Citrus Sinensis ID: 018575

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350----
MLPLSSFHPTFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSSK
cccccccccEEEEccccccccHHHHHHHccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccEEEEcccEEEEEcccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccEEEEEEccHHHHHHHHHHHHccccccEEEEEEEEEccccccEEEEccccccccccEEEEEEcccccccccccccccEEEEEEEEEEccccccccccHHHHHcccHHHHHHHHHHcccccccEEEEEEEccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHcc
ccccEEEEccHHHHHHHHHHHHHHcHHHHHHHHHcccEEEccEEEcccEEEccccEEEEEcccccccccccccccccccccccccEEEEcccEEEEEcccccEEccccccccccccHHHHHHHHHHcccccccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHcccEEEEEEEEEcccccccccEEEcccccccHHHccEEEEcccccEccccccccccEEHHHHHHHccccccccccHHHHcccccEEEEEEcccHHHHHcccEEEEEEEccccccEEEEEHHHccccccccccccccccccccccccHHHHHHHcccEccccccEEEEEccccHHHHHHHHHHcc
mlplssfhptftltpkavprFRKTFFSLasmsnpteptsqnapqtqqnyptplspplpaiskdieltramsassksslyklsrsdvlyedewlvavnkpqgvyceSVLASvpcllagdsaesksgrlsegtkLNLLELHLAnrldrdtsgvMVITKSHKVASKLVKAFTDHKVSKTYIALCigpapkwkrITIIsghgrskfgAWRVYAAsdvgrvlpggsvvRDMVTSFEVLSvngegsfkepselqeheeNNIVVEKKAVLDADAKKNEILVrafprsgrthqIRLHCQYLGisirgdvkyegvyewngkrydghelhaeslsfdhpvtgcpvmvqaplplwgtealqsssk
mlplssfhptftltpkavpRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMsassksslyklsrsdVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGdsaesksgrlsegtkLNLLELHLanrldrdtsgVMVITKSHKVASKLVKaftdhkvsktyialcigpapkWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNgegsfkepselqeheennIVVEKkavldadakkNEILVrafprsgrthqirLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWgtealqsssk
MLPLSSFHPTFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTramsassksslyklsrsDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKlnllelhlanrlDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSSK
*****************VPRFRKTFF*****************************************************KLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAG**************KLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSV*******************IVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGT********
*******HPTFTLTPKAVPRFRKTFFSL****************************************************LSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASD**********VRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSSK
MLPLSSFHPTFTLTPKAVPRFRKTFFSLASM******************PTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGD*********SEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGT********
*LPLSSFHPTFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSSK
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MLPLSSFHPTFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSSK
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query354 2.2.26 [Sep-21-2011]
Q7XA65322 RNA pseudourine synthase yes no 0.855 0.940 0.588 1e-101
Q2QNM3345 RNA pseudourine synthase yes no 0.785 0.805 0.624 2e-98
Q45480303 Uncharacterized RNA pseud yes no 0.610 0.712 0.272 9e-16
Q8FIP7319 Ribosomal large subunit p yes no 0.573 0.636 0.281 3e-14
Q89AH2315 Ribosomal large subunit p yes no 0.725 0.815 0.260 3e-14
Q8D8G1315 Ribosomal large subunit p yes no 0.658 0.739 0.267 4e-14
O50310327 Uncharacterized RNA pseud yes no 0.649 0.703 0.264 5e-14
Q8PHN2331 Ribosomal large subunit p yes no 0.567 0.607 0.278 1e-13
P0AA40319 Ribosomal large subunit p yes no 0.573 0.636 0.277 1e-13
P0AA39319 Ribosomal large subunit p N/A no 0.573 0.636 0.277 1e-13
>sp|Q7XA65|PUS1_ARATH RNA pseudourine synthase 1 OS=Arabidopsis thaliana GN=At1g56345 PE=2 SV=1 Back     alignment and function desciption
 Score =  367 bits (943), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 197/335 (58%), Positives = 241/335 (71%), Gaps = 32/335 (9%)

Query: 23  KTFFSLASMSNP--TEP-------TSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSAS 73
           + FFS    +N   T+P         +   +   NYP P+S P P ISKDIEL RAM AS
Sbjct: 5   RNFFSFTFSANSIITKPYFAIPIKAMEATSELNLNYPKPISAPPPPISKDIELRRAMEAS 64

Query: 74  SKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKL 133
           SKSSL+ L+R D+LYEDE+L+AVNKP+GVYCE+VL S P ++   S+E            
Sbjct: 65  SKSSLFNLTRDDILYEDEYLMAVNKPKGVYCEAVLRSAPQIVLDSSSE------------ 112

Query: 134 NLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITI 193
                HLANRLDRDTSGVM+ITKSHKVA+KLVKAFT+HK+ K+YIALCIG +P W+R+T+
Sbjct: 113 ----YHLANRLDRDTSGVMIITKSHKVAAKLVKAFTEHKIRKSYIALCIGSSPNWRRVTV 168

