Citrus Sinensis ID: 037167

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---
LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSVGSERIRGIQIDSLP
cHHHHHHHHcccccccHHHHHHHHHcccEEEccEEccccccccccccEEEEEccccccccccccccEEEEcccEEEEEccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccEEEEEEccHHHHHHHHHHHHcccccccccHHHHHHHcccccEEEEEEEEEEcccccEEEEcccccccccccccEEEEccccccccEEEEEEEEEcccccEEEEEEEEcccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHcccccccHHHccccccccc
ccHHHHHHHHHcccccHHHHHHHHHcccEEEccEEEcccccEEccccEEEEEcccccccccccccEEEEEcccEEEEEcccccEEcccccccccHHHHHHHHHccccccccccccccccEEEEEcccccEEEEEEccHHHHHHHHHHHHcccccccccccHHHHHccccEEEEEEEEEccccccccEEEccccccccccHHHEEEEEcccccccEEHHEHHHHcccccEEEEEEEEEcccccEEEEEHHHccccccccccccccccccccccHHHHcccccccccccHHHHHcccccHHHHHHHcccEccccccEEEEEccccHHHHHHHHHHHHccccccccccEEEEcccc
LTLIEFYstkhknsaplQGWLQRIQngqitvdgrvvndpniilsagselvyhrlpwkepdvPYLLEVLyedddlialnkpsglqvlpgglfqQRTVLNQLQWRaskqssslssqashpvpvhrlgrgtsgILLCAKTKLAKTCIAgyfadktsvidadSTVMELSQRKITKIYRALVHgivdedkviikqpigivrypgvakglyvaspsgkpalskvdvlerdvqrnCTLVQVEIQSGRPHQIRIHLAFLghpllgdplyvaggqpksfdsefadgtfaqdggyerpvnpvpgdcgyYLHAYQLflshpttnevikitaplpsvlktreegrevdksvgserirgiqidslp
LTLIEFYStkhknsaplqGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQssslssqashpvpvhrlgrgTSGILLCAKTKLAKTCIAGYfadktsvidadSTVMELSQRKITKIYRALvhgivdedkviikqPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKItaplpsvlktreegrevdksvgserirgiqidslp
LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPyllevlyedddlIALNKPSGLQVLPGGLFQQRTVLNQLQWRaskqssslssqasHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSVGSERIRGIQIDSLP
*****FY*******APLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQW*******************HRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLP******************************
LTLIEFYSTKHK*****QGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREV******************
LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQ******************PVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKT************SERIRGIQIDSLP
LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKT****ADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSVGSERIRGIQIDSLP
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSVGSERIRGIQIDSLP
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 ?
Query353 2.2.26 [Sep-21-2011]
Q5M721369 RNA pseudourine synthase yes no 0.934 0.894 0.701 1e-133
Q0DST9397 RNA pseudourine synthase yes no 0.954 0.848 0.658 1e-125
P72970291 Uncharacterized RNA pseud N/A no 0.793 0.962 0.408 4e-52
Q8DEV0325 Ribosomal large subunit p yes no 0.745 0.809 0.316 4e-28
Q9CKA6324 Ribosomal large subunit p yes no 0.733 0.799 0.315 2e-27
Q87S65325 Ribosomal large subunit p yes no 0.736 0.8 0.313 4e-27
O67638316 Uncharacterized RNA pseud yes no 0.745 0.832 0.305 4e-27
P33640320 Ribosomal large subunit p yes no 0.730 0.806 0.328 6e-27
Q9KU20324 Ribosomal large subunit p yes no 0.736 0.802 0.319 8e-27
P44445324 Ribosomal large subunit p yes no 0.767 0.836 0.297 2e-26
>sp|Q5M721|PUS5_ARATH RNA pseudourine synthase 5 OS=Arabidopsis thaliana GN=At3g52260 PE=2 SV=2 Back     alignment and function desciption
 Score =  474 bits (1221), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 235/335 (70%), Positives = 277/335 (82%), Gaps = 5/335 (1%)

Query: 2   TLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPDV 61
           T+ EFY TK+K+SAPL GW+QRIQNGQI +DG VV DPN +L +GS+LVY RLPWKEPD 
Sbjct: 34  TVSEFYFTKYKSSAPLLGWIQRIQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDT 93

Query: 62  PYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQAS-HPVP 120
           PY LEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVL QLQW   K  S + S+ S HPVP
Sbjct: 94  PYSLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVP 153

Query: 121 VHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMEL-SQRKITKIYRALVHG 179
           VHRLGRGTSGILLCAKTKLAKT +A YFA+ TS++ + +   E  + RK++KIYRAL  G
Sbjct: 154 VHRLGRGTSGILLCAKTKLAKTKLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADG 213

Query: 180 IVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSG 239
           IV+ED+V+IKQPIG+VRYPGVA+GLYVASP GKPA SKV VLERD ++NC+LV+VEIQSG
Sbjct: 214 IVEEDEVVIKQPIGVVRYPGVAQGLYVASPEGKPAFSKVFVLERDREKNCSLVKVEIQSG 273

Query: 240 RPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFAD--GTFAQDGGYERPVNPVPGDCG 297
           RPHQIRIHLA++GHPL+GDPLYVAGGQPK FD +  D    FA+DGGY RP   VPGDCG
Sbjct: 274 RPHQIRIHLAYMGHPLVGDPLYVAGGQPKCFDPDLVDDAAAFAEDGGYRRPNQAVPGDCG 333

