Citrus Sinensis ID: 022339

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-------30
MTMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCSSSSSGGNNREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR
ccEEccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccEEEEEEccccccccHHHHHHHccccccHHHHHHHHHcccEEEccEEccccccccccccEEEEEcccccccccccccccccEEEEcccEEEEEcccccEEccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEcccccccEEEEEccHHHHHHHHHHHHcccccEEEEEEEEccccccccEEEccccccccccEEEEEEccccccccEEEEEcc
ccEEEEEcccccEcccccccEcccccccccHHHHcccccccccccccccccccccccEEEEEEEcHHHcccHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEEcccEEEccccEEEEEccccccccccccccccEEEEEcccEEEEEcccccEEccccccccccHHHHHHHHccccccccccHcccccccccccccccccccccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHHcccEEEEEEEEEccccccccEEEccccccccHccEEEEEccccccEEEEEEEEc
mtmlslnsaswgsasctkglqfsptkipfgVFKILRARCsssssggnnrepianyagvqleetvdtKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVshnvkggdmvnctiselqplraeaedipldivyeddnvlvvnkpahmvvhpapgnatgtlvngilhhcslptlassnqeafsdaedisddeefsssisgasirpgivhrldkgtsgllvvakdehshahlseqfKLHTIERVYISLtsgvpsqssgrievpisrdpnnrirmaaipgsnkhgqarhaasr
mtmlslnsaswgsasctkglqfspTKIPFGVFKILRARCSssssggnnrepianYAGVQLEETVDTKAGKLRLDAWissridgisrARVQSSIRSGLVSINGQVVSKVshnvkggdmvNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSssisgasirpgiVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLtsgvpsqssgrievpisrdpnnrirmaaipgsnkhgqarhaasr
MTMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCsssssggnnREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQeafsdaedisddeefsssisGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR
**************SCTKGLQFSPTKIPFGVFKILRARC*************ANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT********************************GIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT*******************************************
*********************FSPTKIPFGVFK***********************GVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDI***********GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR
**************SCTKGLQFSPTKIPFGVFKILRAR********NNREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSN******************SISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG********IEVPISRDPNNRIRMAAIPG*************
*TMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRAR****************YAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT**********************SSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MTMLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCSSSSSGGNNREPIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR
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 ?
Query298 2.2.26 [Sep-21-2011]
Q3ECD0 430 RNA pseudourine synthase no no 0.832 0.576 0.753 1e-104
Q5Z8P2 445 RNA pseudourine synthase yes no 0.815 0.546 0.656 6e-89
P74346327 Uncharacterized RNA pseud N/A no 0.637 0.581 0.397 2e-37
Q45480303 Uncharacterized RNA pseud yes no 0.667 0.656 0.401 8e-37
O50310 327 Uncharacterized RNA pseud yes no 0.657 0.599 0.390 6e-36
O67638316 Uncharacterized RNA pseud yes no 0.620 0.585 0.377 6e-35
Q45826316 Uncharacterized RNA pseud yes no 0.624 0.588 0.394 8e-35
P50513317 Ribosomal large subunit p yes no 0.630 0.593 0.422 4e-34
Q9K0B0 374 Ribosomal large subunit p yes no 0.610 0.486 0.406 4e-31
Q9JVB6 374 Ribosomal large subunit p yes no 0.610 0.486 0.411 2e-30
>sp|Q3ECD0|PUS2_ARATH RNA pseudourine synthase 2, chloroplastic OS=Arabidopsis thaliana GN=At1g76050 PE=2 SV=1 Back     alignment and function desciption
 Score =  376 bits (966), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 190/252 (75%), Positives = 216/252 (85%), Gaps = 4/252 (1%)

Query: 51  PIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSH 110
           P  N AG+++EE VD   GK+RLD+WISSRI+G+SRARVQSSIR GLV++NG+VV KVSH
Sbjct: 62  PRVNNAGLRIEEIVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSH 121

Query: 111 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 170
           NVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGTLVN
Sbjct: 122 NVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVN 181

Query: 171 GILHHCSLPTLASSN--QEAFSDAEDISDDEEFSSSIS--GASIRPGIVHRLDKGTSGLL 226
           GILHHCSLP +  SN  ++  SD E  SDDEE ++S S   AS+RPGIVHRLDKGT+GLL
Sbjct: 182 GILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTTGLL 241