Query: 194 ISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEEN 253
            SGHGRSK GAWRVYAA DVGRVLPGGS VRDM T+FEV+SVN   +  E  EL+  + N
Sbjct: 169 SSGHGRSKHGAWRVYAALDVGRVLPGGSFVRDMETTFEVVSVNSVKN--ESCELE--DVN 224

Query: 254 NIVV---EKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN 310
           +++V   E++     D     ++VRAFPRSGRTHQIRLHCQYLGI IRGDVKY GVYEWN
Sbjct: 225 HVIVAEGERELSCGGDDDDVVVVVRAFPRSGRTHQIRLHCQYLGIPIRGDVKYHGVYEWN 284

Query: 311 GKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWG 345
           G+ ++GHELHAE LS DHPVTG  ++++APLP W 
Sbjct: 285 GRTFEGHELHAECLSLDHPVTGDSIVIRAPLPYWA 319

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q2QNM3|PUS1_ORYSJ RNA pseudourine synthase 1 OS=Oryza sativa subsp. japonica GN=Os12g0560500 PE=2 SV=1 Back     alignment and function description
>sp|Q45480|YLYB_BACSU Uncharacterized RNA pseudouridine synthase YlyB OS=Bacillus subtilis (strain 168) GN=ylyB PE=3 SV=3 Back     alignment and function description
>sp|Q8FIP7|RLUC_ECOL6 Ribosomal large subunit pseudouridine synthase C OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|Q89AH2|RLUC_BUCBP Ribosomal large subunit pseudouridine synthase C OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|Q8D8G1|RLUC_VIBVU Ribosomal large subunit pseudouridine synthase C OS=Vibrio vulnificus (strain CMCP6) GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|O50310|Y723_CHLP8 Uncharacterized RNA pseudouridine synthase Cpar_0723 OS=Chlorobaculum parvum (strain NCIB 8327) GN=Cpar_0723 PE=3 SV=1 Back     alignment and function description
>sp|Q8PHN2|RLUD_XANAC Ribosomal large subunit pseudouridine synthase D OS=Xanthomonas axonopodis pv. citri (strain 306) GN=rluD PE=3 SV=1 Back     alignment and function description
>sp|P0AA40|RLUC_SHIFL Ribosomal large subunit pseudouridine synthase C OS=Shigella flexneri GN=rluC PE=3 SV=1 Back     alignment and function description
>sp|P0AA39|RLUC_ECOLI Ribosomal large subunit pseudouridine synthase C OS=Escherichia coli (strain K12) GN=rluC PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query354
449454141366 PREDICTED: RNA pseudourine synthase 1-li 0.951 0.920 0.671 1e-132
449490929366 PREDICTED: LOW QUALITY PROTEIN: RNA pseu 0.951 0.920 0.668 1e-132
255542880321 ribosomal pseudouridine synthase, putati 0.892 0.984 0.755 1e-123
359487663348 PREDICTED: RNA pseudourine synthase 1-li 0.881 0.896 0.678 1e-118
224122944261 predicted protein [Populus trichocarpa] 0.711 0.965 0.736 1e-114
357441873 1262 Lon protease-like protein [Medicago trun 0.858 0.240 0.642 1e-109
296089768274 unnamed protein product [Vitis vinifera] 0.737 0.952 0.691 1e-106
326492367346 predicted protein [Hordeum vulgare subsp 0.819 0.838 0.601 1e-103
357162113308 PREDICTED: RNA pseudourine synthase 1-li 0.813 0.935 0.608 1e-101
297853522321 pseudouridine synthase family protein [A 0.737 0.813 0.651 1e-101
>gi|449454141|ref|XP_004144814.1| PREDICTED: RNA pseudourine synthase 1-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  479 bits (1232), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 237/353 (67%), Positives = 278/353 (78%), Gaps = 16/353 (4%)

Query: 6   SFHPTFTLTPKAVPRFRKT-------FFSLA-SMSNPTEPTSQNAPQTQQNYPTPLSPPL 57
           S HP F+++PK    F  T       F S++ SM++ +EP + N P T +NYP PLSPPL
Sbjct: 6   SLHPNFSISPKTFTEFPFTKSFCFHRFKSVSNSMTDSSEPVTGNCPSTAENYPVPLSPPL 65

Query: 58  PAISKDIELTRAMSASSKSSLYKLSRSDVLYEDEWLVAVNKPQGVYCESVLASVPCLLAG 117
           PAISK++EL RAM ASSKSSLY LS +DV+YEDEWL+AVNKPQG+YCE+VLA+VP LL G
Sbjct: 66  PAISKNLELARAMVASSKSSLYALSANDVIYEDEWLIAVNKPQGIYCENVLAAVPRLL-G 124

Query: 118 DSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTY 177
           DSA +       G K +L ELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDH VSK+Y
Sbjct: 125 DSANA-------GIKTSLPELHLANRLDRDTSGVMVITKSHKVASKLVKAFTDHTVSKSY 177

