Citrus Sinensis ID: 020729

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--
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
cccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHccHHHHHcccccccHHHHHHHHHHHHHHHHccccEEEEccccHHHHHHHHHHHccccccEEEEEcccccccEEEEEEEcccccccccccEEEEEEEcccccccccccHHHHHHHHccccccccccEEEEcccEEEEEEcHHHHHHHHHcccccccEEEEEEEEccccccccccccEEEEEEEcHHHHHHHHHccccccHHHHHHHHHcccEEEccEEEcccccccccccEEEEEEccEEEEEEEccccccEEEEEEEEcc
cccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHcccccEEEEEcccccHHHHHEEEEccccccccccccEEEEEEccccccccccHHHHHHHHHHccccHcccccEEEccccEEEEEEcHHHHHHHHHHHHHHcccEEEEEEEcHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEcccccEEccccEEEEEcccEEEEEEEcccccccEEEEEEEEc
MAAISLAAPWILRRAVrtfslpqpllhlnpgscfhgthrpftfptslrhtASGIRHLIQAVKGNFDDLlkgvgdknAIEEVKHILEMARRASSRRevlhsdfltppvLKESMMALEKLADVKAvaqggypqaercrlsvghpealtsdpDIVAALSitgnfgfqpcshgdflGSILGTGIAREKIGDIilqgekgaqflvVPELADYLITSLEkvgnvsvsctripllaleyepprtksfktIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTtvtkngttlrtgdivsvsgkgrikigeinstrkGKFAVELIQYL
maaislaapwILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSlekvgnvsvSCTRIPLlaleyepprtksfKTIEASLRVDALASAGFklsrsklvnlisngdvrvnwttvtkngttlrtgdivsvsgkgrikigeinstrkgkfAVELIQYL
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
***ISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMA********VLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI***
****S*AAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTAS**RHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
***ISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
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 ?
Query322 2.2.26 [Sep-21-2011]
P71020257 Putative RNA-binding prot yes no 0.714 0.894 0.309 4e-21
>sp|P71020|YLMH_BACSU Putative RNA-binding protein YlmH OS=Bacillus subtilis (strain 168) GN=ylmH PE=4 SV=1 Back     alignment and function desciption
 Score =  102 bits (254), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 121/242 (50%), Gaps = 12/242 (4%)

Query: 81  VKHILEMARRASSRREVLHSDFLTPPVLKESMM--ALEKLADVKAVAQGGYPQAERCRLS 138
           +   LE  R    +  +  +DFL P   +E ++  A+   ADV     GGY +AER R +
Sbjct: 16  IDQALEWKRIVQEQYRMKLTDFLDP---REQVILSAVTGQADVGLAFSGGYDRAERKR-A 71

Query: 139 VGHPEALT---SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKG 195
           +  PE +T   SD ++  A ++     F    H   LG+++G G+ R+K GDI+   E  
Sbjct: 72  ILFPEYITPEESDFEL-QAFNVRYADKFVSVDHRSLLGALMGIGLKRQKFGDIVF-SETA 129

Query: 196 AQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASA 255
            Q +V  + AD++   L + G  +VS  +I L  L       +      +SLR+DA+ ++
Sbjct: 130 VQLIVSADTADFVAAQLTQAGKAAVSLEKIDLSDLNIPAVDVEIRDDTVSSLRLDAVCAS 189

Query: 256 GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN-STRKGKF 314
             + SR K   L+ NG V+VNW  V      +  GD++S+ G GR  + +I   T+K K+
Sbjct: 190 MSRQSRQKSQTLVKNGLVKVNWKVVEDPSYIVAEGDMLSIRGFGRCSLTKIEGKTKKDKW 249

Query: 315 AV 316
            V
Sbjct: 250 RV 251

Bacillus subtilis (strain 168) (taxid: 224308)