Query: 298 YYLHAYQLFLSH-PTTNEVIKITAPLPSVLKTREE 331
           Y+LHA+Q+ L +   T++V+KI APLP +L+TR E
Sbjct: 334 YHLHAHQVELPNLLNTHKVVKIVAPLPPILQTRCE 368

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q0DST9|PUS5_ORYSJ RNA pseudourine synthase 5 OS=Oryza sativa subsp. japonica GN=Os03g0288500 PE=2 SV=2 Back     alignment and function description
>sp|P72970|Y1592_SYNY3 Uncharacterized RNA pseudouridine synthase slr1592 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1592 PE=3 SV=1 Back     alignment and function description
>sp|Q8DEV0|RLUD_VIBVU Ribosomal large subunit pseudouridine synthase D OS=Vibrio vulnificus (strain CMCP6) GN=rluD PE=3 SV=1 Back     alignment and function description
>sp|Q9CKA6|RLUD_PASMU Ribosomal large subunit pseudouridine synthase D OS=Pasteurella multocida (strain Pm70) GN=rluD PE=3 SV=1 Back     alignment and function description
>sp|Q87S65|RLUD_VIBPA Ribosomal large subunit pseudouridine synthase D OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) GN=rluD 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|P33640|RLUD_PSEAE Ribosomal large subunit pseudouridine synthase D OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=rluD PE=3 SV=2 Back     alignment and function description
>sp|Q9KU20|RLUD_VIBCH Ribosomal large subunit pseudouridine synthase D OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rluD PE=3 SV=1 Back     alignment and function description
>sp|P44445|RLUD_HAEIN Ribosomal large subunit pseudouridine synthase D OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) 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 ?
Query353
224100817377 predicted protein [Populus trichocarpa] 0.949 0.888 0.775 1e-150
296086047347 unnamed protein product [Vitis vinifera] 0.889 0.904 0.759 1e-140
225449104348 PREDICTED: RNA pseudourine synthase 5-li 0.889 0.902 0.757 1e-139
356576201371 PREDICTED: RNA pseudourine synthase 5-li 0.940 0.894 0.710 1e-138
357443349371 RNA pseudourine synthase [Medicago trunc 0.934 0.889 0.718 1e-137
449485927371 PREDICTED: RNA pseudourine synthase 5-li 0.949 0.902 0.701 1e-136
449452164371 PREDICTED: RNA pseudourine synthase 5-li 0.949 0.902 0.698 1e-135
42572641369 RNA pseudourine synthase 5 [Arabidopsis 0.934 0.894 0.701 1e-131
297819936387 pseudouridine synthase family protein [A 0.943 0.860 0.686 1e-130
10045559376 putative protein [Arabidopsis thaliana] 0.934 0.877 0.687 1e-129
>gi|224100817|ref|XP_002312025.1| predicted protein [Populus trichocarpa] gi|222851845|gb|EEE89392.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  536 bits (1380), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 262/338 (77%), Positives = 295/338 (87%), Gaps = 3/338 (0%)

Query: 1   LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEPD 60
           LTLI FYS+K+KNSAPLQGWLQRI NGQIT+DG VV +P  IL  G ELVYHRLPW+EPD
Sbjct: 39  LTLIHFYSSKYKNSAPLQGWLQRIHNGQITIDGEVVKEPKAILRDGMELVYHRLPWREPD 98

Query: 61  VPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVP 120
            PYLL+VLYEDDD++ALNKP GLQVLPGGLFQQRTVL QLQWRASK SSSL+ Q SHPVP
Sbjct: 99  APYLLQVLYEDDDMVALNKPPGLQVLPGGLFQQRTVLMQLQWRASKGSSSLAIQGSHPVP 158

Query: 121 VHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVI-DADSTVMELSQ-RKITKIYRALVH 178
           VHRLGRGTSGILLCAKTK+AKT +A YFAD TS+I D+ +  ME S+ RKI+KIYRALV+
Sbjct: 159 VHRLGRGTSGILLCAKTKVAKTSLAAYFADGTSLIGDSSNANMEQSKRRKISKIYRALVN 218

Query: 179 GIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQS 238
           GI+++DK+IIKQPIG +RYPGVAKGLYVASPSGKPALSKV+VLERD Q N TLVQVEI+S
Sbjct: 219 GILNQDKIIIKQPIGTMRYPGVAKGLYVASPSGKPALSKVEVLERDSQLNQTLVQVEIES 278

Query: 239 GRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGY 298
           GRPHQIRIHL+F+GHPLLGDPLY  GGQP  FDSE  D +FA+DGGYERP  PVPGDCGY
Sbjct: 279 GRPHQIRIHLSFIGHPLLGDPLYDVGGQPMCFDSEHEDESFAEDGGYERPAKPVPGDCGY 338

Query: 299 YLHAYQLFLSHPTTNE-VIKITAPLPSVLKTREEGREV 335
           YLHA+QL LSHPT NE VIKITAPLPS+L+T+ E  E+
Sbjct: 339 YLHAHQLVLSHPTKNEQVIKITAPLPSILRTQAETEEL 376