Query: 178 IALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNG 237
           IA C+G +PKWK+I + SGHGRSKFG WRVYAA+DVGR LPGGSVVRDM T FEVLSVNG
Sbjct: 178 IAFCVGTSPKWKKINVKSGHGRSKFGVWRVYAAADVGRSLPGGSVVRDMETYFEVLSVNG 237

Query: 238 EGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISI 297
           + + +E  + +  EE  IVV  K+++D D+ K+EIL+RA PRSGRTHQIRLHCQYLGI I
Sbjct: 238 KNTMEELQKFRRGEEETIVVHTKSLVDIDSHKDEILIRARPRSGRTHQIRLHCQYLGIPI 297

Query: 298 RGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQ 350
           RGDVKYEGV EWN K YD HELHAESL F HPVTG P+ +QAPLP W ++ALQ
Sbjct: 298 RGDVKYEGVTEWNEKIYDSHELHAESLYFVHPVTGIPLKLQAPLPSWASQALQ 350

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449490929|ref|XP_004158751.1| PREDICTED: LOW QUALITY PROTEIN: RNA pseudourine synthase 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255542880|ref|XP_002512503.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223548464|gb|EEF49955.1| ribosomal pseudouridine synthase, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|359487663|ref|XP_002278016.2| PREDICTED: RNA pseudourine synthase 1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|224122944|ref|XP_002318955.1| predicted protein [Populus trichocarpa] gi|222857331|gb|EEE94878.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357441873|ref|XP_003591214.1| Lon protease-like protein [Medicago truncatula] gi|355480262|gb|AES61465.1| Lon protease-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|296089768|emb|CBI39587.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|326492367|dbj|BAK01967.1| predicted protein [Hordeum vulgare subsp. vulgare] Back     alignment and taxonomy information
>gi|357162113|ref|XP_003579309.1| PREDICTED: RNA pseudourine synthase 1-like [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|297853522|ref|XP_002894642.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297340484|gb|EFH70901.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query354
TAIR|locus:2824464322 AT1G56345 [Arabidopsis thalian 0.782 0.860 0.58 1.6e-86
TIGR_CMR|SPO_3392215 SPO_3392 "ribosomal large subu 0.265 0.437 0.343 5.6e-14
TIGR_CMR|GSU_0671296 GSU_0671 "ribosomal large subu 0.175 0.209 0.492 2.5e-13
TIGR_CMR|CPS_2290360 CPS_2290 "ribosomal large subu 0.192 0.188 0.493 5.1e-13
UNIPROTKB|P0AA41260 truC [Escherichia coli K-12 (t 0.194 0.265 0.383 1.3e-11
UNIPROTKB|Q9KTL4244 truC "tRNA pseudouridine synth 0.203 0.295 0.337 1.4e-11
TIGR_CMR|VC_0888244 VC_0888 "pseudouridine synthas 0.203 0.295 0.337 1.4e-11
TIGR_CMR|CJE_1416322 CJE_1416 "ribosomal large subu 0.220 0.242 0.428 8.6e-11
TIGR_CMR|GSU_3353296 GSU_3353 "RNA pseudouridine sy 0.370 0.442 0.292 9.3e-11
TIGR_CMR|CHY_1119301 CHY_1119 "ribosomal large subu 0.259 0.305 0.326 1.6e-10
TAIR|locus:2824464 AT1G56345 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 865 (309.6 bits), Expect = 1.6e-86, P = 1.6e-86
 Identities = 174/300 (58%), Positives = 212/300 (70%)

Query:    48 NYPTPLSPPLPAISKDIELTXXXXXXXXXXXXXXXXXDVLYEDEWLVAVNKPQGVYCESV 107
             NYP P+S P P ISKDIEL                  D+LYEDE+L+AVNKP+GVYCE+V
Sbjct:    39 NYPKPISAPPPPISKDIELRRAMEASSKSSLFNLTRDDILYEDEYLMAVNKPKGVYCEAV 98

Query:   108 LASVPCLLAGDSAESKSGRLSEGTKXXXXXXXXXXXXDRDTSGVMVITKSHKVASKLVKA 167
             L S P ++   S+E     L+                DRDTSGVM+ITKSHKVA+KLVKA
Sbjct:    99 LRSAPQIVLDSSSEY---HLAN-------------RLDRDTSGVMIITKSHKVAAKLVKA 142

Query:   168 FTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMV 227
             FT+HK+ K+YIALCIG +P W+R+T+ SGHGRSK GAWRVYAA DVGRVLPGGS VRDM 
Sbjct:   143 FTEHKIRKSYIALCIGSSPNWRRVTVSSGHGRSKHGAWRVYAALDVGRVLPGGSFVRDME 202

Query:   228 TSFEVLSVNGEGSFKEPSELQEHEENNIVV---EKKAVLDADAKKNEILVRAFPRSGRTH 284
             T+FEV+SVN   +  E  EL++   N+++V   E++     D     ++VRAFPRSGRTH
Sbjct:   203 TTFEVVSVNSVKN--ESCELED--VNHVIVAEGERELSCGGDDDDVVVVVRAFPRSGRTH 258

Query:   285 QIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLPLW 344
             QIRLHCQYLGI IRGDVKY GVYEWNG+ ++GHELHAE LS DHPVTG  ++++APLP W
Sbjct:   259 QIRLHCQYLGIPIRGDVKYHGVYEWNGRTFEGHELHAECLSLDHPVTGDSIVIRAPLPYW 318
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0005739 "mitochondrion" evidence=ISM
GO:0009451 "RNA modification" evidence=IEA
GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS
GO:0006457 "protein folding" evidence=RCA
GO:0009408 "response to heat" evidence=RCA
GO:0009644 "response to high light intensity" evidence=RCA
GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA
GO:0042542 "response to hydrogen peroxide" evidence=RCA
TIGR_CMR|SPO_3392 SPO_3392 "ribosomal large subunit pseudouridine synthase A" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_0671 GSU_0671 "ribosomal large subunit pseudouridine synthase C" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_2290 CPS_2290 "ribosomal large subunit pseudouridine synthase C" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|P0AA41 truC [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KTL4 truC "tRNA pseudouridine synthase C" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0888 VC_0888 "pseudouridine synthase Rlu family protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|CJE_1416 CJE_1416 "ribosomal large subunit pseudouridine synthases, RluA family" [Campylobacter jejuni RM1221 (taxid:195099)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_3353 GSU_3353 "RNA pseudouridine synthase family protein" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1119 CHY_1119 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q2QNM3PUS1_ORYSJ5, ., 4, ., 9, 9, ., -0.62410.78530.8057yesno
Q7XA65PUS1_ARATH5, ., 4, ., 9, 9, ., -0.58800.85590.9409yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer5.4.990.691

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query354
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 3e-44
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 1e-37
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 7e-33
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine is 8e-24
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 8e-23
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 2e-21
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 7e-19
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 9e-16
cd02558246 cd02558, PSRA_1, Pseudouridine synthase, a subgrou 2e-15
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 7e-12
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; 7e-11
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 5e-09
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 5e-09
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy 4e-08
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylat 5e-06
cd02553167 cd02553, PseudoU_synth_RsuA, Pseudouridine synthas 1e-04
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
 Score =  153 bits (389), Expect = 3e-44
 Identities = 78/261 (29%), Positives = 109/261 (41%), Gaps = 54/261 (20%)

Query: 85  DVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRL 144
           D+LYEDE L+ VNKP G      L   P    G    +    L    +  +    + +RL
Sbjct: 79  DILYEDEDLLVVNKPAG------LVVHP--GGGHHEGTLVNALLRHCQDGVERPGIVHRL 130

Query: 145 DRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITI---ISGHGRSK 201
           D+DTSG++++ K+ + A +L + F   KV KTY+AL  G        TI   I    +++
Sbjct: 131 DKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGH-LPEDEGTIDAPIGRDPKNR 189

Query: 202 FGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVEKKA 261
                V   S            +  +T +EVL   G+                       
Sbjct: 190 KKMAVVKEGS-----------GKPAITHYEVLERFGDNYT-------------------- 218

Query: 262 VLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHA 321
                      LV   P +GRTHQIR+H  +LG  I GD  Y G  +  G       LHA
Sbjct: 219 -----------LVELKPETGRTHQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHA 267

Query: 322 ESLSFDHPVTGCPVMVQAPLP 342
             LSF HP+TG  +  +APLP
Sbjct: 268 YKLSFTHPLTGEELEFEAPLP 288

Length = 289
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C Back     alignment and domain information
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase Back     alignment and domain information
>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2 Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|224108 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|211327 cd02553, PseudoU_synth_RsuA, Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 354
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
PRK11112257 tRNA pseudouridine synthase C; Provisional 100.0
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 100.0
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 100.0
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 100.0
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 100.0
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 100.0
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 100.0
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 100.0
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 99.98
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 99.97
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 99.97
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.97
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.97
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.96
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.96
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.95
TIGR00093128 pseudouridine synthase. This model identifies pane 99.95
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.93
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 99.15
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.71
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 97.43
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.4
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 97.35
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 97.32
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.28
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 97.26
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 97.18
PRK14124308 tRNA pseudouridine synthase B; Provisional 97.14
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 97.13
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 97.12
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 97.1
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 97.09
PRK14123305 tRNA pseudouridine synthase B; Provisional 97.07
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 97.03
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 97.01
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 97.0
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 96.99
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 96.97
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 96.97
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 96.93
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 96.88
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 96.8
PRK14122312 tRNA pseudouridine synthase B; Provisional 96.69
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 96.36
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 96.3
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 96.15
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 95.98
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 92.81
KOG2559318 consensus Predicted pseudouridine synthase [Transl 91.21
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 87.58
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 81.59
COG1188100 Ribosome-associated heat shock protein implicated 81.42
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=1.4e-57  Score=420.90  Aligned_cols=283  Identities=29%  Similarity=0.384  Sum_probs=208.0

Q ss_pred             ccccCCCCCCCcccccccccCCCCCCCCCCCCCCccccCCCCCCCCCCcccccc-eeEEeeccccccccccc-CCCccEE
Q 018575           10 TFTLTPKAVPRFRKTFFSLASMSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKD-IELTRAMSASSKSSLYK-LSRSDVL   87 (354)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~-v~~~~~~~~~~~~~~~~-~~~~~Il   87 (354)
                      .|+++..+.++|+|+||+....-+|..+.+++.+|.+.-...++.+.+....|+ +.+.......+ ..... -.+++||
T Consensus         3 ~~~v~~~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~-~~~~~~~~~l~Il   81 (289)
T COG0564           3 EFEVPEEEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEE-EKLVPEDIPLDIL   81 (289)
T ss_pred             eEEeChhhcCCCHHHHHHHccCcCHHHHHHHHHCCCEEECCEEccCCeeeCCCCEEEEeccccccc-ccccccCCCccEE
Confidence            467777889999999999832268999999999887743443344332222222 22222111110 00010 0136799


Q ss_pred             EeCCcEEEEECCCCCccccccccccc-cccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHHHH
Q 018575           88 YEDEWLVAVNKPQGVYCESVLASVPC-LLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKLVK  166 (354)
Q Consensus        88 yed~~~lvvnKP~Gl~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l~~  166 (354)
                      |||+++||||||+|++||+....... ++.....     .....    ...+++||||||+||||||+|||..++..|++
T Consensus        82 yED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~-----~~~~~----~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~  152 (289)
T COG0564          82 YEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLR-----HCQDG----VERPGIVHRLDKDTSGLLLVAKNREAARELSE  152 (289)
T ss_pred             EecCCEEEEECCCCCcCcCCCCCccHhHHHHHHH-----hcccc----CCceeeeccCCCCCceEEEEECCHHHHHHHHH
Confidence            99999999999999999987433222 1111110     00000    15799999999999999999999999999999


Q ss_pred             HhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCCCCcc
Q 018575          167 AFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSE  246 (354)
Q Consensus       167 ~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~~~~~  246 (354)
                      +|+++.+.|+|+|+|.|.++. +.+.|+.++++..........       ...+. .+.|.|.|+++...          
T Consensus       153 ~f~~r~v~K~Y~Alv~G~~~~-~~~~i~~pi~r~~~~~~~~~v-------~~~~~-gk~A~T~~~~l~~~----------  213 (289)
T COG0564         153 QFKQRKVKKTYLALVRGHLPE-DEGTIDAPIGRDPKNRKKMAV-------VKEGS-GKPAITHYEVLERF----------  213 (289)
T ss_pred             HHhcCcCcEEEEEEEECcccC-CCCEEeeeeecCCcCCceEEE-------eccCC-CCceEEEEEehhcc----------
Confidence            999999999999999999876 457899999887765544332       11222 47899999998652          


Q ss_pred             hhcccccceeeeeehhhccCCCCc-eEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCCCCCCCceeeeeeeE
Q 018575          247 LQEHEENNIVVEKKAVLDADAKKN-EILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHELHAESLS  325 (354)
Q Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~-~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~~~~~~~~LHa~~L~  325 (354)
                                            .. .|+++|+|.||||||||+||+++||||+||.+||...........+++|||++|.
T Consensus       214 ----------------------~~~~tlv~~~~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~~~~~~~~r~~LHA~~l~  271 (289)
T COG0564         214 ----------------------GDNYTLVELKPETGRTHQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHAYKLS  271 (289)
T ss_pred             ----------------------CCceEEEEEEeCCCCHhHHHHHHHHCCCCeeCCcccCCchhhcccCcchhhhhhceeE
Confidence                                  23 6999999999999999999999999999999999853222334678999999999


Q ss_pred             eeCCCCCCceEEEcCCCh
Q 018575          326 FDHPVTGCPVMVQAPLPL  343 (354)
Q Consensus       326 f~~P~~~~~~~~~aplP~  343 (354)
                      |.||.+++.+.|++|+|.
T Consensus       272 f~hp~t~~~~~~~a~~p~  289 (289)
T COG0564         272 FTHPLTGEELEFEAPLPE  289 (289)
T ss_pred             ccCCCCCCEEEEecCCCC
Confidence            999999999999999984

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>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) Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>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 Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA Back     alignment and domain information
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query354
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 5e-12
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 1e-10
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 8e-06
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 3e-04
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 6e-04
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 Back     alignment and structure 
Iteration: 1

 Score = 68.6 bits (166), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/263 (26%), Positives = 109/263 (41%), Gaps = 60/263 (22%)
Query: 86  VLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKXXXXXXXXXXXXD 145
           +LYED+ ++ +NKP G            ++ G  A     R  E               D
Sbjct: 7   ILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLE----------LVHRLD 56
Query: 146 RDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAW 205
           RDTSGV+++ K       L +   +  + K Y+AL  G                     W
Sbjct: 57  RDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQ--------------------W 96
Query: 206 RVYAASDVGRVLPGGSVVRDMVTSFE-VLSVNGEGSFKEPSELQEHEENNIVVEKKAVLD 264
           + +  S          ++++++ S E ++ V+ EG   +PSE          VE++    
Sbjct: 97  QSHVKS------VQAPLLKNILQSGERIVRVSQEG---KPSE------TRFKVEERYAF- 140
Query: 265 ADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWN------GKRYDGHE 318
                   LVR  P +GRTHQIR+H QY G  I  D +Y G  E++      G   +   
Sbjct: 141 ------ATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRY-GDREFDRQLTEAGTGLNRLF 193
Query: 319 LHAESLSFDHPVTGCPVMVQAPL 341
           LHA +L F HP TG  + ++AP+
Sbjct: 194 LHAAALKFTHPGTGEVMRIEAPM 216
>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of Pseudouridine Synthase Rluc From Escherichia Coli Length = 228 Back     alignment and structure
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325 Back     alignment and structure
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 Back     alignment and structure
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query354
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 3e-38
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 5e-35
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 3e-29
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-05
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 7e-05
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 6e-04
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217 Back     alignment and structure
 Score =  134 bits (341), Expect = 3e-38
 Identities = 62/279 (22%), Positives = 89/279 (31%), Gaps = 96/279 (34%)

Query: 85  DVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSE-GTKLNLLELH---- 139
            +LY+D+ ++ VNKP G      L SVP            GRL E    +          
Sbjct: 13  VILYQDDHIMVVNKPSG------LLSVP------------GRLEEHKDSVMTRIQRDYPQ 54

Query: 140 --LANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGH 197
               +RLD  TSGV+V+  +     +L + F + +  K Y+A                  
Sbjct: 55  AESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARV---------------W 99

Query: 198 GRSKFGAWRVYAASDVGRV-LPGG---------SVVRDM----VTSFEVLSVNGEGSFKE 243
           G               G V LP            V  +      T +EV+    + +   
Sbjct: 100 GHPS---------PAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTA-- 148

Query: 244 PSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKY 303
                                         V   P +GR+HQ+R+H   LG  I GD  Y
Sbjct: 149 -----------------------------RVVLKPITGRSHQLRVHMLALGHPILGDRFY 179

Query: 304 EGVYEWNGKRYDGHELHAESLSFDHPVTGCPVMVQAPLP 342
                          LHAE L+  HP  G  +  +AP  
Sbjct: 180 AS--PEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPAD 216
>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 Back     alignment and structure
>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 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>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* Length = 234 Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Length = 243 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query354
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 100.0
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 100.0
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 100.0
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 100.0
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 100.0
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 100.0
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 99.97
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 96.77
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 96.76
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 96.66
2aus_C334 Pseudouridine synthase; isomerase, structural prot 96.64
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 96.63
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 96.47
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 96.21
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 94.03
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 93.71
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 91.64
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 89.71
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 86.6
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 86.19
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 85.25
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 84.44
>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 Back     alignment and structure
Probab=100.00  E-value=8.4e-57  Score=424.66  Aligned_cols=281  Identities=20%  Similarity=0.254  Sum_probs=174.1

Q ss_pred             CccccCCCCCCCcccccccccC-CCCCCCCCCCCCCccccCCCCCCCCCCcccccceeEEeecccccccccccC------
Q 018575            9 PTFTLTPKAVPRFRKTFFSLAS-MSNPTEPTSQNAPQTQQNYPTPLSPPLPAISKDIELTRAMSASSKSSLYKL------   81 (354)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~------   81 (354)
                      .++++++++.+||+|+||+... ..||..++++|..|.|            .|||.++......+.+. +.+.+      
T Consensus         6 ~~~~v~~~~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V------------~VNG~~v~~~~~~v~~g-D~I~v~~~~~~   72 (325)
T 1v9f_A            6 LTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRV------------LVNGKVCDKPKEKVLGG-EQVAINAEIEE   72 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEECCccCCchHHHHHHhhccccCHHHHHHHHHCCCE------------EECCEEccCCCCEeCCC-CEEEEeccccc
Confidence            3577888889999999999886 7899999999999988            44444322222222221 11111      


Q ss_pred             --------CCccEEEeCCcEEEEECCCCCccccccccc-cccccccccccccCCCccccccccccccccccCCCCCceEE
Q 018575           82 --------SRSDVLYEDEWLVAVNKPQGVYCESVLASV-PCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVM  152 (354)
Q Consensus        82 --------~~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGll  152 (354)
                              .++.|+|||++|+|||||+|++||+..... .++++...     ..+....  +...+++|||||++|||||
T Consensus        73 ~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~-----~~~~~~~--~~~~~~~vhRLD~~TSGll  145 (325)
T 1v9f_A           73 EARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALL-----HYYPPIA--DVPRAGIVHRLDKDTTGLM  145 (325)
T ss_dssp             ---CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHH-----HHCGGGG--GSGGGGBCCCCCTTCEEEE
T ss_pred             cccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHH-----HHHHhcC--CCCceeeecCCCCCCeeEE
Confidence                    135799999999999999999999754321 22211110     0111110  1146899999999999999


Q ss_pred             EEEeCHHHHHHHHHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCCceeEeeecCCccccCCCcccccceeeEEE
Q 018575          153 VITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEV  232 (354)
Q Consensus       153 llAk~~~~a~~l~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~t~~~v  232 (354)
                      |||||+++++.|+++|+++.++|+|+|+|.|.++.  .+.|+.+++++.....+...       ..+   .+.+.|+|++
T Consensus       146 l~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~--~g~i~~~i~~~~~~~~~~~v-------~~~---gk~a~t~~~v  213 (325)
T 1v9f_A          146 VVAKTVPAQTRLVESLQRREITREYEAVAIGHMTA--GGTVDEPISRHPTKRTHMAV-------HPM---GKPAVTHYRI  213 (325)
T ss_dssp             EEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCC--CEEEECCEEECSSCTTCEEE-------CTT---SBCCEEEEEE
T ss_pred             EEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCC--CCEEeeeeeECCCCCEEEEE-------CCC---CeeEEEEEEE
Confidence            99999999999999999999999999999999875  57888888776544333321       122   2678899999


Q ss_pred             eeecCCCCCCCCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCccccCC-
Q 018575          233 LSVNGEGSFKEPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNG-  311 (354)
Q Consensus       233 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~~~-  311 (354)
                      +..                                ..++++++|+|.|||+||||+||+++||||+||.+||+...... 
T Consensus       214 l~~--------------------------------~~~~slv~~~l~TGR~HQIRvhla~lG~PI~GD~~Yg~~~~~~~~  261 (325)
T 1v9f_A          214 MEH--------------------------------FRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKG  261 (325)
T ss_dssp             EEE--------------------------------CSSEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTT
T ss_pred             eEE--------------------------------cCCeEEEEEEECCCCcHHHHHHHHhCCCceeCChhhCCccccccc
Confidence            875                                24579999999999999999999999999999999997521000 


Q ss_pred             ---------CCCCCceeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018575          312 ---------KRYDGHELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS  353 (354)
Q Consensus       312 ---------~~~~~~~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~  353 (354)
                               ....+++|||++|+|.||.+++.+.|+||+|.+|.++|+.|+
T Consensus       262 ~~~~~~~~~~~~~r~~LHA~~L~f~hP~~~~~~~~~aplp~~~~~~l~~l~  312 (325)
T 1v9f_A          262 ASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMR  312 (325)
T ss_dssp             CCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             cchhhhhhccCCcChhhheeeeEeeCCCCCCEEEEEecCcHHHHHHHHHhc
Confidence                     124689999999999999999999999999999999999875
>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 Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>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* Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure
>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} Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 354
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 5e-23
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 2e-16
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 Back     information, alignment and structure

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 = 93.5 bits (231), Expect = 5e-23
 Identities = 66/269 (24%), Positives = 92/269 (34%), Gaps = 70/269 (26%)

Query: 86  VLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELH------ 139
           ++YED+ ++ +NKP G       A                 LS G    L  L       
Sbjct: 3   IMYEDDHILVLNKPSG------TAVHG-----------GSGLSFGVIEGLRALRPEARFL 45

Query: 140 -LANRLDRDTSGVMVITKSHKVASKLVKAFTDHKVSKTYIALCIGPAPKWKRITIISGHG 198
            L +RLDRDTSGV+++ K       L +   +  + K Y+AL  G      +        
Sbjct: 46  ELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLK 105

Query: 199 RSKFGAWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFKEPSELQEHEENNIVVE 258
                  R+   S  G+            T F+V                          
Sbjct: 106 NILQSGERIVRVSQEGK---------PSETRFKVEERYA--------------------- 135

Query: 259 KKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEWNGKRYDGHE 318
                         LVR  P +GRTHQIR+H QY G  I  D +Y            G  
Sbjct: 136 -----------FATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTG 184

Query: 319 -----LHAESLSFDHPVTGCPVMVQAPLP 342
                LHA +L F HP TG  + ++AP+ 
Sbjct: 185 LNRLFLHAAALKFTHPGTGEVMRIEAPMD 213
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query354
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 100.0
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 99.96
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 99.93
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 97.67
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 97.21
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 97.09
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 97.07
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 96.87
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 96.85
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 96.68
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 96.49
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.5e-56  Score=399.01  Aligned_cols=216  Identities=30%  Similarity=0.363  Sum_probs=168.8

Q ss_pred             cEEEeCCcEEEEECCCCCccccccccccccccccccccccCCCccccccccccccccccCCCCCceEEEEEeCHHHHHHH
Q 018575           85 DVLYEDEWLVAVNKPQGVYCESVLASVPCLLAGDSAESKSGRLSEGTKLNLLELHLANRLDRDTSGVMVITKSHKVASKL  164 (354)
Q Consensus        85 ~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~vhRLDk~TSGllllAk~~~~a~~l  164 (354)
                      .|||||++|||||||+||+||+......+.+.....     .. .    +...+++|||||++||||||||||.++++.|
T Consensus         2 ~IlyeD~~ilvvnKP~gl~~h~~~~~~~~~~~~l~~-----~~-~----~~~~~~~vHRLD~~TSGlll~Ak~~~~~~~l   71 (227)
T d1v9ka_           2 VIMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA-----LR-P----EARFLELVHRLDRDTSGVLLVAKKRSALRSL   71 (227)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHH-----HS-T----TCSCCEESSCCCTTCEEEEEEESSHHHHHHH
T ss_pred             EEEEeCCCEEEEECCCCCccCCCCCCcchHHHHHHH-----hC-C----CCcccceeeeccceeeeeeeeecchHHHHHH
Confidence            599999999999999999999754332222221110     00 1    1146889999999999999999999999999


Q ss_pred             HHHhhcCccceEEEEEEeCCCCCCCceEEecCCCCCCCC--ceeEeeecCCccccCCCcccccceeeEEEeeecCCCCCC
Q 018575          165 VKAFTDHKVSKTYIALCIGPAPKWKRITIISGHGRSKFG--AWRVYAASDVGRVLPGGSVVRDMVTSFEVLSVNGEGSFK  242 (354)
Q Consensus       165 ~~~f~~~~v~K~Y~A~v~G~~~~~~~~~i~~~i~~~~~~--~~~~~~~~~~~~~~~~g~~~~~a~t~~~vl~~~~~~~~~  242 (354)
                      +++|+++.+.|+|+|+|.|.++. ....+..++......  ...+       +...+   .+.+.|.|+++..       
T Consensus        72 ~~~f~~~~v~K~Y~a~~~G~~~~-~~~~~~~~~~~~~~~~~~~~~-------~~~~~---gk~a~t~~~~l~~-------  133 (227)
T d1v9ka_          72 HEQLREKGMQKDYLALVRGQWQS-HVKSVQAPLLKNILQSGERIV-------RVSQE---GKPSETRFKVEER-------  133 (227)
T ss_dssp             HHHHHTTCSEEEEEEEEESCCCT-TCCEECCCEEEEECTTSCEEE-------EECTT---SBCCCEEEEEEEE-------
T ss_pred             HHHHhcccccceecccccCcccc-ccCccccccccccccceeeee-------ecCCC---Ccccceeehhhhh-------
Confidence            99999999999999999999875 444555544332111  1111       01112   3677888888765       


Q ss_pred             CCcchhcccccceeeeeehhhccCCCCceEEEEEEeCCCchhHHHHHHhhcCCceecCCCCCCcccc-----CCCCCCCc
Q 018575          243 EPSELQEHEENNIVVEKKAVLDADAKKNEILVRAFPRSGRTHQIRLHCQYLGISIRGDVKYEGVYEW-----NGKRYDGH  317 (354)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQIRvhla~lG~PIvGD~~Yg~~~~~-----~~~~~~~~  317 (354)
                                               ...+++++|+|.||||||||+||+++||||+||.+||+....     ......++
T Consensus       134 -------------------------~~~~slv~~~~~TGRtHQIRvHla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~rl  188 (227)
T d1v9ka_         134 -------------------------YAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRL  188 (227)
T ss_dssp             -------------------------CSSEEEEEEEESSCCTTHHHHHHHHTTCCBTTCTTTSCHHHHHHHHHTTCCCCSC
T ss_pred             -------------------------cCCcEEEEEEeccCchHHHHHHHhhcCceeccCcccccccccccchhcccCcchH
Confidence                                     356899999999999999999999999999999999975321     12346789


Q ss_pred             eeeeeeeEeeCCCCCCceEEEcCCChhHHHHHHhcc
Q 018575          318 ELHAESLSFDHPVTGCPVMVQAPLPLWGTEALQSSS  353 (354)
Q Consensus       318 ~LHa~~L~f~~P~~~~~~~~~aplP~~f~~~l~~l~  353 (354)
                      +|||++|+|.||.||+.+.|+||+|++|+++|++|+
T Consensus       189 ~LHa~~L~f~hP~t~~~~~~~aplP~~f~~~l~~Lk  224 (227)
T d1v9ka_         189 FLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKMR  224 (227)
T ss_dssp             CEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             HHHccccEeECCCCCCEEEEEecCcHHHHHHHHHHH
Confidence            999999999999999999999999999999999985
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure