Citrus Sinensis ID: 041166

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130---
Protein Sequence
LTLIEFYSTKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDAD
Secondary Structure (PSIPRED)
cEEEEEccEEEcccccccccccEEEEEEcccccccccccEEEEEEcccEEEEEcccccEEcccccccccHHHHHHHHHHcccccccccccccccEEEEccccccEEEEEEccHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEcccccccccccccccEEEEEcccccccccccccEEEEEcccEEEEEcccccEEcccccccccHHHHHHHHHccccccccccEEccccEEEEccccccEEEEEEccHHHHHHHHHHHHccccEEccc
Coil and Loop (DISEMBL)
LTLIEFYstkhknsaplqgagselvyhrlpwkepdvpyLLEVfyedddlialnkpsglqvlpgglfqQRTVLKQLQWRaskqssslssqashpvpvhrlgrgtsgILLCAKTKLAKTCIAAYfadktsvvdad
Flexible Loop (DISEMBL)
LTLIEFYstkhknsaplqgagSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQssslssqashpvpvhrlgrgTSGILLCAKTKLAKTCIAAyfadktsvvdad
Low Complexity Region (SEG)
LTLIEFYSTKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRaskqssslssqasHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDAD
Disordered region (IsUnstruct)
********************GSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQW*******************HRLGRGTSGILLCAKTKLAKTCIAAYFADKT******
Disordered Region (DISOPRED)
LTLIEF*STKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSS**SQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD********
Disordered Region (DISEMBL)
LTLIEFYSTKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQL*******************PVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDAD
Disordered Region (DISPRO)
LTLIEFYSTKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LTLIEFYSTKHKNSAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDAD
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	133	2.2.26 [Sep-21-2011]
Q5M721	369	RNA pseudourine synthase	no	no	0.969	0.349	0.651	2e-47
Q0DST9	397	RNA pseudourine synthase	yes	no	0.932	0.312	0.614	3e-43
P72970	291	Uncharacterized RNA pseud	N/A	no	0.766	0.350	0.446	1e-17
P50513	317	Ribosomal large subunit p	yes	no	0.729	0.305	0.366	2e-09
P70870	326	Ribosomal large subunit p	yes	no	0.669	0.273	0.337	3e-08
Q9KU20	324	Ribosomal large subunit p	yes	no	0.601	0.246	0.367	3e-07
Q87N15	315	Ribosomal large subunit p	yes	no	0.578	0.244	0.395	5e-07
Q9KQH0	315	Ribosomal large subunit p	no	no	0.578	0.244	0.406	5e-07
Q8PHN2	331	Ribosomal large subunit p	yes	no	0.586	0.235	0.376	6e-07
Q8D8G1	315	Ribosomal large subunit p	yes	no	0.578	0.244	0.395	7e-07

>sp|Q5M721|PUS5_ARATH RNA pseudourine synthase 5 OS=Arabidopsis thaliana GN=At3g52260 PE=2 SV=2

 Score =  187 bits (475), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 101/155 (65%), Positives = 111/155 (71%), Gaps = 26/155 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           T+ EFY TK+K+SAPL G                         +GS+LVY RLPWKEPD 
Sbjct: 34  TVSEFYFTKYKSSAPLLGWIQRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDT 93

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQAS-HPVP 95
           PY LEV YEDDDLIALNKPSGLQVLPGGLFQQRTVL QLQW   K  S + S+ S HPVP
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           VHRLGRGTSGILLCAKTKLAKT +AAYFA+ TS+V
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLV 188

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

>sp|Q0DST9|PUS5_ORYSJ RNA pseudourine synthase 5 OS=Oryza sativa subsp. japonica GN=Os03g0288500 PE=2 SV=2

 Score =  173 bits (438), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 94/153 (61%), Positives = 106/153 (69%), Gaps = 29/153 (18%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           TLIEFYST +K+SAPL G                          GS+LVYHRLPW+EP  
Sbjct: 51  TLIEFYSTSYKSSAPLPGWIKRIRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFA 110

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQ----ASH 92
           P+LL+V YEDDD+IALNKPSGLQVLP GLFQQRTVL QLQ +  K  SS  S+     SH
Sbjct: 111 PHLLDVLYEDDDMIALNKPSGLQVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSH 170

Query: 93  PVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125
           PVPVHRLGRGTSG+LLCAKTKLAK  +AAYFA+
Sbjct: 171 PVPVHRLGRGTSGLLLCAKTKLAKAQLAAYFAE 203

Oryza sativa subsp. japonica (taxid: 39947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|P72970|Y1592_SYNY3 Uncharacterized RNA pseudouridine synthase slr1592 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1592 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 50/112 (44%), Positives = 69/112 (61%), Gaps = 10/112 (8%)

Query: 14  SAPLQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLK 73
           + PLQ AG  L Y R PW EP+VP  L V + D+DL A++KPSGL VLPGG F   TVL+
Sbjct: 36  TYPLQ-AGQTLTYWRSPWVEPEVPLQLSVLHRDEDLWAIDKPSGLPVLPGGDFVYHTVLE 94

Query: 74  QLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD 125
           QL+ +  ++S           P+HRLG GTSG+LL  ++ L +  ++  F +
Sbjct: 95  QLKIQYPQESL---------FPLHRLGTGTSGLLLLGRSTLGRRELSRQFRE 137

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|P50513|RLUD_ZYMMO Ribosomal large subunit pseudouridine synthase D OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=rluD PE=3 SV=2

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/101 (36%), Positives = 57/101 (56%), Gaps = 4/101 (3%)

Query: 28  RLPWKEP-DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSL 86
           R    EP D+P  LE+ +ED+ L+ +NKP+G+ V P       T++  L +  + + S +
Sbjct: 71  RPAHNEPQDIP--LEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLYHCAGKLSGI 128

Query: 87  SSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
              A  P  VHR+ + TSG+L+ AKT  A   +AA FAD +
Sbjct: 129 GGVAR-PGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHS 168

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Zymomonas mobilis (strain ATCC 31821 / ZM4 / CP4) (taxid: 264203)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|P70870|RLUD_BORBU Ribosomal large subunit pseudouridine synthase D OS=Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) GN=rluD PE=3 SV=2

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 45/89 (50%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRL 99
           + + YED ++I LNKP G+   PG      TV+  L +       + + +   P  VHRL
Sbjct: 84  IAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVNFLLYHIKSLKINFNEEKIRPGIVHRL 143

Query: 100 GRGTSGILLCAKTKLAKTCIAAYFADKTS 128
            + TSG+L+CAK       +A  F DK +
Sbjct: 144 DKDTSGVLICAKNISTLRFLAQQFKDKRT 172

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (taxid: 224326)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|Q9KU20|RLUD_VIBCH Ribosomal large subunit pseudouridine synthase D OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rluD PE=3 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 47/87 (54%), Gaps = 7/87 (8%)

Query: 31  WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQA 90
           W+  D+P  L + YEDDD+I +NKP    V PG     +TVL  L +  S       ++ 
Sbjct: 77  WEAQDLP--LNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYSP-----IAEV 129

Query: 91  SHPVPVHRLGRGTSGILLCAKTKLAKT 117
                VHRL + T+G+++ AKT  A+T
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQT 156

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (taxid: 243277)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|Q87N15|RLUC_VIBPA Ribosomal large subunit pseudouridine synthase C OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) GN=rluC PE=3 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 45/86 (52%), Gaps = 9/86 (10%)

Query: 42  VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGR 101
           + YEDD ++ LNKPSG  V  G           L++ A +   +L  QA     VHR+ R
Sbjct: 96  IIYEDDHMLILNKPSGTAVHGGS---------GLKFGAIEALRALRPQARFLELVHRIDR 146

Query: 102 GTSGILLCAKTKLAKTCIAAYFADKT 127
            TSGILL AK + A   + A F +KT
Sbjct: 147 DTSGILLVAKKRSALRHLQAQFREKT 172

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

Vibrio parahaemolyticus (taxid: 670)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

>sp|Q9KQH0|RLUC_VIBCH Ribosomal large subunit pseudouridine synthase C OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rluC PE=3 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 35/86 (40%), Positives = 44/86 (51%), Gaps = 9/86 (10%)

Query: 42  VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGR 101
           + YEDD L+ LNKPSG  V  G           L + A +   +L  QA     VHR+ R
Sbjct: 97  IVYEDDHLLILNKPSGTAVHGGS---------GLHFGAIEALRALRPQARFLELVHRIDR 147

Query: 102 GTSGILLCAKTKLAKTCIAAYFADKT 127
            TSGILL AK + A   + A F +KT
Sbjct: 148 DTSGILLVAKKRSALRHLQAQFREKT 173

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

Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (taxid: 243277)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

>sp|Q8PHN2|RLUD_XANAC Ribosomal large subunit pseudouridine synthase D OS=Xanthomonas axonopodis pv. citri (strain 306) GN=rluD PE=3 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 51/85 (60%), Gaps = 7/85 (8%)

Query: 35  DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPV 94
           D+P  L V YED+ ++ ++KP+GL V PG     RT++  L +R      +L+S     V
Sbjct: 87  DIP--LSVLYEDEQVLVIDKPAGLVVHPGAGNPDRTLVNALLFR----DPALASVPRAGV 140

Query: 95  PVHRLGRGTSGILLCAKTKLAKTCI 119
            VHRL + TSG+++ A+T  A+T +
Sbjct: 141 -VHRLDKDTSGVMVVARTVQAQTAL 164

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Xanthomonas axonopodis pv. citri (strain 306) (taxid: 190486)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|Q8D8G1|RLUC_VIBVU Ribosomal large subunit pseudouridine synthase C OS=Vibrio vulnificus (strain CMCP6) GN=rluC PE=3 SV=1

 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 45/86 (52%), Gaps = 9/86 (10%)

Query: 42  VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGR 101
           + YEDD L+ LNKPSG  V  G           L++ A +   +L  +A     VHR+ R
Sbjct: 96  IIYEDDHLLVLNKPSGTAVHGGS---------GLKFGAIEALRALRPEARFLELVHRIDR 146

Query: 102 GTSGILLCAKTKLAKTCIAAYFADKT 127
            TSGILL AK + A   + A F +KT
Sbjct: 147 DTSGILLVAKKRSALRHLQAQFREKT 172

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

Vibrio vulnificus (taxid: 672)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 4

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	133
225449104	348	PREDICTED: RNA pseudourine synthase 5-li	1.0	0.382	0.689	5e-54
296086047	347	unnamed protein product [Vitis vinifera]	1.0	0.383	0.691	5e-54
224100817	377	predicted protein [Populus trichocarpa]	0.977	0.344	0.690	9e-54
357443349	371	RNA pseudourine synthase [Medicago trunc	0.992	0.355	0.624	7e-49
356576201	371	PREDICTED: RNA pseudourine synthase 5-li	0.969	0.347	0.610	6e-47
22331748	294	RNA pseudourine synthase 5 [Arabidopsis	0.984	0.445	0.643	6e-46
449452164	371	PREDICTED: RNA pseudourine synthase 5-li	0.962	0.345	0.636	7e-46
449485927	371	PREDICTED: RNA pseudourine synthase 5-li	0.962	0.345	0.636	7e-46
17978940	294	AT3g52260/T25B15_30 [Arabidopsis thalian	0.984	0.445	0.643	8e-46
10045559	376	putative protein [Arabidopsis thaliana]	0.969	0.343	0.651	1e-45

>gi|225449104|ref|XP_002276664.1| PREDICTED: RNA pseudourine synthase 5-like [Vitis vinifera]

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 109/158 (68%), Positives = 121/158 (76%), Gaps = 25/158 (15%)

Query: 1   LTLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPD 35
           LTLI++YS+KHKNSAPLQG                         AGS+LVYHRLPW+EPD
Sbjct: 29  LTLIDYYSSKHKNSAPLQGWLQRINKGQITVDGTVVTEPKTILRAGSKLVYHRLPWQEPD 88

Query: 36  VPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP 95
            PYLLE+ YEDDD+IALNKPSGLQVLPGGLFQQRTVL QLQWRA+KQ+S  + Q SH VP
Sbjct: 89  APYLLEILYEDDDVIALNKPSGLQVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVP 148

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDAD 133
           VHRLGRGTSGILLCAKTKLAKT +AAYFAD TSVV  +
Sbjct: 149 VHRLGRGTSGILLCAKTKLAKTRLAAYFADGTSVVGGN 186

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296086047|emb|CBI31488.3| unnamed protein product [Vitis vinifera]

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 112/162 (69%), Positives = 123/162 (75%), Gaps = 29/162 (17%)

Query: 1   LTLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPD 35
           LTLI++YS+KHKNSAPLQG                         AGS+LVYHRLPW+EPD
Sbjct: 29  LTLIDYYSSKHKNSAPLQGWLQRINKGQITVDGTVVTEPKTILRAGSKLVYHRLPWQEPD 88

Query: 36  VPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP 95
            PYLLE+ YEDDD+IALNKPSGLQVLPGGLFQQRTVL QLQWRA+KQ+S  + Q SH VP
Sbjct: 89  APYLLEILYEDDDVIALNKPSGLQVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVP 148

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV----DAD 133
           VHRLGRGTSGILLCAKTKLAKT +AAYFAD TSVV    DAD
Sbjct: 149 VHRLGRGTSGILLCAKTKLAKTRLAAYFADGTSVVGGNRDAD 190

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224100817|ref|XP_002312025.1| predicted protein [Populus trichocarpa] gi|222851845|gb|EEE89392.1| predicted protein [Populus trichocarpa]

 Score =  214 bits (545), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 107/155 (69%), Positives = 118/155 (76%), Gaps = 25/155 (16%)

Query: 1   LTLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPD 35
           LTLI FYS+K+KNSAPLQG                          G ELVYHRLPW+EPD
Sbjct: 39  LTLIHFYSSKYKNSAPLQGWLQRIHNGQITIDGEVVKEPKAILRDGMELVYHRLPWREPD 98

Query: 36  VPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP 95
            PYLL+V YEDDD++ALNKP GLQVLPGGLFQQRTVL QLQWRASK SSSL+ Q SHPVP
Sbjct: 99  APYLLQVLYEDDDMVALNKPPGLQVLPGGLFQQRTVLMQLQWRASKGSSSLAIQGSHPVP 158

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           VHRLGRGTSGILLCAKTK+AKT +AAYFAD TS++
Sbjct: 159 VHRLGRGTSGILLCAKTKVAKTSLAAYFADGTSLI 193

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357443349|ref|XP_003591952.1| RNA pseudourine synthase [Medicago truncatula] gi|358349060|ref|XP_003638558.1| RNA pseudourine synthase [Medicago truncatula] gi|355481000|gb|AES62203.1| RNA pseudourine synthase [Medicago truncatula] gi|355504493|gb|AES85696.1| RNA pseudourine synthase [Medicago truncatula]

 Score =  198 bits (503), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 98/157 (62%), Positives = 114/157 (72%), Gaps = 25/157 (15%)

Query: 1   LTLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPD 35
           LTLIEFYSTK+K+SAPLQG                          GS+LVYHR+PWKEPD
Sbjct: 31  LTLIEFYSTKYKSSAPLQGWLQRIKSDQITLDARVVTDPNTILRVGSKLVYHRIPWKEPD 90

Query: 36  VPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP 95
            P+ +EV YEDDD+IALNKPSGLQVLPGGLFQQRTVL QLQW  + +S+  + Q  HPVP
Sbjct: 91  APHTIEVLYEDDDIIALNKPSGLQVLPGGLFQQRTVLTQLQWETNNKSTIEAHQKPHPVP 150

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDA 132
           VHRLGRGTSGILLCAKTKLA+  +A+YFAD TS ++ 
Sbjct: 151 VHRLGRGTSGILLCAKTKLARARLASYFADGTSRIEG 187

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576201|ref|XP_003556222.1| PREDICTED: RNA pseudourine synthase 5-like [Glycine max]