Query: 227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 286
           VVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRIE+PI RD +NRIRMAAIPG 
Sbjct: 242 VVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRIRMAAIPGG 301

Query: 287 NKHGQARHAASR 298
            + G+ARHAASR
Sbjct: 302 VRGGRARHAASR 313

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q5Z8P2|PUS2_ORYSJ RNA pseudourine synthase 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os06g0717400 PE=2 SV=1 Back     alignment and function description
>sp|P74346|Y1629_SYNY3 Uncharacterized RNA pseudouridine synthase slr1629 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1629 PE=3 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|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|O67638|Y1758_AQUAE Uncharacterized RNA pseudouridine synthase aq_1758 OS=Aquifex aeolicus (strain VF5) GN=aq_1758 PE=3 SV=1 Back     alignment and function description
>sp|Q45826|Y901_CHLAA Uncharacterized RNA pseudouridine synthase Caur_0901 OS=Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) GN=Caur_0901 PE=3 SV=2 Back     alignment and function description
>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 Back     alignment and function description
>sp|Q9K0B0|RLUD_NEIMB Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup B (strain MC58) GN=rluD PE=3 SV=1 Back     alignment and function description
>sp|Q9JVB6|RLUD_NEIMA Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=rluD PE=3 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 ?
Query298
224065743 444 predicted protein [Populus trichocarpa] 0.963 0.646 0.696 1e-107
255556673 399 ribosomal pseudouridine synthase, putati 0.822 0.614 0.775 1e-103
449450654 453 PREDICTED: RNA pseudourine synthase 2, c 0.953 0.626 0.657 1e-103
359492029 433 PREDICTED: RNA pseudourine synthase 2, c 0.973 0.669 0.654 1e-102
449500428 452 PREDICTED: LOW QUALITY PROTEIN: RNA pseu 0.949 0.626 0.661 1e-102
42563248313 RNA pseudourine synthase 2 [Arabidopsis 0.832 0.792 0.753 1e-102
42572121 430 RNA pseudourine synthase 2 [Arabidopsis 0.832 0.576 0.753 1e-102
6721111 980 T4O12.25 [Arabidopsis thaliana] 0.832 0.253 0.679 3e-98
297839485 930 T4O12.25 [Arabidopsis lyrata subsp. lyra 0.791 0.253 0.737 7e-96
357467069 465 RNA pseudourine synthase [Medicago trunc 0.989 0.634 0.589 1e-95
>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa] gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 209/300 (69%), Positives = 242/300 (80%), Gaps = 13/300 (4%)

Query: 3   MLSLNSASWGSASCTKGLQFSPTKIPFGVFKILRARCSSSSSGGNNREP--IANYAGVQL 60
           MLS++S S  SA  +  L   PT       ++L    SS+    +N+ P    NY+GV+L
Sbjct: 30  MLSISSVSRCSAP-SFFLSQKPT-----ASRLLTVHSSSTREPNSNQNPGQRINYSGVKL 83

Query: 61  EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNC 120
           EE+VD+K+GK RLD+WISSRI GISRARVQSSI+SGLVS+NG+V+ KVSHNVK GD VNC
Sbjct: 84  EESVDSKSGKSRLDSWISSRISGISRARVQSSIKSGLVSVNGKVIDKVSHNVKAGDKVNC 143

Query: 121 TISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT 180
            ISELQPLRAE E+IPLDIVYED+NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT
Sbjct: 144 VISELQPLRAEPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT 203

Query: 181 LASSNQEAFSDAEDISDDEE--FSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHL 238
           ++S  QE  S AED+SDD++    SS   AS+RPGIVHRLDKGTSGLLVVAKDEHSHAHL
Sbjct: 204 VSS--QEVLSGAEDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGLLVVAKDEHSHAHL 261

Query: 239 SEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR 298
           SEQFKLHTI+RVY+SLT GVP+  +GRI+VPI RD +NRIRMAAI   N+ GQARHAASR
Sbjct: 262 SEQFKLHTIKRVYVSLTCGVPAPMAGRIDVPIGRDVSNRIRMAAIVEPNR-GQARHAASR 320