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|296086047|emb|CBI31488.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225449104|ref|XP_002276664.1| PREDICTED: RNA pseudourine synthase 5-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356576201|ref|XP_003556222.1| PREDICTED: RNA pseudourine synthase 5-like [Glycine max] Back     alignment and taxonomy information
>gi|357443349|ref|XP_003591952.1| RNA pseudourine synthase [Medicago truncatula] gi|358349060|ref|XP_003638558.1| RNA pseudourine synthase [Medicago truncatula] gi|355481000|gb|AES62203.1| RNA pseudourine synthase [Medicago truncatula] gi|355504493|gb|AES85696.1| RNA pseudourine synthase [Medicago truncatula] Back     alignment and taxonomy information
>gi|449485927|ref|XP_004157313.1| PREDICTED: RNA pseudourine synthase 5-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449452164|ref|XP_004143830.1| PREDICTED: RNA pseudourine synthase 5-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|42572641|ref|NP_974416.1| RNA pseudourine synthase 5 [Arabidopsis thaliana] gi|229891781|sp|Q5M721.2|PUS5_ARATH RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA pseudouridylate synthase 5; AltName: Full=RNA-uridine isomerase 5 gi|332645400|gb|AEE78921.1| RNA pseudourine synthase 5 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297819936|ref|XP_002877851.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297323689|gb|EFH54110.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|10045559|emb|CAC07917.1| putative protein [Arabidopsis thaliana] 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 ?
Query353
UNIPROTKB|Q9KU20324 rluD "Ribosomal large subunit 0.399 0.435 0.349 3.4e-19
TIGR_CMR|VC_0709324 VC_0709 "ribosomal large subun 0.399 0.435 0.349 3.4e-19
UNIPROTKB|Q4K5V9320 rluD "Pseudouridine synthase" 0.407 0.45 0.349 2e-18
TIGR_CMR|DET_1375300 DET_1375 "ribosomal large subu 0.266 0.313 0.363 2.6e-17
TIGR_CMR|SPO_1408342 SPO_1408 "ribosomal large subu 0.818 0.845 0.266 2.7e-17
TIGR_CMR|CHY_1505305 CHY_1505 "ribosomal large subu 0.300 0.347 0.383 3.7e-16
TIGR_CMR|SPO_3392215 SPO_3392 "ribosomal large subu 0.277 0.455 0.343 4.6e-15
TIGR_CMR|CBU_0757327 CBU_0757 "ribosomal large subu 0.450 0.486 0.286 9.2e-15
UNIPROTKB|P33643326 rluD "23S rRNA pseudouridine s 0.422 0.457 0.309 1.5e-14
TIGR_CMR|CHY_1119301 CHY_1119 "ribosomal large subu 0.305 0.358 0.396 3.1e-14
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
 Score = 187 (70.9 bits), Expect = 3.4e-19, Sum P(2) = 3.4e-19
 Identities = 58/166 (34%), Positives = 85/166 (51%)

Query:   161 VMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDV 220
             V  L +R +T+ Y A+V G +    +I K PIG  R+    + L   SP GK A++   V
Sbjct:   159 VRALQKRDVTREYEAIVIGTMTAGGMIDK-PIG--RH-STKRTLMSVSPMGKHAVTHYRV 214

Query:   221 LERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQ---PKSFDSEFADG 277
              E    R  T +++ +++GR HQIR+H+A+L HPLLGD  Y  GG+   PK    E  + 
Sbjct:   215 AEHF--REHTRLRLRLETGRTHQIRVHMAYLQHPLLGDTAY--GGRARIPKGATEELTE- 269

Query:   278 TFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVIKITAPLP 323
                +D  ++R            LHA  L   HP T E ++  AP+P
Sbjct:   270 -MIRD--FDRQA----------LHAVMLKFEHPVTGEELEFHAPVP 302
GO:0000154 "rRNA modification" evidence=ISS
GO:0009982 "pseudouridine synthase activity" evidence=ISS
TIGR_CMR|VC_0709 VC_0709 "ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
UNIPROTKB|Q4K5V9 rluD "Pseudouridine synthase" [Pseudomonas protegens Pf-5 (taxid:220664)] 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
TIGR_CMR|SPO_1408 SPO_1408 "ribosomal large subunit pseudouridine synthase D" [Ruegeria pomeroyi DSS-3 (taxid:246200)] 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|SPO_3392 SPO_3392 "ribosomal large subunit pseudouridine synthase A" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_0757 CBU_0757 "ribosomal large subunit pseudouridine synthase D" [Coxiella burnetii RSA 493 (taxid:227377)] 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|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) ?
Q5M721PUS5_ARATH5, ., 4, ., 9, 9, ., -0.70140.93480.8943yesno
Q0DST9PUS5_ORYSJ5, ., 4, ., 9, 9, ., -0.65800.95460.8488yesno

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 Layer5.4.99LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00018225001
SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (353 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00019724001
RecName- Full=Pseudouridylate synthase; EC=5.4.99.-; (304 aa)
  •   • 0.414