 Score =  191 bits (486), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 94/154 (61%), Positives = 112/154 (72%), Gaps = 25/154 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           TLIEFYSTK+K+SAPLQG                          GS+L+YHRLPWKEPD 
Sbjct: 32  TLIEFYSTKYKSSAPLQGWLQRIKSGQITVDGGVVTDSNTVLRVGSKLIYHRLPWKEPDA 91

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPV 96
           P++++V YEDDD+IALNKPSGLQVLPGGL+QQRT+L QLQW A+ Q +    +  HPVPV
Sbjct: 92  PHMIDVLYEDDDMIALNKPSGLQVLPGGLYQQRTILTQLQWEANNQGTCEMHKRLHPVPV 151

Query: 97  HRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           HRLGRGTSGILLCAKTKLA+  +A++FAD TS V
Sbjct: 152 HRLGRGTSGILLCAKTKLARARLASHFADGTSHV 185

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22331748|ref|NP_190794.2| RNA pseudourine synthase 5 [Arabidopsis thaliana] gi|56744228|gb|AAW28554.1| At3g52260 [Arabidopsis thaliana] gi|332645401|gb|AEE78922.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]

 Score =  188 bits (478), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 101/157 (64%), Positives = 112/157 (71%), Gaps = 26/157 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           T+ EFY TK+K+SAPL G                         +GS+LVY RLPWKEPD 
Sbjct: 34  TVSEFYFTKYKSSAPLLGWIQRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDT 93

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQAS-HPVP 95
           PY LEV YEDDDLIALNKPSGLQVLPGGLFQQRTVL QLQW   K  S + S+ S HPVP
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDA 132
           VHRLGRGTSGILLCAKTKLAKT +AAYFA+ TS+V +
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGS 190

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452164|ref|XP_004143830.1| PREDICTED: RNA pseudourine synthase 5-like [Cucumis sativus]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 98/154 (63%), Positives = 113/154 (73%), Gaps = 26/154 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           +LI FYS K+K+SAPL+G                          GS+LVY RLPWKEPD 
Sbjct: 35  SLIHFYSWKYKSSAPLEGWLQRIKNEQITIDGEVITDPETILRIGSDLVYRRLPWKEPDT 94

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPV 96
           PYLLE+ YED+++IALNKPSGLQVLPGG+FQQRTVL QLQW +SKQS S+S +  HPVPV
Sbjct: 95  PYLLEILYEDNEMIALNKPSGLQVLPGGVFQQRTVLTQLQWWSSKQSFSVSEEL-HPVPV 153

Query: 97  HRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           HRLGRGTSGILLCAKTKLA+T  AAYFA+ TS V
Sbjct: 154 HRLGRGTSGILLCAKTKLARTQFAAYFAEGTSSV 187

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449485927|ref|XP_004157313.1| PREDICTED: RNA pseudourine synthase 5-like [Cucumis sativus]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 98/154 (63%), Positives = 113/154 (73%), Gaps = 26/154 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           +LI FYS K+K+SAPL+G                          GS+LVY RLPWKEPD 
Sbjct: 35  SLIHFYSWKYKSSAPLEGWLQRIKNEQITIDGEVITDPETILRIGSDLVYRRLPWKEPDT 94

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPV 96
           PYLLE+ YED+++IALNKPSGLQVLPGG+FQQRTVL QLQW +SKQS S+S +  HPVPV
Sbjct: 95  PYLLEILYEDNEMIALNKPSGLQVLPGGVFQQRTVLTQLQWWSSKQSFSVSEEL-HPVPV 153

Query: 97  HRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           HRLGRGTSGILLCAKTKLA+T  AAYFA+ TS V
Sbjct: 154 HRLGRGTSGILLCAKTKLARTQFAAYFAEGTSSV 187

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|17978940|gb|AAL47436.1| AT3g52260/T25B15_30 [Arabidopsis thaliana]

 Score =  188 bits (477), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 101/157 (64%), Positives = 112/157 (71%), Gaps = 26/157 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           T+ EFY TK+K+SAPL G                         +GS+LVY RLPWKEPD 
Sbjct: 34  TVSEFYFTKYKSSAPLLGWIQRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDT 93

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQAS-HPVP 95
           PY LEV YEDDDLIALNKPSGLQVLPGGLFQQRTVL QLQW   K  S + S+ S HPVP
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVVDA 132
           VHRLGRGTSGILLCAKTKLAKT +AAYFA+ TS+V +
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGS 190

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|10045559|emb|CAC07917.1| putative protein [Arabidopsis thaliana]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 101/155 (65%), Positives = 111/155 (71%), Gaps = 26/155 (16%)

Query: 2   TLIEFYSTKHKNSAPLQG-------------------------AGSELVYHRLPWKEPDV 36
           T+ EFY TK+K+SAPL G                         +GS+LVY RLPWKEPD 
Sbjct: 34  TVSEFYFTKYKSSAPLLGWIQRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDT 93

Query: 37  PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQAS-HPVP 95
           PY LEV YEDDDLIALNKPSGLQVLPGGLFQQRTVL QLQW   K  S + S+ S HPVP
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV 130
           VHRLGRGTSGILLCAKTKLAKT +AAYFA+ TS+V
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLV 188

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	133
TIGR_CMR|DET_1375	300	DET_1375 "ribosomal large subu	0.691	0.306	0.333	3.5e-07
UNIPROTKB|Q9KU20	324	rluD "Ribosomal large subunit	0.601	0.246	0.356	4.1e-07
TIGR_CMR|VC_0709	324	VC_0709 "ribosomal large subun	0.601	0.246	0.356	4.1e-07
TIGR_CMR|CPS_4520	227	CPS_4520 "ribosomal large subu	0.684	0.400	0.327	1e-06
TIGR_CMR|CHY_1505	305	CHY_1505 "ribosomal large subu	0.706	0.308	0.316	1.7e-06
TIGR_CMR|CPS_3649	304	CPS_3649 "tRNA pseudouridine s	0.654	0.286	0.333	2.1e-06
UNIPROTKB|Q4K5V9	320	rluD "Pseudouridine synthase"	0.676	0.281	0.309	3.9e-06
TIGR_CMR|SPO_1408	342	SPO_1408 "ribosomal large subu	0.631	0.245	0.364	4.4e-06
UNIPROTKB|P0AA37	219	rluA [Escherichia coli K-12 (t	0.631	0.383	0.309	4.4e-06
SGD|S000002194	462	PUS9 "Mitochondrial tRNA:pseud	0.601	0.173	0.329	9.3e-06

TIGR_CMR|DET_1375 DET_1375 "ribosomal large subunit pseudouridine synthase, RluA family" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 122 (48.0 bits), Expect = 3.5e-07, P = 3.5e-07
 Identities = 32/96 (33%), Positives = 48/96 (50%)

Query:    32 KEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXX 91
             K  D+P  LE+ ++D DL+ +NKP GL V P       T++  +                
Sbjct:    72 KAEDIP--LEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVL--ALEPEMEDFDDPL 127

Query:    92 HPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
              P  VHRL + TSG+LL AK + A   ++A F ++T
Sbjct:   128 RPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERT 163

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|Q9KU20 rluD "Ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 122 (48.0 bits), Expect = 4.1e-07, P = 4.1e-07
 Identities = 31/87 (35%), Positives = 44/87 (50%)

Query:    31 WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXX 90
             W+  D+P  L + YEDDD+I +NKP    V PG     +TVL  L +             
Sbjct:    77 WEAQDLP--LNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYSPIAEVPRAGI 134

Query:    91 XHPVPVHRLGRGTSGILLCAKTKLAKT 117
                  VHRL + T+G+++ AKT  A+T
Sbjct:   135 -----VHRLDKDTTGLMVVAKTVPAQT 156

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|VC_0709 VC_0709 "ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 122 (48.0 bits), Expect = 4.1e-07, P = 4.1e-07
 Identities = 31/87 (35%), Positives = 44/87 (50%)

Query:    31 WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXX 90
             W+  D+P  L + YEDDD+I +NKP    V PG     +TVL  L +             
Sbjct:    77 WEAQDLP--LNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYSPIAEVPRAGI 134

Query:    91 XHPVPVHRLGRGTSGILLCAKTKLAKT 117
                  VHRL + T+G+++ AKT  A+T
Sbjct:   135 -----VHRLDKDTTGLMVVAKTVPAQT 156

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|CPS_4520 CPS_4520 "ribosomal large subunit pseudouridine synthase A" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 115 (45.5 bits), Expect = 1.0e-06, P = 1.0e-06
 Identities = 35/107 (32%), Positives = 51/107 (47%)

Query:    20 AGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRX 79
             A  + +Y  LP   P  PYL ++ Y+DDD++ LNK SG+  +PG L + +  L+    R 
Sbjct:     3 ANPDFIY--LP---PMSPYL-DIIYQDDDIVVLNKASGILSVPGRLPEHQDCLQNRVQRV 56

Query:    80 XXXXXXXXXXXXHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
                             VHRL   TSGI++ A  K A   I+  F  +
Sbjct:    57 LPTATI----------VHRLDMATSGIMIMALNKPAHVAISRQFEQR 93

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|CHY_1505 CHY_1505 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 116 (45.9 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 31/98 (31%), Positives = 49/98 (50%)

Query:    32 KEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXX 91
             K  ++P  L++ YED+DL+ +NK +G+ V P       T++  L +              
Sbjct:    76 KPEEIP--LDIVYEDEDLVVVNKKAGMVVHPAEGNWDGTLVNALLYHCQNLSGIGGVL-- 131

Query:    92 HPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSV 129
              P  VHRL + TSG+L+ AK  LA   +A    +K +V
Sbjct:   132 RPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAV 169

GO:0001522 "pseudouridine synthesis" evidence=ISS

GO:0009451 "RNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|CPS_3649 CPS_3649 "tRNA pseudouridine synthase C" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 115 (45.5 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 32/96 (33%), Positives = 53/96 (55%)

Query:    33 EPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXH 92
             EP+ P +L++ Y+D+ ++A++KP+GL       F  R+ + + +               +
Sbjct:    15 EPEKP-VLDILYQDEYMVAVDKPAGL-------FVHRSYMDKDEI-YFALQLVRDQVGQY 65

Query:    93 PVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS 128
               PVHRL R TSG+LL A TK   T ++  FA+K+S
Sbjct:    66 VYPVHRLDRPTSGVLLFALTKDVATKLSEAFANKSS 101

GO:0003824 "catalytic activity" evidence=ISS

GO:0009451 "RNA modification" evidence=ISS

UNIPROTKB|Q4K5V9 rluD "Pseudouridine synthase" [Pseudomonas protegens Pf-5 (taxid:220664)]

 Score = 113 (44.8 bits), Expect = 3.9e-06, P = 3.9e-06
 Identities = 30/97 (30%), Positives = 47/97 (48%)

Query:    31 WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXX 90
             W   D+   L++ YEDDD++ +NKP+GL V P       T+L  L               
Sbjct:    76 WIAQDIE--LDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHIPDIINVPRAGI 133

Query:    91 XHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
                  VHRL + T+G+++ AKT  A+T + A    ++
Sbjct:   134 -----VHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRS 165

GO:0006364 "rRNA processing" evidence=ISS

TIGR_CMR|SPO_1408 SPO_1408 "ribosomal large subunit pseudouridine synthase D" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 113 (44.8 bits), Expect = 4.4e-06, P = 4.4e-06
 Identities = 31/85 (36%), Positives = 43/85 (50%)

Query:    40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPVPVHRL 99
             L V YEDDDLI ++KP+G+ V P       T++  L                 P  VHR+
Sbjct:    85 LVVVYEDDDLIVIDKPAGMVVHPAPGTPSGTLVNALL-AHCGDNLSGVGGVKRPGIVHRI 143

Query:   100 GRGTSGILLCAKTKLAKTCIAAYFA 124
              + TSG+L+ AK+  A   +AA FA
Sbjct:   144 DKDTSGLLVVAKSDAAHHGLAAQFA 168

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|P0AA37 rluA [Escherichia coli K-12 (taxid:83333)]

 Score = 109 (43.4 bits), Expect = 4.4e-06, P = 4.4e-06
 Identities = 30/97 (30%), Positives = 52/97 (53%)

Query:    31 WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQR-TVLKQLQWRXXXXXXXXXXX 89
             +  P  P+L+ + Y+DD ++ +NKPSGL  +PG L + + +V+ ++Q R           
Sbjct:     6 YNPPQEPWLV-ILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQ-RDYPQAES---- 59

Query:    90 XXHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
                   VHRL   TSG+++ A TK A+  +   F ++
Sbjct:    60 ------VHRLDMATSGVIVVALTKAAERELKRQFRER 90

GO:0031118 "rRNA pseudouridine synthesis" evidence=IMP

GO:0031119 "tRNA pseudouridine synthesis" evidence=IMP

GO:0009451 "RNA modification" evidence=IMP

GO:0009982 "pseudouridine synthase activity" evidence=IEA;IDA;IMP

GO:0001522 "pseudouridine synthesis" evidence=IMP

GO:0008033 "tRNA processing" evidence=IMP

GO:0006364 "rRNA processing" evidence=IMP

GO:0003723 "RNA binding" evidence=IEA

GO:0000455 "enzyme-directed rRNA pseudouridine synthesis" evidence=IMP

SGD|S000002194 PUS9 "Mitochondrial tRNA:pseudouridine synthase" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 112 (44.5 bits), Expect = 9.3e-06, P = 9.3e-06
 Identities = 30/91 (32%), Positives = 49/91 (53%)

Query:    23 ELVYHRLPWKEPDVPYL-LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXX 81
             +L+ H++   EP V    ++V +EDD+++ ++KPSG+ V P G ++  T+ K LQ     
Sbjct:   170 DLITHQVHRHEPPVTSRPIKVIFEDDNIMVIDKPSGIPVHPTGRYRFNTITKMLQNNLGF 229

Query:    82 XXXXXXXXXXHPVPVHRLGRGTSGILLCAKT 112
                          P +RL R TSG++  AKT
Sbjct:   230 VVN----------PCNRLDRLTSGLMFLAKT 250

GO:0009451 "RNA modification" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISM;IMP

GO:0031119 "tRNA pseudouridine synthesis" evidence=IMP;IDA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;IMP;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0016853 "isomerase activity" evidence=IEA

GO:0008033 "tRNA processing" 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

Fail to connect to STRING server

---

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	133
COG0564	289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	2e-21
TIGR00005	299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	3e-18
cd02869	185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	6e-14
cd02557	213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	2e-13
cd02558	246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	4e-12
cd02563	223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	2e-10
PRK11180	325	PRK11180, rluD, 23S rRNA pseudouridine synthase D;	3e-10
pfam00849	149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	2e-09
PRK10158	219	PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy	4e-08
PRK11112	257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	8e-08
PRK11025	317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	3e-07
cd02550	154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	9e-04
TIGR01621	217	TIGR01621, RluA-like, pseudouridine synthase Rlu f	0.002

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

 Score = 86.2 bits (214), Expect = 2e-21
 Identities = 33/100 (33%), Positives = 49/100 (49%), Gaps = 9/100 (9%)

Query: 28  RLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLS 87
                  D+P  L++ YED+DL+ +NKP+GL V PGG   + T++  L            
Sbjct: 68  EEKLVPEDIP--LDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALL-------RHCQ 118

Query: 88  SQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
                P  VHRL + TSG+LL AK + A   ++  F  + 
Sbjct: 119 DGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRK 158

Length = 289

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

 Score = 78.1 bits (193), Expect = 3e-18
 Identities = 36/98 (36%), Positives = 51/98 (52%), Gaps = 8/98 (8%)

Query: 33  EPDVPYL---LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQ 89
           E +VP     L++ +ED+D+I +NKPSGL V PGG     TVL  L          ++  
Sbjct: 62  EHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALL----AHCPPIAGV 117

Query: 90  ASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
                 VHRL R TSG+++ AKT LA   +     ++T
Sbjct: 118 ER-VGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT 154

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|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family

 Score = 64.7 bits (158), Expect = 6e-14
 Identities = 26/79 (32%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 49  LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILL 108
           L+ +NKP+GL V PG      T++  L                 P  VHRL + TSG+LL
Sbjct: 1   LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEF-----RPGLVHRLDKDTSGLLL 55

Query: 109 CAKTKLAKTCIAAYFADKT 127
            AK K A   ++  F ++ 
Sbjct: 56  VAKNKKAAAKLSKQFKERK 74

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

 Score = 63.4 bits (155), Expect = 2e-13
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 13/87 (14%)

Query: 27  HRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSL 86
           H  P     +    ++ +EDDDL+ ++KPSG+ V P G ++  TV + L+     +    
Sbjct: 7   HEPPVTNDPI----KIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILK----SEYGL- 57

Query: 87  SSQASHPVPVHRLGRGTSGILLCAKTK 113
               +   P HRL R TSG+LL AKT 
Sbjct: 58  ----TELRPCHRLDRLTSGLLLFAKTS 80

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

 Score = 60.4 bits (147), Expect = 4e-12
 Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 9/92 (9%)

Query: 20  AGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRA 79
            G+ + Y+R    EP +P+   + ++D+ L+  +KP  L V P G +   T+L +L  R 
Sbjct: 19  PGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRL--RR 76

Query: 80  SKQSSSLSSQASHPVPVHRLGRGTSGILLCAK 111
              +  L        P HRL R T+G++L +K
Sbjct: 77  QTGNPDL-------TPAHRLDRLTAGLVLFSK 101

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

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 31/89 (34%), Positives = 41/89 (46%), Gaps = 10/89 (11%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLK-QLQWRASKQSSSLSSQASHPVPVHR 98
           LE+ Y+D+ L+A+NKPSGL V    L +  T    Q       Q         H  PVHR
Sbjct: 1   LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQ---------HVYPVHR 51

Query: 99  LGRGTSGILLCAKTKLAKTCIAAYFADKT 127
           L R TSG+LL A +      +   F +  
Sbjct: 52  LDRPTSGVLLFALSSEVARKLGEQFTEHR 80

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

 Score = 56.2 bits (136), Expect = 3e-10
 Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 23/95 (24%)

Query: 31  WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQA 90
           ++  D+P  L++ YEDDD++ +NKP  L V PG      TVL  L               
Sbjct: 77  FEPQDIP--LDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHY------------ 122

Query: 91  SHP----VP----VHRLGRGTSGILLCAKTKLAKT 117
            +P    VP    VHRL + T+G+++ AKT  A+T
Sbjct: 123 -YPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQT 156

Length = 325

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

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 49  LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILL 108
            I +NKP+G+ V P                 +              PVHRL R TSG+LL
Sbjct: 1   YIVVNKPAGVPVHPTDPSDLL--------SLTALLLVAELGKFRLYPVHRLDRNTSGLLL 52

Query: 109 CAKTKLAKTCIAAYFADKT 127
            AK   A   +   F ++ 
Sbjct: 53  LAKDGEAANKLNKLFPERK 71

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

 Score = 49.6 bits (118), Expect = 4e-08
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 13/98 (13%)

Query: 30  PWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQR-TVLKQLQWRASKQSSSLSS 88
            +  P  P+L+ + Y+D+ ++ +NKPSGL  +PG L + + +V+ ++Q R   Q+ S   
Sbjct: 5   NYNPPQEPWLV-ILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQ-RDYPQAES--- 59

Query: 89  QASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
                  VHRL   TSG+++ A TK A+  +   F ++
Sbjct: 60  -------VHRLDMATSGVIVVALTKAAERELKRQFRER 90

Length = 219

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

 Score = 48.9 bits (117), Expect = 8e-08
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 10/72 (13%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQ-ASHPVPVHR 98
           LE+ Y+D+ L+A+NKP+G  V    L +  TV   +Q        ++  Q   H    HR
Sbjct: 2   LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVF-VMQ--------TVRDQIGQHVFTAHR 52

Query: 99  LGRGTSGILLCA 110
           L R TSG+LL A
Sbjct: 53  LDRPTSGVLLMA 64

Length = 257

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 42  VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGR 101
           + YEDD ++ LNKPSG  V  GG      V++ L+        +L  +A     VHRL R
Sbjct: 95  ILYEDDHILVLNKPSGTAV-HGGSGLSFGVIEGLR--------ALRPEARFLELVHRLDR 145

Query: 102 GTSGILLCAKTKLA 115
            TSG+LL AK + A
Sbjct: 146 DTSGVLLVAKKRSA 159

Length = 317

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 19/68 (27%), Positives = 25/68 (36%), Gaps = 18/68 (26%)

Query: 49  LIALNKPSGLQVLPGGLFQQRTVL----KQLQWRASKQSSSLSSQASHPVPVHRLGRGTS 104
           ++ LNKPSGL   P    +  TV+    K    R                   RL + TS
Sbjct: 1   ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVH--------------AAGRLDKDTS 46

Query: 105 GILLCAKT 112
           G+LL    
Sbjct: 47  GLLLLTND 54

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 15/90 (16%)

Query: 39  LLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP--V 96
           + E+ +   D + +NK  G+ V         T L Q           +++Q        V
Sbjct: 1   MFEILFTHPDFLLINKHPGISVHKD---DGETGLLQE----------VATQLGVGQVWLV 47

Query: 97  HRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
           HRL + TSGILL A    + + ++  FA +
Sbjct: 48  HRLDKMTSGILLLALNAESASELSQGFAKR 77

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	133
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	99.96
cd02558	246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	99.95
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	99.94
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	99.94
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	99.93
cd02557	213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	99.92
PRK10158	219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	99.9
TIGR01621	217	RluA-like pseudouridine synthase Rlu family protei	99.9
PRK11112	257	tRNA pseudouridine synthase C; Provisional	99.9
cd02563	223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	99.9
KOG1919	371	consensus RNA pseudouridylate synthases [RNA proce	99.88
PF00849	164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.81
cd02550	154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.79
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	99.79
cd02869	185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	99.76
cd02556	167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.73
cd02870	146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.73
cd02553	167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.72
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	99.71
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	99.69
cd02566	168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.66
PRK11394	217	23S rRNA pseudouridine synthase E; Provisional	99.57
cd02555	177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.53
cd02554	164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.48
cd02868	226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	99.32
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.2
cd02572	182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	97.83
PRK00989	230	truB tRNA pseudouridine synthase B; Provisional	97.72
PRK04099	273	truB tRNA pseudouridine synthase B; Provisional	97.64
cd00506	210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	97.62
TIGR00431	209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	97.6
PRK00020	244	truB tRNA pseudouridine synthase B; Provisional	97.48
PRK02484	294	truB tRNA pseudouridine synthase B; Provisional	97.47
PRK03287	298	truB tRNA pseudouridine synthase B; Provisional	97.45
PRK14123	305	tRNA pseudouridine synthase B; Provisional	97.41
PRK14124	308	tRNA pseudouridine synthase B; Provisional	97.4
PRK14846	345	truB tRNA pseudouridine synthase B; Provisional	97.4
PRK00130	290	truB tRNA pseudouridine synthase B; Provisional	97.4
PRK05389	305	truB tRNA pseudouridine synthase B; Provisional	97.37
PRK02193	279	truB tRNA pseudouridine synthase B; Provisional	97.34
PRK04270	300	H/ACA RNA-protein complex component Cbf5p; Reviewe	97.32
PRK05033	312	truB tRNA pseudouridine synthase B; Provisional	97.32
cd02573	277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	97.32
PRK01528	292	truB tRNA pseudouridine synthase B; Provisional	97.32
PRK02755	295	truB tRNA pseudouridine synthase B; Provisional	97.27
PRK01550	304	truB tRNA pseudouridine synthase B; Provisional	97.23
PRK01851	303	truB tRNA pseudouridine synthase B; Provisional	97.22
PRK14122	312	tRNA pseudouridine synthase B; Provisional	96.97
TIGR00425	322	CBF5 rRNA pseudouridine synthase, putative. This f	96.84
PRK04642	300	truB tRNA pseudouridine synthase B; Provisional	96.83
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	96.66
COG0130	271	TruB Pseudouridine synthase [Translation, ribosoma	96.65
cd02867	312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	96.41
KOG2559	318	consensus Predicted pseudouridine synthase [Transl	95.48
cd01291	87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	90.33

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

Probab=99.96  E-value=3.4e-29  Score=196.69  Aligned_cols=105  Identities=31%  Similarity=0.460  Sum_probs=88.2

Q ss_pred             CCCcEEEEecCCCCC--C--CCCCCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCccc
Q 041166           19 GAGSELVYHRLPWKE--P--DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPV   94 (133)
Q Consensus        19 ~~g~~v~~~~~~~~~--~--~~~~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~   94 (133)
                      ..||.+.+.......  .  +.+.++.|||||++++|||||+||+|||++.+...|+++++..++...       ..+++
T Consensus        53 ~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-------~~~~~  125 (289)
T COG0564          53 KPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-------VERPG  125 (289)
T ss_pred             CCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhcccc-------CCcee
Confidence            388999887644222  1  223347899999999999999999999998888899999998775432       46889


Q ss_pred             ccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           95 PVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        95 ~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      +||||||+|||+||||||..++..|+++|++|+|.+
T Consensus       126 ~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K  161 (289)
T COG0564         126 IVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKK  161 (289)
T ss_pred             eeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcE
Confidence            999999999999999999999999999999998765

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

Probab=99.95  E-value=5.2e-27  Score=180.50  Aligned_cols=105  Identities=27%  Similarity=0.418  Sum_probs=88.4

Q ss_pred             CCCCCcEEEEecCCCCCCCCCCCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCccccc
Q 041166           17 LQGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPV   96 (133)
Q Consensus        17 ~~~~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~v   96 (133)
                      ....||.|.++....+++..+.+++|||||++|+|||||+|++|||+++....|+...+...+.         ...+++|
T Consensus        16 ~l~~gd~i~~~~~~~~~~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~---------~~~~~~v   86 (246)
T cd02558          16 PYRPGTFVWYYRELPDEPPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG---------NPDLTPA   86 (246)
T ss_pred             eecCCCEEEEeCCCCCCCCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC---------CCccccc
Confidence            3569999998765444444455689999999999999999999999988777888888765432         3467799


Q ss_pred             ccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           97 HRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        97 hRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      ||||++|||+||||||+++++.++++|++++|.+
T Consensus        87 hRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K  120 (246)
T cd02558          87 HRLDRLTAGLVLFSKRPETRGAYQTLFARREVSK  120 (246)
T ss_pred             ccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccE
Confidence            9999999999999999999999999999998875

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.

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=99.94  E-value=1.7e-26  Score=183.75  Aligned_cols=125  Identities=25%  Similarity=0.299  Sum_probs=99.3

Q ss_pred             ChHHHHHhhhCCCCCCCC------------------------CCCcEEEEecCCCCC---CCCCCCcceEEECCcEEEEE
Q 041166            1 LTLIEFYSTKHKNSAPLQ------------------------GAGSELVYHRLPWKE---PDVPYLLEVFYEDDDLIALN   53 (133)
Q Consensus         1 ~~l~~~~~~~~~~~~~~~------------------------~~g~~v~~~~~~~~~---~~~~~~~~vlyed~~~lvvn   53 (133)
                      .||++||.+.|...++..                        .+||.|.+...+..+   .+...+++|||||++++|||
T Consensus        18 ~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvn   97 (325)
T PRK11180         18 QRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVIN   97 (325)
T ss_pred             ccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEE
Confidence            478999999887655551                        278888887543221   12234689999999999999


Q ss_pred             CCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           54 KPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        54 KP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      ||+||+|||+++....|+.+.+...+.....     ..++++|||||++|||+||||||..++..|+++|++++|.+
T Consensus        98 KP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~-----~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K  169 (325)
T PRK11180         98 KPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITR  169 (325)
T ss_pred             CCCCCeEeCCCCCCCCcHHHHHHHHhhhccC-----CcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcce
Confidence            9999999998877677999888866543211     34678999999999999999999999999999999998865

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=99.94  E-value=3.9e-26  Score=179.31  Aligned_cols=124  Identities=31%  Similarity=0.407  Sum_probs=97.8

Q ss_pred             hHHHHHhhhCCCCCCCC------------------------CCCcEEEEecCCCCC---CCCCCCcceEEECCcEEEEEC
Q 041166            2 TLIEFYSTKHKNSAPLQ------------------------GAGSELVYHRLPWKE---PDVPYLLEVFYEDDDLIALNK   54 (133)
Q Consensus         2 ~l~~~~~~~~~~~~~~~------------------------~~g~~v~~~~~~~~~---~~~~~~~~vlyed~~~lvvnK   54 (133)
                      ||++||...|...++..                        .+||.|.+...+..+   +....+++|+|||++++||||
T Consensus         7 rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnK   86 (299)
T TIGR00005         7 RLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINK   86 (299)
T ss_pred             hHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEEC
Confidence            78899998887555541                        278888885433222   122235789999999999999


Q ss_pred             CCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           55 PSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        55 P~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      |+|++||+.++....|+.+.+..++....     ....+++|||||++|||+||||||.++++.++++|++++|.+
T Consensus        87 P~g~~~~~~~~~~~~tl~~~l~~~~~~~~-----~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K  157 (299)
T TIGR00005        87 PSGLVVHPGGGNPFGTVLNALLAHCPPIA-----GVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTK  157 (299)
T ss_pred             CCCCeEeCCCCCCcccHHHHHHHhccccc-----CCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcce
Confidence            99999999887777889998876653211     135788999999999999999999999999999999998865

modifies uracil-65 in transfer RNAs to pseudouridine.

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=99.93  E-value=2.3e-25  Score=176.87  Aligned_cols=121  Identities=30%  Similarity=0.339  Sum_probs=90.9

Q ss_pred             ChHHHHHhhhCCCCCCCC-----------------------CCCcEEEEecCCCCC----CC-------CCCCcceEEEC
Q 041166            1 LTLIEFYSTKHKNSAPLQ-----------------------GAGSELVYHRLPWKE----PD-------VPYLLEVFYED   46 (133)
Q Consensus         1 ~~l~~~~~~~~~~~~~~~-----------------------~~g~~v~~~~~~~~~----~~-------~~~~~~vlyed   46 (133)
                      .||++||...+...++..                       ..||.|.+......+    |.       ...+++|||||
T Consensus        20 ~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed   99 (317)
T PRK11025         20 QRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYED   99 (317)
T ss_pred             chHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEEC
Confidence            378999998887655551                       268888875322211    11       12356899999


Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcC
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK  126 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~  126 (133)
                      ++++|||||+|++|||+.+.. .++.+.+......        ...+++|||||++|||+||||||..+++.|+++|+++
T Consensus       100 ~~~lvvnKP~gl~~~~~~~~~-~~~~~~~~~~~~~--------~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~  170 (317)
T PRK11025        100 DHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPE--------ARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK  170 (317)
T ss_pred             CCEEEEECCCCCcCcCCCCCC-ccHHHHHHHhccC--------CCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhC
Confidence            999999999999999987653 3556655543211        2346789999999999999999999999999999999


Q ss_pred             Cccc
Q 041166          127 TSVV  130 (133)
Q Consensus       127 ~v~~  130 (133)
                      +|.+
T Consensus       171 ~v~K  174 (317)
T PRK11025        171 GMQK  174 (317)
T ss_pred             CccE
Confidence            8865

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like

Probab=99.92  E-value=2.8e-25  Score=167.57  Aligned_cols=91  Identities=34%  Similarity=0.485  Sum_probs=77.9

Q ss_pred             CCCCCCC-CCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeee
Q 041166           31 WKEPDVP-YLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLC  109 (133)
Q Consensus        31 ~~~~~~~-~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~  109 (133)
                      .+||+.+ .+++|||||++++|||||+|++|++++.....|+.+.|...+.         ...+++|||||++|||+|||
T Consensus         6 ~~~~~~~~~~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~---------~~~~~~vhRLD~~TSGllll   76 (213)
T cd02557           6 RHEPPVTNDPIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG---------LTELRPCHRLDRLTSGLLLF   76 (213)
T ss_pred             ccCCCCCCCCCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC---------CCCccCccCCCCCCceEEEE
Confidence            4555544 5899999999999999999999999877667788888875432         24678999999999999999


Q ss_pred             ecChHHHHHHHHHHHcCCccc
Q 041166          110 AKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus       110 Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      |||+++++.|+++|++++|++
T Consensus        77 ak~~~~~~~l~~~f~~~~v~K   97 (213)
T cd02557          77 AKTSQTASRLQQQIRSREVKK   97 (213)
T ss_pred             ECCHHHHHHHHHHHHcCCccE
Confidence            999999999999999998875

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.