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255556673|ref|XP_002519370.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223541437|gb|EEF42987.1| ribosomal pseudouridine synthase, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449450654|ref|XP_004143077.1| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|359492029|ref|XP_003634352.1| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Vitis vinifera] gi|302141717|emb|CBI18920.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449500428|ref|XP_004161095.1| PREDICTED: LOW QUALITY PROTEIN: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|42563248|ref|NP_177732.2| RNA pseudourine synthase 2 [Arabidopsis thaliana] gi|332197668|gb|AEE35789.1| RNA pseudourine synthase 2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|42572121|ref|NP_974151.1| RNA pseudourine synthase 2 [Arabidopsis thaliana] gi|122215273|sp|Q3ECD0.1|PUS2_ARATH RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName: Full=RNA pseudouridylate synthase 2; AltName: Full=RNA-uridine isomerase 2; Flags: Precursor gi|332197669|gb|AEE35790.1| RNA pseudourine synthase 2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|6721111|gb|AAF26765.1|AC007396_14 T4O12.25 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297839485|ref|XP_002887624.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata] gi|297333465|gb|EFH63883.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|357467069|ref|XP_003603819.1| RNA pseudourine synthase [Medicago truncatula] gi|355492867|gb|AES74070.1| RNA pseudourine synthase [Medicago truncatula] 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 ?
Query298
TAIR|locus:2204355 430 AT1G76050 [Arabidopsis thalian 0.832 0.576 0.714 1.3e-91
TIGR_CMR|GSU_0082322 GSU_0082 "ribosomal large subu 0.382 0.354 0.426 7.5e-42
TIGR_CMR|CHY_1505305 CHY_1505 "ribosomal large subu 0.392 0.383 0.411 9.3e-38
TIGR_CMR|DET_1375300 DET_1375 "ribosomal large subu 0.338 0.336 0.392 2.2e-36
UNIPROTKB|Q4K5V9320 rluD "Pseudouridine synthase" 0.392 0.365 0.406 2.1e-32
UNIPROTKB|P33643326 rluD "23S rRNA pseudouridine s 0.392 0.358 0.403 5.5e-32
TIGR_CMR|CPS_3915324 CPS_3915 "ribosomal large subu 0.392 0.361 0.403 2.3e-31
UNIPROTKB|Q9KU20324 rluD "Ribosomal large subunit 0.395 0.364 0.393 1.3e-30
TIGR_CMR|VC_0709324 VC_0709 "ribosomal large subun 0.395 0.364 0.393 1.3e-30
TIGR_CMR|SPO_1408 342 SPO_1408 "ribosomal large subu 0.714 0.622 0.380 2.1e-29
TAIR|locus:2204355 AT1G76050 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 913 (326.5 bits), Expect = 1.3e-91, P = 1.3e-91
 Identities = 180/252 (71%), Positives = 202/252 (80%)

Query:    51 PIANYAGVQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSH 110
             P  N AG+++EE VD   GK+RLD+WISSRI+G+SRARVQSSIR GLV++NG+VV KVSH
Sbjct:    62 PRVNNAGLRIEEIVDAAKGKIRLDSWISSRINGVSRARVQSSIRLGLVTVNGRVVDKVSH 121

Query:   111 NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 170
             NVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGTLVN
Sbjct:   122 NVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGTLVN 181

Query:   171 GILHHCSLPTLASSNQXXXXXXXXXXXXX----XXXXXXXGASIRPGIVHRLDKGTSGLL 226
             GILHHCSLP +  SN                          AS+RPGIVHRLDKGT+GLL
Sbjct:   182 GILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTTGLL 241

Query:   227 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 286
             VVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRIE+PI RD +NRIRMAAIPG 
Sbjct:   242 VVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRIRMAAIPGG 301

Query:   287 NKHGQARHAASR 298
              + G+ARHAASR
Sbjct:   302 VRGGRARHAASR 313
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0009451 "RNA modification" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM
GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS
TIGR_CMR|GSU_0082 GSU_0082 "ribosomal large subunit pseudouridine synthase D" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1505 CHY_1505 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|DET_1375 DET_1375 "ribosomal large subunit pseudouridine synthase, RluA family" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
UNIPROTKB|Q4K5V9 rluD "Pseudouridine synthase" [Pseudomonas protegens Pf-5 (taxid:220664)] Back     alignment and assigned GO terms
UNIPROTKB|P33643 rluD "23S rRNA pseudouridine synthase" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_3915 CPS_3915 "ribosomal large subunit pseudouridine synthase D" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KU20 rluD "Ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0709 VC_0709 "ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_1408 SPO_1408 "ribosomal large subunit pseudouridine synthase D" [Ruegeria pomeroyi DSS-3 (taxid:246200)] 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

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 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

Your Input:
grail3.0003012502
hypothetical protein (444 aa)
(Populus trichocarpa)
Predicted Functional Partners:
fgenesh4_pg.C_scaffold_18203000001
Predicted protein (261 aa)
• •   • 0.825
estExt_Genewise1_v1.C_LG_VIII2938
hypothetical protein (232 aa)
• •   • 0.707
eugene3.94380001
Predicted protein (290 aa)
•     • 0.655
eugene3.149220001
Predicted protein (326 aa)
•     • 0.564
gw1.X.4012.1
isoleucyl-tRNA synthetase (1029 aa)
•  •    0.561
estExt_fgenesh4_pg.C_LG_VIII0269
hypothetical protein (397 aa)
  •   • 0.498
eugene3.34300002
Pseudouridylate synthase (225 aa)
  •   • 0.473
gw1.IX.3521.1
hypothetical protein; GTPase of unknown physiological role (By similarity) (489 aa)
•     • 0.451
gw1.XVIII.1881.1
hypothetical protein (281 aa)
•     • 0.434
estExt_fgenesh4_pm.C_1500028
hypothetical protein (326 aa)
  •   • 0.405

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 ?
Query298
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 3e-65
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 7e-57
PRK11180 325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; 4e-47
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 7e-36
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 2e-18
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 5e-14
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine is 4e-13
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 5e-13
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d 2e-11
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 7e-09
smart0036360 smart00363, S4, S4 RNA-binding domain 3e-08
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy 4e-08
pfam0147948 pfam01479, S4, S4 domain 2e-06
COG2302257 COG2302, COG2302, Uncharacterized conserved protei 4e-06
COG1188100 COG1188, COG1188, Ribosome-associated heat shock p 4e-05
PRK11112 257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 5e-05
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 6e-05
TIGR03069257 TIGR03069, PS_II_S4, photosystem II S4 domain prot 8e-05
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylat 1e-04
cd02558246 cd02558, PSRA_1, Pseudouridine synthase, a subgrou 2e-04
COG1189245 COG1189, COG1189, Predicted rRNA methylase [Transl 3e-04
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
 Score =  206 bits (525), Expect = 3e-65
 Identities = 95/241 (39%), Positives = 131/241 (54%), Gaps = 36/241 (14%)

Query: 59  QLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMV 118
            LE  V  +    RLD +++  +  ISR+R+Q  IR G V +NG+ V K S+ +K GD+V
Sbjct: 1   MLEFEVPEEEAGQRLDKFLAKLL-PISRSRIQKLIRKGRVRVNGKKV-KPSYKLKPGDVV 58

Query: 119 NCTISEL-QPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
              + E  +  +   EDIPLDI+YED+++LVVNKPA +VVHP  G+  GTLVN +L HC 
Sbjct: 59  RIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQ 118

Query: 178 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAH 237
                                            RPGIVHRLDK TSGLL+VAK+  +   
Sbjct: 119 D-----------------------------GVERPGIVHRLDKDTSGLLLVAKNREAARE 149

Query: 238 LSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAAS 297
           LSEQFK   +++ Y++L  G   +  G I+ PI RDP NR +MA +      G  + A +
Sbjct: 150 LSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVK----EGSGKPAIT 205

Query: 298 R 298
            
Sbjct: 206 H 206

Length = 289
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family 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|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>gnl|CDD|238095 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
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>gnl|CDD|201819 pfam01479, S4, S4 domain Back     alignment and domain information
>gnl|CDD|225185 COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>gnl|CDD|224109 COG1188, 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
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional 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|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein 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|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|224110 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 298
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
PRK11180 325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 99.96
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 99.96
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 99.96
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 99.95
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 99.94
KOG1919 371 consensus RNA pseudouridylate synthases [RNA proce 99.93
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 99.92
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 99.92
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 99.92
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 99.91
PRK11112 257 tRNA pseudouridine synthase C; Provisional 99.9
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 99.85
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 99.82
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 99.79
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 99.79
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.77
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 99.76
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.69
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.69
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.68
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.67
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 99.3
TIGR00093128 pseudouridine synthase. This model identifies pane 99.21
cd02868 226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 99.15
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 99.04
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 99.0
smart0036360 S4 S4 RNA-binding domain. 98.5
COG1188100 Ribosome-associated heat shock protein implicated 98.5
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 98.28
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 98.21
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 98.21
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 98.19
CHL00113201 rps4 ribosomal protein S4; Reviewed 98.16
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 98.05
PRK05327203 rpsD 30S ribosomal protein S4; Validated 98.02
COG2302257 Uncharacterized conserved protein, contains S4-lik 97.8
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 97.76
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.69
PRK1150770 ribosome-associated protein; Provisional 97.67
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 97.57
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.46
PRK00989 230 truB tRNA pseudouridine synthase B; Provisional 97.36
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.33
PRK04099 273 truB tRNA pseudouridine synthase B; Provisional 97.32
PRK00020 244 truB tRNA pseudouridine synthase B; Provisional 97.27
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 97.27
PRK00130 290 truB tRNA pseudouridine synthase B; Provisional 97.18
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 97.14
PRK14124 308 tRNA pseudouridine synthase B; Provisional 97.13
PRK03287 298 truB tRNA pseudouridine synthase B; Provisional 97.12
PRK02484 294 truB tRNA pseudouridine synthase B; Provisional 97.11
PRK14123 305 tRNA pseudouridine synthase B; Provisional 97.1
PRK02755 295 truB tRNA pseudouridine synthase B; Provisional 97.09
PRK05389 305 truB tRNA pseudouridine synthase B; Provisional 97.07
PRK02193 279 truB tRNA pseudouridine synthase B; Provisional 97.04
cd02573 277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 97.03
PRK04270 300 H/ACA RNA-protein complex component Cbf5p; Reviewe 96.98
PRK05033 312 truB tRNA pseudouridine synthase B; Provisional 96.98
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 96.97
PRK01550 304 truB tRNA pseudouridine synthase B; Provisional 96.96
PRK01528 292 truB tRNA pseudouridine synthase B; Provisional 96.95
COG250173 S4-like RNA binding protein [Replication, recombin 96.93
PRK01851 303 truB tRNA pseudouridine synthase B; Provisional 96.9
PRK14122 312 tRNA pseudouridine synthase B; Provisional 96.84
TIGR00425 322 CBF5 rRNA pseudouridine synthase, putative. This f 96.55
PRK04642 300 truB tRNA pseudouridine synthase B; Provisional 96.5
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 96.47
cd02867 312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 96.43
PLN00189194 40S ribosomal protein S9; Provisional 96.42
COG0130 271 TruB Pseudouridine synthase [Translation, ribosoma 96.14
PRK04313237 30S ribosomal protein S4e; Validated 95.99
PTZ00155181 40S ribosomal protein S9; Provisional 95.79
PLN00036261 40S ribosomal protein S4; Provisional 95.72
PTZ00223273 40S ribosomal protein S4; Provisional 95.62
PTZ00118262 40S ribosomal protein S4; Provisional 95.57
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosoma 92.72
PRK0177795 hypothetical protein; Validated 91.08
PRK13354410 tyrosyl-tRNA synthetase; Provisional 89.68
PF1445181 Ub-Mut7C: Mut7-C ubiquitin 89.46
COG4332203 Uncharacterized protein conserved in bacteria [Fun 88.39
PRK05912408 tyrosyl-tRNA synthetase; Validated 88.24
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 87.62
PF06353142 DUF1062: Protein of unknown function (DUF1062); In 85.66
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 85.24
PRK0836470 sulfur carrier protein ThiS; Provisional 84.42
cd0075480 MoaD Ubiquitin domain of MoaD-like proteins. MoaD 82.22
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=3.4e-41  Score=314.17  Aligned_cols=195  Identities=47%  Similarity=0.748  Sum_probs=172.9

Q ss_pred             EEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccc-cccccCCCCeee
Q 022339           61 EETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQP-LRAEAEDIPLDI  139 (298)
Q Consensus        61 ~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~-~~~~~~~~~~~I  139 (298)
                      ++.|..+.+++|||+||++.++ +||+.++++|++|.|.|||+++. ++++|..||+|++...+... ....+++.+++|
T Consensus         3 ~~~v~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~I   80 (289)
T COG0564           3 EFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDI   80 (289)
T ss_pred             eEEeChhhcCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccccccccccCCCccE
Confidence            4566778899999999999666 99999999999999999999996 99999999999998865442 334456777999


Q ss_pred             eecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCC
Q 022339          140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD  219 (298)
Q Consensus       140 lyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD  219 (298)
                      ||||+++||||||+||+|||++++..+|++++++.++..                             ...++++|||||
T Consensus        81 lyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~-----------------------------~~~~~~~vHRLD  131 (289)
T COG0564          81 LYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQD-----------------------------GVERPGIVHRLD  131 (289)
T ss_pred             EEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhccc-----------------------------cCCceeeeccCC
Confidence            999999999999999999999999999999999987631                             135788999999


Q ss_pred             CCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCCeEEEEcCCC
Q 022339          220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS  286 (298)
Q Consensus       220 ~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~~~~~~~~~~  286 (298)
                      ++||||||+|||..++..|+++|+++.+.|+|+|+|.|.+..++++|+.||+++..++.++.+....
T Consensus       132 kdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~  198 (289)
T COG0564         132 KDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEG  198 (289)
T ss_pred             CCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEECcccCCCCEEeeeeecCCcCCceEEEeccC
Confidence            9999999999999999999999999999999999999999998999999999998887777665443

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional 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
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] 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
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 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
>PRK11112 tRNA pseudouridine synthase C; Provisional 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
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like 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
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like 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
>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
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like 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
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain 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
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated 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
>PRK02484 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
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02193 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
>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
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional 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
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK01777 hypothetical protein; Validated Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>PF14451 Ub-Mut7C: Mut7-C ubiquitin Back     alignment and domain information
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated 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
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function 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
>PRK08364 sulfur carrier protein ThiS; Provisional Back     alignment and domain information
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins 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 ?
Query298
1v9f_A 325 Crystal Structure Of Catalytic Domain Of Pseudourid 1e-29
1qyu_A 349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 2e-28
1prz_A 252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 3e-20
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 1e-06
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 5e-06
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 6e-06
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325 Back     alignment and structure 
Iteration: 1

 Score =  126 bits (316), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 113/227 (49%), Gaps = 28/227 (12%)
Query: 58  VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDM 117
           VQL  TV       RLD  ++      SR+R++  I    V +NG+V  K    V GG+ 
Sbjct: 4   VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQ 63
Query: 118 VNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
           V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+  
Sbjct: 64  VAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY- 122
Query: 178 LPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKDEHSHAH 237
            P +A                            R GIVHRLDK T+GL+VVAK   +   
Sbjct: 123 -PPIADVP-------------------------RAGIVHRLDKDTTGLMVVAKTVPAQTR 156
Query: 238 LSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIP 284
           L E  +   I R Y ++  G  + + G ++ PISR P  R  MA  P
Sbjct: 157 LVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHP 202
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349 Back     alignment and structure
>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252 Back     alignment and structure
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 Back     alignment and structure
>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-induced Rna Structure Length = 217 Back     alignment and structure
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query298
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; 2e-95
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 4e-61
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 2e-50
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 6e-09
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 3e-05
>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
 Score =  283 bits (727), Expect = 2e-95
 Identities = 81/238 (34%), Positives = 114/238 (47%), Gaps = 34/238 (14%)

Query: 58  VQLEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDM 117
           VQL  TV       RLD  ++      SR+R++  I    V +NG+V  K    V GG+ 
Sbjct: 4   VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQ 63

Query: 118 VNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS 177
           V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+  
Sbjct: 64  VAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY- 122

Query: 178 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAH 237
                                      I+    R GIVHRLDK T+GL+VVAK   +   
Sbjct: 123 -------------------------PPIAD-VPRAGIVHRLDKDTTGLMVVAKTVPAQTR 156

Query: 238 LSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA 295
           L E  +   I R Y ++  G  + + G ++ PISR P  R  MA  P        + A
Sbjct: 157 LVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHPMG------KPA 207
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217 Back     alignment and structure
>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
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Length = 92 Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Length = 133 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query298
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; 100.0
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 99.97
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 99.97
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 99.97
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 99.93
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 99.91
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 99.88
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 99.87
2gml_A 237 Ribosomal large subunit pseudouridine synthase F; 99.75
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.88
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.84
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 98.64
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.63
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.61
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 98.39
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 98.29
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 98.19
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 98.17
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 98.03
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 97.95
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 97.67
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 97.28
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 97.09
1k8w_A 327 TRNA pseudouridine synthase B; protein-RNA complex 96.83
1r3e_A 309 TRNA pseudouridine synthase B; RNA modification, p 96.73
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 96.71
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 96.7
1sgv_A 316 TRNA pseudouridine synthase B; hinged motion, tRNA 96.55
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 96.46
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 96.17
3iz6_D265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 94.75
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 94.68
3u5c_E261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 94.02
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 90.34
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 90.01
1fm0_D81 Molybdopterin convertin factor, subunit 1; molybde 89.23
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 88.96
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 83.99
2ktl_A164 Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s 81.99
>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=3.7e-39  Score=303.75  Aligned_cols=196  Identities=39%  Similarity=0.611  Sum_probs=107.8

Q ss_pred             EEEEEcCCCccchHHHHHHhccCCcCHHHHHHHHHCCceEECCEEeccccccccCCCEEeeccccccccccccCCCCeee
Q 022339           60 LEETVDTKAGKLRLDAWISSRIDGISRARVQSSIRSGLVSINGQVVSKVSHNVKGGDMVNCTISELQPLRAEAEDIPLDI  139 (298)
Q Consensus        60 ~~~~v~~~~~g~rLdk~L~~~~~~~Sr~~~~~lI~~G~V~VNGk~v~~~~~~v~~gD~I~i~~~~~~~~~~~~~~~~~~I  139 (298)
                      ++++|+..++++|||+||++.++.+||+.++++|++|.|+|||+++.++++.|.+||+|++...........++..+++|
T Consensus         6 ~~~~v~~~~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~i   85 (325)
T 1v9f_A            6 LTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDI   85 (325)
T ss_dssp             ----------------------------------------------------------------------CCCCCCCCCE
T ss_pred             EEEEECCccCCchHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeE
Confidence            45677888899999999999876899999999999999999999865899999999999997654332223345667899


Q ss_pred             eecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCCCceecccCC
Q 022339          140 VYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLD  219 (298)
Q Consensus       140 lyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~vhRLD  219 (298)
                      ||||++++|||||+||+||+.++....|+++.|..++..  ..                         ...++++|||||
T Consensus        86 lyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~--~~-------------------------~~~~~~~vhRLD  138 (325)
T 1v9f_A           86 VYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPP--IA-------------------------DVPRAGIVHRLD  138 (325)
T ss_dssp             EEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGG--GG-------------------------GSGGGGBCCCCC
T ss_pred             EEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHh--cC-------------------------CCCceeeecCCC
Confidence            999999999999999999998887778999999877521  00                         124678999999


Q ss_pred             CCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCCeEEEEc
Q 022339          220 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI  283 (298)
Q Consensus       220 ~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~~~~~~~  283 (298)
                      ++||||||||+|..+++.|+.+|+.+.++|+|+|+|.|.+.. +|+|+.||.++..++.++.+.
T Consensus       139 ~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~-~g~i~~~i~~~~~~~~~~~v~  201 (325)
T 1v9f_A          139 KDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMAVH  201 (325)
T ss_dssp             TTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCC-CEEEECCEEECSSCTTCEEEC
T ss_pred             CCCeeEEEEEcCHHHHHHHHHHHHcCCeeEEEEEEEeCCCCC-CCEEeeeeeECCCCCEEEEEC
Confidence            999999999999999999999999999999999999999977 899999999987666666554
>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
>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
>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
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>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
>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
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A 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
>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
>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
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus} 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
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D Back     alignment and structure
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D* Back     alignment and structure
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>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
>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
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} 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
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Back     alignment and structure
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W Back     alignment and structure
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E Back     alignment and structure
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Back     alignment and structure
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Back     alignment and structure
>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D Back     alignment and structure
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Back     alignment and structure
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Back     alignment and structure
>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4} 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 298
d1v9fa_ 250 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 8e-25
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 3e-18
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-te 2e-07
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-te 1e-06
d1dm9a_104 d.66.1.3 (A:) Heat shock protein 15 kD {Escherichi 0.002
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250 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 D, RluD
species: Escherichia coli [TaxId: 562]

 Score = 98.1 bits (243), Expect = 8e-25
 Identities = 56/156 (35%), Positives = 77/156 (49%), Gaps = 28/156 (17%)

Query: 131 EAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFS 190
           E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+               
Sbjct: 2   EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY-------------- 47

Query: 191 DAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERV 250
                               R GIVHRLDK T+GL+VVAK   +   L E  +   I R 
Sbjct: 48  -------------PPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 94

Query: 251 YISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 286
           Y ++       + G ++ PISR P  R  MA  P  
Sbjct: 95  YEAVA-IGHMTAGGTVDEPISRHPTKRTHMAVHPMG 129
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58 Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Length = 59 Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Length = 104 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 ?
Query298
d1v9fa_ 250 Ribosomal large subunit pseudouridine synthase D, 99.94
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 99.92
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 99.71
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 99.64
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 99.18
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 99.15
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 98.76
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 98.74
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 98.07
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 97.89
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 97.87
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 97.24
d1k8wa5 242 Pseudouridine synthase II TruB {Escherichia coli [ 97.15
d1r3ea2 228 Pseudouridine synthase II TruB {Thermotoga maritim 96.94
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 96.85
d1sgva2 233 Pseudouridine synthase II TruB {Mycobacterium tube 96.82
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 96.68
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 96.6
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {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 D, RluD
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=4e-27  Score=212.06  Aligned_cols=127  Identities=45%  Similarity=0.758  Sum_probs=107.6

Q ss_pred             ccCCCCeeeeecCCcEEEEeCCCCceeecCCCCCCccHHHHHHhhcCCCccccccccccccccccccccccccccCCCCC
Q 022339          131 EAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASI  210 (298)
Q Consensus       131 ~~~~~~~~IlyeD~~llvvnKPaGl~v~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~  210 (298)
                      +|++.+++|||||+++||||||+||+|||+.++..+|+++.|..++....                           ...
T Consensus         2 ~P~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~---------------------------~~~   54 (250)
T d1v9fa_           2 EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIA---------------------------DVP   54 (250)
T ss_dssp             CCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGG---------------------------GSG
T ss_pred             CCCCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhcc---------------------------CCC
Confidence            35678899999999999999999999999988888899999988753100                           224


Q ss_pred             CceecccCCCCCceeEEEEcCHHHHHHHHHHHhcCeeceEEEEEEeeecCCCCcEEEccceeCCCCCeEEEEcCC
Q 022339          211 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPG  285 (298)
Q Consensus       211 ~~~~vhRLD~~TSGLlL~Ak~~~~~~~L~~~f~~~~i~K~YlAlv~G~~~~~~g~I~~pl~~~~~~~~~~~~~~~  285 (298)
                      .+++|||||++||||||||||+.+++.|+.+|+++.|.|+|+|++.|.+ ..++.++.|+.........+.+.+.
T Consensus        55 ~~~~vHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~v~K~Y~a~~~g~~-~~~~~~~~~~~~~~~~~~~~~~~~~  128 (250)
T d1v9fa_          55 RAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHM-TAGGTVDEPISRHPTKRTHMAVHPM  128 (250)
T ss_dssp             GGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCC-CCCEEEECCEEECSSCTTCEEECTT
T ss_pred             ceeEEeecCCCCcceEEEecccHHHHhhhhhhccceEeEEeeeeecccc-ccccccccccccCCcccceeEECCC
Confidence            5678999999999999999999999999999999999999999999988 4567888888877666555555543
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {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
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} 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
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} 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
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} 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