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 ?
Query353
TIGR00005299 TIGR00005, rluA_subfam, pseudouridine synthase, Rl 1e-68
COG0564289 COG0564, RluA, Pseudouridylate synthases, 23S RNA- 6e-67
cd02869185 cd02869, PseudoU_synth_RluCD_like, Pseudouridine s 1e-50
PRK11180325 PRK11180, rluD, 23S rRNA pseudouridine synthase D; 2e-39
cd02557213 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth 1e-37
cd02563223 cd02563, PseudoU_synth_TruC, tRNA pseudouridine is 4e-27
pfam00849149 pfam00849, PseudoU_synth_2, RNA pseudouridylate sy 7e-27
PRK11025317 PRK11025, PRK11025, 23S rRNA pseudouridylate synth 3e-23
PRK11112257 PRK11112, PRK11112, tRNA pseudouridine synthase C; 1e-21
cd02558246 cd02558, PSRA_1, Pseudouridine synthase, a subgrou 2e-21
PRK10158219 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy 5e-19
cd02550154 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine 3e-15
TIGR01621217 TIGR01621, RluA-like, pseudouridine synthase Rlu f 1e-11
COG1187248 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylat 2e-07
cd02870146 cd02870, PseudoU_synth_RsuA_like, Pseudouridine sy 2e-06
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d 3e-04
smart0036360 smart00363, S4, S4 RNA-binding domain 0.004
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family Back     alignment and domain information 
 Score =  217 bits (554), Expect = 1e-68
 Identities = 109/313 (34%), Positives = 152/313 (48%), Gaps = 47/313 (15%)

Query: 20  WLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEP-DVPYL---LEVLYEDDDLI 75
             + I+NGQ+ V+G+V  +P + +  G + +  R+P +E  +VP     L++L+ED+D+I
Sbjct: 24  IQKLIENGQVKVNGKVTANPKLKVKDG-DRITVRVPEEEEHEVPPQDIPLDILFEDEDII 82

Query: 76  ALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCA 135
            +NKPSGL V PGG     TVLN L          ++        VHRL R TSG+++ A
Sbjct: 83  VINKPSGLVVHPGGGNPFGTVLNALL----AHCPPIAGVER-VGIVHRLDRDTSGLMVVA 137

Query: 136 KTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIV 195
           KT LA                      +L  R +TK Y ALVHG  D     +  P+G V
Sbjct: 138 KTPLA----------------LRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRV 181

Query: 196 RYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPL 255
                       S  GKPA++   VLER    N +LV+ E+++GR HQIR+HL +LGHPL
Sbjct: 182 PNN-RGLMAVHPSSEGKPAVTHFRVLERF--GNASLVECELETGRTHQIRVHLQYLGHPL 238

Query: 256 LGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEV 315
            GDPLY      K       +G                      LHAY+L   HP T E+
Sbjct: 239 AGDPLY----GNKPVPGNNLNGL--------------LNFDRQALHAYELGFIHPATGEI 280

Query: 316 IKITAPLPSVLKT 328
           ++  APLP+ L  
Sbjct: 281 LEFEAPLPADLVL 293

In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine [Protein synthesis, tRNA and rRNA base modification]. Length = 299
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] 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|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional 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|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase Back     alignment and domain information
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate 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|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; 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|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621 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|211347 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases, RsuA subfamily 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|214638 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 353
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 100.0
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 100.0
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 100.0
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 100.0
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 100.0
PRK11112257 tRNA pseudouridine synthase C; Provisional 100.0
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 100.0
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 100.0
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 100.0
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 100.0
KOG1919371 consensus RNA pseudouridylate synthases [RNA proce 100.0
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 100.0
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 100.0
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 100.0
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 100.0
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 100.0
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 100.0
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 100.0
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 100.0
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 100.0
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 99.98
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 99.97
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 99.96
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 99.96
TIGR00093128 pseudouridine synthase. This model identifies pane 99.94
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 99.93
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 99.17
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 99.09
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 98.88
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 98.58
smart0036360 S4 S4 RNA-binding domain. 98.15
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 97.96
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 97.92
COG1188100 Ribosome-associated heat shock protein implicated 97.91
CHL00113201 rps4 ribosomal protein S4; Reviewed 97.86
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 97.76
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 97.76
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 97.72
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 97.7
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 97.7
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 97.67
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 97.64
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 97.62
PRK05327203 rpsD 30S ribosomal protein S4; Validated 97.6
TIGR00478228 tly hemolysin TlyA family protein. Hemolysins are 97.57
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 97.52
PRK14123305 tRNA pseudouridine synthase B; Provisional 97.52
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 97.51
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 97.51
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 97.5
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 97.48
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 97.48
PRK14846345 truB tRNA pseudouridine synthase B; Provisional 97.47
PRK14124308 tRNA pseudouridine synthase B; Provisional 97.45
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 97.45
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 97.44
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 97.44
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 97.43
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 97.43
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 97.4
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 97.39
COG2302257 Uncharacterized conserved protein, contains S4-lik 97.36
PRK14122312 tRNA pseudouridine synthase B; Provisional 97.26
PRK1150770 ribosome-associated protein; Provisional 97.22
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 97.22
COG1189245 Predicted rRNA methylase [Translation, ribosomal s 97.2
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 97.19
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 97.05
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 96.99
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 96.72
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 96.6
COG250173 S4-like RNA binding protein [Replication, recombin 96.48
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 96.4
PRK04313237 30S ribosomal protein S4e; Validated 96.01
PLN00036261 40S ribosomal protein S4; Provisional 95.74
PLN00189194 40S ribosomal protein S9; Provisional 95.66
PTZ00223273 40S ribosomal protein S4; Provisional 95.61
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 95.59
PTZ00118262 40S ribosomal protein S4; Provisional 95.52
PTZ00155181 40S ribosomal protein S9; Provisional 94.54
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosoma 93.61
PRK13354410 tyrosyl-tRNA synthetase; Provisional 90.81
PRK05912408 tyrosyl-tRNA synthetase; Validated 89.04
PF1445181 Ub-Mut7C: Mut7-C ubiquitin 88.77
PRK0177795 hypothetical protein; Validated 86.37
KOG2559318 consensus Predicted pseudouridine synthase [Transl 86.35
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 84.18
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information 
Probab=100.00  E-value=1e-64  Score=471.80  Aligned_cols=272  Identities=38%  Similarity=0.580  Sum_probs=227.4

Q ss_pred             CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCC--CC--CCCCccEEEECCcEEE
Q 037167            1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKE--PD--VPYLLEVLYEDDDLIA   76 (353)
Q Consensus         1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~--~~--~~~~~~Ilyed~~~iv   76 (353)
                      +||..||.+ +.. .||+.+.++|++|.|+|||+++. ++++|..||+|.+.......  ..  .+.+++|||||++++|
T Consensus        13 ~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llV   89 (289)
T COG0564          13 QRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLV   89 (289)
T ss_pred             CCHHHHHHH-ccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEE
Confidence            478888888 665 79999999999999999999997 99999999999885432111  11  1234789999999999


Q ss_pred             EECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhccccccc
Q 037167           77 LNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVID  156 (353)
Q Consensus        77 vnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~  156 (353)
                      ||||+||+|||++.+...|+++++..+....       ..++++||||||+||||||+|||..++..|+++|++      
T Consensus        90 vnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~------  156 (289)
T COG0564          90 VNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-------VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQ------  156 (289)
T ss_pred             EECCCCCcCcCCCCCccHhHHHHHHHhcccc-------CCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhc------
Confidence            9999999999998888899999887664322       257899999999999999999999999999999987      


Q ss_pred             cchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCC-CCcceeEEEEEEEeCCCCeEEEEEE
Q 037167          157 ADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPS-GKPALSKVDVLERDVQRNCTLVQVE  235 (353)
Q Consensus       157 ~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~-gk~a~t~~~vl~~~~~~~~sll~~~  235 (353)
                                +.+.|+|+|+|.|.++++++.|+.|+++.....  ....+.... |++|.|.|+++++... ..||++|+
T Consensus       157 ----------r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~--~~~~v~~~~~gk~A~T~~~~l~~~~~-~~tlv~~~  223 (289)
T COG0564         157 ----------RKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNR--KKMAVVKEGSGKPAITHYEVLERFGD-NYTLVELK  223 (289)
T ss_pred             ----------CcCcEEEEEEEECcccCCCCEEeeeeecCCcCC--ceEEEeccCCCCceEEEEEehhccCC-ceEEEEEE
Confidence                      589999999999999988899999999875433  223333333 8999999999998742 26999999


Q ss_pred             eCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCccccccccceeeeeecCCCCCE
Q 037167          236 IQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEV  315 (353)
Q Consensus       236 l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~  315 (353)
                      |.||||||||+||+++||||+||.+||....             ....+.          .|++|||++|.|.||.+++.
T Consensus       224 ~~TGRTHQIRVHl~~lghPI~GD~~Yg~~~~-------------~~~~~~----------~r~~LHA~~l~f~hp~t~~~  280 (289)
T COG0564         224 PETGRTHQIRVHLAHLGHPIVGDPLYGGKDK-------------SAGAGL----------KRQALHAYKLSFTHPLTGEE  280 (289)
T ss_pred             eCCCCHhHHHHHHHHCCCCeeCCcccCCchh-------------hcccCc----------chhhhhhceeEccCCCCCCE
Confidence            9999999999999999999999999996310             000011          24899999999999999999


Q ss_pred             EEEEeCCch
Q 037167          316 IKITAPLPS  324 (353)
Q Consensus       316 ~~~~aplP~  324 (353)
                      +.|++|+|.
T Consensus       281 ~~~~a~~p~  289 (289)
T COG0564         281 LEFEAPLPE  289 (289)
T ss_pred             EEEecCCCC
Confidence            999999984

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>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
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family 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
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification] Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional 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
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] 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
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB 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
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like 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
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family 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
>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
>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
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type 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
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family 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
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein 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
>PRK02193 truB 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
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 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
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] 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
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] 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
>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
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated Back     alignment and domain information
>PF14451 Ub-Mut7C: Mut7-C ubiquitin Back     alignment and domain information
>PRK01777 hypothetical protein; Validated 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query353
1v9f_A325 Crystal Structure Of Catalytic Domain Of Pseudourid 3e-16
1prz_A252 Crystal Structure Of Pseudouridine Synthase Rlud Ca 1e-14
1qyu_A349 Structure Of The Catalytic Domain Of 23s Rrna Pseud 3e-14
1xpi_A231 Crystal Structure Of The Catalytic Domain Of E. Col 3e-13
1v9k_A228 The Crystal Structure Of The Catalytic Domain Of Ps 1e-12
2i82_A217 Crystal Structure Of Pseudouridine Synthase Rlua: I 1e-10
>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 = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 116/249 (46%), Gaps = 40/249 (16%)
Query: 75  IALNKPSGLQVLPGGLFQQRTVLNQLQWRXXXXXXXXXXXXXHPVPVHRLGRGTSGILLC 134
           I +NKP  L V PG      TVLN L                    VHRL + T+G+++ 
Sbjct: 93  IIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGI-----VHRLDKDTTGLMVV 147
Query: 135 AKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGI 194
           AKT  A+T +                V  L +R+IT+ Y A+  G +     +  +PI  
Sbjct: 148 AKTVPAQTRL----------------VESLQRREITREYEAVAIGHMTAGGTV-DEPIS- 189
Query: 195 VRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHP 254
            R+P     + V  P GKPA++   ++E    R  T +++ +++GR HQIR+H+A + HP
Sbjct: 190 -RHPTKRTHMAV-HPMGKPAVTHYRIMEH--FRVHTRLRLRLETGRTHQIRVHMAHITHP 245
Query: 255 LLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNE 314
           L+GDP+Y  GG+P+              G  E  ++ +       LHA  L L HP +  
Sbjct: 246 LVGDPVY--GGRPRP-----------PKGASEAFISTLRKFDRQALHATMLRLYHPISGI 292
Query: 315 VIKITAPLP 323
            ++  AP+P
Sbjct: 293 EMEWHAPIP 301
>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
>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231 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
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query353
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 9e-57
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 2e-56
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 1e-55
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 2e-06
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 3e-06
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 2e-04
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 2e-04
>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 =  186 bits (475), Expect = 9e-57
 Identities = 87/321 (27%), Positives = 146/321 (45%), Gaps = 68/321 (21%)

Query: 17  LQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVY-----HRLPWKEPDVPYLLEVLYED 71
           ++ W   I + ++ V+G+V + P   +  G ++           ++  D+P  L+++YED
Sbjct: 35  IKEW---ILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIP--LDIVYED 89

Query: 72  DDLIALNKPSGLQVLPG-----GLFQQRTVLNQLQWRASKQSSSLSSQASHPVP----VH 122
           +D+I +NKP  L V PG     G     TVLN L       +          VP    VH
Sbjct: 90  EDIIIINKPRDLVVHPGAGNPDG-----TVLNALLHYYPPIAD---------VPRAGIVH 135

Query: 123 RLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVD 182
           RL + T+G+++ AKT  A+T +      +                 IT+ Y A+  G + 
Sbjct: 136 RLDKDTTGLMVVAKTVPAQTRLVESLQRRE----------------ITREYEAVAIGHMT 179

Query: 183 EDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQSGRPH 242
               +  +PI   R+P     + V  P GKPA++   ++E    R  T +++ +++GR H
Sbjct: 180 AGGTV-DEPIS--RHPTKRTHMAV-HPMGKPAVTHYRIMEHF--RVHTRLRLRLETGRTH 233

Query: 243 QIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLHA 302
           QIR+H+A + HPL+GDP+Y  GG+P+                +   +          LHA
Sbjct: 234 QIRVHMAHITHPLVGDPVY--GGRPRPPKGASEA--------FISTLRKFDRQA---LHA 280

Query: 303 YQLFLSHPTTNEVIKITAPLP 323
             L L HP +   ++  AP+P
Sbjct: 281 TMLRLYHPISGIEMEWHAPIP 301
>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
>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
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Length = 217 Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Length = 189 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query353
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
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 100.0
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 100.0
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 100.0
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 99.97
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.5
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.39
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.17
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.11
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 98.09
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 97.99
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 97.88
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 97.87
3hp7_A291 Hemolysin, putative; structural genomics, APC64019 97.66
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 97.64
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 97.47
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 97.22
2aus_C334 Pseudouridine synthase; isomerase, structural prot 97.14
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 97.14
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 97.14
3j20_E243 30S ribosomal protein S4E; archaea, archaeal, KINK 97.13
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 97.1
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 97.1
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 97.08
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 96.98
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 95.4
3iz6_D265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 94.87
2xzm_W260 40S ribosomal protein S4; ribosome, translation; 3 94.86
3u5c_E261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 93.94
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 90.51
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 90.18
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 89.7
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 85.06
1fm0_D81 Molybdopterin convertin factor, subunit 1; molybde 83.19
2ktl_A164 Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s 81.56
>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=1.1e-63  Score=474.64  Aligned_cols=295  Identities=28%  Similarity=0.405  Sum_probs=189.7

Q ss_pred             CcHHHHHHhhcCCCCCHHHHHHHHHcCCEEECCEEccCCCceecCCCEEEEeeCCCCCC---CCCCCccEEEECCcEEEE
Q 037167            1 LTLIEFYSTKHKNSAPLQGWLQRIQNGQITVDGRVVNDPNIILSAGSELVYHRLPWKEP---DVPYLLEVLYEDDDLIAL   77 (353)
Q Consensus         1 ~~l~~~l~~~~~~~~sr~~~~~~I~~G~V~vNg~~v~~~~~~v~~gd~i~~~~~~~~~~---~~~~~~~Ilyed~~~ivv   77 (353)
                      |||.+||.+.+.. +||+.++++|++|+|+|||+++.++++.|++||.|.+...+..++   ..+.+++|+|||++++||
T Consensus        17 ~RLd~~L~~~~~~-~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvv   95 (325)
T 1v9f_A           17 QRLDQALAEMFPD-YSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIII   95 (325)
T ss_dssp             ------------------------------------------------------------CCCCCCCCCEEEECSSEEEE
T ss_pred             chHHHHHHhhccc-cCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEE
Confidence            5889999988744 699999999999999999998668999999999998864332111   123357899999999999


Q ss_pred             ECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHHHHHHHHhhcccccccc
Q 037167           78 NKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDA  157 (353)
Q Consensus        78 nKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~L~~~f~~g~~~~~~  157 (353)
                      |||+||+||+++.....|+++.+..++.....     ..++++|||||++||||||||+|+++++.|+++|.+       
T Consensus        96 nKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~-----~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~-------  163 (325)
T 1v9f_A           96 NKPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQR-------  163 (325)
T ss_dssp             EECSSCCSSCBTTBSSSSHHHHHHHHCGGGGG-----SGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHT-------
T ss_pred             ECCCCCeEecCCCCCCccHHHHHHHHHHhcCC-----CCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHc-------
Confidence            99999999998777678999888755432111     246889999999999999999999999999999976       


Q ss_pred             chhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEEEEeCCCCeEEEEEEeC
Q 037167          158 DSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVEIQ  237 (353)
Q Consensus       158 ~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl~~~~~~~~sll~~~l~  237 (353)
                               +.|+|+|+|+|.|.+++ ++.|+.||++........+  + ..+|++|.|.|++++..  .+.|+++|+|.
T Consensus       164 ---------~~v~K~Y~a~v~G~~~~-~g~i~~~i~~~~~~~~~~~--v-~~~gk~a~t~~~vl~~~--~~~slv~~~l~  228 (325)
T 1v9f_A          164 ---------REITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMA--V-HPMGKPAVTHYRIMEHF--RVHTRLRLRLE  228 (325)
T ss_dssp             ---------TCSEEEEEEEEESCCCC-CEEEECCEEECSSCTTCEE--E-CTTSBCCEEEEEEEEEC--SSEEEEEEEES
T ss_pred             ---------CCeeEEEEEEEeCCCCC-CCEEeeeeeECCCCCEEEE--E-CCCCeeEEEEEEEeEEc--CCeEEEEEEEC
Confidence                     68999999999999987 7899999988654333222  2 35799999999999986  36899999999


Q ss_pred             CCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCcccccccc-ccCCCCCCCCCCCCccccccccceeeeeecCCCCCEE
Q 037167          238 SGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTF-AQDGGYERPVNPVPGDCGYYLHAYQLFLSHPTTNEVI  316 (353)
Q Consensus       238 TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~-~~~~~~~r~~~~~~~~~~l~LHa~~l~f~hp~~~~~~  316 (353)
                      ||||||||+||+++||||+||.+||....  +....  ...+ .....+.          +++|||++|+|.||.+|+.+
T Consensus       229 TGR~HQIRvhla~lG~PI~GD~~Yg~~~~--~~~~~--~~~~~~~~~~~~----------r~~LHA~~L~f~hP~~~~~~  294 (325)
T 1v9f_A          229 TGRTHQIRVHMAHITHPLVGDPVYGGRPR--PPKGA--SEAFISTLRKFD----------RQALHATMLRLYHPISGIEM  294 (325)
T ss_dssp             CCCTTHHHHHHHHTTCCBTTCTTTTCCCC--CCTTC--CHHHHHHHHHCC----------SCSEEEEEEEEECTTTCCEE
T ss_pred             CCCcHHHHHHHHhCCCceeCChhhCCccc--ccccc--chhhhhhccCCc----------ChhhheeeeEeeCCCCCCEE
Confidence            99999999999999999999999995311  10000  0000 0000111          48999999999999999999


Q ss_pred             EEEeCCchhHHHHHHhccccc
Q 037167          317 KITAPLPSVLKTREEGREVDK  337 (353)
Q Consensus       317 ~~~aplP~~f~~~~~~l~~~~  337 (353)
                      .|+||+|.+|+.+++.|+.+.
T Consensus       295 ~~~aplp~~~~~~l~~l~~~~  315 (325)
T 1v9f_A          295 EWHAPIPQDMVELIEVMRADF  315 (325)
T ss_dssp             EEECCCCHHHHHHHHHHHHHH
T ss_pred             EEEecCcHHHHHHHHHhcccc
Confidence            999999999999999987643
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>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
>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
>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_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
>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
>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
>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
>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
>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
>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 353
d1v9fa_250 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 3e-33
d1v9ka_227 d.265.1.3 (A:) Ribosomal large subunit pseudouridi 4e-29
>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 =  121 bits (304), Expect = 3e-33
 Identities = 73/272 (26%), Positives = 120/272 (44%), Gaps = 42/272 (15%)

Query: 56  WKEPDVPYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQA 115
           ++  D+P  L+++YED+D+I +NKP  L V PG      TVLN L            +  
Sbjct: 1   FEPQDIP--LDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI-----ADV 53

Query: 116 SHPVPVHRLGRGTSGILLCAKTKLAKTCIAGYFADKTSVIDADSTVMELSQRKITKIYRA 175
                VHRL + T+G+++ AKT  A+T +                      R+IT+ Y A
Sbjct: 54  PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQR----------------REITREYEA 97

Query: 176 LVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVLERDVQRNCTLVQVE 235
           +  G +             +      +      P GKPA++   ++E    R  T +++ 
Sbjct: 98  VAIGHMTAG----GTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEH--FRVHTRLRLR 151

Query: 236 IQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGD 295
           +++GR HQIR+H+A + HPL+GDP+Y    +P               G  E  ++ +   
Sbjct: 152 LETGRTHQIRVHMAHITHPLVGDPVYGGRPRPP-------------KGASEAFISTLRKF 198

Query: 296 CGYYLHAYQLFLSHPTTNEVIKITAPLPSVLK 327
               LHA  L L HP +   ++  AP+P  + 
Sbjct: 199 DRQALHATMLRLYHPISGIEMEWHAPIPQDMV 230
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227 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 ?
Query353
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 100.0
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 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 99.05
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 99.0
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 98.38
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 98.33
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 97.77
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 97.59
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 97.58
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 97.53
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 97.38
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 97.34
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 97.32
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 97.28
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 97.22
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 96.83
>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=100.00  E-value=1.6e-58  Score=421.07  Aligned_cols=239  Identities=31%  Similarity=0.466  Sum_probs=192.3

Q ss_pred             CCCccEEEECCcEEEEECCCCCccccCCCCCcchHHHHHHHHHhhcCCCccCCCCCCcccccCCCCCceEEEEEeChHHH
Q 037167           62 PYLLEVLYEDDDLIALNKPSGLQVLPGGLFQQRTVLNQLQWRASKQSSSLSSQASHPVPVHRLGRGTSGILLCAKTKLAK  141 (353)
Q Consensus        62 ~~~~~Ilyed~~~ivvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~  141 (353)
                      +.+++|||||+++||||||+||+|||++.+...|+++.+.........     ...+++|||||++||||||||||++++
T Consensus         5 ~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~~~-----~~~~~~vHRLDr~TSGlll~Ak~~~a~   79 (250)
T d1v9fa_           5 DIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIAD-----VPRAGIVHRLDKDTTGLMVVAKTVPAQ   79 (250)
T ss_dssp             CCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGG-----SGGGGBCCCCCTTCEEEEEEESSHHHH
T ss_pred             CCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhccC-----CCceeEEeecCCCCcceEEEecccHHH
Confidence            346889999999999999999999999887788998888765443211     245789999999999999999999999


Q ss_pred             HHHHHHhhccccccccchhhhhhccceEEEEEEEEEeeeeCCCceEEecceeeecCCCcccceEeeCCCCCcceeEEEEE
Q 037167          142 TCIAGYFADKTSVIDADSTVMELSQRKITKIYRALVHGIVDEDKVIIKQPIGIVRYPGVAKGLYVASPSGKPALSKVDVL  221 (353)
Q Consensus       142 ~~L~~~f~~g~~~~~~~~~~~~~~~~~v~K~Y~alv~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~gk~a~t~~~vl  221 (353)
                      +.|+++|++                +.|.|+|+|+|.|.++. .+.++.|+......   .......++|++|.|+|+++
T Consensus        80 ~~l~~~f~~----------------~~v~K~Y~a~~~g~~~~-~~~~~~~~~~~~~~---~~~~~~~~~gk~a~T~~~~l  139 (250)
T d1v9fa_          80 TRLVESLQR----------------REITREYEAVAIGHMTA-GGTVDEPISRHPTK---RTHMAVHPMGKPAVTHYRIM  139 (250)
T ss_dssp             HHHHHHHHT----------------TCSEEEEEEEEESCCCC-CEEEECCEEECSSC---TTCEEECTTSBCCEEEEEEE
T ss_pred             Hhhhhhhcc----------------ceEeEEeeeeecccccc-ccccccccccCCcc---cceeEECCCCeeccccchhh
Confidence            999999987                58999999999999875 46677777654322   22334567899999999999


Q ss_pred             EEeCCCCeEEEEEEeCCCchhHHHHHHHHcCCCeeCCcCCCCCCCCCCCCccccccccccCCCCCCCCCCCCcccccccc
Q 037167          222 ERDVQRNCTLVQVEIQSGRPHQIRIHLAFLGHPLLGDPLYVAGGQPKSFDSEFADGTFAQDGGYERPVNPVPGDCGYYLH  301 (353)
Q Consensus       222 ~~~~~~~~sll~~~l~TGR~HQIR~hla~lG~PIvGD~~Yg~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~l~LH  301 (353)
                      +..  .+.|+++|+|.|||+||||+||+++||||+||.+||......  ... .........++.          |++||
T Consensus       140 ~~~--~~~slv~~~~~TGR~HQIRvHla~lG~PIlGD~~YG~~~~~~--~~~-~~~~~~~~~~~~----------r~~LH  204 (250)
T d1v9fa_         140 EHF--RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPP--KGA-SEAFISTLRKFD----------RQALH  204 (250)
T ss_dssp             EEC--SSEEEEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCC--TTC-CHHHHHHHHHCC----------SCSEE
T ss_pred             hcc--cCceeEEEEecccchHHHHHHHHHhCCccceeccCccccccc--ccc-cHHHHHHHhccc----------hhhhh
Confidence            987  489999999999999999999999999999999999642211  000 000000001112          48999


Q ss_pred             ceeeeeecCCCCCEEEEEeCCchhHHHHHHhcccccccc
Q 037167          302 AYQLFLSHPTTNEVIKITAPLPSVLKTREEGREVDKSVG  340 (353)
Q Consensus       302 a~~l~f~hp~~~~~~~~~aplP~~f~~~~~~l~~~~~~~  340 (353)
                      |++|+|.||.+|+.+.|+||+|++|.++++.|+++....
T Consensus       205 A~~L~f~hP~t~~~~~~~aplP~df~~~l~~L~~~~~~~  243 (250)
T d1v9fa_         205 ATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEH  243 (250)
T ss_dssp             EEEEEEECTTTCCEEEEECCCCHHHHHHHHHHHHHHHHH
T ss_pred             cCccccccCCCCCeEEEEeCCcHHHHHHHHHHhhHHHhc
Confidence            999999999999999999999999999999998876553
>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
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} 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
>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
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} 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
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} 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