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

Probab=99.90  E-value=1.6e-23  Score=158.69  Aligned_cols=81  Identities=32%  Similarity=0.554  Sum_probs=68.9

Q ss_pred             CcceEEECCcEEEEECCCCceeecCCC-CCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166           39 LLEVFYEDDDLIALNKPSGLQVLPGGL-FQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT  117 (133)
Q Consensus        39 ~~~vlyed~~~lvvnKP~gl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~  117 (133)
                      .++|||||++|+|||||+|++||++.. ....++.+.+...+           ..+++|||||++||||||||||.++++
T Consensus        13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~-----------~~~~~vhRLDr~TSGlll~Akt~~~~~   81 (219)
T PRK10158         13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY-----------PQAESVHRLDMATSGVIVVALTKAAER   81 (219)
T ss_pred             CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC-----------CCCCEECCCCCCCceEEEEECCHHHHH
Confidence            478999999999999999999998763 33457777665432           247799999999999999999999999


Q ss_pred             HHHHHHHcCCccc
Q 041166          118 CIAAYFADKTSVV  130 (133)
Q Consensus       118 ~l~~~f~~~~v~~  130 (133)
                      .|+++|++++|.+
T Consensus        82 ~l~~~f~~~~v~K   94 (219)
T PRK10158         82 ELKRQFREREPKK   94 (219)
T ss_pred             HHHHHHHhCCccE
Confidence            9999999998865

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

Probab=99.90  E-value=1.2e-23  Score=159.15  Aligned_cols=80  Identities=25%  Similarity=0.357  Sum_probs=67.9

Q ss_pred             cceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHH
Q 041166           40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCI  119 (133)
Q Consensus        40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l  119 (133)
                      ++|||||++++|||||+||+||++..  ..++...+.....         ...+++|||||++|||+||||||+++++.|
T Consensus         2 ~~ilyed~~~lvvnKP~Gl~v~~~~~--~~~l~~~l~~~~~---------~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L   70 (217)
T TIGR01621         2 FEILFTHPDFLLINKHPGISVHKDDG--ETGLLQEVATQLG---------VGQVWLVHRLDKMTSGILLLALNAESASEL   70 (217)
T ss_pred             ceEEEeCCCEEEEECCCCCeECCCCC--cChHHHHHHHhcC---------CCCccEecCCCCCCceEEEEEcCHHHHHHH
Confidence            57999999999999999999998764  2466666653321         346889999999999999999999999999


Q ss_pred             HHHHHcCCccc
Q 041166          120 AAYFADKTSVV  130 (133)
Q Consensus       120 ~~~f~~~~v~~  130 (133)
                      +++|++++|.+
T Consensus        71 ~~~~~~~~v~K   81 (217)
T TIGR01621        71 SQGFAKRKIEK   81 (217)
T ss_pred             HHHHhcCCccE
Confidence            99999999875

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.

>PRK11112 tRNA pseudouridine synthase C; Provisional

Probab=99.90  E-value=1.7e-23  Score=161.88  Aligned_cols=81  Identities=33%  Similarity=0.465  Sum_probs=65.8

Q ss_pred             cceEEECCcEEEEECCCCceeecCCCCCcch--HHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166           40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRT--VLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT  117 (133)
Q Consensus        40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~  117 (133)
                      ++|||||++|+|||||+||+||++......+  +...+...+          ...+++|||||++||||||||||.++++
T Consensus         2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~VHRLDr~TSGlll~Ak~~~~~~   71 (257)
T PRK11112          2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI----------GQHVFTAHRLDRPTSGVLLMALSSEVAR   71 (257)
T ss_pred             CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh----------CCCceeeccCCCCCeeEEEEECCHHHHH
Confidence            5799999999999999999999875443333  223332221          2357799999999999999999999999


Q ss_pred             HHHHHHHcCCccc
Q 041166          118 CIAAYFADKTSVV  130 (133)
Q Consensus       118 ~l~~~f~~~~v~~  130 (133)
                      .|+++|++++|.+
T Consensus        72 ~L~~~f~~~~v~K   84 (257)
T PRK11112         72 LLAQQFEQHQIQK   84 (257)
T ss_pred             HHHHHHHhCCcce
Confidence            9999999999875

>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=99.90  E-value=2.1e-23  Score=158.23  Aligned_cols=81  Identities=38%  Similarity=0.566  Sum_probs=65.6

Q ss_pred             cceEEECCcEEEEECCCCceeecCCCCCcch--HHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166           40 LEVFYEDDDLIALNKPSGLQVLPGGLFQQRT--VLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT  117 (133)
Q Consensus        40 ~~vlyed~~~lvvnKP~gl~v~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~  117 (133)
                      ++|||||++++|||||+|++|||+++....+  +...+...+          ...+++|||||++||||||||||+++++
T Consensus         1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~Ak~~~~~~   70 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL----------GQHVYPVHRLDRPTSGVLLFALSSEVAR   70 (223)
T ss_pred             CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc----------CCCcccccCCCCCCeEEEEEEECHHHHH
Confidence            4699999999999999999999886443322  223332221          2467899999999999999999999999


Q ss_pred             HHHHHHHcCCccc
Q 041166          118 CIAAYFADKTSVV  130 (133)
Q Consensus       118 ~l~~~f~~~~v~~  130 (133)
                      .|+++|++++|.+
T Consensus        71 ~l~~~f~~~~v~K   83 (223)
T cd02563          71 KLGEQFTEHRVHK   83 (223)
T ss_pred             HHHHHHhcCceeE
Confidence            9999999998865

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

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

Probab=99.88  E-value=1.2e-22  Score=163.73  Aligned_cols=119  Identities=27%  Similarity=0.379  Sum_probs=98.7

Q ss_pred             HHHHHhhhCCCCCCC-----------------------CCCCcEEEEecCCCCCCCCCCCcceEEECCcEEEEECCCCce
Q 041166            3 LIEFYSTKHKNSAPL-----------------------QGAGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALNKPSGLQ   59 (133)
Q Consensus         3 l~~~~~~~~~~~~~~-----------------------~~~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvnKP~gl~   59 (133)
                      +.+++..+|....++                       .+.||.+....+.++.+....++.|+|||++++|||||+|++
T Consensus        46 ~~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~vhrh~p~~~~~~~~Iv~ed~~~vVvnKP~gip  125 (371)
T KOG1919|consen   46 LVDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHTVHRHEPPVAYLPIRIVFEDKDYVVVNKPHGIP  125 (371)
T ss_pred             hHHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEeeccCCCCccccccceEEecCCEEEEeCCCCCc
Confidence            567777777777655                       247888876544444455556899999999999999999999


Q ss_pred             eecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           60 VLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        60 v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      |||++.+..+++...+.....         ...+++|||||+.|||+|+|||+++++..++++|+++++.+
T Consensus       126 Vhp~g~~~~n~i~~~l~~~~~---------~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k  187 (371)
T KOG1919|consen  126 VHPTGRYRENTITKILAALHK---------VEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKK  187 (371)
T ss_pred             eeccCccccccchHHHHHhcc---------ccccccccccCccccceEEEEechhHhHHHHHHHhccccee
Confidence            999999999999888876521         56788999999999999999999999999999999997764

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

Probab=99.81  E-value=3.9e-20  Score=132.91  Aligned_cols=78  Identities=32%  Similarity=0.456  Sum_probs=57.7

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT  127 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~  127 (133)
                      +|+|||||+||+|++.+....................     ..++++|||||++||||||||+|.++++.|+++|++++
T Consensus         1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~   75 (164)
T PF00849_consen    1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDD-----PPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRK   75 (164)
T ss_dssp             SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTT-----SGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCeEecCCCCCcccccchhhhhhhhccC-----CCceEECCCCCccccCCeeccCCcccccccccccccCC
Confidence            6899999999999998854444444444433333222     67899999999999999999999999999999999998


Q ss_pred             ccc
Q 041166          128 SVV  130 (133)
Q Consensus       128 v~~  130 (133)
                      +.+
T Consensus        76 ~~K   78 (164)
T PF00849_consen   76 VEK   78 (164)
T ss_dssp             SEE
T ss_pred             CcE
Confidence            765

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 ....

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

Probab=99.79  E-value=1.6e-19  Score=129.79  Aligned_cols=69  Identities=26%  Similarity=0.315  Sum_probs=57.4

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS  128 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v  128 (133)
                      ++|+|||+|++||++.+....++...+....          ..++++|||||++|||+||||+|+++++.|+++  ++++
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~----------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~v   68 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH----------GPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREI   68 (154)
T ss_pred             CEEEECCCCCEEecCCCCCCCcHHHhhhccc----------CCceeEeccCCCCCeeEEEEEcCHHHHHHHhhh--hccC
Confidence            5899999999999988776678777654221          356889999999999999999999999999998  5555


Q ss_pred             c
Q 041166          129 V  129 (133)
Q Consensus       129 ~  129 (133)
                      .
T Consensus        69 ~   69 (154)
T cd02550          69 E   69 (154)
T ss_pred             c
Confidence            4

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.

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=99.79  E-value=7.7e-20  Score=139.29  Aligned_cols=73  Identities=22%  Similarity=0.159  Sum_probs=55.0

Q ss_pred             ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      ++++++|||||+||+|||+... ..|+...+...          ...++++|||||++||||||||||..+++.|..  .
T Consensus        58 ~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~----------~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~  124 (232)
T PRK10839         58 HGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP----------VAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--P  124 (232)
T ss_pred             CCCEEEEEECCCCeEecccCCC-CCeEEEecccc----------cccCceecCCCCCCceeEEEEecCHHHHHHHhC--C
Confidence            3568999999999999987543 35655443211          034678999999999999999999999988885  4


Q ss_pred             cCCccc
Q 041166          125 DKTSVV  130 (133)
Q Consensus       125 ~~~v~~  130 (133)
                      ++.|.+
T Consensus       125 ~~~i~K  130 (232)
T PRK10839        125 RHHCEK  130 (232)
T ss_pred             CCCCCe
Confidence            555543

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

Probab=99.76  E-value=2.2e-18  Score=125.92  Aligned_cols=77  Identities=34%  Similarity=0.433  Sum_probs=63.4

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS  128 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v  128 (133)
                      ++|+|||+|++|++.......++...+........     ....+++|||||++|||+||||+++++++.|.++|+++.+
T Consensus         1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~   75 (185)
T cd02869           1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLG-----EEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKV   75 (185)
T ss_pred             CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcC-----CCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCce
Confidence            58999999999999888777788777632222211     1467889999999999999999999999999999999887


Q ss_pred             cc
Q 041166          129 VV  130 (133)
Q Consensus       129 ~~  130 (133)
                      .+
T Consensus        76 ~K   77 (185)
T cd02869          76 KK   77 (185)
T ss_pred             eE
Confidence            64

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.

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

Probab=99.73  E-value=4.5e-18  Score=123.98  Aligned_cols=71  Identities=20%  Similarity=0.185  Sum_probs=57.6

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT  127 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~  127 (133)
                      .++|+|||+|++||+.......|+.+.+..+.          ..++++|||||++|||+||||+|.++++.|..  .+++
T Consensus         1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~----------~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~--~~~~   68 (167)
T cd02556           1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG----------IPRWISVGRLDLNTEGLLLFTNDGELANRLMH--PSNE   68 (167)
T ss_pred             CEEEEECCCCcEECccCCCCCccHHHhhhhhc----------cCceEEcCcCCCCCeeEEEEECCHHHHHHHhC--CcCC
Confidence            37899999999999866555678888776431          34678999999999999999999999999974  5666


Q ss_pred             ccc
Q 041166          128 SVV  130 (133)
Q Consensus       128 v~~  130 (133)
                      |.+
T Consensus        69 i~K   71 (167)
T cd02556          69 IER   71 (167)
T ss_pred             CCe
Confidence            653

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.

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

Probab=99.73  E-value=1.4e-18  Score=123.83  Aligned_cols=68  Identities=25%  Similarity=0.235  Sum_probs=54.0

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS  128 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v  128 (133)
                      |+|+|||+|++|++.......++.+.+...           ..++++|||||++|||+||||+|.++++.|..  +++.|
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~-----------~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~i   67 (146)
T cd02870           1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV-----------GERLFPVGRLDYDTEGLLLLTNDGELANRLTH--PRYGV   67 (146)
T ss_pred             CEEEECCCCcEecccCCCCCCEEeeecccc-----------CCCEEECCCCCCCCeeEEEEeCCHHHHHHhhC--ccCCC
Confidence            589999999999987765556776554311           35688999999999999999999999999976  34444


Q ss_pred             c
Q 041166          129 V  129 (133)
Q Consensus       129 ~  129 (133)
                      .
T Consensus        68 ~   68 (146)
T cd02870          68 E   68 (146)
T ss_pred             C
Confidence            4

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

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

Probab=99.72  E-value=8.8e-18  Score=122.51  Aligned_cols=69  Identities=25%  Similarity=0.332  Sum_probs=55.1

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCc
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTS  128 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v  128 (133)
                      |+|+|||+|++||++. ....|+.+.+..++.         ..++++|||||++|||+||||||.++++.+..  ++++|
T Consensus         2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~---------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~--~~~~i   69 (167)
T cd02553           2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR---------RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHV   69 (167)
T ss_pred             EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc---------cCCeEEcccCCCCCEEEEEEEeCHHHHHHhhC--CcCCC
Confidence            7999999999999654 446788888875532         35688999999999999999999998887765  34555


Q ss_pred             c
Q 041166          129 V  129 (133)
Q Consensus       129 ~  129 (133)
                      .
T Consensus        70 ~   70 (167)
T cd02553          70 P   70 (167)
T ss_pred             c
Confidence            4

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.

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=99.71  E-value=2e-17  Score=130.19  Aligned_cols=65  Identities=23%  Similarity=0.302  Sum_probs=54.9

Q ss_pred             EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHH
Q 041166           44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAA  121 (133)
Q Consensus        44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~  121 (133)
                      +||++++|+|||+|++||++... ..|+.+.+..            ..++++|||||++||||||||+|.++++.|..
T Consensus        64 ~ed~~~lvlnKP~G~~~~~~~~~-~~tv~~~l~~------------~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~  128 (290)
T PRK10475         64 AEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH------------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR  128 (290)
T ss_pred             cCCCeEEEEECCCCCCcCCCCCC-CCcHHHHhhc------------cccccccccCCCCCcceEEEecCHHHHHHhhC
Confidence            47889999999999999977653 5688777742            13578999999999999999999999999866

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=99.69  E-value=8.2e-17  Score=126.64  Aligned_cols=73  Identities=19%  Similarity=0.169  Sum_probs=59.0

Q ss_pred             ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      ||+.|+++|||+|++|++.......|+.+.+....          ..++++|||||++||||||||++.++++.|..  .
T Consensus        65 e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~~----------~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~--p  132 (289)
T PRK10700         65 QICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLR----------GARWIAVGRLDVNTCGLLLFTTDGELANRLMH--P  132 (289)
T ss_pred             cCCeEEEEECCCCCEeecCCCCCCccHHHHhhhhc----------CCceeEccCCCCCCceEEEEEcCHHHHHHHhC--c
Confidence            44679999999999999886555679988886421          34678999999999999999999999999975  4


Q ss_pred             cCCcc
Q 041166          125 DKTSV  129 (133)
Q Consensus       125 ~~~v~  129 (133)
                      ++.|.
T Consensus       133 ~~~i~  137 (289)
T PRK10700        133 SREVE  137 (289)
T ss_pred             cCCCC
Confidence            55544

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE

Probab=99.66  E-value=1.4e-16  Score=116.29  Aligned_cols=61  Identities=23%  Similarity=0.259  Sum_probs=48.8

Q ss_pred             EEEEECCCCceeecCCC-CCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHH
Q 041166           49 LIALNKPSGLQVLPGGL-FQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAY  122 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~  122 (133)
                      ++|+|||+|++||++.. ....|+.+.+.             ..++++|||||++|||+||||+|+++++.|...
T Consensus         1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~-------------~~~~~~v~RLD~~TsGlll~a~d~~~~~~l~~~   62 (168)
T cd02566           1 LILFNKPYGVLSQFTDESEKHKTLKDYID-------------DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDP   62 (168)
T ss_pred             CEEEECCCCCEEecCCCcCCCccHHHHcC-------------cCCeEEccCCCCCCeEEEEEEeCHHHHHHHHCC
Confidence            58999999999998764 34467766552             135679999999999999999999887777664

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.