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 ?
Query322
225461477321 PREDICTED: putative RNA-binding protein 0.996 1.0 0.751 1e-138
147798253269 hypothetical protein VITISV_010260 [Viti 0.829 0.992 0.831 1e-129
449457021319 PREDICTED: putative RNA-binding protein 0.975 0.984 0.725 1e-129
359807576324 uncharacterized protein LOC100793767 [Gl 0.978 0.972 0.689 1e-128
18404337320 RNA-binding S4 domain-containing protein 0.990 0.996 0.693 1e-127
357452969325 hypothetical protein MTR_2g085340 [Medic 0.990 0.981 0.655 1e-121
217074322325 unknown [Medicago truncatula] 0.990 0.981 0.655 1e-121
224114944268 predicted protein [Populus trichocarpa] 0.826 0.992 0.805 1e-120
297847696 759 hypothetical protein ARALYDRAFT_314636 [ 0.897 0.380 0.648 1e-113
242054411304 hypothetical protein SORBIDRAFT_03g03447 0.816 0.865 0.730 1e-112
>gi|225461477|ref|XP_002282453.1| PREDICTED: putative RNA-binding protein ylmH [Vitis vinifera] gi|302142996|emb|CBI20291.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 242/322 (75%), Positives = 279/322 (86%), Gaps = 1/322 (0%)

Query: 1   MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQA 60
           MAA     P +LR+A+ +F LP  L H+N    ++   R F   T L  +ASG+ HL QA
Sbjct: 1   MAATGFTTPSVLRKALHSF-LPLRLTHINNTLFYYKNLRSFPLSTHLNSSASGMCHLAQA 59

Query: 61  VKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLAD 120
           +KG+ + LLKGV D++ IE VKHILEMA+RAS+RREVLH+DFLTPPVLKESM+ LEKLAD
Sbjct: 60  MKGDANSLLKGVADRSTIEAVKHILEMAKRASARREVLHTDFLTPPVLKESMIVLEKLAD 119

Query: 121 VKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGI 180
           +KAVAQGGYPQAERCRLSVGH E LT+ PDIVAAL ITGNFGFQ CSHGDFLG+ILGTGI
Sbjct: 120 MKAVAQGGYPQAERCRLSVGHSEVLTTAPDIVAALRITGNFGFQSCSHGDFLGAILGTGI 179

Query: 181 AREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSF 240
           AREK+GDIILQGEKGAQ L+VPEL D+L++SLEKVGNVSVSCT++PLLALEYE PRT +F
Sbjct: 180 AREKLGDIILQGEKGAQVLIVPELVDFLVSSLEKVGNVSVSCTKMPLLALEYEEPRTTTF 239

Query: 241 KTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR 300
           KTIE SLRVDALASAGFKLSRSKLV+LISNGDVRVNWTTVTKNGTTL+TGD+VSVSGKGR
Sbjct: 240 KTIELSLRVDALASAGFKLSRSKLVDLISNGDVRVNWTTVTKNGTTLKTGDVVSVSGKGR 299

Query: 301 IKIGEINSTRKGKFAVELIQYL 322
           +KIGEINST+KGK+AVELI++L
Sbjct: 300 LKIGEINSTKKGKYAVELIRFL 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147798253|emb|CAN67613.1| hypothetical protein VITISV_010260 [Vitis vinifera] Back     alignment and taxonomy information
>gi|449457021|ref|XP_004146247.1| PREDICTED: putative RNA-binding protein YlmH-like [Cucumis sativus] gi|449495519|ref|XP_004159865.1| PREDICTED: putative RNA-binding protein YlmH-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|359807576|ref|NP_001241156.1| uncharacterized protein LOC100793767 [Glycine max] gi|255642537|gb|ACU21532.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|18404337|ref|NP_564622.1| RNA-binding S4 domain-containing protein [Arabidopsis thaliana] gi|16648939|gb|AAL24321.1| Unknown protein [Arabidopsis thaliana] gi|24899783|gb|AAN65106.1| Unknown protein [Arabidopsis thaliana] gi|27311617|gb|AAO00774.1| Unknown protein [Arabidopsis thaliana] gi|30984534|gb|AAP42730.1| At1g53120 [Arabidopsis thaliana] gi|332194772|gb|AEE32893.1| RNA-binding S4 domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|357452969|ref|XP_003596761.1| hypothetical protein MTR_2g085340 [Medicago truncatula] gi|355485809|gb|AES67012.1| hypothetical protein MTR_2g085340 [Medicago truncatula] Back     alignment and taxonomy information
>gi|217074322|gb|ACJ85521.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|224114944|ref|XP_002316899.1| predicted protein [Populus trichocarpa] gi|222859964|gb|EEE97511.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297847696|ref|XP_002891729.1| hypothetical protein ARALYDRAFT_314636 [Arabidopsis lyrata subsp. lyrata] gi|297337571|gb|EFH67988.1| hypothetical protein ARALYDRAFT_314636 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|242054411|ref|XP_002456351.1| hypothetical protein SORBIDRAFT_03g034470 [Sorghum bicolor] gi|241928326|gb|EES01471.1| hypothetical protein SORBIDRAFT_03g034470 [Sorghum bicolor] 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 ?
Query322
TAIR|locus:2037048320 AT1G53120 [Arabidopsis thalian 0.990 0.996 0.693 1.6e-116
UNIPROTKB|P74082259 sll1252 "Sll1252 protein" [Syn 0.782 0.972 0.464 3.6e-57
UNIPROTKB|Q3AAH6246 CHY_2039 "S4 domain protein" [ 0.736 0.963 0.373 2.5e-33
TIGR_CMR|CHY_2039246 CHY_2039 "S4 domain protein" [ 0.736 0.963 0.373 2.5e-33
UNIPROTKB|Q81WE2255 BAS3748 "S4 domain protein" [B 0.717 0.905 0.3 2.4e-21
TIGR_CMR|BA_4036255 BA_4036 "S4 domain protein" [B 0.717 0.905 0.3 2.4e-21
UNIPROTKB|Q71XY5258 LMOf2365_2060 "S4 domain prote 0.683 0.852 0.300 1.5e-19
TAIR|locus:2037048 AT1G53120 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1148 (409.2 bits), Expect = 1.6e-116, P = 1.6e-116
 Identities = 224/323 (69%), Positives = 271/323 (83%)

Query:     1 MAAISLAAPW-ILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQ 59
             MA  SLA PW ILR A R+ +     LH N  +       P +FP  LR +A    +  +
Sbjct:     1 MAVTSLAPPWVILRLAFRSVAASS-CLHTNQKTLITNLSIPTSFP--LRQSALRRCYSAE 57

Query:    60 AVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLA 119
             A+KG+ D LLKGVGD+   +EVK ILEMARRASS+REVLH+DFLTPP++KES+  LEK A
Sbjct:    58 AIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREVLHTDFLTPPIVKESVSLLEKFA 117

Query:   120 DVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTG 179
             DVK VAQGGYP+AERCR+S+GHP+ LTSDPDIVAALSITGNFGFQPCSHGDFLG+ILGTG
Sbjct:   118 DVKIVAQGGYPEAERCRISIGHPDVLTSDPDIVAALSITGNFGFQPCSHGDFLGAILGTG 177

Query:   180 IAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKS 239
             I+REK+GDI++Q EKGAQ L+VPEL D+++T+L+KVGNV V+C++IPLLALEYEPPRT S
Sbjct:   178 ISREKLGDILIQEEKGAQVLIVPELVDFVVTALDKVGNVGVTCSKIPLLALEYEPPRTNS 237

Query:   240 FKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG 299
             FKT+EASLR+DA+ASAGFK+SRSKLV+LIS+ DVRVNW TVTKNGT ++TGD+VSVSGKG
Sbjct:   238 FKTVEASLRIDAVASAGFKISRSKLVDLISSKDVRVNWATVTKNGTIVKTGDVVSVSGKG 297

Query:   300 RIKIGEINSTRKGKFAVELIQYL 322
             R+KIGEIN T+KGKFAVE+I+YL
Sbjct:   298 RLKIGEINETKKGKFAVEIIRYL 320
GO:0003723 "RNA binding" evidence=IEA;ISS
GO:0008150 "biological_process" evidence=ND
GO:0009507 "chloroplast" evidence=ISM;IDA
UNIPROTKB|P74082 sll1252 "Sll1252 protein" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)] Back     alignment and assigned GO terms
UNIPROTKB|Q3AAH6 CHY_2039 "S4 domain protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2039 CHY_2039 "S4 domain protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|Q81WE2 BAS3748 "S4 domain protein" [Bacillus anthracis (taxid:1392)] Back     alignment and assigned GO terms
TIGR_CMR|BA_4036 BA_4036 "S4 domain protein" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q71XY5 LMOf2365_2060 "S4 domain protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)] 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 ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00027695001
SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (412 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00032279001
SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (162 aa)
•     • 0.532
GSVIVG00000690001
RecName- Full=Pyrroline-5-carboxylate reductase; EC=1.5.1.2; (276 aa)
•       0.470

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 ?
Query322
PLN00051267 PLN00051, PLN00051, RNA-binding S4 domain-containi 1e-168
TIGR03069257 TIGR03069, PS_II_S4, photosystem II S4 domain prot 1e-113
COG2302257 COG2302, COG2302, Uncharacterized conserved protei 5e-65
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d 5e-10
smart0036360 smart00363, S4, S4 RNA-binding domain 9e-10
pfam0147948 pfam01479, S4, S4 domain 5e-06
>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information 
 Score =  468 bits (1207), Expect = e-168
 Identities = 190/267 (71%), Positives = 223/267 (83%)

Query: 56  HLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMAL 115
            L  A  G+ D  L GV D    EEVK ILEMA RAS R EV H+DFLTPP++K+SM AL
Sbjct: 1   ILAAAAAGDADSALLGVVDPAHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAAL 60

Query: 116 EKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSI 175
           EKLADVKAVA GGY QAERCRLS+G PE LTS PDIVAALS++GNF F P SHGDFLG+I
Sbjct: 61  EKLADVKAVAWGGYAQAERCRLSIGRPEVLTSQPDIVAALSVSGNFMFDPASHGDFLGAI 120

Query: 176 LGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPP 235
           LGTGI R+K+GDI++QGE+GAQ LVVPEL ++L +SL KV  V V C  IPL ALE EPP
Sbjct: 121 LGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRAIPLSALEVEPP 180

Query: 236 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV 295
           R +SFK++EASLR+DALASAGF++SRSKLV+LIS+GDVRVNW  VTKNGTTL+TGD+VSV
Sbjct: 181 RVESFKSVEASLRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSV 240

Query: 296 SGKGRIKIGEINSTRKGKFAVELIQYL 322
           SGKGR+++GEIN+T+KGKFAVELI+YL
Sbjct: 241 SGKGRLEVGEINTTKKGKFAVELIRYL 267

Length = 267
>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein 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|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
>gnl|CDD|201819 pfam01479, S4, S4 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 322
PLN00051267 RNA-binding S4 domain-containing protein; Provisio 100.0
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members 100.0
COG2302257 Uncharacterized conserved protein, contains S4-lik 100.0
KOG4837248 consensus Uncharacterized conserved protein [Funct 99.93
TIGR01017200 rpsD_bact ribosomal protein S4, bacterial/organell 99.2
PRK05327203 rpsD 30S ribosomal protein S4; Validated 99.14
PF0147948 S4: S4 domain; InterPro: IPR002942 Ribosomes are t 99.12
TIGR0298859 YaaA_near_RecF S4 domain protein YaaA. This small 99.05
COG1188100 Ribosome-associated heat shock protein implicated 98.94
PRK10348133 ribosome-associated heat shock protein Hsp15; Prov 98.76
smart0036360 S4 S4 RNA-binding domain. 98.53
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The 98.5
CHL00113201 rps4 ribosomal protein S4; Reviewed 98.46
COG0522205 RpsD Ribosomal protein S4 and related proteins [Tr 98.22
PRK10475 290 23S rRNA pseudouridine synthase F; Provisional 98.18
TIGR00478 228 tly hemolysin TlyA family protein. Hemolysins are 98.16
PRK10839 232 16S rRNA pseudouridylate synthase A; Provisional 98.15
TIGR00005 299 rluA_subfam pseudouridine synthase, RluA family. m 98.05
PRK11180 325 rluD 23S rRNA pseudouridine synthase D; Provisiona 98.01
COG1187 248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 97.95
COG1189 245 Predicted rRNA methylase [Translation, ribosomal s 97.88
PRK11025 317 23S rRNA pseudouridylate synthase C; Provisional 97.88
COG0564 289 RluA Pseudouridylate synthases, 23S RNA-specific [ 97.83
PRK10700 289 23S rRNA pseudouridylate synthase B; Provisional 97.71
PRK1150770 ribosome-associated protein; Provisional 97.59
PRK04051177 rps4p 30S ribosomal protein S4P; Validated 97.51
PF0388074 DbpA: DbpA RNA binding domain ; InterPro: IPR00558 97.4
PF1327565 S4_2: S4 domain; PDB: 1P9K_A. 97.35
TIGR01018162 rpsD_arch ribosomal protein S4(archaeal type)/S9(e 97.08
PLN00189194 40S ribosomal protein S9; Provisional 96.84
PTZ00155181 40S ribosomal protein S9; Provisional 96.47
COG250173 S4-like RNA binding protein [Replication, recombin 96.0
KOG4837248 consensus Uncharacterized conserved protein [Funct 95.31
COG4332203 Uncharacterized protein conserved in bacteria [Fun 95.26
PF06353142 DUF1062: Protein of unknown function (DUF1062); In 94.14
PRK04313 237 30S ribosomal protein S4e; Validated 92.74
PTZ00118 262 40S ribosomal protein S4; Provisional 92.22
PTZ00223 273 40S ribosomal protein S4; Provisional 92.18
PLN00036 261 40S ribosomal protein S4; Provisional 92.1
PRK13354410 tyrosyl-tRNA synthetase; Provisional 90.62
PRK05912408 tyrosyl-tRNA synthetase; Validated 90.29
PF1445181 Ub-Mut7C: Mut7-C ubiquitin 88.36
COG1471 241 RPS4A Ribosomal protein S4E [Translation, ribosoma 87.79
PRK0177795 hypothetical protein; Validated 83.37
>PLN00051 RNA-binding S4 domain-containing protein; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.6e-72  Score=529.80  Aligned_cols=257  Identities=72%  Similarity=1.099  Sum_probs=240.7

Q ss_pred             hHHhhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEecCCCC
Q 020729           65 FDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEA  144 (322)
Q Consensus        65 ~~~ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i~~~~~  144 (322)
                      -..+++|+.+ +++.++++++||+++|.++|.+++|+||||+|+.++.+++++..++++.++|||++|||+|++|+|+++
T Consensus        11 ~~~i~~h~~~-ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~   89 (267)
T PLN00051         11 DSALLGVVDP-AHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEV   89 (267)
T ss_pred             hhHHHhhcCh-hhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHh
Confidence            3478999885 559999999999999999999999999999999999999988889999999999999999999975554


Q ss_pred             CCCCcCceEEEEEecCCCCcCCCchhhHHHHHcCCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEEE
Q 020729          145 LTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTR  224 (322)
Q Consensus       145 ~~~~~~~i~~l~i~~~~kF~~lsHrD~LGaLm~LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~  224 (322)
                      ++.+++|+++++|++++||.+|+|||||||||||||+||+||||++.++++||++|+++|++||++||+|||+++|++++
T Consensus        90 ~~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~V~~~~  169 (267)
T PLN00051         90 LTSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRA  169 (267)
T ss_pred             ccccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhccceeEEEEE
Confidence            42223599999999999999999999999999999999999999996555799999999999999999999999999999


Q ss_pred             ecCccccCCCCCceeEeecccccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeecCeEEEE
Q 020729          225 IPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIG  304 (322)
Q Consensus       225 i~~~~l~~~~~~~k~~~~~vaS~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg~GR~~i~  304 (322)
                      ++++++..|+++|++++.+++|+|||++++..+++||++++++|++|+|+|||++++++++.|++||+|||||+|||++.
T Consensus       170 ~~~~~~~~~~~~~~e~~~~vas~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~GR~~i~  249 (267)
T PLN00051        170 IPLSALEVEPPRVESFKSVEASLRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRLEVG  249 (267)
T ss_pred             ecHHHcCCCccceEEccCCcCcccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeCCEEEEE
Confidence            99999888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccccceEEEEEEeC
Q 020729          305 EINSTRKGKFAVELIQYL  322 (322)
Q Consensus       305 ei~~TKKgR~~i~l~ry~  322 (322)
                      +++.|||||++|++++|+
T Consensus       250 ~~~~TKKgr~~i~i~ky~  267 (267)
T PLN00051        250 EINTTKKGKFAVELIRYL  267 (267)
T ss_pred             EEecccCCcEEEEEEecC
Confidence            988999999999999985

>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>KOG4837 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated 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
>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
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain 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
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>TIGR00478 tly hemolysin TlyA family protein Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK11507 ribosome-associated protein; Provisional Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4P; Validated Back     alignment and domain information
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [] Back     alignment and domain information
>PF13275 S4_2: S4 domain; PDB: 1P9K_A Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>PLN00189 40S ribosomal protein S9; Provisional Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>KOG4837 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown] 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
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PLN00036 40S ribosomal protein S4; Provisional 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
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK01777 hypothetical protein; Validated Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query322
2fph_X165 YLMH; division protein, bacteria, GRAM+, DNA bindi 9e-43
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-05
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; 4e-05
1vio_A 243 Ribosomal small subunit pseudouridine synthase A; 3e-04
1ksk_A 234 Ribosomal small subunit pseudouridine synthase A; 6e-04
>2fph_X YLMH; division protein, bacteria, GRAM+, DNA binding protein; 1.70A {Streptococcus pneumoniae} Length = 165 Back     alignment and structure
 Score =  144 bits (365), Expect = 9e-43
 Identities = 30/155 (19%), Positives = 60/155 (38%), Gaps = 4/155 (2%)

Query: 75  KNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAER 134
                 +   +E  ++         + F+ P   K  +  L K   +   + G +  +E 
Sbjct: 8   IEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEK-LLKILAKTYGLACSSSGEFVSSEY 66

Query: 135 CRLSVGHPEALTSDPDI-VAALSITGNFGFQPCSHGDFLGSILGT-GIAREKIGDIILQG 192
            R+ +          D  ++   I  +  F+  +H   LG+++   GI R+  GDI++  
Sbjct: 67  VRVLLYPDYFQPEFSDFEISLQEIVYSNKFEYLTHAKILGTVINQLGIERKLFGDILVDE 126

Query: 193 EKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPL 227
           E  AQ ++  +        L+K+G + VS    P 
Sbjct: 127 E-RAQIMINQQFLLLFQDGLKKIGRIPVSLEERPF 160
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query322
2fph_X165 YLMH; division protein, bacteria, GRAM+, DNA bindi 100.0
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 98.92
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.9
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.85
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-bindin 98.66
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, uni 98.65
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spi 98.58
3r8n_D205 30S ribosomal protein S4; protein biosynthesis, RN 98.58
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protei 98.45
1ksk_A 234 Ribosomal small subunit pseudouridine synthase A; 98.43
3dh3_A 290 Ribosomal large subunit pseudouridine synthase F; 98.35
1vio_A 243 Ribosomal small subunit pseudouridine synthase A; 98.33
3hp7_A 291 Hemolysin, putative; structural genomics, APC64019 98.33
3j20_D180 30S ribosomal protein S4P; archaea, archaeal, KINK 98.33
2xzm_D181 Ribosomal protein S4 containing protein; ribosome, 98.26
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; 98.16
3u5c_J197 40S ribosomal protein S9-A; translation, ribosome, 97.75
3iz6_C195 40S ribosomal protein S9 (S4P); eukaryotic ribosom 97.17
3kbg_A 213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 96.82
3j20_E 243 30S ribosomal protein S4E; archaea, archaeal, KINK 96.77
2g0c_A76 ATP-dependent RNA helicase DBPA; RNA recognition m 94.03
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 93.57
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 93.36
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase; truncation, based 92.72
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 89.27
3u5c_E 261 RP5, S7, YS6, 40S ribosomal protein S4-A; translat 88.74
2ktl_A164 Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s 87.59
2xzm_W 260 40S ribosomal protein S4; ribosome, translation; 3 87.43
3iz6_D 265 40S ribosomal protein S4 (S4E); eukaryotic ribosom 86.84
>2fph_X YLMH; division protein, bacteria, GRAM+, DNA binding protein; 1.70A {Streptococcus pneumoniae} Back     alignment and structure
Probab=100.00  E-value=1.6e-47  Score=336.14  Aligned_cols=159  Identities=18%  Similarity=0.296  Sum_probs=145.8

Q ss_pred             hhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCChHHHHHHHHHhhccCCeEEEEcCCCcccceeEEEecCCCCCC-
Q 020729           68 LLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT-  146 (322)
Q Consensus        68 ll~~~~~~~~~~~i~~l~d~~~~a~~~~~~~~TdFL~P~e~~~~~~~l~~~~~i~~~~~GGy~~AERkr~~i~~~~~~~-  146 (322)
                      +++|+. +++++++++++||+++|.++|.+.+|+||||+|+.++.+++++. ++++.++|||++|||+|++|+ |+|++ 
T Consensus         2 ~~~hf~-~~e~~~i~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~i~~~~-~~~~~~~GGy~~AER~r~~i~-p~~~~~   78 (165)
T 2fph_X            2 IYQHFS-IEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTY-GLACSSSGEFVSSEYVRVLLY-PDYFQP   78 (165)
T ss_dssp             CCCCCC-GGGHHHHHHHHHHHHHHHHHTSCEECCCBCHHHHHHHHHHHHHT-TCEEEEGGGTSCCSSBCEEEE-CTTCCC
T ss_pred             hhhhcC-hhhHHHHHHHHHHHHHHHHhCCEEECCCCCHHHHHHHHHHHhcc-CcEEEEeCCCcHHheeEEEEe-cccccC
Confidence            578887 45679999999999999999999999999999999999999876 799999999999999999995 55544 


Q ss_pred             CCcC-ceEEEEEecCCCCcCCCchhhHHHHHc-CCCCCCCcccEEEecCCeEEEEechhHHHHHHhccceeeceEEEEEE
Q 020729          147 SDPD-IVAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTR  224 (322)
Q Consensus       147 ~~~~-~i~~l~i~~~~kF~~lsHrD~LGaLm~-LGI~RekiGDI~v~~~~~a~v~v~~ei~~fi~~nl~kVg~~~V~~~~  224 (322)
                      +..+ |+++++|++|+||++++|||||||||| |||+|+++|||++.+ ++||++|+++|++||.+||+|||+++|++++
T Consensus        79 ~~~d~~i~~l~i~~~~kF~~l~Hrd~LGaLm~~LGI~Re~iGDI~v~~-~~~qv~v~~~i~~~i~~nl~kIg~~~V~~~~  157 (165)
T 2fph_X           79 EFSDFEISLQEIVYSNKFEYLTHAKILGTVINQLGIERKLFGDILVDE-ERAQIMINQQFLLLFQDGLKKIGRIPVSLEE  157 (165)
T ss_dssp             CGGGGCEEEEEEESCCCCHHHHHHHHHSCSSSCCCCCGGGEEEEECSS-SCCEEEEEGGGHHHHHHHCCEETTEECEEEE
T ss_pred             cccCCceEEEEEecccccccCCHHHHHHHHHHhcCCCHhhcCCEEEEC-CEEEEEEcHHHHHHHHHHHhhccCeeEEEEE
Confidence            3334 899999999999999999999999999 999999999999966 4899999999999999999999999999999


Q ss_pred             ecCccc
Q 020729          225 IPLLAL  230 (322)
Q Consensus       225 i~~~~l  230 (322)
                      ++++++
T Consensus       158 i~~~~l  163 (165)
T 2fph_X          158 RPFTEK  163 (165)
T ss_dssp             CCGGGC
T ss_pred             eCHHHc
Confidence            998776
>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
>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
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} 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
>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
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B 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
>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
>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
>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
>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4} Back     alignment and structure
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W 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

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 322
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-te 5e-10
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-te 2e-07
d1p9ka_79 d.66.1.6 (A:) Hypothetical protein YbcJ {Escherich 2e-04
>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

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

 Score = 52.4 bits (126), Expect = 5e-10
 Identities = 12/53 (22%), Positives = 21/53 (39%)

Query: 246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 298
           SLR+D   +    L+RS+    I    V++N   V      +   D +    +
Sbjct: 1   SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDE 53
>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
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Length = 79 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 ?
Query322
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Hae 99.36
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Esc 99.29
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 99.16
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId 98.7
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus 98.55
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562 98.4
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 98.38
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 97.17
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain 96.78
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=99.36  E-value=1.7e-13  Score=98.42  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=50.0

Q ss_pred             ccHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 020729          246 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  297 (322)
Q Consensus       246 S~RLD~~Ls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~Vk~GD~IsVrg  297 (322)
                      |||||.+|+.....||++++++|++|+|.|||+++++|++.|++||.|+++|
T Consensus         1 smRLD~~Ls~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~~~g   52 (58)
T d1vioa2           1 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFED   52 (58)
T ss_dssp             CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETT
T ss_pred             CcHHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeCCCCCCCCCCCEEEECC
Confidence            7999999999889999999999999999999999999999999999999975
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {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
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {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
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure