPPAKVSW-------QNEQRLRFALKEPQPGQIRRMCES-VGLEVVALRRIR  154 (177)
T ss_pred             -----------c-CCe---ecceEEEEE-------cCCCEEEEEEECCcChHHHHHHHH-cCCeEEEEEEEE
Confidence                       0 000   012233322       134799999999999999999997 999999998874

This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.

>PRK11394 23S rRNA pseudouridine synthase E; Provisional

Probab=99.88  E-value=3.4e-23  Score=179.00  Aligned_cols=126  Identities=25%  Similarity=0.382  Sum_probs=83.8

Q ss_pred             CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEecccee-ee
Q 023907           27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGK-VV  105 (275)
Q Consensus        27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~-~~  105 (275)
                      .++++|||||++||||||||+|+.+++.|.++  ++.              +.|+|+|+|.|.+.......   +.. ..
T Consensus        70 ~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~--~~~--------------i~K~Y~~~v~g~~~~~~l~~---l~~Gv~  130 (217)
T PRK11394         70 QGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GKR--------------TGKIYYVQVEGIPTQDALEA---LRNGVT  130 (217)
T ss_pred             CCeEEecCCCCCCeeEEEEECCHHHHHHHhCc--ccC--------------CCEEEEEEECCCCCHHHHHH---HhCCeE
Confidence            46899999999999999999999999999986  322              99999999999986543211   100 00


Q ss_pred             ccCCce--eeEEEecCC-CCCCCcceEEEEEEeee-cCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCCCCCCCC
Q 023907          106 VDNGKS--DRITVVNND-QIMSAQHAVTRYQVIKP-SCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       106 ~~~~~~--~~~~~~~~~-~~~~~k~a~t~~~~l~~-~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~~Yg~~  178 (275)
                      ..++..  ..+...... ...      ..+..+.. ...+.++++|+|.|||+||||+||++ +||||+||.+|+-.
T Consensus       131 i~~~~~~p~~~~~i~~~~~~~------~~~~~~~~~~~~~~s~l~I~L~eGR~hQIRrm~a~-lG~pVl~L~Ry~iG  200 (217)
T PRK11394        131 LNDGPTLPAGAELVDEPAWLW------PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAH-VGFPTLRLIRYAMG  200 (217)
T ss_pred             ECCccccccEEEEeccccccc------ccccccccccCCCceEEEEEEeCCCCHHHHHHHHH-cCCeEeeeEEEEEC
Confidence            011110  000000000 000      00111111 11357899999999999999999997 99999999999754

>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like

Probab=99.80  E-value=2.1e-19  Score=149.59  Aligned_cols=106  Identities=17%  Similarity=0.180  Sum_probs=77.2

Q ss_pred             CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceeeec
Q 023907           27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVV  106 (275)
Q Consensus        27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~~~  106 (275)
                      .++++|||||++|||+||||+|..+++.|+.+...                +.|+|+|.|.|.+.+...  ..      .
T Consensus        31 ~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~----------------~~K~Y~V~v~~~l~~~~l--~~------l   86 (164)
T cd02554          31 PRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNN----------------HEKEYLVTVNKPITDEFI--EG------M   86 (164)
T ss_pred             CCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcC----------------CCeEEEEEECCCCCHHHH--HH------H
Confidence            57999999999999999999999999999887776                899999999998865311  00      0


Q ss_pred             cCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeCC
Q 023907          107 DNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGD  172 (275)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD  172 (275)
                      ..|.    .. .        .+.|....+... +. +.++|.+.+||+||||+||++ +|+||+-=
T Consensus        87 ~~G~----~~-~--------~~~~~~~~v~~~-~~-~~l~i~l~eGr~~qIRrm~~~-~G~~V~~L  136 (164)
T cd02554          87 SNGV----VI-L--------GTVTKPCKVERL-AK-DKFRIVLTQGLNRQIRRMCEA-LGYRVTDL  136 (164)
T ss_pred             hCCC----EE-C--------CeEEcceEEEEC-CC-CEEEEEEECCcCHHHHHHHHH-cCCEEEEE
Confidence            1111    11 1        112222222222 12 359999999999999999997 99999853

This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=99.80  E-value=1.4e-19  Score=163.70  Aligned_cols=121  Identities=17%  Similarity=0.216  Sum_probs=82.2

Q ss_pred             CcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEeccc
Q 023907           11 RSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP   90 (275)
Q Consensus        11 ~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~   90 (275)
                      .++.+++..+    ....+++|||||++||||||||+|.++++.|...  .+              .+.|+|+|+|.|.+
T Consensus        89 ~tv~d~l~~~----~~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p--~~--------------~i~K~Y~v~V~G~~  148 (289)
T PRK10700         89 PTVFDRLPKL----RGARWIAVGRLDVNTCGLLLFTTDGELANRLMHP--SR--------------EVEREYAVRVFGQV  148 (289)
T ss_pred             ccHHHHhhhh----cCCceeEccCCCCCCceEEEEEcCHHHHHHHhCc--cC--------------CCCeEEEEEEccCC
Confidence            4555555431    2346789999999999999999999999999763  32              39999999999988


Q ss_pred             CCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCcee
Q 023907           91 RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIV  170 (275)
Q Consensus        91 ~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIv  170 (275)
                      ++...  .. +     ..|    +.+ .+     .......++.+... ...++++|++.+||+||||+||++ +|+||+
T Consensus       149 ~~~~l--~~-l-----~~G----v~l-~~-----~~~~~~~v~~~~~~-~~~s~l~v~L~EGk~hQIRrm~~~-lG~~V~  208 (289)
T PRK10700        149 DDAKL--RQ-L-----SRG----VQL-ED-----GPAAFKTIKFSGGE-GINQWYNVTLTEGRNREVRRLWEA-VGVQVS  208 (289)
T ss_pred             CHHHH--HH-H-----HcC----CEe-CC-----ceeeeEEEEeccCC-CCceEEEEEEeCCccHHHHHHHHH-cCCEEe
Confidence            65321  11 1     112    111 11     11111222222211 245899999999999999999997 999998


Q ss_pred             C
Q 023907          171 G  171 (275)
Q Consensus       171 G  171 (275)
                      .
T Consensus       209 ~  209 (289)
T PRK10700        209 R  209 (289)
T ss_pred             E
Confidence            3

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=99.75  E-value=1.6e-18  Score=156.56  Aligned_cols=124  Identities=15%  Similarity=0.196  Sum_probs=83.7

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      +++|.......++.+++..      ...+++|||||++||||||||+|.++++.|.++...                +.|
T Consensus        78 ~~~~~~~~~~~tv~~~l~~------~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~----------------i~K  135 (290)
T PRK10475         78 IVSTTEDGERDNIVDFVNH------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGND----------------HEK  135 (290)
T ss_pred             CCcCCCCCCCCcHHHHhhc------cccccccccCCCCCcceEEEecCHHHHHHhhCcCCC----------------CCe
Confidence            3456554444555555442      246889999999999999999999999999775443                999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.+.+.  .+...      ..|.    .+ .+..   .+++.  +..+     ..++++|++.+||+||||+|
T Consensus       136 ~Y~v~V~g~~~~~--~l~~l------~~Gv----~l-~~~~---~~~~~--v~~~-----~~~~~~i~l~eGk~rqIRrm  192 (290)
T PRK10475        136 EYLVTVDKPITDE--FIRGM------GAGV----PI-LGTV---TKKCK--VKKE-----APFVFRITLVQGLNRQIRRM  192 (290)
T ss_pred             EEEEEECCCCCHH--HHHHH------hCCc----EE-CCEE---ecceE--EEec-----CCcEEEEEEECCcCHHHHHH
Confidence            9999999988543  22111      1121    11 0000   01111  1111     13579999999999999999


Q ss_pred             HHhcCCCcee
Q 023907          161 CAEVLGTPIV  170 (275)
Q Consensus       161 la~~lG~PIv  170 (275)
                      |++ +|+||+
T Consensus       193 ~~~-~G~~V~  201 (290)
T PRK10475        193 CEH-FGYEVT  201 (290)
T ss_pred             HHH-cCCEEe
Confidence            997 999997

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=99.68  E-value=3.4e-17  Score=143.85  Aligned_cols=114  Identities=19%  Similarity=0.280  Sum_probs=81.6

Q ss_pred             CCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccceee
Q 023907           25 YSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKV  104 (275)
Q Consensus        25 ~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~~~  104 (275)
                      ...++++|+|||++|+|+|||++|++.++.|.++-.+                +.|+|+|.|.|.+.+..  ++.-    
T Consensus        97 ~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~P~~~----------------~~K~Y~v~v~g~~~~~~--l~~l----  154 (248)
T COG1187          97 RKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMHPSSE----------------VEKEYLVRVEGPVTEED--LEKL----  154 (248)
T ss_pred             cccceeeccccCCCCeeEEEEeCCHHHHHHhcCCCCC----------------CCEEEEEEEecCCCHHH--HHHH----
Confidence            4456999999999999999999999999999887766                99999999999776432  1110    


Q ss_pred             eccCCceeeEEEecCCCCCCCcceEEEEEEeeecCC-cEEEEEEEeCcCchhHHHHHHHhcCCCceeCCC
Q 023907          105 VVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCH-GYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDY  173 (275)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~-~~slv~~~~~TGR~HQIR~hla~~lG~PIvGD~  173 (275)
                        ..|    +.+.      ++....+....+..... ..+++++.|.+||+||||.||++ +|+|++.=.
T Consensus       155 --~~G----v~l~------d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQVRRm~~a-~G~~V~~L~  211 (248)
T COG1187         155 --RKG----VTLD------DGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEA-VGLEVLRLK  211 (248)
T ss_pred             --hCC----cEec------CcccccceeEEEEecCCCCceEEEEEEeCCcCHHHHHHHHH-cCCEEeEEE
Confidence              011    1111      11222223222222212 57999999999999999999997 999998533

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like

Probab=98.08  E-value=1e-05  Score=70.74  Aligned_cols=43  Identities=35%  Similarity=0.286  Sum_probs=36.8

Q ss_pred             CCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           28 PPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        28 ~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      ..++|||||++|||||+||+++.+  ++.+.|.++.              +.|+|+|..
T Consensus        33 ~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~--------------~~K~Y~~~~   75 (226)
T cd02868          33 VLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNH--------------PTRVYTIRG   75 (226)
T ss_pred             eeeEccccCCCCceEEEEEeChhH--hHHHHHHhcC--------------CCeEEEEEE
Confidence            367889999999999999999876  5888898865              899999644

This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).

>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

Probab=96.57  E-value=0.0097  Score=43.96  Aligned_cols=22  Identities=9%  Similarity=0.060  Sum_probs=19.6

Q ss_pred             CCCCCcccccCCCCCceEEEEE
Q 023907           25 YSEPPRLVHRLDRDSSGILVMG   46 (275)
Q Consensus        25 ~~~~~~~vhRLD~~TSGllllA   46 (275)
                      ...+++.++++|+.++|+++++
T Consensus        22 ~~~~i~~aG~kDk~a~t~q~v~   43 (87)
T cd01291          22 PPKRVGYAGRKDKRAVTTQLVS   43 (87)
T ss_pred             ChheEEECccCCCCeeEEEEEc
Confidence            3457899999999999999999

Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like

Probab=92.70  E-value=0.42  Score=40.51  Aligned_cols=56  Identities=20%  Similarity=0.072  Sum_probs=40.1

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-+..  .++.+.+.+                -.|+|.|.+.
T Consensus        16 ~~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~--Tk~~~~~~~----------------~~K~Y~a~v~   71 (182)
T cd02572          16 HEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRA--TRLVKSQQE----------------AGKEYVCVMR   71 (182)
T ss_pred             HHHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHH--hhhhHHHhC----------------CCCEEEEEEE
Confidence            3344433333344689999999999999999999973  445556655                5799998774

This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family

Probab=91.27  E-value=0.74  Score=39.92  Aligned_cols=56  Identities=21%  Similarity=0.144  Sum_probs=40.6

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+....+.....++...+-||-..||||+++-+..  .++...+.+                ..|+|.|.+.
T Consensus        14 ~~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~----------------~~K~Y~~~~~   69 (210)
T cd00506          14 HDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA----------------ATKDYTAIGR   69 (210)
T ss_pred             HHHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc----------------CCceEEEEEE
Confidence            3344434333345689999999999999999999974  445556665                6899999763

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker

>PRK00989 truB tRNA pseudouridine synthase B; Provisional

Probab=90.69  E-value=0.65  Score=40.77  Aligned_cols=57  Identities=19%  Similarity=0.044  Sum_probs=41.2

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+.||-..||||+++-.. .+.++.+.+.+                ..|+|.|.+.
T Consensus        23 ~dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~~----------------~~K~Y~~~~~   79 (230)
T PRK00989         23 FSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILLF----------------EDKEYAAVAH   79 (230)
T ss_pred             HHHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhcC----------------CCcEEEEEEE
Confidence            344443433334568999999999999999999886 34456666655                6799999764

>TIGR00431 TruB tRNA pseudouridine 55 synthase

Probab=89.09  E-value=1.3  Score=38.36  Aligned_cols=56  Identities=16%  Similarity=0.102  Sum_probs=40.7

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+++...-+.....++...+-||-..||||+++-+...  ++...+.+                -.|+|.|.+.
T Consensus        16 ~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~~----------------~~K~Y~~~~~   71 (209)
T TIGR00431        16 FDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLTD----------------LDKEYRAEIR   71 (209)
T ss_pred             HHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHcC----------------CCCeEEEEEE
Confidence            34444333333446789999999999999999999754  56666665                6899998763

TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific

>PRK00020 truB tRNA pseudouridine synthase B; Provisional

Probab=88.12  E-value=1.7  Score=38.46  Aligned_cols=55  Identities=16%  Similarity=0.106  Sum_probs=40.4

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      .+++...-+.....++...+-||-..||||+++-...  .++...+.+                ..|+|.|.+
T Consensus        24 ~dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~----------------~~K~Y~a~~   78 (244)
T PRK00020         24 NHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRA--TKISGRMLE----------------ADKTYQATL   78 (244)
T ss_pred             HHHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHH--hhhhHHhcc----------------CCcEEEEEE
Confidence            4455544443445689999999999999999999973  445555555                579999976

>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones

Probab=87.16  E-value=0.66  Score=37.98  Aligned_cols=42  Identities=29%  Similarity=0.298  Sum_probs=31.7

Q ss_pred             CCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           27 EPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        27 ~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      .++...+.||-..||||+++-+..  .++.+.+.+                ..|+|.|..
T Consensus         7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~----------------~~K~Y~~~~   48 (149)
T PF01509_consen    7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN----------------SDKEYVATI   48 (149)
T ss_dssp             SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT----------------SEEEEEEEE
T ss_pred             ceeccccccCCcceEEEEEEECCc--chHHHHhhc----------------cCCEEEEEE
Confidence            467889999999999999999873  336666665                679999965

Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....

>PRK04099 truB tRNA pseudouridine synthase B; Provisional

Probab=87.15  E-value=2  Score=38.73  Aligned_cols=56  Identities=16%  Similarity=0.151  Sum_probs=41.1

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+..+-+.....+....+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        16 ~~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~----------------~~K~Y~a~~~   71 (273)
T PRK04099         16 NAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK----------------TPKTYRATLW   71 (273)
T ss_pred             HHHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc----------------CCceEEEEEE
Confidence            4455544443345689999999999999999999975  336666655                5799998763

>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like

Probab=85.78  E-value=2.6  Score=38.08  Aligned_cols=56  Identities=16%  Similarity=0.150  Sum_probs=40.7

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-+..  .++...+.+                ..|+|.|.+.
T Consensus        14 ~~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~~~~~   69 (277)
T cd02573          14 HDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD----------------ADKTYRATVR   69 (277)
T ss_pred             HHHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC----------------CCcEEEEEEE
Confidence            3444433333344579999999999999999999974  346666665                6799999764

This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.

>PRK02193 truB tRNA pseudouridine synthase B; Provisional

Probab=85.65  E-value=2.6  Score=38.17  Aligned_cols=56  Identities=16%  Similarity=0.146  Sum_probs=40.2

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+.+                ..|+|.|.+.
T Consensus        14 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~   69 (279)
T PRK02193         14 FKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDED--TKLIDYLDQ----------------KDKTYIAKIK   69 (279)
T ss_pred             HHHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChh--hhhhHHhcc----------------CCcEEEEEEE
Confidence            4444433333344689999999999999999999974  345555554                6799999763

>PRK02484 truB tRNA pseudouridine synthase B; Provisional

Probab=84.40  E-value=3.2  Score=37.84  Aligned_cols=56  Identities=16%  Similarity=0.091  Sum_probs=40.6

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+.||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        17 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~   72 (294)
T PRK02484         17 HDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTE----------------AGKVYEGEIT   72 (294)
T ss_pred             HHHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChh--hhhhHHhcc----------------CCcEEEEEEE
Confidence            4455533333345689999999999999999999974  335555655                5799999764

>PRK14123 tRNA pseudouridine synthase B; Provisional

Probab=84.04  E-value=3.4  Score=37.89  Aligned_cols=56  Identities=13%  Similarity=0.105  Sum_probs=40.7

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-.+.+  ++.+.+..                ..|+|.|.+.
T Consensus        17 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~----------------~~K~Y~~~~~   72 (305)
T PRK14123         17 HDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD----------------MGKAYEATVS   72 (305)
T ss_pred             HHHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC----------------CCcEEEEEEE
Confidence            34444333333456899999999999999999999754  45666655                6799999763

>PRK14124 tRNA pseudouridine synthase B; Provisional

Probab=84.00  E-value=4.1  Score=37.42  Aligned_cols=56  Identities=14%  Similarity=0.221  Sum_probs=40.9

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+..                -.|+|.|.+.
T Consensus        17 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~   72 (308)
T PRK14124         17 HDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKN----------------EKKVYYVKMR   72 (308)
T ss_pred             HHHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhc----------------CCceEEEEEE
Confidence            4455544343345689999999999999999999974  335566665                5799999763

>PRK03287 truB tRNA pseudouridine synthase B; Provisional

Probab=83.84  E-value=3.4  Score=37.76  Aligned_cols=56  Identities=21%  Similarity=0.254  Sum_probs=40.0

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        23 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~----------------~~K~Y~a~~~   78 (298)
T PRK03287         23 HDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERA--TKLLGHLTL----------------TDKSYTATIR   78 (298)
T ss_pred             HHHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChh--hhhhHHHhc----------------CCcEEEEEEE
Confidence            4444433333345689999999999999999999963  445555655                5799999763

>PRK14846 truB tRNA pseudouridine synthase B; Provisional

Probab=83.22  E-value=4.2  Score=37.80  Aligned_cols=56  Identities=18%  Similarity=0.143  Sum_probs=40.1

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++...+.+                ..|+|.|.+.
T Consensus        17 ~dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~~----------------~~K~Y~a~~~   72 (345)
T PRK14846         17 AQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLID----------------ARKTYIFTVK   72 (345)
T ss_pred             HHHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChh--hhhhHHHhc----------------CCceEEEEEE
Confidence            3444433333345689999999999999999999974  445555555                6799998763

>PRK00130 truB tRNA pseudouridine synthase B; Provisional

Probab=82.97  E-value=4.2  Score=37.03  Aligned_cols=56  Identities=16%  Similarity=0.074  Sum_probs=40.5

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        16 ~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~~   71 (290)
T PRK00130         16 FDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME----------------GKKTYRAEIK   71 (290)
T ss_pred             HHHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc----------------CCcEEEEEEE
Confidence            3444433333344689999999999999999999974  336666665                5799999764

>PRK05389 truB tRNA pseudouridine synthase B; Provisional

Probab=82.25  E-value=4.2  Score=37.30  Aligned_cols=55  Identities=16%  Similarity=0.068  Sum_probs=39.5

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+
T Consensus        27 ~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~a~~   81 (305)
T PRK05389         27 TEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEA--TKTVPYVMD----------------GTKRYRFTV   81 (305)
T ss_pred             HHHHHHHHHHhcccccCCcccCCCCCceEEEEEEChh--hhhhHHhcc----------------CCcEEEEEE
Confidence            4444433333344678999999999999999999973  445555554                579999976

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed

Probab=82.23  E-value=4.1  Score=37.23  Aligned_cols=56  Identities=20%  Similarity=0.110  Sum_probs=39.8

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....+....+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        36 ~~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~~----------------~~K~Y~~~~~   91 (300)
T PRK04270         36 HEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALLE----------------SGKEYVCVMH   91 (300)
T ss_pred             HHHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChH--hhhhHHhcc----------------CCcEEEEEEE
Confidence            3344433332334578999999999999999999874  445566655                5799998763

>PRK01851 truB tRNA pseudouridine synthase B; Provisional

Probab=80.47  E-value=6.1  Score=36.21  Aligned_cols=56  Identities=13%  Similarity=0.083  Sum_probs=40.1

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-...  .++.+.+.+                -.|+|.|.+.
T Consensus        30 ~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~----------------~~K~Y~~~~~   85 (303)
T PRK01851         30 NDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLD----------------ADKTYEATLR   85 (303)
T ss_pred             HHHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHH--HhhhHHhcc----------------cCeEEEEEEE
Confidence            3444433333345678999999999999999999974  335566655                5799999763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	275
1xpi_A	231	Crystal Structure Of The Catalytic Domain Of E. Col		7e-13
1v9k_A	228	The Crystal Structure Of The Catalytic Domain Of Ps		2e-12
2i82_A	217	Crystal Structure Of Pseudouridine Synthase Rlua: I		7e-10
1v9f_A	325	Crystal Structure Of Catalytic Domain Of Pseudourid		7e-07
1prz_A	252	Crystal Structure Of Pseudouridine Synthase Rlud Ca		7e-06
1qyu_A	349	Structure Of The Catalytic Domain Of 23s Rrna Pseud		7e-06

>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231

Iteration: 1
 Score = 70.9 bits (172), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 79/146 (54%), Gaps = 22/146 (15%)
Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           LVHRLDRD+SG+L++ + +++   LH   REK               +Q+ Y ALV G  
Sbjct: 51  LVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQKDYLALVRGQW 96
Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
           +     + APL K ++ +G  +RI  V+ +     + + TR++V +      T ++ SP+
Sbjct: 97  QSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEERYAFA-TLVRCSPV 149
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH  +  G PI  D +YG
Sbjct: 150 TGRTHQIRVHT-QYAGHPIAFDDRYG 174

>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of Pseudouridine Synthase Rluc From Escherichia Coli Length = 228

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 78/146 (53%), Gaps = 22/146 (15%)
Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           LVHRLDRD+SG+L++ + +++   LH   REK                Q+ Y ALV G  
Sbjct: 48  LVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------XQKDYLALVRGQW 93
Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
           +     + APL K ++ +G  +RI  V+ +     + + TR++V +      T ++ SP+
Sbjct: 94  QSHVKSVQAPLLKNILQSG--ERIVRVSQE----GKPSETRFKVEERYAFA-TLVRCSPV 146
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH  +  G PI  D +YG
Sbjct: 147 TGRTHQIRVHT-QYAGHPIAFDDRYG 171

>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-induced Rna Structure Length = 217

Iteration: 1
 Score = 60.8 bits (146), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 69/145 (47%), Gaps = 22/145 (15%)
Query: 32  VHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPR 91
           VHRLD  +SG++V+  T+ +   L   FRE              R  ++ Y A V G P 
Sbjct: 58  VHRLDXATSGVIVVALTKAAERELKRQFRE--------------REPKKQYVARVWGHPS 103
Query: 92  CSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLT 151
            ++G++  PL   + D     +  V       + + A T Y+V++ +      + L P+T
Sbjct: 104 PAEGLVDLPL---ICDWPNRPKQKVCYE----TGKPAQTEYEVVEYAADNTARVVLKPIT 156
Query: 152 GRKHQLRVHCAEVLGTPIVGDYKYG 176
           GR HQLRVH    LG PI+GD  Y 
Sbjct: 157 GRSHQLRVHXL-ALGHPILGDRFYA 180

>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 72/146 (49%), Gaps = 25/146 (17%)
Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           +VHRLD+D++G++V+ +T  + T L                  ++R + R Y A+ +G  
Sbjct: 133 IVHRLDKDTTGLMVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 177
Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
             + G +  P+ +       + R  +  +      + AVT Y++++     +T L+L   
Sbjct: 178 MTAGGTVDEPISR-----HPTKRTHMAVHPM---GKPAVTHYRIME-HFRVHTRLRLRLE 228
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH A +   P+VGD  YG
Sbjct: 229 TGRTHQIRVHMAHIT-HPLVGDPVYG 253

>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           +VHRLD+D++G+ V+ +T  + T L                  ++R + R Y A+ +G  
Sbjct: 60  IVHRLDKDTTGLXVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 104
Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
             + G +  P+ +       + R     +      + AVT Y++ +     +T L+L   
Sbjct: 105 XTAGGTVDEPISR-----HPTKRTHXAVHP---XGKPAVTHYRIXE-HFRVHTRLRLRLE 155
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH A +   P+VGD  YG
Sbjct: 156 TGRTHQIRVHXAHIT-HPLVGDPVYG 180

>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 31  LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTP 90
           +VHRLD+D++G+ V+ +T  + T L                  ++R + R Y A+ +G  
Sbjct: 157 IVHRLDKDTTGLXVVAKTVPAQTRLVESL--------------QRREITREYEAVAIGH- 201
Query: 91  RCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPL 150
             + G +  P+ +       + R     +      + AVT Y++ +     +T L+L   
Sbjct: 202 XTAGGTVDEPISR-----HPTKRTHXAVHPM---GKPAVTHYRIXE-HFRVHTRLRLRLE 252
Query: 151 TGRKHQLRVHCAEVLGTPIVGDYKYG 176
           TGR HQ+RVH A +   P+VGD  YG
Sbjct: 253 TGRTHQIRVHXAHIT-HPLVGDPVYG 277

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	275
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	9e-35
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	3e-34
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	1e-23
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	2e-04
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	2e-04

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Length = 228

 Score =  124 bits (313), Expect = 9e-35
 Identities = 50/148 (33%), Positives = 78/148 (52%), Gaps = 22/148 (14%)

Query: 29  PRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVG 88
             LVHRLDRD+SG+L++ + +++   LH   REK               +Q+ Y ALV G
Sbjct: 46  LELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQKDYLALVRG 91

Query: 89  TPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLS 148
             +     + APL K ++ +G+  RI  V+ +     + + TR++V +      T ++ S
Sbjct: 92  QWQSHVKSVQAPLLKNILQSGE--RIVRVSQE----GKPSETRFKVEE-RYAFATLVRCS 144

Query: 149 PLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
           P+TGR HQ+RVH     G PI  D +YG
Sbjct: 145 PVTGRTHQIRVHTQY-AGHPIAFDDRYG 171

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217

 Score =  122 bits (308), Expect = 3e-34
 Identities = 47/157 (29%), Positives = 68/157 (43%), Gaps = 40/157 (25%)

Query: 29  PRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVG 88
              VHRLD  +SG++V+  T+ +   L   FRE+                ++ Y A V G
Sbjct: 55  AESVHRLDMATSGVIVVALTKAAERELKRQFRERE--------------PKKQYVARVWG 100

Query: 89  TPRCSKGVISAPLG---------KVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSC 139
            P  ++G++  PL          KV  + GK                 A T Y+V++ + 
Sbjct: 101 HPSPAEGLVDLPLICDWPNRPKQKVCYETGK----------------PAQTEYEVVEYAA 144

Query: 140 HGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
                + L P+TGR HQLRVH    LG PI+GD  Y 
Sbjct: 145 DNTARVVLKPITGRSHQLRVHMLA-LGHPILGDRFYA 180

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325

 Score = 96.4 bits (241), Expect = 1e-23
 Identities = 44/158 (27%), Positives = 71/158 (44%), Gaps = 43/158 (27%)

Query: 29  PR--LVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV 86
           PR  +VHRLD+D++G++V+ +T  + T L    + +               + R Y A+ 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE--------------ITREYEAVA 174

Query: 87  VGTPRCSKGVISAPLGK--------VVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPS 138
           +G    + G +  P+ +         V   GK                 AVT Y++++  
Sbjct: 175 IGHMT-AGGTVDEPISRHPTKRTHMAVHPMGK----------------PAVTHYRIME-H 216

Query: 139 CHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYG 176
              +T L+L   TGR HQ+RVH A  +  P+VGD  YG
Sbjct: 217 FRVHTRLRLRLETGRTHQIRVHMAH-ITHPLVGDPVYG 253

>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 34/152 (22%), Positives = 58/152 (38%), Gaps = 38/152 (25%)

Query: 23  YDYSEPPRLVH--RLDRDSSGILVM---GRTQTSATVLHSIFR-EKTFSASKEDNDNEKR 76
            ++     +    RLDRDS G+LV+   G  Q  A +     R  K              
Sbjct: 36  KEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQ--ARLTQPGKRTGKI------------- 80

Query: 77  ILQRWYWALVVGTPRCSKGVISAPLGK-VVVDNG--KSDRITVVNNDQIMSAQHAVTRYQ 133
                Y+  V G P  ++  +   L   V +++G        +V+    +  ++   R +
Sbjct: 81  -----YYVQVEGIP--TQDAL-EALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 132

Query: 134 VIKPSCHGYTWLKLSPLT-GRKHQLRVHCAEV 164
              P+    +WLK++ L  GR  Q+R   A V
Sbjct: 133 KSIPT----SWLKIT-LYEGRNRQVRRMTAHV 159

>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Length = 217

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 34/152 (22%), Positives = 58/152 (38%), Gaps = 38/152 (25%)

Query: 23  YDYSEPPRLVH--RLDRDSSGILVM---GRTQTSATVLHSIFR-EKTFSASKEDNDNEKR 76
            ++     +    RLDRDS G+LV+   G  Q  A +     R  K              
Sbjct: 64  KEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQ--ARLTQPGKRTGKI------------- 108

Query: 77  ILQRWYWALVVGTPRCSKGVISAPLGK-VVVDNG--KSDRITVVNNDQIMSAQHAVTRYQ 133
                Y+  V G P  ++  +   L   V +++G        +V+    +  ++   R +
Sbjct: 109 -----YYVQVEGIP--TQDAL-EALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 160

Query: 134 VIKPSCHGYTWLKLSPLT-GRKHQLRVHCAEV 164
              P+    +WLK++ L  GR  Q+R   A V
Sbjct: 161 KSIPT----SWLKIT-LYEGRNRQVRRMTAHV 187

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	100.0
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	100.0
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	100.0
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	99.97
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	99.96
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	99.95
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	99.94
2gml_A	237	Ribosomal large subunit pseudouridine synthase F;	99.91
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	99.89

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A

Probab=100.00  E-value=2.3e-45  Score=320.49  Aligned_cols=206  Identities=30%  Similarity=0.442  Sum_probs=164.0

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+...++.+.+....  .....+++|||||++||||||||+|+++++.|+++|+++.              ++|
T Consensus        20 ~~~~~~~~~~~~l~~~l~~~~--~~~~~~~~VhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~--------------v~K   83 (228)
T 1v9k_A           20 TAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQK   83 (228)
T ss_dssp             SCSSCCSSSBCCHHHHHHHHS--TTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTC--------------SEE
T ss_pred             CeEecCCChHHHHHHHHHHHc--CCCCccceEecCCCCCeEEEEEEeCHHHHHHHHHHHHhCC--------------eeE
Confidence            578887776666655544322  1234689999999999999999999999999999999866              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++...|.|+.+|.+.....|.. .+.+.     .+++.|.|.|++++.. .++|+++|+|.|||+||||+|
T Consensus        84 ~Y~a~v~G~~~~~~~~i~~~l~~~~~~~g~~-~~~~~-----~~gk~a~t~~~vl~~~-~~~slv~~~l~TGR~HQIR~h  156 (228)
T 1v9k_A           84 DYLALVRGQWQSHVKSVQAPLLKNILQSGER-IVRVS-----QEGKPSETRFKVEERY-AFATLVRCSPVTGRTHQIRVH  156 (228)
T ss_dssp             EEEEEEESCCCTTCCEECCCEEEEECTTSCE-EEEEC-----TTSBCCCEEEEEEEEC-SSEEEEEEEESSCCTTHHHHH
T ss_pred             EEEEEEecccCCCCCEEeCceeccCCCCCce-EEEEC-----CCCcEEEEEEEEEEEc-CCeEEEEEEECCCCchHHHHH
Confidence            9999999999988899999998764433322 22232     2378999999999987 679999999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907          161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ  240 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~  240 (275)
                      |++ +||||+||.+||....               +..+..              ......+++|||++|.|++|     
T Consensus       157 la~-lG~PI~gD~~YG~~~~---------------~~~~~~--------------~~~~~~r~~LHa~~l~f~hP-----  201 (228)
T 1v9k_A          157 TQY-AGHPIAFDDRYGDREF---------------DRQLTE--------------AGTGLNRLFLHAAALKFTHP-----  201 (228)
T ss_dssp             HHH-TTCCBTTCTTTSCHHH---------------HHHHHH--------------TTCCCCSCCEEEEEEEEECT-----
T ss_pred             HHH-CCCcEecCcccCCccc---------------cchhhc--------------ccCCCCChhhccceeEeeCC-----
Confidence            997 9999999999996421               000000              00013579999999999998     


Q ss_pred             hhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                .+++.+.|+||+|++|..+++.|+
T Consensus       202 ----------~t~~~~~~~aplp~~~~~~l~~l~  225 (228)
T 1v9k_A          202 ----------GTGEVMRIEAPMDEGLKRCLQKMR  225 (228)
T ss_dssp             ----------TTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             ----------CCCCEEEEEeCCcHHHHHHHHHhh
Confidence                      478999999999999999998875

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=100.00  E-value=1.3e-43  Score=324.46  Aligned_cols=210  Identities=27%  Similarity=0.401  Sum_probs=162.6

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhc-CCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTY-DYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~-~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++.+. ..++.+.+..++.. .....+++|||||++||||||||+|+++++.|+++|.++.              +
T Consensus       101 ~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~--------------v  166 (325)
T 1v9f_A          101 LVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE--------------I  166 (325)
T ss_dssp             CCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTC--------------S
T ss_pred             CeEecCCCCCCccHHHHHHHHHHhcCCCCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCC--------------e
Confidence            578876654 34565555444432 1234689999999999999999999999999999999876              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|+|.|.++. +|.|+.||.+....   ..++.+..     +++.|.|.|++++.. .++|+++|+|.|||+||||
T Consensus       167 ~K~Y~a~v~G~~~~-~g~i~~~i~~~~~~---~~~~~v~~-----~gk~a~t~~~vl~~~-~~~slv~~~l~TGR~HQIR  236 (325)
T 1v9f_A          167 TREYEAVAIGHMTA-GGTVDEPISRHPTK---RTHMAVHP-----MGKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIR  236 (325)
T ss_dssp             EEEEEEEEESCCCC-CEEEECCEEECSSC---TTCEEECT-----TSBCCEEEEEEEEEC-SSEEEEEEEESCCCTTHHH
T ss_pred             eEEEEEEEeCCCCC-CCEEeeeeeECCCC---CEEEEECC-----CCeeEEEEEEEeEEc-CCeEEEEEEECCCCcHHHH
Confidence            99999999999987 89999999874322   22333332     479999999999997 6899999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +||++ +||||+||.+||+....          .......+...              .....+++|||++|.|+||   
T Consensus       237 vhla~-lG~PI~GD~~Yg~~~~~----------~~~~~~~~~~~--------------~~~~~r~~LHA~~L~f~hP---  288 (325)
T 1v9f_A          237 VHMAH-ITHPLVGDPVYGGRPRP----------PKGASEAFIST--------------LRKFDRQALHATMLRLYHP---  288 (325)
T ss_dssp             HHHHH-TTCCBTTCTTTTCCCCC----------CTTCCHHHHHH--------------HHHCCSCSEEEEEEEEECT---
T ss_pred             HHHHh-CCCceeCChhhCCcccc----------ccccchhhhhh--------------ccCCcChhhheeeeEeeCC---
Confidence            99997 99999999999964210          00000000000              0013578999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                  .+++.+.|+||+|++|..+++.|+
T Consensus       289 ------------~~~~~~~~~aplp~~~~~~l~~l~  312 (325)
T 1v9f_A          289 ------------ISGIEMEWHAPIPQDMVELIEVMR  312 (325)
T ss_dssp             ------------TTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             ------------CCCCEEEEEecCcHHHHHHHHHhc
Confidence                        478999999999999999999875

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}

Probab=100.00  E-value=4.1e-43  Score=304.13  Aligned_cols=185  Identities=30%  Similarity=0.419  Sum_probs=149.4

Q ss_pred             CCccCCCC--CcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIG--IRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~--~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++.+  ...++.+.+...+     ..+++|||||++||||||||+|+++++.|+++|.++.              +
T Consensus        30 ~~~~~~~~~~~~~tl~~~l~~~~-----~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~~~~--------------v   90 (217)
T 2i82_A           30 LLSVPGRLEEHKDSVMTRIQRDY-----PQAESVHRLDMATSGVIVVALTKAAERELKRQFRERE--------------P   90 (217)
T ss_dssp             SBSSCCSSGGGCCBHHHHHHHHC-----TTCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTC--------------S
T ss_pred             CeEeCCCCCCchhHHHHHHHHHC-----CCCceeecCCCCCeEEEEEEeCHHHHHHHHHHHHhCC--------------e
Confidence            57887654  4456655555332     3578999999999999999999999999999999977              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      +|+|+|+|.|.++..+|.|+.||...... +.  +..+..    .+++.|.|.|++++....++++++|+|.|||+||||
T Consensus        91 ~K~Y~a~v~G~~~~~~g~i~~~l~~~~~~-~~--~~~v~~----~~gk~a~t~~~vl~~~~~~~slv~~~l~TGR~HQIR  163 (217)
T 2i82_A           91 KKQYVARVWGHPSPAEGLVDLPLICDWPN-RP--KQKVCY----ETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLR  163 (217)
T ss_dssp             EEEEEEEEESCCSSSEEEEECCEEECGGG-TT--CEEECT----TTCBCCEEEEEEEEEETTTEEEEEEEESSCCTTHHH
T ss_pred             eEEEEEEEecccCCCCcEEecceeecCCC-Cc--EEEEeC----CCCcEEEEEEEEEEECCCCeEEEEEEECCCCcHHHH
Confidence            99999999999988889999998764211 11  122221    247899999999998733389999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +||++ +||||+||.+||.....                                    ....+++|||++|.|+||   
T Consensus       164 ~hla~-lG~PIvGD~~Yg~~~~~------------------------------------~~~~r~~LHa~~l~f~hP---  203 (217)
T 2i82_A          164 VHMLA-LGHPILGDRFYASPEAR------------------------------------AMAPRLLLHAEMLTITHP---  203 (217)
T ss_dssp             HHHHH-TTCCBTTCTTTSCHHHH------------------------------------HTCSSCCEEEEEEEEECT---
T ss_pred             HHHHH-CCCcEECccccCCcccc------------------------------------CCCCCceeeeeEeEEcCC---
Confidence            99996 99999999999964210                                    003479999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLP  263 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP  263 (275)
                                  .+++.+.|+||+|
T Consensus       204 ------------~~~~~~~~~ap~p  216 (217)
T 2i82_A          204 ------------AYGNSMTFKAPAD  216 (217)
T ss_dssp             ------------TTCCEEEEECCCC
T ss_pred             ------------CCCCEEEEEecCC
Confidence                        4789999999998

>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}

Probab=99.97  E-value=1.2e-32  Score=233.49  Aligned_cols=147  Identities=22%  Similarity=0.296  Sum_probs=105.6

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      |+||++.+. ..++.+++.       ...+++|||||++||||||||+|+++++.|+++  ++.              ++
T Consensus        22 ~~~~~~~~~~~~tl~~~l~-------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~--------------v~   78 (189)
T 2oml_A           22 VLPQFTDEAGRKTLKEFIP-------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GKR--------------TG   78 (189)
T ss_dssp             BCSCSSCCTTCBCGGGTCC-------CSSCEESSCCCTTCEEEEEEESCHHHHHHHHST--TSC--------------CC
T ss_pred             CEecCCCCCCCCCHHHHcC-------CCCceECCCCCCCCeeEEEEEcCHHHHHHHhCc--cCC--------------Cc
Confidence            577876553 445544432       136899999999999999999999999999987  333              99


Q ss_pred             eEEEEEEecccCCCc-cEEeccceeeeccCCce--eeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhH
Q 023907           80 RWYWALVVGTPRCSK-GVISAPLGKVVVDNGKS--DRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQ  156 (275)
Q Consensus        80 K~Y~alv~G~~~~~~-g~i~~~l~~~~~~~~~~--~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQ  156 (275)
                      |+|+|+|.|.++... +.++.++..   +++..  ..+.....    ....+.|.|+++.....++|+++|+|.|||+||
T Consensus        79 K~Y~a~v~G~~~~~~~~~i~~~i~~---~~~~~~~~~~~~~~~----~~~~~~t~~~v~~~~~~~~slv~~~l~TGR~HQ  151 (189)
T 2oml_A           79 KIYYVQVEGIPTQDALEALRNGVTL---NDGPTLPAGAELVDE----PAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQ  151 (189)
T ss_dssp             EEEEEEEESCCCHHHHHHHHHCCEE---TTEECCCCEEEEECC----CTTCCCCSSCCC-CTTSCEEEEEEEESCCCTTH
T ss_pred             EEEEEEEcCCCCHHHHHHHHcCcee---CCceeeeeEEEEecc----cccccccccccccccCCCcEEEEEEEeeCCCHH
Confidence            999999999987644 345555432   12211  11111111    012346777777765347899999999999999


Q ss_pred             HHHHHHhcCCCceeCCCCCCCC
Q 023907          157 LRVHCAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       157 IR~hla~~lG~PIvGD~~Yg~~  178 (275)
                      ||+||++ +||||+||.+||..
T Consensus       152 IRvhla~-lG~PI~gD~~Y~~g  172 (189)
T 2oml_A          152 VRRMTAH-VGFPTLRLIRYAMG  172 (189)
T ss_dssp             HHHHHHH-TTCCEEEEEEEEET
T ss_pred             HHHHHHH-cCCcCcceEEEEEC
Confidence            9999997 99999999999854

>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}

Probab=99.96  E-value=3.7e-31  Score=228.97  Aligned_cols=146  Identities=23%  Similarity=0.313  Sum_probs=98.5

Q ss_pred             CCccCCCCC-cCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcc
Q 023907            1 MPVQGGIGI-RRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQ   79 (275)
Q Consensus         1 l~v~~g~~~-~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~   79 (275)
                      |+||++.+. ..++.+++    .   ...+++|||||++||||||||+|+++++.|++++  +.              ++
T Consensus        50 l~~~~~~~~~~~tl~~~l----~---~~~~~~VhRLDr~TSGllllAk~~~~~~~L~~~~--~~--------------v~  106 (217)
T 2olw_A           50 VLPQFTDEAGRKTLKEFI----P---VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPG--KR--------------TG  106 (217)
T ss_dssp             BCSCSSCCTTSBCGGGTC----C---CCSCEESSCCCTTCEEEEEEESCHHHHHHHHCTT--CC--------------CC
T ss_pred             CEeccCCCCCCccHHHHh----C---cCCceECCCCCCCCeeEEEEEcCHHHHHHHHccc--cc--------------CC
Confidence            467875542 44544433    2   1368999999999999999999999999999873  33              99


Q ss_pred             eEEEEEEecccCCCc-cEEeccceeeeccCCce--eeEEEecCCCCCCCcceEEEEEEeeec-CCcEEEEEEEeCcCchh
Q 023907           80 RWYWALVVGTPRCSK-GVISAPLGKVVVDNGKS--DRITVVNNDQIMSAQHAVTRYQVIKPS-CHGYTWLKLSPLTGRKH  155 (275)
Q Consensus        80 K~Y~alv~G~~~~~~-g~i~~~l~~~~~~~~~~--~~~~~~~~~~~~~~k~a~t~~~~l~~~-~~~~slv~~~~~TGR~H  155 (275)
                      |+|+|+|.|.++... +.++.++..   ++|..  ..+.+....     ..+.+.+..+... ..++|+++|+|.|||+|
T Consensus       107 K~Y~A~V~G~~~~~~~~~i~~~i~~---~~g~~~~~~~~~~~~~-----~~~~~~~~~v~~~~~~~~slv~~~l~TGRtH  178 (217)
T 2olw_A          107 KIYYVQVEGIPTQDALEALRNGVTL---NDGPTLPAGAELVDEP-----AWLWPRNPPIRERKSIPTSWLKITLYEGRNR  178 (217)
T ss_dssp             EEEEEEEESCCCHHHHHHHHHCCEE---TTEECCCCEEEEECCC-----TTCCCCSSCCC-CCSSCEEEEEEEESCCCTT
T ss_pred             EEEEEEEccCCCHHHHHHHhCCEEe---CCCcccceEEEEecCC-----ccccccccceeccCCCCcEEEEEEECcCCCH
Confidence            999999999987654 344444431   12211  111111110     0011111112121 14689999999999999


Q ss_pred             HHHHHHHhcCCCceeCCCCCCCC
Q 023907          156 QLRVHCAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       156 QIR~hla~~lG~PIvGD~~Yg~~  178 (275)
                      |||+||++ +||||+||.+||..
T Consensus       179 QIRvhla~-lG~PIvgD~rY~~g  200 (217)
T 2olw_A          179 QVRRMTAH-VGFPTLRLIRYAMG  200 (217)
T ss_dssp             HHHHHHHH-TTCCEEEEEEEEET
T ss_pred             HHHHHHHH-CCCcEeCCEEEEEC
Confidence            99999997 99999999999854

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=99.95  E-value=4e-29  Score=218.44  Aligned_cols=136  Identities=17%  Similarity=0.135  Sum_probs=97.0

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+...++.+++.    ......+++|||||++|||+||||+|++++..+..  .++.              ++|
T Consensus        74 ~~~~~~~~~~~tl~~~l~----~~~~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~--------------v~K  133 (234)
T 1ksk_A           74 YVCSTDDPDHPTVLYFLD----EPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHH--------------CEK  133 (234)
T ss_dssp             CBSSSSCSSSCBGGGGCC----CTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSC--------------CCE
T ss_pred             CEeCCCCCCCCcHHHHhh----hhhcCCeeEcCCCCCCCeeEEEEEcCHHHHHHHhC--CCCC--------------CCe
Confidence            578877665555554433    22224689999999999999999999998887765  3333              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++...  ++.+..      |    +.+ .+ .....++|.  |++++     .++++|+|.|||+||||+|
T Consensus       134 ~Y~a~v~g~~~~~~--i~~~~~------g----~~~-~~-~~~~~~~a~--~~~~~-----~s~~~~~l~tGR~HQIR~h  192 (234)
T 1ksk_A          134 TYLVTLESPVADDT--AEQFAK------G----VQL-HN-EKDLTKPAV--LEVIT-----PTQVRLTISEGRYHQVKRM  192 (234)
T ss_dssp             EEEEEESSCCCTTH--HHHHHH------C----CCC-TT-CSSCCCCCE--EEEEE-----TTEEEEEESCCCTTHHHHH
T ss_pred             EEEEEEccCCCHHH--HHHHHC------C----eEE-CC-CCcccceEE--EEEeC-----CeEEEEEEccCCCHHHHHH
Confidence            99999999987642  333211      1    001 00 001245554  56664     4799999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCC
Q 023907          161 CAEVLGTPIVGDYKYGWQ  178 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~  178 (275)
                      |++ +||||+||.+|+..
T Consensus       193 ~~~-lG~pi~gd~ry~~g  209 (234)
T 1ksk_A          193 FAA-VGNHVVELHRERIG  209 (234)
T ss_dssp             HHH-TTCCEEEEEEEEET
T ss_pred             HHH-cCCeEeeeEEEEEC
Confidence            996 99999999999643

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=99.94  E-value=4e-28  Score=213.32  Aligned_cols=136  Identities=18%  Similarity=0.175  Sum_probs=94.4

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+...++.+++...    ....+++|||||++||||||||+|++++..+..  .++              .++|
T Consensus        73 ~~~~~~~~~~~tl~~~l~~~----~~~~~~~vhRLD~~TsGlll~ak~~~~a~~l~~--~~~--------------~v~K  132 (243)
T 1vio_A           73 CVCSNDDGDYPTIYQFFDYP----LAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITS--PKH--------------HCEK  132 (243)
T ss_dssp             CBSSCCC--CCBGGGGSCTT----GGGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTS--------------CCCE
T ss_pred             CEeCCCCCCCCcHHHHHhHH----hcCCEeEccCCCCCCeEEEEEEECHHHHHHHhC--CCC--------------CCCE
Confidence            57787655455554443321    223689999999999999999999998777654  333              3999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++..  .++.+..      |    +.+...  ...+++|.  |++++     .++++|+|.|||+||||+|
T Consensus       133 ~Y~a~v~g~~~~~--~i~~~~~------g----~~~~~~--~~~~~~a~--~~~l~-----~sl~~~~l~tGR~HQIR~h  191 (243)
T 1vio_A          133 TYLVTLADPVEEN--YSAACAE------G----ILLRGE--KEPTKPAK--LEILD-----DYNVNLTISEGRYHQVKRM  191 (243)
T ss_dssp             EEEEEESSCCCTT--HHHHHHH------C----CCCTTC--SSCCCCCE--EEECS-----SSEEEEEESCCCTTHHHHH
T ss_pred             EEEEEEeCCCCHH--HHHHHhC------C----eEECCC--CccceeEE--EEEeC-----CEEEEEEEccCCcHHHHHH
Confidence            9999999998764  2333321      1    011110  01245565  45554     5899999999999999999


Q ss_pred             HHhcCCCceeCCC--CCCCC
Q 023907          161 CAEVLGTPIVGDY--KYGWQ  178 (275)
Q Consensus       161 la~~lG~PIvGD~--~Yg~~  178 (275)
                      |++ +||||+||.  .||..
T Consensus       192 l~~-lG~pI~gd~r~~~G~~  210 (243)
T 1vio_A          192 FAA-LGNKVVGLHRWKIGDV  210 (243)
T ss_dssp             HHH-TTCCEEEEEEEEETTE
T ss_pred             HHH-CCCeEcccEEEEECCE
Confidence            996 999999999  55643

>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}

Probab=99.91  E-value=2.3e-25  Score=194.12  Aligned_cols=129  Identities=15%  Similarity=0.164  Sum_probs=93.2

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      +++|++.....+|.+++    ..  ...+++|||||++||||||||+|.+++..|.+.-..                |+|
T Consensus        25 ~vs~~~~~~~~tv~dll----~~--~~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~p~~~----------------v~K   82 (237)
T 2gml_A           25 IVSTTEDGERDNIVDFV----NH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGND----------------HEK   82 (237)
T ss_dssp             CBCCSSSSCSSBHHHHS----CC--SSCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHHH----------------SCE
T ss_pred             CEeCCCCCCCCCHHHHh----hc--cCCeeEecCCCCCCeeEEEEEcCHHHHHHHhCccCC----------------CCE
Confidence            35665444445554443    22  347899999999999999999999999999986444                999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.+++..  ++. +     ..|.    .+ .     +++.+.+.++++.     .++++|+|.|||+||||+|
T Consensus        83 ~Y~a~V~G~~~~~~--i~~-l-----~~Gv----~l-~-----~~~~~~a~~~~l~-----~s~l~i~L~tGR~HQIRr~  139 (237)
T 2gml_A           83 EYLVTVDKPITEEF--IRG-M-----SAGV----PI-L-----GTVTKKCKVKKEA-----PFVFRITLVQGLNRQIRRM  139 (237)
T ss_dssp             EEEEEESSCCCHHH--HHH-H-----SSCC----EE-T-----TEECCCCEEEEEE-----TTEEEEEECCCSTTHHHHH
T ss_pred             EEEEEEcccCCHHH--HHH-H-----HcCe----Ee-C-----CcccccEEEEEeC-----CEEEEEEEecCCcHHHHHH
Confidence            99999999886532  111 1     1121    11 1     1223334556653     3699999999999999999


Q ss_pred             HHhcCCCceeCCCCC
Q 023907          161 CAEVLGTPIVGDYKY  175 (275)
Q Consensus       161 la~~lG~PIvGD~~Y  175 (275)
                      |++ +||||+||..|
T Consensus       140 ~a~-lG~pV~~L~R~  153 (237)
T 2gml_A          140 CEH-FGYEVKKLERT  153 (237)
T ss_dssp             HHH-TTCCEEEEEEE
T ss_pred             HHH-cCCCEeeeEEE
Confidence            997 99999999886

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=99.89  E-value=4.5e-24  Score=191.70  Aligned_cols=130  Identities=15%  Similarity=0.166  Sum_probs=92.6

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |++|++.+...++.+++.    .  ...+++|||||++||||||||+|.+++..|.++...                ++|
T Consensus        78 ~~~~~~~~~~~tl~~~l~----~--~~~~~~VhRLD~dTSGLllla~d~~~~~~L~~~~~~----------------v~K  135 (290)
T 3dh3_A           78 IVSTTEDGERDNIVDFVN----H--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGND----------------HEK  135 (290)
T ss_dssp             CBCCCCSSCTTBHHHHHT----C--SSCCEESSCCCTTCEEEEEEESCTTHHHHHHCGGGC----------------CCE
T ss_pred             cccCCCCCCCCcHHHHhh----c--cCceeeeccCCCCCcceEEEcCCHHHHHHHHHhhCC----------------cCE
Confidence            467776665556555543    2  567999999999999999999999999998875332                999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.+++..  +.. +     ..|..    + .+.   ..+++.  ++.+     +.++++|+|.|||+||||+|
T Consensus       136 ~Y~a~V~G~~~~~~--i~~-l-----~~Gv~----l-~~~---~~~~~~--v~~~-----~~~~l~l~l~tGR~HQIR~~  192 (290)
T 3dh3_A          136 EYLVTVDKPITEEF--IRG-M-----SAGVP----I-LGT---VTKKCK--VKKE-----APFVFRITLVQGLNRQIRRM  192 (290)
T ss_dssp             EEEEEESSCCCHHH--HHH-H-----HTCCB----C-SSS---BCCCCE--EEEC-----SSSEEEEEESCCCTTHHHHH
T ss_pred             EEEEEECCCCCHHH--HHH-H-----hcCcc----c-CCc---ccceEE--EEEc-----CCeEEEEEEeCCCChHHHHH
Confidence            99999999886532  111 1     11110    0 110   012232  2222     34799999999999999999


Q ss_pred             HHhcCCCceeCCCCCC
Q 023907          161 CAEVLGTPIVGDYKYG  176 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg  176 (275)
                      |++ +||||+++..|.
T Consensus       193 ~~~-lG~pV~~L~R~~  207 (290)
T 3dh3_A          193 CEH-FGYEVKKLERTR  207 (290)
T ss_dssp             HHH-TTCCEEEEEEEE
T ss_pred             HHH-cCCeEEEeEEEE
Confidence            997 999999998874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	275
d1v9ka_	227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	3e-14
d1v9fa_	250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	4e-11

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

 Score = 68.0 bits (165), Expect = 3e-14
 Identities = 63/273 (23%), Positives = 106/273 (38%), Gaps = 68/273 (24%)

Query: 1   MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFR 60
             V GG G+   + E          +    LVHRLDRD+SG+L++ + +++   LH   R
Sbjct: 19  TAVHGGSGLSFGVIEGLRA--LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLR 76

Query: 61  EKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNND 120
           E              + +Q+ Y ALV G  +     + APL K ++ +G+  RI  V+ +
Sbjct: 77  E--------------KGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE--RIVRVSQE 120

Query: 121 QIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQTH 180
                + + TR++V +      T ++ SP+TGR HQ+RVH     G PI  D +YG +  
Sbjct: 121 ----GKPSETRFKVEE-RYAFATLVRCSPVTGRTHQIRVHTQYA-GHPIAFDDRYGDREF 174

Query: 181 RKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ 240
            +      + L                              RL LH   +          
Sbjct: 175 DRQLTEAGTGL-----------------------------NRLFLHAAALKFT------- 198

Query: 241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVL 273
                        E +++ AP+   ++R    +
Sbjct: 199 --------HPGTGEVMRIEAPMDEGLKRCLQKM 223

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

 Score = 59.6 bits (143), Expect = 4e-11
 Identities = 56/277 (20%), Positives = 92/277 (33%), Gaps = 66/277 (23%)

Query: 1   MPVQGGIGIRRS--IDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSI 58
           + V  G G      ++ L              +VHRLD+D++G++V+ +T  + T L   
Sbjct: 26  LVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVES 85

Query: 59  FREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVN 118
            + +  +   E                +   P     +   P+GK               
Sbjct: 86  LQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGK--------------- 130

Query: 119 NDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVGDYKYGWQ 178
                    AVT Y++++     +T L+L   TGR HQ+RVH A +   P+VGD  YG +
Sbjct: 131 --------PAVTHYRIME-HFRVHTRLRLRLETGRTHQIRVHMAHI-THPLVGDPVYGGR 180

Query: 179 THRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA 238
                                        G      S L K  R  LH   + L      
Sbjct: 181 PRPPK------------------------GASEAFISTLRKFDRQALHATMLRLY----- 211

Query: 239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS 275
                      +S    ++  AP+P  M    +V+ +
Sbjct: 212 ---------HPISG-IEMEWHAPIPQDMVELIEVMRA 238

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	275
d1v9ka_	227	Ribosomal large subunit pseudouridine synthase C,	100.0
d1v9fa_	250	Ribosomal large subunit pseudouridine synthase D,	100.0
d1vioa1	174	Ribosomal small subunit pseudouridine 516 synthase	99.84
d1kska4	172	Ribosomal small subunit pseudouridine 516 synthase	99.77
d1k8wa5	242	Pseudouridine synthase II TruB {Escherichia coli [	86.9
d1r3ea2	228	Pseudouridine synthase II TruB {Thermotoga maritim	84.3
d1sgva2	233	Pseudouridine synthase II TruB {Mycobacterium tube	80.75
d2ey4a2	245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	80.11

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.3e-48  Score=338.77  Aligned_cols=207  Identities=29%  Similarity=0.441  Sum_probs=168.3

Q ss_pred             CCccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcce
Q 023907            1 MPVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQR   80 (275)
Q Consensus         1 l~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K   80 (275)
                      |+||++.+...++.+.+..+.  .....+++|||||++||||||||||+++++.|+++|+++.              +.|
T Consensus        19 l~~h~~~~~~~~~~~~l~~~~--~~~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~--------------v~K   82 (227)
T d1v9ka_          19 TAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG--------------MQK   82 (227)
T ss_dssp             SCSSCCSSSBCCHHHHHHHHS--TTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTTC--------------SEE
T ss_pred             CccCCCCCCcchHHHHHHHhC--CCCcccceeeeccceeeeeeeeecchHHHHHHHHHHhccc--------------ccc
Confidence            689998887777655554332  3456789999999999999999999999999999999977              999


Q ss_pred             EEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHH
Q 023907           81 WYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVH  160 (275)
Q Consensus        81 ~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~h  160 (275)
                      +|+|+|.|.++...+.++.++.......+. ..+.+.     .+++.+.|.|++++.. .++++|+|+|.||||||||+|
T Consensus        83 ~Y~a~~~G~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-----~~gk~a~t~~~~l~~~-~~~slv~~~~~TGRtHQIRvH  155 (227)
T d1v9ka_          83 DYLALVRGQWQSHVKSVQAPLLKNILQSGE-RIVRVS-----QEGKPSETRFKVEERY-AFATLVRCSPVTGRTHQIRVH  155 (227)
T ss_dssp             EEEEEEESCCCTTCCEECCCEEEEECTTSC-EEEEEC-----TTSBCCCEEEEEEEEC-SSEEEEEEEESSCCTTHHHHH
T ss_pred             eecccccCccccccCcccccccccccccee-eeeecC-----CCCcccceeehhhhhc-CCcEEEEEEeccCchHHHHHH
Confidence            999999999999889999988765433322 122222     2378999999999998 789999999999999999999


Q ss_pred             HHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchhhh
Q 023907          161 CAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQAIQ  240 (275)
Q Consensus       161 la~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~~~  240 (275)
                      ||+ +||||+||.+||....               ++.+..              .....+|++|||++|.|+||     
T Consensus       156 la~-lG~PIvGD~~Yg~~~~---------------~~~~~~--------------~~~~~~rl~LHa~~L~f~hP-----  200 (227)
T d1v9ka_         156 TQY-AGHPIAFDDRYGDREF---------------DRQLTE--------------AGTGLNRLFLHAAALKFTHP-----  200 (227)
T ss_dssp             HHH-TTCCBTTCTTTSCHHH---------------HHHHHH--------------TTCCCCSCCEEEEEEEEECT-----
T ss_pred             Hhh-cCceeccCcccccccc---------------cccchh--------------cccCcchHHHHccccEeECC-----
Confidence            996 9999999999997531               110000              00114689999999999998     


Q ss_pred             hhhccCCCCCCCCccEEEEcCCchHHHHHHHHhcC
Q 023907          241 KVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLNS  275 (275)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~~  275 (275)
                                .+++.+.|+||+|++|.++|+.|++
T Consensus       201 ----------~t~~~~~~~aplP~~f~~~l~~Lk~  225 (227)
T d1v9ka_         201 ----------GTGEVMRIEAPMDEGLKRCLQKMRN  225 (227)
T ss_dssp             ----------TTCCEEEEECCCCHHHHHHHHHHHH
T ss_pred             ----------CCCCEEEEEecCcHHHHHHHHHHHh
Confidence                      5889999999999999999999863

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.2e-47  Score=335.41  Aligned_cols=210  Identities=28%  Similarity=0.408  Sum_probs=161.7

Q ss_pred             CCccCCCCCc-CcHHHHHHHHhh-cCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCc
Q 023907            1 MPVQGGIGIR-RSIDELAATCLT-YDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRIL   78 (275)
Q Consensus         1 l~v~~g~~~~-~sl~~l~~~~l~-~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v   78 (275)
                      |+||++.+.. .++.+.+..++. ......+++|||||++||||||||||+.+++.|+++|+++.              |
T Consensus        26 l~~hp~~~~~~~t~~~~l~~~~~~~~~~~~~~~vHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~--------------v   91 (250)
T d1v9fa_          26 LVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE--------------I   91 (250)
T ss_dssp             CCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTC--------------S
T ss_pred             CCCcCCCCCCCccHHHHHHHHhhhccCCCceeEEeecCCCCcceEEEecccHHHHhhhhhhccce--------------E
Confidence            6899876643 344444333333 23445688999999999999999999999999999999977              9


Q ss_pred             ceEEEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHH
Q 023907           79 QRWYWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLR  158 (275)
Q Consensus        79 ~K~Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR  158 (275)
                      .|+|+|++.|.++. .+.++.++....   .....+.+..     .+++|.|.|++++.. .++|+++|+|.|||+||||
T Consensus        92 ~K~Y~a~~~g~~~~-~~~~~~~~~~~~---~~~~~~~~~~-----~gk~a~T~~~~l~~~-~~~slv~~~~~TGR~HQIR  161 (250)
T d1v9fa_          92 TREYEAVAIGHMTA-GGTVDEPISRHP---TKRTHMAVHP-----MGKPAVTHYRIMEHF-RVHTRLRLRLETGRTHQIR  161 (250)
T ss_dssp             EEEEEEEEESCCCC-CEEEECCEEECS---SCTTCEEECT-----TSBCCEEEEEEEEEC-SSEEEEEEEESCCCTTHHH
T ss_pred             eEEeeeeecccccc-ccccccccccCC---cccceeEECC-----CCeeccccchhhhcc-cCceeEEEEecccchHHHH
Confidence            99999999999865 457777776532   2222333333     379999999999998 8999999999999999999


Q ss_pred             HHHHhcCCCceeCCCCCCCCccccccccCCCCCCcCCCcccccccccccccccCcCcccccccccccccceeeccCCchh
Q 023907          159 VHCAEVLGTPIVGDYKYGWQTHRKWKQFHPSDLSKDSNEEIPKEKTLHFGLDLESGSILEKQPRLHLHCKEMTLPNVSQA  238 (275)
Q Consensus       159 ~hla~~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~LHa~~l~f~~~~~~  238 (275)
                      +|||+ +||||+||.+||+.....          ....+.+.              ......+|++|||++|+|+||   
T Consensus       162 vHla~-lG~PIlGD~~YG~~~~~~----------~~~~~~~~--------------~~~~~~~r~~LHA~~L~f~hP---  213 (250)
T d1v9fa_         162 VHMAH-ITHPLVGDPVYGGRPRPP----------KGASEAFI--------------STLRKFDRQALHATMLRLYHP---  213 (250)
T ss_dssp             HHHHH-TTCCBTTCTTTTCCCCCC----------TTCCHHHH--------------HHHHHCCSCSEEEEEEEEECT---
T ss_pred             HHHHH-hCCccceeccCccccccc----------ccccHHHH--------------HHHhccchhhhhcCccccccC---
Confidence            99997 999999999999764210          00111000              000114689999999999998   


Q ss_pred             hhhhhccCCCCCCCCccEEEEcCCchHHHHHHHHhc
Q 023907          239 IQKVQLSSGCDVSKLETLKLVAPLPSHMQRSWDVLN  274 (275)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~aplP~~f~~~~~~l~  274 (275)
                                  .+++.+.|+||||++|.++|+.|+
T Consensus       214 ------------~t~~~~~~~aplP~df~~~l~~L~  237 (250)
T d1v9fa_         214 ------------ISGIEMEWHAPIPQDMVELIEVMR  237 (250)
T ss_dssp             ------------TTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             ------------CCCCeEEEEeCCcHHHHHHHHHHh
Confidence                        478999999999999999999885

>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal small subunit pseudouridine 516 synthase RsuA
species: Haemophilus influenzae [TaxId: 727]

Probab=99.84  E-value=3.3e-22  Score=165.01  Aligned_cols=134  Identities=17%  Similarity=0.222  Sum_probs=86.1

Q ss_pred             CccCCCCCcCcHHHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceE
Q 023907            2 PVQGGIGIRRSIDELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRW   81 (275)
Q Consensus         2 ~v~~g~~~~~sl~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~   81 (275)
                      .+|...+...++-++    +.......+++|||||++||||||||+|.++++.+......                +.|+
T Consensus        15 ~~~~~~~~~~~v~~~----l~~~~~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~~~~~----------------~~k~   74 (174)
T d1vioa1          15 VCSNDDGDYPTIYQF----FDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHH----------------CEKT   74 (174)
T ss_dssp             BSSCCC--CCBGGGG----SCTTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSC----------------CCEE
T ss_pred             EeCCCCCCCCcHHHh----CcccccCceEEEecCChhHhceEEEeecccccccccccccc----------------eeee
Confidence            345544555554443    33344556899999999999999999999998887654333                8999


Q ss_pred             EEEEEecccCCCccEEeccceeeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHH
Q 023907           82 YWALVVGTPRCSKGVISAPLGKVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHC  161 (275)
Q Consensus        82 Y~alv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hl  161 (275)
                      |.+.+.+.+.+...  . .+.......|.             ........++.++     .+.+++.|.|||+||||+||
T Consensus        75 y~v~v~~~~~~~~~--~-~l~~~v~~~g~-------------~~~~~~~~~~~~~-----~~~~~i~l~tGR~hQIR~~~  133 (174)
T d1vioa1          75 YLVTLADPVEENYS--A-ACAEGILLRGE-------------KEPTKPAKLEILD-----DYNVNLTISEGRYHQVKRMF  133 (174)
T ss_dssp             EEEEESSCCCTTHH--H-HHHHCCCCTTC-------------SSCCCCCEEEECS-----SSEEEEEESCCCTTHHHHHH
T ss_pred             eeeEEecccchhhH--H-HHhCCceecCc-------------cccceeeeecccc-----CcEEEEEEecccchHHHHHH
Confidence            99999988865431  1 11100000110             0111222333332     23589999999999999999


Q ss_pred             HhcCCCceeCCC--CCCC
Q 023907          162 AEVLGTPIVGDY--KYGW  177 (275)
Q Consensus       162 a~~lG~PIvGD~--~Yg~  177 (275)
                      ++ +||||++-.  .||.
T Consensus       134 ~~-~g~pI~~L~Ri~~g~  150 (174)
T d1vioa1         134 AA-LGNKVVGLHRWKIGD  150 (174)
T ss_dssp             HH-TTCCEEEEEEEEETT
T ss_pred             HH-cCCEEEEEEEEEEcc
Confidence            97 999998643  3554

>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal small subunit pseudouridine 516 synthase RsuA
species: Escherichia coli [TaxId: 562]

Probab=99.77  E-value=3.4e-20  Score=152.58  Aligned_cols=111  Identities=19%  Similarity=0.199  Sum_probs=78.9

Q ss_pred             cCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEecccCCCccEEeccce
Q 023907           23 YDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVVGTPRCSKGVISAPLG  102 (275)
Q Consensus        23 ~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~g~i~~~l~  102 (275)
                      ......+++|||||++|||+||||+|+++++.|.++..+                ++|+|+|.+.|.+......   .+.
T Consensus        30 ~~~~~~l~~vgRLD~~tsGLlL~tndg~~~~~l~~~~~~----------------i~k~Y~v~v~~~i~~~~~~---~l~   90 (172)
T d1kska4          30 EPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHH----------------CEKTYLVTLESPVADDTAE---QFA   90 (172)
T ss_dssp             CTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTTSC----------------CCEEEEEEESSCCCTTHHH---HHH
T ss_pred             ccccCcEEEeecCCccccccEEEecccceeeeecccccc----------------ccEEEEEEEeccCCHHHHH---Hhh
Confidence            344557899999999999999999999999998876554                8999999999988764321   111


Q ss_pred             eeeccCCceeeEEEecCCCCCCCcceEEEEEEeeecCCcEEEEEEEeCcCchhHHHHHHHhcCCCceeC
Q 023907          103 KVVVDNGKSDRITVVNNDQIMSAQHAVTRYQVIKPSCHGYTWLKLSPLTGRKHQLRVHCAEVLGTPIVG  171 (275)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~k~a~t~~~~l~~~~~~~slv~~~~~TGR~HQIR~hla~~lG~PIvG  171 (275)
                      .     |.      .-     ++..+.+.+..++..  +.++++|++.|||+||||+||++ +|+||+.
T Consensus        91 ~-----gv------~i-----~~~~~~~~~~~v~~~--~~~~l~i~l~~Gr~~qIR~~~~~-lg~~V~~  140 (172)
T d1kska4          91 K-----GV------QL-----HNEKDLTKPAVLEVI--TPTQVRLTISEGRYHQVKRMFAA-VGNHVVE  140 (172)
T ss_dssp             H-----CC------CC-----TTCSSCCCCCEEEEE--ETTEEEEEESCCCTTHHHHHHHH-TTCCEEE
T ss_pred             c-----ce------EE-----cCccccccceEEeec--cCcEEEEEEecCccHHHHHHHHH-cCCEEeE
Confidence            1     10      00     011222222233332  22469999999999999999997 9999973

>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Escherichia coli [TaxId: 562]

Probab=86.90  E-value=0.35  Score=39.52  Aligned_cols=55  Identities=11%  Similarity=0.139  Sum_probs=39.4

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      .+++..+-+.....++...+.||-..||+|+++-+..  .++...+.+                -.|+|.|.+
T Consensus        18 ~~vv~~~k~~l~~kKvGh~GTLDP~AsGvL~i~ig~a--TK~~~~~~~----------------~~K~Y~~~i   72 (242)
T d1k8wa5          18 NDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEA--TKFSQYLLD----------------SDKRYRVIA   72 (242)
T ss_dssp             HHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGG--GGGTHHHHT----------------SCEEEEEEE
T ss_pred             HHHHHHHHHHhCCCcCCcCCcCCCcccceEEEEEchh--hhhhhhhhh----------------hhheeeEEE
Confidence            4455544443445678999999999999999999763  334455554                579999876

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Thermotoga maritima [TaxId: 2336]

Probab=84.30  E-value=0.34  Score=39.20  Aligned_cols=56  Identities=16%  Similarity=0.322  Sum_probs=39.3

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .++++..-+.....++...++||-..||||+++-+...  ++...+.+                ..|+|.|.+.
T Consensus        17 ~~~v~~vk~~l~~~KvGh~GTLDP~AsGvL~i~ig~~t--kl~~~~~~----------------~~K~Y~~~~~   72 (228)
T d1r3ea2          17 HDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGT--RILEFYKD----------------LKKVYWVKMR   72 (228)
T ss_dssp             HHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGG--GGGGGGTT----------------SCEEEEEEEE
T ss_pred             HHHHHHHHHHhCCCccCcCcccCCcceeeEEEEEcccc--cchhhhhc----------------ccceEEEEEE
Confidence            34444343334456889999999999999999998633  34444444                6799998763

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=80.75  E-value=0.54  Score=38.09  Aligned_cols=55  Identities=18%  Similarity=0.293  Sum_probs=39.5

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEE
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALV   86 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv   86 (275)
                      .++++...+.....++...++||-..||||+++-...  .++.+.+.+                -.|+|.|.+
T Consensus        18 ~~~v~~vk~~~~~kKvGh~GTLDP~AtGvL~i~ig~a--TK~~~~~~~----------------~~K~Y~~~~   72 (233)
T d1sgva2          18 HDVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERA--TKILGLLTA----------------APKSYAATI   72 (233)
T ss_dssp             HHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGG--GGGGGGTTT----------------SCEEEEEEE
T ss_pred             HHHHHHHHHHhCcCccccCcCCCCcceeeEEEEechh--hhhhhhhcc----------------CceEEEEEE
Confidence            4444544444456688999999999999999999863  344444444                579999976

>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.11  E-value=1.1  Score=36.40  Aligned_cols=56  Identities=21%  Similarity=0.114  Sum_probs=41.0

Q ss_pred             HHHHHHHhhcCCCCCCcccccCCCCCceEEEEEeCHHHHHHHHHHHHhccccccccccccccCCcceEEEEEEe
Q 023907           14 DELAATCLTYDYSEPPRLVHRLDRDSSGILVMGRTQTSATVLHSIFREKTFSASKEDNDNEKRILQRWYWALVV   87 (275)
Q Consensus        14 ~~l~~~~l~~~~~~~~~~vhRLD~~TSGllllAk~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~v~K~Y~alv~   87 (275)
                      .+.+...-+.....++...+-||-..||||+++-.+.  .++.+.+.+                ..|+|.|.+.
T Consensus        56 ~~vv~~vkk~l~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~~~~----------------~~K~Y~~~~~  111 (245)
T d2ey4a2          56 HEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKA--TRVVQALLP----------------AGKEYVALMH  111 (245)
T ss_dssp             HHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGG--GGGHHHHTT----------------SCEEEEEEEE
T ss_pred             HHHHHHHHHHhCcCCCCcCccCCCcceeeEEEEecHH--HHHHHHhcc----------------CCcEEEEEEE
Confidence            3444544343445688999999999999999999764  345556655                6899999874