>PRK11394 23S rRNA pseudouridine synthase E; Provisional

Probab=99.57  E-value=4.4e-15  Score=112.58  Aligned_cols=68  Identities=16%  Similarity=0.180  Sum_probs=54.8

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcC
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK  126 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~  126 (133)
                      ..|+++|||+|++|+........++.+.+.             ..++++|||||++|||+||||+|.++++.|...  ++
T Consensus        39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~-------------~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~--~~  103 (217)
T PRK11394         39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP--GK  103 (217)
T ss_pred             CEEEEEECCCCCEEeeCCccCCcchHHhcc-------------cCCeEEecCCCCCCeeEEEEECCHHHHHHHhCc--cc
Confidence            458999999999999655544567777653             236789999999999999999999999999985  44


Q ss_pred             Ccc
Q 041166          127 TSV  129 (133)
Q Consensus       127 ~v~  129 (133)
                      .|.
T Consensus       104 ~i~  106 (217)
T PRK11394        104 RTG  106 (217)
T ss_pred             CCC
Confidence            443

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

Probab=99.53  E-value=1.7e-14  Score=106.29  Aligned_cols=70  Identities=16%  Similarity=0.158  Sum_probs=50.1

Q ss_pred             CcEEEEECCCCceeecCC--------CCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGG--------LFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTC  118 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~--------~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~  118 (133)
                      .-++++|||+|++|....        .....++...+...           ..++++|||||++||||||||+|+++++.
T Consensus         4 ~~y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~-----------~~~l~~VgRLD~dTsGLLl~t~d~~~~~~   72 (177)
T cd02555           4 PVTLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGH-----------FARLAPIGPLDKDASGLLVFSQDGRVLRK   72 (177)
T ss_pred             cEEEEEECCCceEecCCCcccccccccccccchhhhhhhc-----------CCceeEecCCCCCCeeEEEEECCHHHHHH
Confidence            347899999999986433        11112333333322           23688999999999999999999999999


Q ss_pred             HHHHHHcCCcc
Q 041166          119 IAAYFADKTSV  129 (133)
Q Consensus       119 l~~~f~~~~v~  129 (133)
                      |....  +.|.
T Consensus        73 L~~~~--~~i~   81 (177)
T cd02555          73 LIGDA--SRLE   81 (177)
T ss_pred             HhChh--cCCC
Confidence            99853  4444

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.

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

Probab=99.48  E-value=7.9e-14  Score=101.68  Aligned_cols=63  Identities=19%  Similarity=0.266  Sum_probs=51.7

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      |+++|||+|++|+++.. ...|+.+.+..            ..++++|||||++|||+||||+|.++++.|.....
T Consensus         2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~------------~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~   64 (164)
T cd02554           2 YIAYNKPVGIDCTLERA-DEDNIIDFVNP------------PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADN   64 (164)
T ss_pred             EEEEECCCCcEeecCCC-CCCcHHHHhcC------------cCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhc
Confidence            68999999999998754 34677766531            24688999999999999999999999999976443

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.

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like

Probab=99.32  E-value=2.5e-12  Score=98.10  Aligned_cols=66  Identities=23%  Similarity=0.201  Sum_probs=48.5

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT  127 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~  127 (133)
                      .++|||||+||.+++..    +++...+...++.        ....++|||||+.|||+|+||++..+  ++.++|.++.
T Consensus         1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~~--------~k~~~~vhrLD~~aSGvl~~a~~~~t--kl~~~~~~~~   66 (226)
T cd02868           1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFPE--------DKVLVGVHRLDAFSSGVLVLGVNHGN--KLLSHLYSNH   66 (226)
T ss_pred             CEEEEEcCCCCChhHHH----HHHHHHHHHHccc--------cceeeEccccCCCCceEEEEEeChhH--hHHHHHHhcC
Confidence            47999999999876432    3444434333321        22366789999999999999999987  6999998864

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).

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

Probab=99.20  E-value=9.5e-12  Score=95.97  Aligned_cols=111  Identities=20%  Similarity=0.136  Sum_probs=72.3

Q ss_pred             hHHHHHhhhCCCCCCCCC---CCcEEEEecCCCCCC------CC----CCCcceEE-ECCcEEEEECCCCceeecCCCCC
Q 041166            2 TLIEFYSTKHKNSAPLQG---AGSELVYHRLPWKEP------DV----PYLLEVFY-EDDDLIALNKPSGLQVLPGGLFQ   67 (133)
Q Consensus         2 ~l~~~~~~~~~~~~~~~~---~g~~v~~~~~~~~~~------~~----~~~~~vly-ed~~~lvvnKP~gl~v~~~~~~~   67 (133)
                      ||.+||+..--.|.+...   .+..|.++......+      ..    ...-.+.+ +..-|+++|||.|+.|.......
T Consensus         4 RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~~~~~~~~~~y~llnKP~G~v~s~~D~~g   83 (248)
T COG1187           4 RLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGKRIELKEERVYLLLNKPRGYVSSTEDDEG   83 (248)
T ss_pred             chHHHHHHcCCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCEEeeccccceEEEEECCCCeEecccCCCC
Confidence            788999887766666632   222222222111111      10    01122444 34449999999999998664445


Q ss_pred             cchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHH
Q 041166           68 QRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIA  120 (133)
Q Consensus        68 ~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~  120 (133)
                      ..|+.+.+....+        ...++++|.|||++|+|+||++.+++.++.|.
T Consensus        84 r~tv~D~lp~~~~--------~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~  128 (248)
T COG1187          84 RPTVFDLLPERLP--------RKKRLFPVGRLDKDTEGLLLLTNDGELAHRLM  128 (248)
T ss_pred             Cceeeeecccccc--------cccceeeccccCCCCeeEEEEeCCHHHHHHhc
Confidence            6788877763311        15679999999999999999999999888763

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like

Probab=97.83  E-value=5.1e-05  Score=56.29  Aligned_cols=59  Identities=20%  Similarity=0.180  Sum_probs=45.2

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-++.||-..||+|+++-+. + .++.+.|.
T Consensus         2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~---------~kkvGH~GTLDp~A~GvLiv~~g~-~-Tk~~~~~~   60 (182)
T cd02572           2 YGVINLDKPSGPSSH--------EVVAWIKRILG---------VEKTGHSGTLDPKVTGCLPVCIDR-A-TRLVKSQQ   60 (182)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCcCeeEEEEEECH-H-hhhhHHHh
Confidence            469999999999775        56777877664         346777999999999999999887 3 34444443

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

>PRK00989 truB tRNA pseudouridine synthase B; Provisional

Probab=97.72  E-value=6.5e-05  Score=57.61  Aligned_cols=60  Identities=12%  Similarity=0.218  Sum_probs=46.7

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.|+.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-.. ++.+|.+.|.
T Consensus         9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~vG~-~aTkl~~~~~   68 (230)
T PRK00989          9 EGILLVDKPQGRTSF--------SLIRSLTKLIG---------VKKIGHAGTLDPFATGVMVMLIGR-KFTRLSDILL   68 (230)
T ss_pred             CEEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCCCeeEEEEEECC-chhhhHHHhc
Confidence            479999999999776        56788887764         457778999999999999999776 3344555543

>PRK04099 truB tRNA pseudouridine synthase B; Provisional

Probab=97.64  E-value=0.00013  Score=57.26  Aligned_cols=60  Identities=20%  Similarity=0.285  Sum_probs=47.0

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.++++|||+||.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-...  .++.+.+.+
T Consensus         2 ngil~vdKP~g~tS~--------~vv~~ikk~~~---------~kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~   61 (273)
T PRK04099          2 NRLFVANKPAGMSSN--------AFLSRLKRKYG---------VKKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKK   61 (273)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCccCCCCCeeEEEEEEChH--hhhHHHhcc
Confidence            468999999999776        67888887774         4567789999999999999998874  335554443

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family

Probab=97.62  E-value=0.00015  Score=54.87  Aligned_cols=58  Identities=21%  Similarity=0.187  Sum_probs=44.5

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      .+++||||.||-+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-+..  .++...|.
T Consensus         1 Gil~i~KP~g~tS~--------~vv~~ik~~~~---------~kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~   58 (210)
T cd00506           1 GLFAVDKPQGPSSH--------DVVDTIRRIFL---------AEKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLL   58 (210)
T ss_pred             CEEEEEcCCCCCHH--------HHHHHHHHHhC---------ccccCCCCcCCCcCeeEEEEEECHH--HhhhHHHh
Confidence            37999999999776        56777887764         3577779999999999999998873  33444443

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

>TIGR00431 TruB tRNA pseudouridine 55 synthase

Probab=97.60  E-value=0.00019  Score=54.39  Aligned_cols=59  Identities=17%  Similarity=0.293  Sum_probs=46.7

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-+..+  ++...|.
T Consensus         2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~---------~kKvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~   60 (209)
T TIGR00431         2 NGVLLLDKPQGMTSF--------DALAKVRRLLN---------VKKVGHTGTLDPFATGVLPILVGKAT--KLSPYLT   60 (209)
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHhC---------CCcCCCCCCCCCcCceEEEEEEChHh--hhhHHHc
Confidence            368999999999765        57788887774         45677799999999999999998853  4555554

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=97.48  E-value=0.00027  Score=54.63  Aligned_cols=59  Identities=25%  Similarity=0.392  Sum_probs=45.7

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.|+.+|        .++..+++.+.         ..+++-.+-||-..||+|+++-.. + .++...|.
T Consensus        10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~---------~kKvGH~GTLDP~AtGvLiv~iG~-a-TKl~~~l~   68 (244)
T PRK00020         10 DGVLLLDKPVGLSSN--------HALQRAKRTVD---------AAKAGHTGTLDPFATGLLVCCMGR-A-TKISGRML   68 (244)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCCCCcCCcCCCcCeeEEEEEECH-H-hhhhHHhc
Confidence            479999999999776        56788887664         457777999999999999999887 3 34444443

>PRK02484 truB tRNA pseudouridine synthase B; Provisional

Probab=97.47  E-value=0.00031  Score=55.76  Aligned_cols=59  Identities=20%  Similarity=0.219  Sum_probs=46.1

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||+||.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-...  .++.+.+.
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~   61 (294)
T PRK02484          3 NGIINLKKEAGMTSH--------DAVFKLRKILQ---------TKKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMT   61 (294)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCCCeeEEEEEEChh--hhhhHHhc
Confidence            469999999999776        57788887764         4577789999999999999998873  33444444

>PRK03287 truB tRNA pseudouridine synthase B; Provisional

Probab=97.45  E-value=0.00034  Score=55.59  Aligned_cols=60  Identities=17%  Similarity=0.257  Sum_probs=46.5

Q ss_pred             CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      -+.+++||||.|+.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-.. + .++.+.+.
T Consensus         8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~-a-TKl~~~l~   67 (298)
T PRK03287          8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG---------TRKVGHAGTLDPMATGVLVLGVER-A-TKLLGHLT   67 (298)
T ss_pred             cCeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCcCccCCCcceeEEEEEeCh-h-hhhhHHHh
Confidence            3579999999999776        57788887775         346777999999999999999886 3 34444444

>PRK14123 tRNA pseudouridine synthase B; Provisional

Probab=97.41  E-value=0.0004  Score=55.37  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=47.0

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.+++||||.||.+|        .++..+++.+.         ..+++-.+.||-..||+|+++-...+  ++.+.+.+
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~aT--kl~~~l~~   62 (305)
T PRK14123          3 NGILPVYKERGLTSH--------DVVFKLRKILK---------TKKIGHTGTLDPEVAGVLPVCIGNAT--RVSDYVMD   62 (305)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCcCCCCcCeeEEEEEEChhh--hhHHHhcC
Confidence            479999999999776        57788887764         45677899999999999999988743  45555543

>PRK14124 tRNA pseudouridine synthase B; Provisional

Probab=97.40  E-value=0.00046  Score=55.08  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=46.0

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||+|+.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-+..  .++.+.|.
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~   61 (308)
T PRK14124          3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK---------TRKVGHAGTLDPFATGVLIVGVNKA--TRLLEYLK   61 (308)
T ss_pred             ceEEEEECCCCCCHH--------HHHHHHHHHcC---------CCccCcCcCCCCCCcEEEEEEEChH--HhhhHHHh
Confidence            468999999999776        57788887764         3467779999999999999998874  33444444

>PRK14846 truB tRNA pseudouridine synthase B; Provisional

Probab=97.40  E-value=0.00047  Score=55.63  Aligned_cols=59  Identities=15%  Similarity=0.157  Sum_probs=45.8

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-...  .++.+.+.
T Consensus         3 nGiL~idKP~G~TS~--------dvv~~vrk~l~---------~kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~   61 (345)
T PRK14846          3 NYWLNIYKPRGISSA--------QLVSIVKKILG---------KTKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLI   61 (345)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCcCCcCccCCCcCceEEEEEEChh--hhhhHHHh
Confidence            579999999999776        57788887764         4577789999999999999998873  34444443

>PRK00130 truB tRNA pseudouridine synthase B; Provisional

Probab=97.40  E-value=0.00044  Score=54.79  Aligned_cols=60  Identities=23%  Similarity=0.343  Sum_probs=46.7

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.+++||||.|+.+|        .++..+++.+.         ..+++-.+-||-..||+|+++-...  .++.+.|.+
T Consensus         2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~   61 (290)
T PRK00130          2 DGILNILKPPGMTSF--------DVVRKIRKIAK---------IKKVGHTGTLDPLASGVLPVCLGKA--TKIVDYLME   61 (290)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccCcCCCCCCCCeeEEEEEEChh--hhhHHHhcc
Confidence            478999999999776        57788887764         3467779999999999999998873  345555543

>PRK05389 truB tRNA pseudouridine synthase B; Provisional

Probab=97.37  E-value=0.00048  Score=54.91  Aligned_cols=59  Identities=22%  Similarity=0.342  Sum_probs=46.1

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.|+.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-..  +.++.+.|.
T Consensus        13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~--aTkl~~~l~   71 (305)
T PRK05389         13 SGWLILDKPAGMTST--------EAVSKVKWLFD---------AQKAGHAGTLDPLASGVLPIALGE--ATKTVPYVM   71 (305)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCcccCCCCCceEEEEEECh--hhhhhHHhc
Confidence            579999999999776        57788887765         346777899999999999999887  244444444

>PRK02193 truB tRNA pseudouridine synthase B; Provisional

Probab=97.34  E-value=0.00048  Score=54.28  Aligned_cols=57  Identities=23%  Similarity=0.295  Sum_probs=44.0

Q ss_pred             EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           49 LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        49 ~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      ++++|||.||.+|        .+++.+++.+.         ..+++-.+.||-..||+|+++-...  .++.+.+.
T Consensus         2 il~i~KP~G~tS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~   58 (279)
T PRK02193          2 IKLLYKPKGISSF--------KFIKNFAKTNN---------IKKIGHTGTLDPLASGLLLVATDED--TKLIDYLD   58 (279)
T ss_pred             EEEEECCCCCCHH--------HHHHHHHHHcC---------CCccccCccCCCcCeeEEEEEEChh--hhhhHHhc
Confidence            7899999999776        56777777664         4577789999999999999998873  34444443

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

Probab=97.32  E-value=0.00057  Score=54.34  Aligned_cols=61  Identities=18%  Similarity=0.112  Sum_probs=46.8

Q ss_pred             ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      -.+.++++|||.|+.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-+..  .++.+.+.
T Consensus        20 ~~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~---------~kkvGH~GTLDp~A~GvL~v~~g~a--tk~~~~~~   80 (300)
T PRK04270         20 IKFGVVNLDKPPGPTSH--------EVAAWVRDILG---------VEKAGHGGTLDPKVTGVLPVALGKA--TKVVQALL   80 (300)
T ss_pred             cCCCEEEEECCCCCCHH--------HHHHHHHHHhc---------cccccCCCCCCCcCeEEEEEEEChH--hhhhHHhc
Confidence            34589999999999776        56788887664         3467778999999999999998873  44444444

>PRK05033 truB tRNA pseudouridine synthase B; Provisional

Probab=97.32  E-value=0.00062  Score=54.42  Aligned_cols=60  Identities=20%  Similarity=0.303  Sum_probs=46.8

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.+++||||.||.+|        .++..+++.+.         ..+++-...||-..||+|+++-...  .++.+.+.+
T Consensus        10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~   69 (312)
T PRK05033         10 NGVLLLDKPQGMSSN--------DALQKVKRLFN---------ANKAGHTGALDPLATGMLPICLGEA--TKFSQYLLD   69 (312)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcC
Confidence            579999999999776        56788887764         3567778999999999999998874  335555543

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

Probab=97.32  E-value=0.00064  Score=53.55  Aligned_cols=59  Identities=22%  Similarity=0.328  Sum_probs=45.7

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      .+++||||.||.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-+..  .+|.+.+.+
T Consensus         1 Gil~i~KP~G~tS~--------~vv~~vr~~~~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~   59 (277)
T cd02573           1 GILLLDKPAGLTSH--------DVVQKVRRLLG---------TKKVGHTGTLDPLATGVLPIALGEA--TKLSQYLLD   59 (277)
T ss_pred             CEEEEECCCCCCHH--------HHHHHHHHHhC---------cCccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcC
Confidence            47899999999776        56788887765         3467778999999999999998874  345555543

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.

>PRK01528 truB tRNA pseudouridine synthase B; Provisional

Probab=97.32  E-value=0.00062  Score=53.98  Aligned_cols=51  Identities=14%  Similarity=0.153  Sum_probs=42.4

Q ss_pred             CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      .+.+++||||.||.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-..
T Consensus         2 ~~GiL~i~KP~G~TS~--------dvv~~vrk~~~---------~kKvGH~GTLDP~AtGvL~v~vG~   52 (292)
T PRK01528          2 SNYWLNIYKPRGISSA--------KLVSIVKKILG---------KVKIGHAGTLDVEAEGVLPLAVGE   52 (292)
T ss_pred             CCEEEEEeCCCCCCHH--------HHHHHHHHHcC---------CCccCcCccCCCcCceEEEEEECh
Confidence            3579999999999776        56788887764         346777999999999999999887

>PRK02755 truB tRNA pseudouridine synthase B; Provisional

Probab=97.27  E-value=0.00061  Score=54.08  Aligned_cols=60  Identities=20%  Similarity=0.253  Sum_probs=47.2

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-.+-||-..||+|+++-.+.+  ++.+.+.+
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~~   62 (295)
T PRK02755          3 FGFLNLDKPAGLTSH--------DCVARLRRLLR---------LKRVGHGGTLDPAATGVLPIALGKAT--RLLPYLPG   62 (295)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccccCCCCCCcCeeEEEEEEChhh--hhHHHhCC
Confidence            479999999999776        67888887765         35677799999999999999988743  45555543

>PRK01550 truB tRNA pseudouridine synthase B; Provisional

Probab=97.23  E-value=0.00082  Score=53.57  Aligned_cols=60  Identities=23%  Similarity=0.307  Sum_probs=46.1

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHc
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFAD  125 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~  125 (133)
                      +.+++||||+||.+|        .+++.+++.+.         ..+++-..-||-..||+|+++-...  .++.+.+.+
T Consensus         2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~   61 (304)
T PRK01550          2 NGVLLLHKPRGMTSH--------DCVFKLRKILR---------TKKVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTD   61 (304)
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHcC---------CCCcccCCCCCCcCeeEEEEEEChh--hhhhHHhcC
Confidence            469999999999776        56788887764         3466778999999999999998873  335555543

>PRK01851 truB tRNA pseudouridine synthase B; Provisional

Probab=97.22  E-value=0.00095  Score=53.17  Aligned_cols=59  Identities=20%  Similarity=0.204  Sum_probs=46.1

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-...||-..||+|+++-...  .++.+.+.
T Consensus        16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~   74 (303)
T PRK01851         16 DGVLLLDKPLGLSSN--------DALQRAKRLLR---------AKKAGHTGTLDPLATGLLPLCFGEA--TKFSQDLL   74 (303)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC---------cccCCCCCCCCCCCceEEEEEECHH--HhhhHHhc
Confidence            589999999999776        57888887775         3466678999999999999998874  33444444

>PRK14122 tRNA pseudouridine synthase B; Provisional

Probab=96.97  E-value=0.002  Score=51.52  Aligned_cols=58  Identities=17%  Similarity=0.267  Sum_probs=44.8

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      .+++||||.||.+|        .+++.+++.+.         ..+++-..-||-..||+|+++-...  .+|.+.+.
T Consensus         2 ~il~idKP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~   59 (312)
T PRK14122          2 PVYAVDKPLGLTSH--------DVVNRARRALG---------TRRVGHTGTLDPLATGVLVLCTDDS--TKLVPFLS   59 (312)
T ss_pred             cEEEEECCCCCCHH--------HHHHHHHHHhC---------CCCCCCCCCCCCcCeeeEEEEEChh--hhhhHHhc
Confidence            37899999999776        57788887764         3466778999999999999998874  33555553

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative

Probab=96.84  E-value=0.0026  Score=51.09  Aligned_cols=60  Identities=17%  Similarity=0.187  Sum_probs=46.0

Q ss_pred             CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      .+.+++||||.||.+|        .+++.+++.+.         ..+++-..-||-..||+|+++-...  .++.+.+.
T Consensus        33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~---------~kkvGH~GTLDP~A~GvL~v~~G~a--Tkl~~~~~   92 (322)
T TIGR00425        33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN---------VEKTGHGGTLDPKVTGVLPVCIERA--TRLVKSLQ   92 (322)
T ss_pred             CCCEEEEeCCCCCCHH--------HHHHHHHHHhc---------ccccCCCCCCCCCCceEEEEEEChH--hhccHHhc
Confidence            3479999999999776        56788887764         3466678999999999999998873  44444444

This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.

>PRK04642 truB tRNA pseudouridine synthase B; Provisional

Probab=96.83  E-value=0.003  Score=50.30  Aligned_cols=59  Identities=24%  Similarity=0.254  Sum_probs=45.8

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||.||.+|        .+++.+++.+.         ..+++-..-||-..||+|+++-...  .++.+.+.
T Consensus        10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~---------~kKvGH~GTLDP~AtGvL~v~~G~a--Tkl~~~l~   68 (300)
T PRK04642         10 DGILLLDKPAGLSSN--------NALQAARRLLR---------AEKGGHTGSLDPLATGLLPLCFGEA--TKIAGLLL   68 (300)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC---------CCcccCCCccCCcCeeeEEEEEChh--hhhhHHhc
Confidence            579999999999776        57888887765         3466678899999999999998763  44444444

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=96.66  E-value=0.0038  Score=37.24  Aligned_cols=27  Identities=22%  Similarity=0.399  Sum_probs=18.6

Q ss_pred             CCcEEEEecCCCCCCCCCCCcceEEECCcEEEEE
Q 041166           20 AGSELVYHRLPWKEPDVPYLLEVFYEDDDLIALN   53 (133)
Q Consensus        20 ~g~~v~~~~~~~~~~~~~~~~~vlyed~~~lvvn   53 (133)
                      +|+.+.+...+       .+..|+|||++++|+|
T Consensus        44 ~~d~i~i~~~~-------~~~~i~~ed~~~lvv~   70 (70)
T cd00165          44 PGDVIEVDGKS-------IEEDIVYEDKKLLVVN   70 (70)
T ss_pred             CCCEEEEcCCC-------cccceeeccCCEEEeC
Confidence            56666655321       1238999999999986

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=96.65  E-value=0.0049  Score=48.44  Aligned_cols=62  Identities=16%  Similarity=0.144  Sum_probs=47.8

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCC
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT  127 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~  127 (133)
                      .++++|||.|+.+|        .++.++++.+.         ..+.+-..-||-..||+|++|-. ++.+.++-+....+
T Consensus        16 Gil~ldKP~G~tS~--------~~v~~vkkil~---------~~K~GH~GTLDP~atGvLpi~ig-~aTKl~~~l~~~~K   77 (271)
T COG0130          16 GVINLDKPPGPTSH--------EVVAWVKRILG---------VEKAGHGGTLDPLATGVLPICLG-EATKLVQYLLDADK   77 (271)
T ss_pred             ceEEeeCCCCCCHH--------HHHHHHHHHhC---------ccccccccccCCcccceEEEEec-hhHhHHHHHhhCCc
Confidence            89999999999776        67788888876         45666678999999999999988 55555554444433

>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4

Probab=96.41  E-value=0.0095  Score=47.70  Aligned_cols=67  Identities=19%  Similarity=0.195  Sum_probs=44.6

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccC--------------------CCCCCCCcccccccCCCCCceee
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSS--------------------SLSSQASHPVPVHRLGRGTSGIL  107 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~--------------------~~~~~~~~~~~vhRLDr~TSGll  107 (133)
                      .+++||||.||.+|        .+++.+++.+.....                    .......+++-.+-||=..||+|
T Consensus         1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVL   72 (312)
T cd02867           1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVL   72 (312)
T ss_pred             CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeE
Confidence            37999999999775        567777766543100                    00011246777899999999999


Q ss_pred             eeecChHHHHHHHHHH
Q 041166          108 LCAKTKLAKTCIAAYF  123 (133)
Q Consensus       108 l~Ak~~~~~~~l~~~f  123 (133)
                      +++-..- .+.++..+
T Consensus        73 vvgvG~a-TK~l~~~l   87 (312)
T cd02867          73 VVGVGAG-TKQLQDYL   87 (312)
T ss_pred             EEEECcH-HHHHHHHh
Confidence            9998763 44444444

This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).

>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=95.48  E-value=0.011  Score=45.90  Aligned_cols=22  Identities=36%  Similarity=0.354  Sum_probs=19.0

Q ss_pred             cccccccCCCCCceeeeeecCh
Q 041166           92 HPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        92 ~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      .+.++||||-.|||+++|.-+.
T Consensus        90 ~V~v~h~l~~~~sgvl~~gVgh  111 (318)
T KOG2559|consen   90 DVQVVHVLPLATSGVLLFGVGH  111 (318)
T ss_pred             ceeeEEeecccccceEEEecCc
Confidence            3678999999999999998654

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

Probab=90.33  E-value=0.29  Score=31.39  Aligned_cols=21  Identities=10%  Similarity=-0.040  Sum_probs=19.2

Q ss_pred             CCcccccccCCCCCceeeeee
Q 041166           90 ASHPVPVHRLGRGTSGILLCA  110 (133)
Q Consensus        90 ~~~~~~vhRLDr~TSGlll~A  110 (133)
                      ..+++.++++|+.++|+++++
T Consensus        23 ~~~i~~aG~kDk~a~t~q~v~   43 (87)
T cd01291          23 PKRVGYAGRKDKRAVTTQLVS   43 (87)
T ss_pred             hheEEECccCCCCeeEEEEEc
Confidence            567889999999999999998

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).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	133
2i82_A	217	Crystal Structure Of Pseudouridine Synthase Rlua: I		9e-06
1v9f_A	325	Crystal Structure Of Catalytic Domain Of Pseudourid		3e-05
1prz_A	252	Crystal Structure Of Pseudouridine Synthase Rlud Ca		3e-05
1qyu_A	349	Structure Of The Catalytic Domain Of 23s Rrna Pseud		8e-05

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 49/97 (50%), Gaps = 13/97 (13%)
Query: 31  WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQR-TVLKQLQWRXXXXXXXXXXX 89
           +  P  P+L+ + Y+DD +  +NKPSGL  +PG L + + +V  ++Q             
Sbjct: 4   YNPPQEPWLV-ILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTRIQRDYPQAES----- 57
Query: 90  XXHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADK 126
                 VHRL   TSG+++ A TK A+  +   F ++
Sbjct: 58  ------VHRLDXATSGVIVVALTKAAERELKRQFRER 88

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 35  DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
           D+P  L++ YED+D+I +NKP  L V PG      TVL  L                   
Sbjct: 80  DIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 133
Query: 95  PVHRLGRGTSGILLCAKTKLAKT 117
            VHRL + T+G+++ AKT  A+T
Sbjct: 134 -VHRLDKDTTGLMVVAKTVPAQT 155

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 35  DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
           D+P  L++ YED+D+I +NKP  L V PG      TVL  L                   
Sbjct: 7   DIP--LDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 60
Query: 95  PVHRLGRGTSGILLCAKTKLAKT 117
            VHRL + T+G+ + AKT  A+T
Sbjct: 61  -VHRLDKDTTGLXVVAKTVPAQT 82

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 35  DVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRXXXXXXXXXXXXXHPV 94
           D+P  L++ YED+D+I +NKP  L V PG      TVL  L                   
Sbjct: 104 DIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI---- 157
Query: 95  PVHRLGRGTSGILLCAKTKLAKT 117
            VHRL + T+G+ + AKT  A+T
Sbjct: 158 -VHRLDKDTTGLXVVAKTVPAQT 179

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	133
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	2e-17
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	3e-14
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	3e-12

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

 Score = 73.7 bits (182), Expect = 2e-17
 Identities = 27/92 (29%), Positives = 45/92 (48%), Gaps = 18/92 (19%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVP---- 95
           L + Y+DD ++ +NKPSGL  +PG L + +               S+ ++     P    
Sbjct: 12  LVILYQDDHIMVVNKPSGLLSVPGRLEEHKD--------------SVMTRIQRDYPQAES 57

Query: 96  VHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
           VHRL   TSG+++ A TK A+  +   F ++ 
Sbjct: 58  VHRLDMATSGVIVVALTKAAERELKRQFRERE 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 Length = 228

 Score = 65.6 bits (161), Expect = 3e-14
 Identities = 34/89 (38%), Positives = 44/89 (49%), Gaps = 11/89 (12%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPG-GLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHR 98
             + YEDD ++ LNKPSG  V  G GL     V++ L  RA      L  +A     VHR
Sbjct: 2   DVIMYEDDHILVLNKPSGTAVHGGSGLSF--GVIEGL--RA------LRPEARFLELVHR 51

Query: 99  LGRGTSGILLCAKTKLAKTCIAAYFADKT 127
           L R TSG+LL AK + A   +     +K 
Sbjct: 52  LDRDTSGVLLVAKKRSALRSLHEQLREKG 80

>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 = 61.0 bits (149), Expect = 3e-12
 Identities = 31/97 (31%), Positives = 45/97 (46%), Gaps = 23/97 (23%)

Query: 40  LEVFYEDDDLIALNKPSGLQVLPG-----GLFQQRTVLKQLQWRASKQSSSLSSQASHPV 94
           L++ YED+D+I +NKP  L V PG     G     TVL  L       +          V
Sbjct: 83  LDIVYEDEDIIIINKPRDLVVHPGAGNPDG-----TVLNALLHYYPPIAD---------V 128

Query: 95  P----VHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
           P    VHRL + T+G+++ AKT  A+T +      + 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE 165

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	133
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	99.94
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	99.91
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	99.89
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	99.86
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	99.86
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	99.86
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	99.85
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	99.78
2gml_A	237	Ribosomal large subunit pseudouridine synthase F;	99.6
1r3e_A	309	TRNA pseudouridine synthase B; RNA modification, p	97.13
1k8w_A	327	TRNA pseudouridine synthase B; protein-RNA complex	97.07
1sgv_A	316	TRNA pseudouridine synthase B; hinged motion, tRNA	97.06
2aus_C	334	Pseudouridine synthase; isomerase, structural prot	96.99
2apo_A	357	Probable tRNA pseudouridine synthase B; protein-pr	96.88
3u28_A	400	H/ACA ribonucleoprotein complex subunit 4; pseudou	96.8
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	88.84

>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=99.94  E-value=5.3e-27  Score=185.36  Aligned_cols=124  Identities=25%  Similarity=0.306  Sum_probs=77.5

Q ss_pred             hHHHHHhhhCCCCCCCC------------------------CCCcEEEEecCCCCCC---CCCCCcceEEECCcEEEEEC
Q 041166            2 TLIEFYSTKHKNSAPLQ------------------------GAGSELVYHRLPWKEP---DVPYLLEVFYEDDDLIALNK   54 (133)
Q Consensus         2 ~l~~~~~~~~~~~~~~~------------------------~~g~~v~~~~~~~~~~---~~~~~~~vlyed~~~lvvnK   54 (133)
                      ||++||.+.+...++..                        .+||.|.+...+..++   +.+.+++|+|||++++||||
T Consensus        18 RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvvnK   97 (325)
T 1v9f_A           18 RLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINK   97 (325)
T ss_dssp             ----------------------------------------------------------CCCCCCCCCEEEECSSEEEEEE
T ss_pred             hHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEEEC
Confidence            78999998875444441                        2678787765433221   22345789999999999999


Q ss_pred             CCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHHcCCccc
Q 041166           55 PSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKTSVV  130 (133)
Q Consensus        55 P~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~~~~v~~  130 (133)
                      |+||+||+.......|+.+.+..++.....     ..++++|||||++||||||||||.++++.|+++|++++|.+
T Consensus        98 P~G~~~~~~~~~~~~tl~~~l~~~~~~~~~-----~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K  168 (325)
T 1v9f_A           98 PRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITR  168 (325)
T ss_dssp             CSSCCSSCBTTBSSSSHHHHHHHHCGGGGG-----SGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEE
T ss_pred             CCCCeEecCCCCCCccHHHHHHHHHHhcCC-----CCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeE
Confidence            999999998877677999988766643221     34789999999999999999999999999999999998865

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

Probab=99.91  E-value=2.7e-24  Score=161.34  Aligned_cols=81  Identities=33%  Similarity=0.562  Sum_probs=71.0

Q ss_pred             CcceEEECCcEEEEECCCCceeecCCC-CCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166           39 LLEVFYEDDDLIALNKPSGLQVLPGGL-FQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT  117 (133)
Q Consensus        39 ~~~vlyed~~~lvvnKP~gl~v~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~  117 (133)
                      .++|+|||++++|||||+|++||++.. ....|+.+.+...+           .++++|||||++|||+||||||.++++
T Consensus        11 ~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~~tl~~~l~~~~-----------~~~~~vhRLD~~TSGlll~ak~~~~~~   79 (217)
T 2i82_A           11 WLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY-----------PQAESVHRLDMATSGVIVVALTKAAER   79 (217)
T ss_dssp             SCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHC-----------TTCEESSCCCTTCEEEEEEESSHHHHH
T ss_pred             CceEEEECCCEEEEECCCCCeEeCCCCCCchhHHHHHHHHHC-----------CCCceeecCCCCCeEEEEEEeCHHHHH
Confidence            378999999999999999999998754 34578888887553           246799999999999999999999999


Q ss_pred             HHHHHHHcCCccc
Q 041166          118 CIAAYFADKTSVV  130 (133)
Q Consensus       118 ~l~~~f~~~~v~~  130 (133)
                      .|+++|++++|.+
T Consensus        80 ~l~~~f~~~~v~K   92 (217)
T 2i82_A           80 ELKRQFREREPKK   92 (217)
T ss_dssp             HHHHHHHTTCSEE
T ss_pred             HHHHHHHhCCeeE
Confidence            9999999999865

>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=99.89  E-value=2.1e-23  Score=157.55  Aligned_cols=81  Identities=36%  Similarity=0.449  Sum_probs=69.6

Q ss_pred             ceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHH
Q 041166           41 EVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIA  120 (133)
Q Consensus        41 ~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~  120 (133)
                      +|+|||++++|||||+||+|||+.+ ...++...+...+..        ...+++|||||++|||+||||||.++++.|+
T Consensus         3 ~Ilyed~~~lvvnKP~G~~~~~~~~-~~~~l~~~l~~~~~~--------~~~~~~VhRLD~~TSGlll~ak~~~~~~~l~   73 (228)
T 1v9k_A            3 VIMYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPE--------ARFLELVHRLDRDTSGVLLVAKKRSALRSLH   73 (228)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSS-SBCCHHHHHHHHSTT--------CSCCEESSCCCTTCEEEEEEESSHHHHHHHH
T ss_pred             CEEEECCCEEEEECCCCCeEecCCC-hHHHHHHHHHHHcCC--------CCccceEecCCCCCeEEEEEEeCHHHHHHHH
Confidence            5999999999999999999998765 356788777654321        3468899999999999999999999999999


Q ss_pred             HHHHcCCccc
Q 041166          121 AYFADKTSVV  130 (133)
Q Consensus       121 ~~f~~~~v~~  130 (133)
                      ++|++++|.+
T Consensus        74 ~~~~~~~v~K   83 (228)
T 1v9k_A           74 EQLREKGMQK   83 (228)
T ss_dssp             HHHHTTCSEE
T ss_pred             HHHHhCCeeE
Confidence            9999998865

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

Probab=99.86  E-value=5.6e-23  Score=151.17  Aligned_cols=77  Identities=14%  Similarity=0.112  Sum_probs=61.7

Q ss_pred             CcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHH
Q 041166           39 LLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTC  118 (133)
Q Consensus        39 ~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~  118 (133)
                      ...|||||++++|||||+||+||+.......|+.+.+.             ..++++|||||++|||+||||||.++++.
T Consensus         3 ~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~-------------~~~~~~vhRLD~~TSGlll~ak~~~~~~~   69 (189)
T 2oml_A            3 RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------------VQGVYAAGRLDRDSEGLLVLTNNGALQAR   69 (189)
T ss_dssp             -----CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC-------------CSSCEESSCCCTTCEEEEEEESCHHHHHH
T ss_pred             ccccccCCCeEEEEECCCCCEecCCCCCCCCCHHHHcC-------------CCCceECCCCCCCCeeEEEEEcCHHHHHH
Confidence            35699999999999999999999988766678766553             12578999999999999999999999999


Q ss_pred             HHHHHHcCCccc
Q 041166          119 IAAYFADKTSVV  130 (133)
Q Consensus       119 l~~~f~~~~v~~  130 (133)
                      |+++  +++|.+
T Consensus        70 l~~~--~~~v~K   79 (189)
T 2oml_A           70 LTQP--GKRTGK   79 (189)
T ss_dssp             HHST--TSCCCE
T ss_pred             HhCc--cCCCcE
Confidence            9997  555543

>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=99.86  E-value=3.1e-23  Score=156.88  Aligned_cols=77  Identities=21%  Similarity=0.145  Sum_probs=62.8

Q ss_pred             ceEEE-CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHH
Q 041166           41 EVFYE-DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCI  119 (133)
Q Consensus        41 ~vlye-d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l  119 (133)
                      .|+|| |++++|||||+||+|||.... ..|+.+.+...+          ..++++|||||++|||+||||+|.++++.+
T Consensus        56 ~i~~e~d~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~----------~~~~~~vhRLD~~TsGlll~ak~~~~~~~l  124 (234)
T 1ksk_A           56 PLAQQHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEPV----------AWKLHAAGRLDIDTTGLVLMTDDGQWSHRI  124 (234)
T ss_dssp             EECCCCCCCEEEEEECTTCBSSSSCSS-SCBGGGGCCCTT----------GGGCEESSCCCTTCEEEEEEESCHHHHHHH
T ss_pred             EeecCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHhhhhh----------cCCeeEcCCCCCCCeeEEEEEcCHHHHHHH
Confidence            58999 999999999999999998764 678877664322          136789999999999999999999988877


Q ss_pred             HHHHHcCCccc
Q 041166          120 AAYFADKTSVV  130 (133)
Q Consensus       120 ~~~f~~~~v~~  130 (133)
                      ..  ++++|.+
T Consensus       125 ~~--~~~~v~K  133 (234)
T 1ksk_A          125 TS--PRHHCEK  133 (234)
T ss_dssp             HC--TTSCCCE
T ss_pred             hC--CCCCCCe
Confidence            65  4566543

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

Probab=99.86  E-value=9.3e-23  Score=153.21  Aligned_cols=78  Identities=14%  Similarity=0.102  Sum_probs=60.4

Q ss_pred             CCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHH
Q 041166           38 YLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKT  117 (133)
Q Consensus        38 ~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~  117 (133)
                      ..+.|||||++++|||||+|++||+.......|+.+.|.             ..++++|||||++||||||||+|.++++
T Consensus        30 ~~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~tl~~~l~-------------~~~~~~VhRLDr~TSGllllAk~~~~~~   96 (217)
T 2olw_A           30 TRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------------VQGVYAAGRLDRDSEGLLVLTNNGALQA   96 (217)
T ss_dssp             -------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCC-------------CCSCEESSCCCTTCEEEEEEESCHHHHH
T ss_pred             ccCceEeeCCcEEEEECCCCCEeccCCCCCCccHHHHhC-------------cCCceECCCCCCCCeeEEEEEcCHHHHH
Confidence            457899999999999999999999987766678766553             1267899999999999999999999999


Q ss_pred             HHHHHHHcCCccc
Q 041166          118 CIAAYFADKTSVV  130 (133)
Q Consensus       118 ~l~~~f~~~~v~~  130 (133)
                      .|+++  .++|.+
T Consensus        97 ~L~~~--~~~v~K  107 (217)
T 2olw_A           97 RLTQP--GKRTGK  107 (217)
T ss_dssp             HHHCT--TCCCCE
T ss_pred             HHHcc--cccCCE
Confidence            99987  455543

>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=99.85  E-value=9e-23  Score=155.27  Aligned_cols=78  Identities=17%  Similarity=0.161  Sum_probs=61.5

Q ss_pred             cceEEECCc-EEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHH
Q 041166           40 LEVFYEDDD-LIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTC  118 (133)
Q Consensus        40 ~~vlyed~~-~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~  118 (133)
                      .+|+|||++ ++|||||+||+||+.... ..|+.+.|...+          ..++++|||||++|||+||||+|.+++..
T Consensus        54 ~~i~~ed~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~~----------~~~~~~vhRLD~~TsGlll~ak~~~~a~~  122 (243)
T 1vio_A           54 ELLTWIEEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYPL----------AGKLHSAGRLDVDTTGLVLLTDDGQWSHR  122 (243)
T ss_dssp             EECCSSCCCCEEEEEECTTCBSSCCC---CCBGGGGSCTTG----------GGGCEESSCCCTTCEEEEEEESCHHHHHH
T ss_pred             cccccCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHHhHHh----------cCCEeEccCCCCCCeEEEEEEECHHHHHH
Confidence            358999999 999999999999988764 568877665332          13678999999999999999999998777


Q ss_pred             HHHHHHcCCccc
Q 041166          119 IAAYFADKTSVV  130 (133)
Q Consensus       119 l~~~f~~~~v~~  130 (133)
                      +..  ++++|.+
T Consensus       123 l~~--~~~~v~K  132 (243)
T 1vio_A          123 ITS--PKHHCEK  132 (243)
T ss_dssp             HHC--TTSCCCE
T ss_pred             HhC--CCCCCCE
Confidence            654  4566543

>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=99.78  E-value=4.7e-20  Score=143.95  Aligned_cols=66  Identities=23%  Similarity=0.286  Sum_probs=57.1

Q ss_pred             EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHH
Q 041166           44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAY  122 (133)
Q Consensus        44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~  122 (133)
                      |||++|+|+|||+|++||+.... ..|+.+.+..            ..++++|||||++||||||||+|.++++.|...
T Consensus        64 ~ed~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~------------~~~~~~VhRLD~dTSGLllla~d~~~~~~L~~~  129 (290)
T 3dh3_A           64 AEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH------------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRA  129 (290)
T ss_dssp             GGGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTC------------SSCCEESSCCCTTCEEEEEEESCTTHHHHHHCG
T ss_pred             cccceEEEEECCCccccCCCCCC-CCcHHHHhhc------------cCceeeeccCCCCCcceEEEcCCHHHHHHHHHh
Confidence            79999999999999999987754 5688776642            357889999999999999999999999998874

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

Probab=99.60  E-value=7.7e-16  Score=117.04  Aligned_cols=64  Identities=22%  Similarity=0.317  Sum_probs=53.4

Q ss_pred             CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHH
Q 041166           46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAY  122 (133)
Q Consensus        46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~  122 (133)
                      ++.|+|+|||+|++|++... ...|+.+.+..            ..++++|||||++||||||||+|.++++.|...
T Consensus        13 ~~~~lvlnKPaG~vs~~~~~-~~~tv~dll~~------------~~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~p   76 (237)
T 2gml_A           13 DLVLIALNKPVGIVSTTEDG-ERDNIVDFVNH------------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRA   76 (237)
T ss_dssp             CCCEEEEEECTTCBCCSSSS-CSSBHHHHSCC------------SSCCEEESCCCTTCEEEEEEESCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCEeCCCCC-CCCCHHHHhhc------------cCCeeEecCCCCCCeeEEEEEcCHHHHHHHhCc
Confidence            45799999999999998665 45688765531            246889999999999999999999999999874

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A

Probab=97.13  E-value=0.00039  Score=54.41  Aligned_cols=51  Identities=14%  Similarity=0.166  Sum_probs=42.8

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKL  114 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~  114 (133)
                      +.+++||||+||.+|        .++..+++.+.         ..+++-.+.||-..||+|+++-...
T Consensus         3 ~Gil~vdKP~G~TS~--------~vv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a   53 (309)
T 1r3e_A            3 HGILVAYKPKGPTSH--------DVVDEVRKKLK---------TRKVGHGGTLDPFACGVLIIGVNQG   53 (309)
T ss_dssp             CEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGGG
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHhc---------cceecccccCCCCcceeEEEEECHH
Confidence            469999999999776        67888887774         4577789999999999999998663

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A

Probab=97.07  E-value=0.00049  Score=54.23  Aligned_cols=59  Identities=17%  Similarity=0.271  Sum_probs=46.0

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFA  124 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f~  124 (133)
                      +.+++||||+||.+|        .++..+++.+.         ..+++-.+.||-..||+|+++-...+  ++.+.+.
T Consensus        25 ~Gil~vdKP~G~TS~--------dvv~~vr~~l~---------~kKvGH~GTLDP~AtGvL~i~~G~aT--Kl~~~l~   83 (327)
T 1k8w_A           25 NGVLLLDKPQGMSSN--------DALQKVKRIYN---------ANRAGHTGALDPLATGMLPICLGEAT--KFSQYLL   83 (327)
T ss_dssp             CEEEEEEECTTCCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGGGG--GGTHHHH
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHhhc---------cceeccCCCCCCCCeeEEEEEECHHH--hHHHHhc
Confidence            579999999999775        67788887764         45777899999999999999987642  2444443

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2

Probab=97.06  E-value=0.00049  Score=53.98  Aligned_cols=52  Identities=13%  Similarity=0.249  Sum_probs=43.7

Q ss_pred             CCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChH
Q 041166           46 DDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKL  114 (133)
Q Consensus        46 d~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~  114 (133)
                      .+.+++||||+||.+|        .++..+++.+.         ..+++-.+.||-..||+|+++-...
T Consensus         5 ~~Gil~vdKP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a   56 (316)
T 1sgv_A            5 GPGIVVIDKPAGMTSH--------DVVGRCRRIFA---------TRRVGHAGTLDPMATGVLVIGIERA   56 (316)
T ss_dssp             CSEEEEEEECTTCCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGGG
T ss_pred             CCeEEEEECCCCCCHH--------HHHHHHHHHhc---------cccccccccCCCCCeEEEEEEECHH
Confidence            4579999999999776        67888888775         4577889999999999999998663

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A

Probab=96.99  E-value=0.0006  Score=53.83  Aligned_cols=53  Identities=21%  Similarity=0.183  Sum_probs=44.1

Q ss_pred             EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      |-.+.+++||||+|+.+|        .++..+++.+.         ..+++-.+.||-..||+|+++-..
T Consensus        43 ~~~~Gil~vdKP~g~tS~--------~vv~~vr~~~~---------~~KvGH~GTLDP~atGvL~v~~g~   95 (334)
T 2aus_C           43 HIQYGVINLDKPPGPTSH--------EVVAWIKRILN---------LEKAGHGGTLDPKVSGVLPVALER   95 (334)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhC---------cceeccccccCCccceeEEEEeCh
Confidence            445789999999999776        67788887774         457778999999999999999864

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2

Probab=96.88  E-value=0.00085  Score=53.44  Aligned_cols=53  Identities=15%  Similarity=0.132  Sum_probs=44.2

Q ss_pred             EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      |-.+.+++||||+|+.+|        .++..+++.+.         ..+++-...||-..||+|+++-..
T Consensus        63 ~~~~Gil~vdKP~G~TS~--------~vv~~vr~~l~---------~~KvGH~GTLDP~AtGvL~v~~G~  115 (357)
T 2apo_A           63 LIKYGVVVVDKPRGPTSH--------EVSTWVKKILN---------LDKAGHGGTLDPKVTGVLPVALER  115 (357)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhC---------ccccccccccCCCceeEEEEEeCH
Confidence            456789999999999776        67788887774         457788999999999999999864

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A

Probab=96.80  E-value=0.0012  Score=53.30  Aligned_cols=53  Identities=19%  Similarity=0.245  Sum_probs=44.9

Q ss_pred             EECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           44 YEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        44 yed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      |-.+.+++||||+|+.+|        .++..+++.+.         ..+++-...||-..||+|+++-..
T Consensus        56 ~~~~Gil~ldKP~G~TS~--------dvv~~vrr~l~---------~kKvGH~GTLDP~AtGvL~v~iG~  108 (400)
T 3u28_A           56 YISSGVINLDKPSNPSSH--------EVVAWIKRILR---------CEKTGHSGTLDPKVTGCLIVCIDR  108 (400)
T ss_dssp             HHHTEEEEEEECSSSCHH--------HHHHHHHHHHT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             hccCcEEEEECCCCCCHH--------HHHHHHHHHhC---------cCcccccCCCCCCCeEEEEEEECh
Confidence            555789999999999776        67888888875         467788999999999999999865

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}

Probab=88.84  E-value=0.14  Score=32.31  Aligned_cols=16  Identities=6%  Similarity=0.038  Sum_probs=10.9

Q ss_pred             hHHHHHhhhCCCCCCC
Q 041166            2 TLIEFYSTKHKNSAPL   17 (133)
Q Consensus         2 ~l~~~~~~~~~~~~~~   17 (133)
                      ||++||......+++.
T Consensus         2 RLD~~L~~~~~~~sR~   17 (92)
T 2k6p_A            2 RIDKFLQSVGLVKRRV   17 (92)
T ss_dssp             BHHHHSTTTTSCCCCC
T ss_pred             hHHHHHHHCCCCCCHH
Confidence            7999998865433444

---

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	133
d1v9fa_	250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-14
d1v9ka_	227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	3e-10

>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 = 65.4 bits (158), Expect = 2e-14
 Identities = 30/97 (30%), Positives = 47/97 (48%), Gaps = 7/97 (7%)

Query: 31  WKEPDVPYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQA 90
           ++  D+P  L++ YED+D+I +NKP  L V PG      TVL  L            +  
Sbjct: 1   FEPQDIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADV 53

Query: 91  SHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYFADKT 127
                VHRL + T+G+++ AKT  A+T +      + 
Sbjct: 54  PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRRE 90

>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 = 53.8 bits (128), Expect = 3e-10
 Identities = 29/90 (32%), Positives = 38/90 (42%), Gaps = 9/90 (10%)

Query: 42  VFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGR 101
           + YEDD ++ LNKPSG  V  G       +      R          +A     VHRL R
Sbjct: 3   IMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALR---------PEARFLELVHRLDR 53

Query: 102 GTSGILLCAKTKLAKTCIAAYFADKTSVVD 131
            TSG+LL AK + A   +     +K    D
Sbjct: 54  DTSGVLLVAKKRSALRSLHEQLREKGMQKD 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	133
d1v9fa_	250	Ribosomal large subunit pseudouridine synthase D,	99.94
d1v9ka_	227	Ribosomal large subunit pseudouridine synthase C,	99.92
d1vioa1	174	Ribosomal small subunit pseudouridine 516 synthase	99.66
d1kska4	172	Ribosomal small subunit pseudouridine 516 synthase	99.44
d1k8wa5	242	Pseudouridine synthase II TruB {Escherichia coli [	97.37
d1r3ea2	228	Pseudouridine synthase II TruB {Thermotoga maritim	97.26
d1sgva2	233	Pseudouridine synthase II TruB {Mycobacterium tube	97.07
d2ey4a2	245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	96.94
d2apoa2	230	Pseudouridine synthase II TruB {Archaeon Methanoco	96.9

>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=99.94  E-value=8.3e-28  Score=182.30  Aligned_cols=89  Identities=31%  Similarity=0.434  Sum_probs=79.1

Q ss_pred             CCCcceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHH
Q 041166           37 PYLLEVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAK  116 (133)
Q Consensus        37 ~~~~~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~  116 (133)
                      +.+++|||||++++|||||+||+|||++.+..+|+++.+...+.....     ...+++|||||++||||||||||++++
T Consensus         5 ~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~-----~~~~~~vHRLDr~TSGlll~Ak~~~a~   79 (250)
T d1v9fa_           5 DIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQ   79 (250)
T ss_dssp             CCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGG-----SGGGGBCCCCCTTCEEEEEEESSHHHH
T ss_pred             CCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhccC-----CCceeEEeecCCCCcceEEEecccHHH
Confidence            557899999999999999999999999888788999988877654322     457789999999999999999999999


Q ss_pred             HHHHHHHHcCCccc
Q 041166          117 TCIAAYFADKTSVV  130 (133)
Q Consensus       117 ~~l~~~f~~~~v~~  130 (133)
                      +.|+++|++++|.+
T Consensus        80 ~~l~~~f~~~~v~K   93 (250)
T d1v9fa_          80 TRLVESLQRREITR   93 (250)
T ss_dssp             HHHHHHHHTTCSEE
T ss_pred             HhhhhhhccceEeE
Confidence            99999999999875

>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=99.92  E-value=8.3e-26  Score=168.64  Aligned_cols=81  Identities=36%  Similarity=0.464  Sum_probs=68.7

Q ss_pred             ceEEECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHH
Q 041166           41 EVFYEDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIA  120 (133)
Q Consensus        41 ~vlyed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~  120 (133)
                      .|||||++++|||||+||+|||+.... .+++..+......        ...+++|||||++||||||||||.++++.|+
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~-~~~~~~l~~~~~~--------~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l~   72 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRPE--------ARFLELVHRLDRDTSGVLLVAKKRSALRSLH   72 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSB-CCHHHHHHHHSTT--------CSCCEESSCCCTTCEEEEEEESSHHHHHHHH
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCc-chHHHHHHHhCCC--------CcccceeeeccceeeeeeeeecchHHHHHHH
Confidence            399999999999999999999987654 4556666544332        4567899999999999999999999999999


Q ss_pred             HHHHcCCccc
Q 041166          121 AYFADKTSVV  130 (133)
Q Consensus       121 ~~f~~~~v~~  130 (133)
                      ++|++++|..
T Consensus        73 ~~f~~~~v~K   82 (227)
T d1v9ka_          73 EQLREKGMQK   82 (227)
T ss_dssp             HHHHTTCSEE
T ss_pred             HHHhcccccc
Confidence            9999999865

>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=99.66  E-value=9.4e-18  Score=119.93  Aligned_cols=66  Identities=21%  Similarity=0.261  Sum_probs=51.2

Q ss_pred             ECCcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHH
Q 041166           45 EDDDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAA  121 (133)
Q Consensus        45 ed~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~  121 (133)
                      |++.|+++|||+|++|+.+.. ...|+.+.+....          ..++++|||||++||||||||++.+.++.+..
T Consensus         1 e~~~Yi~lNKP~G~~~~~~~~-~~~~v~~~l~~~~----------~~~l~~V~RLD~~TsGLll~t~d~~~~~~l~~   66 (174)
T d1vioa1           1 EEGQYFMLNKPQGCVCSNDDG-DYPTIYQFFDYPL----------AGKLHSAGRLDVDTTGLVLLTDDGQWSHRITS   66 (174)
T ss_dssp             CCCCEEEEEECTTCBSSCCC---CCBGGGGSCTTG----------GGGCEESSCCCTTCEEEEEEESCHHHHHHHHC
T ss_pred             CCCEEEEEECCCCEEeCCCCC-CCCcHHHhCcccc----------cCceEEEecCChhHhceEEEeecccccccccc
Confidence            688999999999999986544 3456655543211          34678999999999999999999998887754

>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=99.44  E-value=1e-14  Score=103.98  Aligned_cols=65  Identities=25%  Similarity=0.156  Sum_probs=49.6

Q ss_pred             cEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHH
Q 041166           48 DLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYF  123 (133)
Q Consensus        48 ~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f  123 (133)
                      -|+++|||+|+.|+..... ..++...+...          ...++++|||||++|||+||||.+.+.++.|....
T Consensus         2 ~yi~lNKP~G~l~s~~~~~-~~~~~~~l~~~----------~~~~l~~vgRLD~~tsGLlL~tndg~~~~~l~~~~   66 (172)
T d1kska4           2 RYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP----------VAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPR   66 (172)
T ss_dssp             CEEEEEECTTCBSSSSCSS-SCBGGGGCCCT----------TGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTT
T ss_pred             EEEEEECCCCEEECCcCCC-CCcEEEecCcc----------ccCcEEEeecCCccccccEEEecccceeeeecccc
Confidence            4899999999999865543 33554433211          14568899999999999999999999999887643

>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=97.37  E-value=7.4e-05  Score=54.81  Aligned_cols=50  Identities=18%  Similarity=0.272  Sum_probs=41.4

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      +.+++||||+|+.++        .+++.+++.+.         ..+++-...||--.||+|+++-+.
T Consensus         4 ~G~l~v~KP~g~tS~--------~vv~~~k~~l~---------~kKvGh~GTLDP~AsGvL~i~ig~   53 (242)
T d1k8wa5           4 NGVLLLDKPQGMSSN--------DALQKVKRIYN---------ANRAGHTGALDPLATGMLPICLGE   53 (242)
T ss_dssp             CEEEEEEECTTCCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             cEEEEEecCCCCCHH--------HHHHHHHHHhC---------CCcCCcCCcCCCcccceEEEEEch
Confidence            679999999999765        56777776654         457778999999999999999865

>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=97.26  E-value=0.00011  Score=53.29  Aligned_cols=50  Identities=14%  Similarity=0.199  Sum_probs=41.5

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      +.+++||||+|+-++        .+++.+++.+.         ..+++-..+||-..||+|+++-+.
T Consensus         3 ~G~l~i~Kp~g~tS~--------~~v~~vk~~l~---------~~KvGh~GTLDP~AsGvL~i~ig~   52 (228)
T d1r3ea2           3 HGILVAYKPKGPTSH--------DVVDEVRKKLK---------TRKVGHGGTLDPFACGVLIIGVNQ   52 (228)
T ss_dssp             CEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC---------CCccCcCcccCCcceeeEEEEEcc
Confidence            578999999999765        56777877764         457778999999999999999875

>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=97.07  E-value=0.00024  Score=51.74  Aligned_cols=50  Identities=14%  Similarity=0.266  Sum_probs=41.3

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      ..+++||||.|+.+|        .++..+++.+.         ..+++-..+||=-.||+|+++-..
T Consensus         4 ~G~l~v~KP~G~TS~--------~~v~~vk~~~~---------~kKvGh~GTLDP~AtGvL~i~ig~   53 (233)
T d1sgva2           4 PGIVVIDKPAGMTSH--------DVVGRCRRIFA---------TRRVGHAGTLDPMATGVLVIGIER   53 (233)
T ss_dssp             SEEEEEEECTTCCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             CEEEEEEcCCCCCHH--------HHHHHHHHHhC---------cCccccCcCCCCcceeeEEEEech
Confidence            579999999999664        56777776664         457788999999999999999865

>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=96.94  E-value=0.00036  Score=51.14  Aligned_cols=58  Identities=22%  Similarity=0.184  Sum_probs=45.6

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecChHHHHHHHHHH
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAAYF  123 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~~~~~~l~~~f  123 (133)
                      ..+++||||.|+.+|        .+++.+++.+.         ..+++-...||=..||+|+++-...  .++.+.|
T Consensus        42 ~G~l~idKP~G~TS~--------~vv~~vkk~l~---------~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~~   99 (245)
T d2ey4a2          42 FGVINLDKPPGPTSH--------EVVAWIKKILN---------LEKAGHGGTLDPKVSGVLPVALEKA--TRVVQAL   99 (245)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGGG--GGGHHHH
T ss_pred             CcEEEEeCCCCCCHH--------HHHHHHHHHhC---------cCCCCcCccCCCcceeeEEEEecHH--HHHHHHh
Confidence            489999999999765        67888887764         4577889999999999999998653  3444444

>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]}

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 Methanococcus jannaschii [TaxId: 2190]

Probab=96.90  E-value=0.00041  Score=50.37  Aligned_cols=50  Identities=16%  Similarity=0.154  Sum_probs=42.5

Q ss_pred             CcEEEEECCCCceeecCCCCCcchHHHHHHHHHhhccCCCCCCCCcccccccCCCCCceeeeeecCh
Q 041166           47 DDLIALNKPSGLQVLPGGLFQQRTVLKQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTK  113 (133)
Q Consensus        47 ~~~lvvnKP~gl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLDr~TSGlll~Ak~~  113 (133)
                      ..+++||||.|+.+|        .+++.+++.+.         ..+++-...||=..||+|+++-..
T Consensus        29 ~G~l~idKP~G~TS~--------~vv~~ikk~l~---------~kKvGH~GTLDP~AtGvL~v~iG~   78 (230)
T d2apoa2          29 YGVVVVDKPRGPTSH--------EVSTWVKKILN---------LDKAGHGGTLDPKVTGVLPVALER   78 (230)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTT---------CSCEEESSCCCTTCEEEEEEEEGG
T ss_pred             CcEEEEECCCCCCHH--------HHHHHHHHHcC---------CCCCCcccccCccceeeeeeeecH
Confidence            479999999999775        67788887765         467888999999999999999876