Citrus Sinensis ID: 022999

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Local Sequence Feature Prediction

Residue Number Marker
--------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-------29
Protein Sequence
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIRSS
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHcccccccEEcccccccccccccccccccccccccccHHHHHHHHccHHHHHcccccccHHHHHHHHHHHHHHHHccccEEEEccccHHHHHHHHHHHccccccEEEEEcccccccEEEEEEEcccccccccccEEEEEEEcccccccccccHHHHHHHHccccccccccEEEEcccEEEEEEcHHHHHHHHHcccccccEEEEEEEEcccccccccccEEEEEEEEEcHHHHHHHHHHHcccHHHHHHHHHcccEEEcEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccEccccccHHHHHHHHHHHcccccEEEEEcccccHHHHHEEEEcccccccccccHEEEEEEccccccccccHHHHHHHHHHcccEHccccEEEEcccccEEEEEcHHHHHHHHHHHHHccccEEEEEEEcHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEEEEEcccc
Coil and Loop (DISEMBL)
MAAISLAAPWILRRAVrtfslpqpllhlnpgscfhgthrpftfptslrhtASGIRHLIQAVKGNFDDLlkgvgdknAIEEVKHILEMARRASSRRevlhsdfltppvLKESMMALEKLADVKAvaqggypqaercrlsvghpealtsdpDIVAALSitgnfgfqpcshgdflGSILGTGIAREKIGDIilqgekgaqflvVPELADYLITSLEkvgnvsvsctripllaleyepprtksfktIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIRSS
Flexible Loop (DISEMBL)
maaislaapwILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSlekvgnvsvSCTRIPLlaleyepprtksfKTIEASLRVDALASAGFKLSRSKLVNLIRYsslaslvqisakasairss
Low Complexity Region (SEG)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIRSS
Disordered region (IsUnstruct)
***ISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMA********VLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQI**********
Disordered Region (DISOPRED)
****S*AAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHT*****HLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKA******
Disordered Region (DISEMBL)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQI**********
Disordered Region (DISPRO)
***ISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASA****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIRSS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	289	2.2.26 [Sep-21-2011]
P71020	257	Putative RNA-binding prot	yes	no	0.633	0.712	0.293	3e-12

>sp|P71020|YLMH_BACSU Putative RNA-binding protein YlmH OS=Bacillus subtilis (strain 168) GN=ylmH PE=4 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/194 (29%), Positives = 95/194 (48%), Gaps = 11/194 (5%)

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 GFKLSRSKLVNLIR 269
             + SR K   L++
Sbjct: 190 MSRQSRQKSQTLVK 203

Bacillus subtilis (strain 168) (taxid: 224308)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	289
225461477	321	PREDICTED: putative RNA-binding protein	0.923	0.831	0.727	1e-109
255586534	231	RNA binding protein, putative [Ricinus c	0.757	0.948	0.812	1e-102
18404337	320	RNA-binding S4 domain-containing protein	0.916	0.828	0.676	1e-101
359807576	324	uncharacterized protein LOC100793767 [Gl	0.972	0.867	0.628	1e-101
449457021	319	PREDICTED: putative RNA-binding protein	0.899	0.815	0.704	1e-101
147798253	269	hypothetical protein VITISV_010260 [Viti	0.737	0.791	0.821	2e-99
357452969	325	hypothetical protein MTR_2g085340 [Medic	0.986	0.876	0.610	5e-97
217074322	325	unknown [Medicago truncatula]	0.986	0.876	0.610	8e-97
224114944	268	predicted protein [Populus trichocarpa]	0.733	0.791	0.793	7e-92
297847696	759	hypothetical protein ARALYDRAFT_314636 [	0.837	0.318	0.617	6e-89

>gi|225461477|ref|XP_002282453.1| PREDICTED: putative RNA-binding protein ylmH [Vitis vinifera] gi|302142996|emb|CBI20291.3| unnamed protein product [Vitis vinifera]

 Score =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 195/268 (72%), Positives = 225/268 (83%), Gaps = 1/268 (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 KTIEASLRVDALASAGFKLSRSKLVNLI 268
           KTIE SLRVDALASAGFKLSRSKLV+LI
Sbjct: 240 KTIELSLRVDALASAGFKLSRSKLVDLI 267

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586534|ref|XP_002533905.1| RNA binding protein, putative [Ricinus communis] gi|223526138|gb|EEF28479.1| RNA binding protein, putative [Ricinus communis]

 Score =  376 bits (965), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 178/219 (81%), Positives = 199/219 (90%)

Query: 51  ASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKE 110
           A GI  L QA+K    DLLK VGDK+ +EEVKHIL+MARRASSRRE LH+DFLTPP+LKE
Sbjct: 13  ALGICQLAQAMKSEVSDLLKSVGDKSVVEEVKHILDMARRASSRREALHTDFLTPPILKE 72

Query: 111 SMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGD 170
           SM+ LEKLAD+KAV QGGYPQAERCRLSVGHPEAL +DPDI+AALSITGNF FQPCSHGD
Sbjct: 73  SMLLLEKLADIKAVGQGGYPQAERCRLSVGHPEALMNDPDIIAALSITGNFAFQPCSHGD 132

Query: 171 FLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLAL 230
           FLGSILGTGI+REK+GDIILQGEKGAQ L VPEL D++++SL+KVGNVSVSC RIPLLAL
Sbjct: 133 FLGSILGTGISREKVGDIILQGEKGAQILTVPELVDFIMSSLDKVGNVSVSCARIPLLAL 192

Query: 231 EYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIR 269
           EYEPPRT++F TIEASLRVDALASAGFK+SRSKLV+LIR
Sbjct: 193 EYEPPRTRTFNTIEASLRVDALASAGFKISRSKLVDLIR 231

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  374 bits (959), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 182/269 (67%), Positives = 221/269 (82%), Gaps = 4/269 (1%)

Query: 1   MAAISLAAPW-ILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQ 59
           MA  SLA PW ILR A R+ +     LH N  +       P +FP  LR +A    +  +
Sbjct: 1   MAVTSLAPPWVILRLAFRSVA-ASSCLHTNQKTLITNLSIPTSFP--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 FKTIEASLRVDALASAGFKLSRSKLVNLI 268
           FKT+EASLR+DA+ASAGFK+SRSKLV+LI
Sbjct: 238 FKTVEASLRIDAVASAGFKISRSKLVDLI 266

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807576|ref|NP_001241156.1| uncharacterized protein LOC100793767 [Glycine max] gi|255642537|gb|ACU21532.1| unknown [Glycine max]

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 186/296 (62%), Positives = 229/296 (77%), Gaps = 15/296 (5%)

Query: 1   MAAISLAAPWILRRAVRTFSLPQP-------LLHLNPGSCFHGTHRPFTFPTSLRHTASG 53
           + A S    W LRRA + F++           L L    C H      +  TSL   ASG
Sbjct: 3   VTASSFGTTWCLRRAAQAFAISHSHILRNNVKLSLQRNFCSH----LLSVSTSL---ASG 55

Query: 54  IRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMM 113
           +   +QA+KG  D LLKGVG+++  +EVKHILEMARRAS +RE+LH+DFLTPPVLKESM 
Sbjct: 56  VSQTVQALKGEVDLLLKGVGERSVTKEVKHILEMARRASLKREILHTDFLTPPVLKESMQ 115

Query: 114 ALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLG 173
            LEKLADVKA+AQGGYPQAERCR+SVGHPE LTSDPDI++ALSITGNF F+PCSHGDFLG
Sbjct: 116 VLEKLADVKAIAQGGYPQAERCRISVGHPEELTSDPDIISALSITGNFQFEPCSHGDFLG 175

Query: 174 SILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYE 233
           SILGTGI REK+GDIILQGE+GAQ +VVPEL ++L+++L KV NV VSCT+IPL++L+YE
Sbjct: 176 SILGTGIVREKLGDIILQGEQGAQIIVVPELVEFLMSTLVKVRNVPVSCTKIPLISLDYE 235

Query: 234 PPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSL-ASLVQISAKASAIRS 288
           PPRTKSFKTIEASLRVDALASAGFK+SRSKLV++I    +  + + ++ K + ++S
Sbjct: 236 PPRTKSFKTIEASLRVDALASAGFKVSRSKLVDMISNGDVRINWIPVTTKGTTLKS 291

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 188/267 (70%), Positives = 223/267 (83%), Gaps = 7/267 (2%)

Query: 3   AISLAAPWILRRAVRTFSLPQPL-LHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAV 61
           A S+AA W LRRA +  S  +PL L+LN   CF+       FP+S   T SGI  L+QAV
Sbjct: 5   ATSIAALWSLRRAAQFSSFRRPLALNLNR-LCFNEAR----FPSSPLGT-SGICQLVQAV 58

Query: 62  KGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADV 121
           KG+ D LL GVGDK  I +VK IL MA+R+ SRREVLH++FLTPPV+KESM+A++KLADV
Sbjct: 59  KGDIDVLLNGVGDKGVIVDVKQILVMAKRSLSRREVLHTNFLTPPVVKESMLAIQKLADV 118

Query: 122 KAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIA 181
           KA+AQGGYP+AERCR+SVGH + LTSDPDI++ALSITGNF F PCSHGDFLGSILGTGIA
Sbjct: 119 KAIAQGGYPEAERCRISVGHADELTSDPDIISALSITGNFTFHPCSHGDFLGSILGTGIA 178

Query: 182 REKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFK 241
           REK+GDI+LQ E GAQ ++VPEL D+LI+SL KVGNV+VSCTRIPL ALEYEPP+TK+FK
Sbjct: 179 REKLGDIMLQEETGAQVVIVPELVDFLISSLRKVGNVTVSCTRIPLTALEYEPPKTKTFK 238

Query: 242 TIEASLRVDALASAGFKLSRSKLVNLI 268
           TIEASLRVDA+ASAGFK+SRSKLV+LI
Sbjct: 239 TIEASLRVDAIASAGFKISRSKLVDLI 265

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147798253|emb|CAN67613.1| hypothetical protein VITISV_010260 [Vitis vinifera]

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 175/213 (82%), Positives = 196/213 (92%)

Query: 56  HLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMAL 115
           HL QA+KG+ + LLKGV D++ IE VKHILEMA+RAS+RREVLH+DFLTPPVLKESM+ L
Sbjct: 3   HLAQAMKGDANSLLKGVADRSTIEAVKHILEMAKRASARREVLHTDFLTPPVLKESMIVL 62

Query: 116 EKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSI 175
           EKLAD+KAVAQGGYPQAERCRLSVGH E LT+ PDIVAAL ITGNFGFQ CSHGDFLG+I
Sbjct: 63  EKLADMKAVAQGGYPQAERCRLSVGHSEVLTTAPDIVAALRITGNFGFQSCSHGDFLGAI 122

Query: 176 LGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPP 235
           LGTGIAREK+GDIILQGEKGAQ L+VPEL D+L++SLEKVGNVSVSCT++PLLALEYE P
Sbjct: 123 LGTGIAREKLGDIILQGEKGAQVLIVPELVDFLVSSLEKVGNVSVSCTKMPLLALEYEEP 182

Query: 236 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLI 268
           RT +FKTIE SLRVDALASAGFKLSRSKLV+LI
Sbjct: 183 RTTTFKTIELSLRVDALASAGFKLSRSKLVDLI 215

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357452969|ref|XP_003596761.1| hypothetical protein MTR_2g085340 [Medicago truncatula] gi|355485809|gb|AES67012.1| hypothetical protein MTR_2g085340 [Medicago truncatula]

 Score =  360 bits (923), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 180/295 (61%), Positives = 225/295 (76%), Gaps = 10/295 (3%)

Query: 1   MAAI--SLAAPWILRRAVRTFSLPQPLLHLNPGSCFHG----THRPFTFPTSLRHTASGI 54
           MAA   S    W LRR  + F+L         G+        T    +F TS   + SG 
Sbjct: 1   MAATTTSFGTAWCLRRVTQAFALSHSHTLRTNGNNLSFQRTLTSHLLSFSTS---SDSGA 57

Query: 55  RHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMA 114
              +QA K   D LLKGVG+K+   EVKH+LEMARRAS +RE+LH++FLTPPVLKESM  
Sbjct: 58  STTVQASKREVDVLLKGVGEKSVENEVKHVLEMARRASLKREILHTNFLTPPVLKESMQV 117

Query: 115 LEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGS 174
           LEKLAD+KA+AQGGYPQAERCR+SVGHP+ LTSDPD+++ALSITGNF F+PCSHGDFLGS
Sbjct: 118 LEKLADIKALAQGGYPQAERCRISVGHPDELTSDPDVISALSITGNFQFEPCSHGDFLGS 177

Query: 175 ILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEP 234
           ILGTGIAREK+GDIILQGE+GAQ +VVPEL ++L ++L+KV NV V+CT+IPL++L+YEP
Sbjct: 178 ILGTGIAREKVGDIILQGEQGAQIIVVPELVEFLTSALDKVRNVPVTCTKIPLISLDYEP 237

Query: 235 PRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSL-ASLVQISAKASAIRS 288
           PRTKSFKTIEASLRVDA+ASAGFK+SRSKLV++I    +  + + I+ K + ++S
Sbjct: 238 PRTKSFKTIEASLRVDAVASAGFKISRSKLVDMISNGDVRINWIPITTKGTTVKS 292

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074322|gb|ACJ85521.1| unknown [Medicago truncatula]

 Score =  359 bits (922), Expect = 8e-97,   Method: Compositional matrix adjust.
 Identities = 180/295 (61%), Positives = 225/295 (76%), Gaps = 10/295 (3%)

Query: 1   MAAI--SLAAPWILRRAVRTFSLPQPLLHLNPGSCFHG----THRPFTFPTSLRHTASGI 54
           MAA   S    W LRR  + F+L         G+        T    +F TS   + SG 
Sbjct: 1   MAATTTSFGTAWCLRRVTQAFALSHSHTLRTNGNNLSFQRTLTSHLLSFSTS---SDSGA 57

Query: 55  RHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMA 114
              +QA K   D LLKGVG+K+   EVKH+LEMARRAS +RE+LH++FLTPPVLKESM  
Sbjct: 58  STTVQASKREVDVLLKGVGEKSVENEVKHVLEMARRASLKREILHTNFLTPPVLKESMRV 117

Query: 115 LEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGS 174
           LEKLAD+KA+AQGGYPQAERCR+SVGHP+ LTSDPD+++ALSITGNF F+PCSHGDFLGS
Sbjct: 118 LEKLADIKALAQGGYPQAERCRISVGHPDELTSDPDVISALSITGNFQFEPCSHGDFLGS 177

Query: 175 ILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEP 234
           ILGTGIAREK+GDIILQGE+GAQ +VVPEL ++L ++L+KV NV V+CT+IPL++L+YEP
Sbjct: 178 ILGTGIAREKVGDIILQGEQGAQIIVVPELVEFLTSALDKVRNVPVTCTKIPLISLDYEP 237

Query: 235 PRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSL-ASLVQISAKASAIRS 288
           PRTKSFKTIEASLRVDA+ASAGFK+SRSKLV++I    +  + + I+ K + ++S
Sbjct: 238 PRTKSFKTIEASLRVDAVASAGFKISRSKLVDMISNGDVRINWIPITTKGTTVKS 292

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114944|ref|XP_002316899.1| predicted protein [Populus trichocarpa] gi|222859964|gb|EEE97511.1| predicted protein [Populus trichocarpa]

 Score =  343 bits (879), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 169/213 (79%), Positives = 189/213 (88%), Gaps = 1/213 (0%)

Query: 56  HLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMAL 115
           H+ QA KG     LKGV DK+ IEEVK IL+MARRAS RREVLH+DFLTPP LKES+  L
Sbjct: 3   HVAQATKGEVV-ALKGVEDKSVIEEVKRILDMARRASLRREVLHTDFLTPPTLKESLHVL 61

Query: 116 EKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSI 175
           EKLADVKA+AQGGYPQAERCRLSVGHPE LTSDPDIVAALSITGNFGFQ CSHGDFLG+I
Sbjct: 62  EKLADVKAIAQGGYPQAERCRLSVGHPETLTSDPDIVAALSITGNFGFQLCSHGDFLGAI 121

Query: 176 LGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPP 235
           LGTGIAR K+GDII+ G K AQ L+VP+L DY+++SL+KVG+VSVSCT IPL A+EYEPP
Sbjct: 122 LGTGIARNKLGDIIVLGGKRAQVLLVPDLVDYIVSSLDKVGDVSVSCTPIPLHAIEYEPP 181

Query: 236 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLI 268
           RTKSFKT+EASLRVDALASAGFK+SRSKLV+LI
Sbjct: 182 RTKSFKTVEASLRVDALASAGFKISRSKLVDLI 214

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  333 bits (853), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 166/269 (61%), Positives = 203/269 (75%), Gaps = 27/269 (10%)

Query: 1   MAAISLAAPWI-LRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQ 59
           MA  SLA PWI LR+  R+ +     LH N  +       P +FP  LRH+A    ++ +
Sbjct: 439 MAVTSLAPPWIILRQTFRSVA-ASSYLHSNHKTLISNLSIPASFP--LRHSALRRCYIAE 495

Query: 60  AVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLA 119
           A+KG+ D LLKGVGD+   +EVK ILEMARRA+S+REVLH+DFLTPP++KES++ L K A
Sbjct: 496 AIKGDVDFLLKGVGDQAVAKEVKQILEMARRAASKREVLHTDFLTPPIVKESVLVLGKFA 555

Query: 120 DVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTG 179
           DVK VAQGGYP+AERCR+S+GHP+ LT+DPDIVAALSITGNFGFQPCSHGDFLG+ILGTG
Sbjct: 556 DVKIVAQGGYPEAERCRISIGHPDVLTNDPDIVAALSITGNFGFQPCSHGDFLGAILGTG 615

Query: 180 IAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKS 239
           I+REK+GDI++Q                       VGNV V+CT+IPLLALEYEPPRT S
Sbjct: 616 ISREKLGDILIQ-----------------------VGNVGVTCTKIPLLALEYEPPRTNS 652

Query: 240 FKTIEASLRVDALASAGFKLSRSKLVNLI 268
           FKT+EASLR+DA+ASAGFK+SRSKLV+LI
Sbjct: 653 FKTVEASLRIDAVASAGFKISRSKLVDLI 681

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	289
TAIR|locus:2037048	320	AT1G53120 [Arabidopsis thalian	0.916	0.828	0.676	1.9e-92
UNIPROTKB|P74082	259	sll1252 "Sll1252 protein" [Syn	0.685	0.764	0.470	2.5e-42
UNIPROTKB|Q3AAH6	246	CHY_2039 "S4 domain protein" [	0.633	0.743	0.376	3.3e-24
TIGR_CMR|CHY_2039	246	CHY_2039 "S4 domain protein" [	0.633	0.743	0.376	3.3e-24
UNIPROTKB|Q81WE2	255	BAS3748 "S4 domain protein" [B	0.629	0.713	0.293	5.7e-11
TIGR_CMR|BA_4036	255	BA_4036 "S4 domain protein" [B	0.629	0.713	0.293	5.7e-11
UNIPROTKB|Q71XY5	258	LMOf2365_2060 "S4 domain prote	0.612	0.686	0.281	9.6e-10

TAIR|locus:2037048 AT1G53120 [Arabidopsis thaliana (taxid:3702)]

 Score = 921 (329.3 bits), Expect = 1.9e-92, P = 1.9e-92
 Identities = 182/269 (67%), Positives = 221/269 (82%)

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 FKTIEASLRVDALASAGFKLSRSKLVNLI 268
             FKT+EASLR+DA+ASAGFK+SRSKLV+LI
Sbjct:   238 FKTVEASLRIDAVASAGFKISRSKLVDLI 266

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)]

 Score = 448 (162.8 bits), Expect = 2.5e-42, P = 2.5e-42
 Identities = 95/202 (47%), Positives = 131/202 (64%)

Query:    68 LLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQG 127
             LLKG  D+ AI  V   ++ A +A    EV+ SDF  PP++ E     + L ++  +  G
Sbjct:     7 LLKGAPDREAIARV---IDQAEQALRTWEVVVSDFCAPPLIAEIQTRFDSLTELHFLPWG 63

Query:   128 GYPQAERCRLSVGHPEA-LTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIG 186
             GYPQAER RL++   E  L ++   + AL + GNF F P SH DFLG++LGTG+ REK+G
Sbjct:    64 GYPQAERQRLAIARAEIPLETEQIPLTALDVAGNFLFDPASHRDFLGALLGTGLVREKVG 123

Query:   187 DIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEAS 246
             DIIL GE+GAQ +VVPE+A+++   L +V  V V    I L  L+  PP+TK   T+EAS
Sbjct:   124 DIILLGERGAQAIVVPEVAEFISLHLTQVRTVPVKAKAIALEELKIRPPKTKEMTTVEAS 183

Query:   247 LRVDALASAGFKLSRSKLVNLI 268
             LR+DA+ASAGF LSRSK+ + +
Sbjct:   184 LRLDAIASAGFGLSRSKMADAV 205

GO:0030096 "plasma membrane-derived thylakoid photosystem II" evidence=IDA

UNIPROTKB|Q3AAH6 CHY_2039 "S4 domain protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 70/186 (37%), Positives = 101/186 (54%)

Query:    84 ILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE 143
             I ++  RA+  + VL +DFL P     +   L    +V     GGYP AE+ R +     
Sbjct:     8 IEDLLSRAAKGQIVL-TDFLDPAAASLTRDLLRNYPEVNYKVDGGYPNAEKVRFAFYPIY 66

Query:   144 ALTSDPDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVP 202
                 D ++ +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL    G Q +V  
Sbjct:    67 VFPEDVELNLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILI-PNGCQVVVDR 125

Query:   203 ELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRS 262
             +L  YLI  L+KV  V V+   I    L     +T+       SLR+D++ ++GF +SRS
Sbjct:   126 DLVPYLIQQLDKVHRVGVTVKEIVREELLLPEAKTREVVAFVKSLRLDSVGASGFGISRS 185

Query:   263 KLVNLI 268
             ++V  I
Sbjct:   186 QMVKEI 191

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CHY_2039 CHY_2039 "S4 domain protein" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 70/186 (37%), Positives = 101/186 (54%)

Query:    84 ILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE 143
             I ++  RA+  + VL +DFL P     +   L    +V     GGYP AE+ R +     
Sbjct:     8 IEDLLSRAAKGQIVL-TDFLDPAAASLTRDLLRNYPEVNYKVDGGYPNAEKVRFAFYPIY 66

Query:   144 ALTSDPDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVP 202
                 D ++ +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL    G Q +V  
Sbjct:    67 VFPEDVELNLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILI-PNGCQVVVDR 125

Query:   203 ELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRS 262
             +L  YLI  L+KV  V V+   I    L     +T+       SLR+D++ ++GF +SRS
Sbjct:   126 DLVPYLIQQLDKVHRVGVTVKEIVREELLLPEAKTREVVAFVKSLRLDSVGASGFGISRS 185

Query:   263 KLVNLI 268
             ++V  I
Sbjct:   186 QMVKEI 191

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q81WE2 BAS3748 "S4 domain protein" [Bacillus anthracis (taxid:1392)]

 Score = 168 (64.2 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 57/194 (29%), Positives = 98/194 (50%)

Query:    81 VKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVG 140
             V  +LE  ++A+   +V  +DFL P   +   M + +  D+     G   +AER R  + 
Sbjct:    15 VDKVLEW-KQAAEYHQVKLTDFLDPRQQQIVTMVIGQ-GDIAVQFDGATSRAERKRALI- 71

Query:   141 HPEALTSDPDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQF 198
             +P+ L  + +   V  L I     F    H   LG+ +  G+ REK GDI+LQ ++ AQ 
Sbjct:    72 YPDYLVVNEEEFQVEGLEIDYPSKFYTLEHRQILGTFMSLGLTREKCGDILLQEDR-AQI 130

Query:   199 LVVPELADYLITSLEKVGNVSVSCTRIP---LLALEYEPPRTKSFKTIEASLRVDALASA 255
             +V  E+  Y+  +L+ +G V VS + +    +L ++ E    KS  T+ +SLR+D + + 
Sbjct:   131 VVAKEVVSYIEMNLQSIGKVKVSLSPVKGEKILQIQ-ETWGEKS-GTV-SSLRLDVMLAE 187

Query:   256 GFKLSRSKLVNLIR 269
                +SR K+   I+
Sbjct:   188 MLHISRQKVQPFIK 201

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_4036 BA_4036 "S4 domain protein" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 168 (64.2 bits), Expect = 5.7e-11, P = 5.7e-11
 Identities = 57/194 (29%), Positives = 98/194 (50%)

Query:    81 VKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVG 140
             V  +LE  ++A+   +V  +DFL P   +   M + +  D+     G   +AER R  + 
Sbjct:    15 VDKVLEW-KQAAEYHQVKLTDFLDPRQQQIVTMVIGQ-GDIAVQFDGATSRAERKRALI- 71

Query:   141 HPEALTSDPDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQF 198
             +P+ L  + +   V  L I     F    H   LG+ +  G+ REK GDI+LQ ++ AQ 
Sbjct:    72 YPDYLVVNEEEFQVEGLEIDYPSKFYTLEHRQILGTFMSLGLTREKCGDILLQEDR-AQI 130

Query:   199 LVVPELADYLITSLEKVGNVSVSCTRIP---LLALEYEPPRTKSFKTIEASLRVDALASA 255
             +V  E+  Y+  +L+ +G V VS + +    +L ++ E    KS  T+ +SLR+D + + 
Sbjct:   131 VVAKEVVSYIEMNLQSIGKVKVSLSPVKGEKILQIQ-ETWGEKS-GTV-SSLRLDVMLAE 187

Query:   256 GFKLSRSKLVNLIR 269
                +SR K+   I+
Sbjct:   188 MLHISRQKVQPFIK 201

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q71XY5 LMOf2365_2060 "S4 domain protein" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)]

 Score = 159 (61.0 bits), Expect = 9.6e-10, P = 9.6e-10
 Identities = 52/185 (28%), Positives = 84/185 (45%)

Query:   100 SDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT-SDPDI-VAALSI 157
             +DFL P     +   +    ++     GG   AER R  + +P+  T ++ D  +A   I
Sbjct:    35 TDFLDPRQRFITETVIGGYDEINVQFFGGVAHAERRRALI-YPDYYTPTEADFEIALFHI 93

Query:   158 TGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGN 217
                  F   +H   LG+++  G+ R+  GDI+  G +  Q LV   + DYL   LEK+G 
Sbjct:    94 RYPVKFTTLTHQKILGTLMSLGMKRDIFGDILNNGTEW-QLLVESTMKDYLTLQLEKIGK 152

Query:   218 VSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLV 277
             V+V      L    Y P   +      +S+R+D + S    +SR K   L+     A LV
Sbjct:   153 VNVMLEETDLANAVYAPVVWEEMGLTVSSMRLDVIISNAHHISRQKAKQLVT----AGLV 208

Query:   278 QISAK 282
             +++ K
Sbjct:   209 KVNWK 213


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.135   0.386    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      289       289   0.00088  115 3  11 22  0.50    33
                                                     33  0.43    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  7
  No. of states in DFA:  591 (63 KB)
  Total size of DFA:  172 KB (2101 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.60u 0.14s 24.74t   Elapsed:  00:00:01
  Total cpu time:  24.60u 0.14s 24.74t   Elapsed:  00:00:01
  Start:  Sat May 11 06:14:36 2013   End:  Sat May 11 06:14:37 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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	Length	Definition	E-value
Query	289
PLN00051	267	PLN00051, PLN00051, RNA-binding S4 domain-containi	1e-129
TIGR03069	257	TIGR03069, PS_II_S4, photosystem II S4 domain prot	2e-86
COG2302	257	COG2302, COG2302, Uncharacterized conserved protei	5e-44

>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein; Provisional

 Score =  366 bits (942), Expect = e-129
 Identities = 147/213 (69%), Positives = 171/213 (80%)

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 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLI 268
           R +SFK++EASLR+DALASAGF++SRSKLV+LI
Sbjct: 181 RVESFKSVEASLRLDALASAGFRMSRSKLVDLI 213

Length = 267

>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein

 Score =  258 bits (662), Expect = 2e-86
 Identities = 100/206 (48%), Positives = 134/206 (65%), Gaps = 7/206 (3%)

Query: 67  DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQ 126
           +LLKG       EE++ +L++A +A    E + SDFL+ P+ +E +     L D+K +A 
Sbjct: 5   ELLKGANYP---EELERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAW 61

Query: 127 GGYPQAERCRLSVGHPEALTSDPDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREK 184
           GGYPQAER R++    +    DPDI  +  L I GNF F P SH DF G++LGTGI REK
Sbjct: 62  GGYPQAERQRIACARSD-NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREK 120

Query: 185 IGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRT-KSFKTI 243
           IGDI + G++GAQ L  PELA++L   L +V +V V C  IPL  L+   PRT K   T+
Sbjct: 121 IGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKCKAIPLEELQIPAPRTPKELTTV 180

Query: 244 EASLRVDALASAGFKLSRSKLVNLIR 269
           EASLR+DA+ASAGF LSRSK+V+ I+
Sbjct: 181 EASLRIDAIASAGFGLSRSKIVDQIK 206

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium [Energy metabolism, Photosynthesis]. Length = 257

>gnl|CDD|225185 COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown]

 Score =  149 bits (379), Expect = 5e-44
 Identities = 71/190 (37%), Positives = 99/190 (52%), Gaps = 5/190 (2%)

Query: 81  VKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVG 140
           +  +LE  ++      V+ +DFL P      +  L  L DVK    GGYP+AER RL + 
Sbjct: 16  IDRVLEWIKQVEKTYTVVVTDFLDPREQAI-LKTLAGLEDVKVSFSGGYPRAERKRLIL- 73

Query: 141 HPEALTSD-PDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQF 198
           +P     +  D  +  L I+    F   +H D LG++L  GI REK GDII++GE GAQ 
Sbjct: 74  YPAYYPLEESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEGE-GAQL 132

Query: 199 LVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFK 258
           +V  ELAD+ +  L K+G   V    I L  L+    + K      +SLR+D + S GF 
Sbjct: 133 IVATELADFFLLHLTKIGKAPVKLEEIDLEELKESTEKWKELDVTVSSLRLDVVISEGFG 192

Query: 259 LSRSKLVNLI 268
           LSR+K   LI
Sbjct: 193 LSRAKAQQLI 202

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	289
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	100.0
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	100.0
COG2302	257	Uncharacterized conserved protein, contains S4-lik	100.0
KOG4837	248	consensus Uncharacterized conserved protein [Funct	99.82
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	98.57
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	98.52
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.48
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	98.08
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	97.66
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	97.29
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	97.13
smart00363	60	S4 S4 RNA-binding domain.	97.06
CHL00113	201	rps4 ribosomal protein S4; Reviewed	96.78
COG1188	100	Ribosome-associated heat shock protein implicated	96.73
PF06353	142	DUF1062: Protein of unknown function (DUF1062); In	96.32
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	96.13
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	95.89
COG4332	203	Uncharacterized protein conserved in bacteria [Fun	95.85
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	95.64
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	93.88
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	92.12
PLN00189	194	40S ribosomal protein S9; Provisional	88.31
PTZ00155	181	40S ribosomal protein S9; Provisional	88.26

>PLN00051 RNA-binding S4 domain-containing protein; Provisional

Probab=100.00  E-value=9.2e-64  Score=463.86  Aligned_cols=223  Identities=65%  Similarity=0.967  Sum_probs=203.5

Q ss_pred             hhccH-HHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEe
Q 022999           61 VKGNF-DDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSV  139 (289)
Q Consensus        61 ~~~~~-~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i  139 (289)
                      -.++. ..+++|+.+ +++.++++++||+++|.+++.+++|+||||+||.++.+++++.+++++.++|||++|||+|++|
T Consensus         6 ~~~~~~~~i~~h~~~-ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~   84 (267)
T PLN00051          6 AAGDADSALLGVVDP-AHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSI   84 (267)
T ss_pred             hccchhhHHHhhcCh-hhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEE
Confidence            33444 368999875 5599999999999999999999999999999999999999888899999999999999999999


Q ss_pred             eCCCCCCCCcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceE
Q 022999          140 GHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVS  219 (289)
Q Consensus       140 ~~p~y~~~~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~  219 (289)
                      +|+++++.+++++++++|++++||.+|+|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++
T Consensus        85 ~p~~~~~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~  164 (267)
T PLN00051         85 GRPEVLTSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVP  164 (267)
T ss_pred             echHhccccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhcccee
Confidence            86665533336899999999999999999999999999999999999999855456999999999999999999999999


Q ss_pred             EEEEEecCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          220 VSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       220 V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      |++++++++++.+|+++|+++.++|||+|||+++|++|++||++++++|++|+|+|||+++.++|
T Consensus       165 V~~~~~~~~~~~~~~~~~~e~~~~vas~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s  229 (267)
T PLN00051        165 VECRAIPLSALEVEPPRVESFKSVEASLRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNG  229 (267)
T ss_pred             EEEEEecHHHcCCCccceEEccCCcCcccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCC
Confidence            99999999998888889999999999999999999999999999999999999999999765444

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=100.00  E-value=6.8e-61  Score=442.61  Aligned_cols=220  Identities=43%  Similarity=0.670  Sum_probs=198.1

Q ss_pred             cHHHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEeeCCC
Q 022999           64 NFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE  143 (289)
Q Consensus        64 ~~~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i~~p~  143 (289)
                      +++.++++++++|+   +++++||+++|.++|.+++|+||||+||.++.+++++..++++.++|||++|||+|++|+|++
T Consensus         2 ~~~~~~~~~~~~ee---~~~~~d~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~   78 (257)
T TIGR03069         2 PREELLKGANYPEE---LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD   78 (257)
T ss_pred             ChHHHHHhCCCHHH---HHHHHHHHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEeccc
Confidence            45678999886342   999999999999999999999999999999999998888999999999999999999998665


Q ss_pred             CCCCC-cCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEE
Q 022999          144 ALTSD-PDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC  222 (289)
Q Consensus       144 y~~~~-~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v  222 (289)
                      ++.+. ++++++++|++++||.+|+|||||||||||||+|+++|||++.++++||++|+++|++||.+||+|||+++|++
T Consensus        79 ~~~~~~df~i~~l~i~~~~kF~~l~Hrd~LGalm~lGi~R~~iGDI~v~~~~~~~v~v~~~i~~~i~~~l~kIg~~~V~~  158 (257)
T TIGR03069        79 NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKC  158 (257)
T ss_pred             ccCCcccCceEEEEEEcccccCCCCHHHHHHHHHHcCCcHhhcCCEEEecCCcEEEEECHHHHHHHHHHhhhccceeEEE
Confidence            54322 35899999999999999999999999999999999999998776656999999999999999999999999999


Q ss_pred             EEecCCcccCCCCCe-eEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEe-cccccc
Q 022999          223 TRIPLLALEYEPPRT-KSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQIS-AKASAI  286 (289)
Q Consensus       223 ~ei~~~~l~~~~~~~-ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~-~~~~~~  286 (289)
                      ++++++++..+++++ +++.++|+|+|||+++++++++||++++++|++|+|+|||+++ .++..+
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v  224 (257)
T TIGR03069       159 KAIPLEELQIPAPRTPKELTTVEASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSREL  224 (257)
T ss_pred             EEeCHHHcCCCCcccceEecCCCccccHHHHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcC
Confidence            999999875555555 9999999999999999999999999999999999999999976 444333

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]

Probab=100.00  E-value=7.7e-61  Score=436.01  Aligned_cols=215  Identities=33%  Similarity=0.446  Sum_probs=199.6

Q ss_pred             HHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEeeCCCCCC
Q 022999           67 DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT  146 (289)
Q Consensus        67 ~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i~~p~y~~  146 (289)
                      .++.|+. .|++.+++|++||+++++++|++..||||||+|+.+....++ ..++++.++||||+|||+|++++|++|..
T Consensus         3 ~iyqhf~-~eer~fidr~l~~~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l~P~y~~~   80 (257)
T COG2302           3 GIYQHFR-AEERPFIDRVLEWIKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLILYPAYYPL   80 (257)
T ss_pred             cHhhhcC-chhHHHHHHHHHHHHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEEcccccCh
Confidence            4677866 567999999999999999999999999999999999888777 78999999999999999999998555543


Q ss_pred             C-CcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEe
Q 022999          147 S-DPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRI  225 (289)
Q Consensus       147 ~-~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei  225 (289)
                      + .++++++++|.|++||.+++||||||+||||||+|+++|||++.+ ++||++|.+++++|+..+|+|||+++|+++++
T Consensus        81 ~~~df~l~l~eI~y~~kF~~l~H~~~LGtll~lGikRe~~GDIiv~~-~~aQliv~~~~~~f~~~~Ltkig~~~V~l~ei  159 (257)
T COG2302          81 EESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEG-EGAQLIVATELADFFLLHLTKIGKAPVKLEEI  159 (257)
T ss_pred             hhcccceEEEEEEcccccccccHHHHHHHHHhccCcHHhhccEEEeC-CeeEEEEehhHHHHHHHHHHhhcCcceEEEEc
Confidence            3 345899999999999999999999999999999999999999876 69999999999999999999999999999999


Q ss_pred             cCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          226 PLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       226 ~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      +++++..+.++|++..++|||||||+|+|++||+||++|+++|++|+|+||++++.++|
T Consensus       160 ~~~~l~~~~~~~~e~~~~vsSlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s  218 (257)
T COG2302         160 DLEELKESTEKWKELDVTVSSLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKAS  218 (257)
T ss_pred             CHHHcccCccceeEEeeeeehhhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEEecccc
Confidence            99999988889999999999999999999999999999999999999999999777444

>KOG4837 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.82  E-value=1.7e-21  Score=173.86  Aligned_cols=210  Identities=54%  Similarity=0.839  Sum_probs=188.8

Q ss_pred             HHHhhccHHHHhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEE
Q 022999           58 IQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL  137 (289)
Q Consensus        58 ~~~~~~~~~~ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl  137 (289)
                      ..|+|++.+.+++.+.+...-..+.+++++|.++.......+|+||.|.       .+..++++.....|||+.||+|++
T Consensus         6 ~~~i~g~~~~~~~~vg~~~v~k~~~~~~~m~~~~~~~r~f~~t~~l~ps-------l~t~F~~v~s~~lpgl~~a~ec~~   78 (248)
T KOG4837|consen    6 SEAIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREFLHTDFLTPS-------LLTKFADVKSVALPGLPEAEECRI   78 (248)
T ss_pred             hhHhhhhhhhhhhcccHHHHHhhcHHHHHHHHHHHhhHHHHhhhhhCch-------hhhccccchhhhcCCCCCChheEe
Confidence            3789999999999999988889999999999999999999999999994       345778999999999999999999


Q ss_pred             EeeCCCCCCCCcCceEEEEEecCCCCCCCCchhhHHHHHhCCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcc
Q 022999          138 SVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGN  217 (289)
Q Consensus       138 ~i~~p~y~~~~~~~i~~L~I~~~~kF~~LsHRD~LGaLmgLGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr  217 (289)
                      -|+.|+....+++..+.+.+..++.|++.+|.||||+++     ||+.|||.++.+   |+.+.+++.+|..+-|.|+| 
T Consensus        79 pi~~~~~~ts~k~~kksl~~td~~dsd~esh~Df~~e~~-----~e~~~D~~Vvk~---~~~i~~~v~sfr~d~llK~G-  149 (248)
T KOG4837|consen   79 PIGHPDVLTSDKDIKKSLSITDNFDSDPESHGDFLGEIL-----REKLGDILVVKE---KVLIVPEVVSFRVDALLKVG-  149 (248)
T ss_pred             eccCccccccchhHHHHhhhccccCCCcccchhHHHHHH-----HHhcCCceeeeh---hhhhhhHHHHHHHHHHHHhc-
Confidence            999998766666667889999999999999999999998     999999998864   58888999999999999999 


Q ss_pred             eEEEEEEecCCcccCCCCCeeEEEEeecccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccccc
Q 022999          218 VSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKASAI  286 (289)
Q Consensus       218 ~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~  286 (289)
                      ..|.+..+++.-+.+. ++.-+++..-.|+|+|+.-++.|.++|+  .++|....|+||-..+.+++.|
T Consensus       150 lgv~rnKVel~fye~e-~R~N~~Kl~kkS~~i~vgds~d~~ig~~--~~~~s~~~~rV~~~tV~~~~t~  215 (248)
T KOG4837|consen  150 LGVTRNKVELLFYEYE-PRTNSFKLVKKSLRIDVGDSADFKIGRS--VDLISSKDVRVNWATVTKNGTI  215 (248)
T ss_pred             cccccchhhHhhhhcc-cccCcccccccceeeecccccceeeecc--cccCCcceEEEeeeeecccceE
Confidence            9999999988766655 6888899999999999999999999999  8899999999998877766654

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=98.57  E-value=2.5e-08  Score=89.69  Aligned_cols=69  Identities=16%  Similarity=0.143  Sum_probs=60.2

Q ss_pred             eEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccchHHHH-HccccccHHHHHHHHHcCCe
Q 022999          195 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLIRYSSL  273 (289)
Q Consensus       195 ~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVv-s~~f~lSRska~~lI~~GkV  273 (289)
                      .+|.++.+++.+|+..++.++|++.+.+  +.+.+                 +|||.++ +.+|..||++|.++|+.|+|
T Consensus        57 ~~Yg~~e~q~~~~~~~a~~~~g~t~~~l--l~~le-----------------~RLD~~L~~~g~~~SR~~ArqlI~~G~V  117 (200)
T TIGR01017        57 FMYGITEKQFRKYFKEAKKLKGNTGENL--LRLLE-----------------SRLDNVVYRLGFAPTRFAARQLVSHGHI  117 (200)
T ss_pred             HHHhchHHHHHHHHHHHhccCCCchhHH--HHHHH-----------------HHHHHHHHHcCCCCCHHHHHHHHHCCCE
Confidence            6899999999999999999999999877  32211                 7999998 77889999999999999999


Q ss_pred             EECcEEecc
Q 022999          274 ASLVQISAK  282 (289)
Q Consensus       274 ~vn~~~~~~  282 (289)
                      .|||+++..
T Consensus       118 ~VNgk~v~~  126 (200)
T TIGR01017       118 LVNGKKVDI  126 (200)
T ss_pred             EECCEEeCC
Confidence            999997643

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=98.52  E-value=2.8e-08  Score=89.50  Aligned_cols=69  Identities=16%  Similarity=0.235  Sum_probs=60.6

Q ss_pred             CeEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccchHHHH-HccccccHHHHHHHHHcCC
Q 022999          194 KGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLIRYSS  272 (289)
Q Consensus       194 ~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVv-s~~f~lSRska~~lI~~Gk  272 (289)
                      ..+|.++.+++.+|+..++.++|++.+.+  +.+.|                 +|||.++ +.+|..||++|.++|..|+
T Consensus        59 ~~~Y~~~e~q~~~~~~~a~~~~g~t~~~l--l~~lE-----------------~RLD~iL~~~g~~~SR~~arqlI~~G~  119 (203)
T PRK05327         59 RRIYGVLEKQFRRYFKEAARRKGNTGENL--LQLLE-----------------SRLDNVVYRLGFAPTRRQARQLVSHGH  119 (203)
T ss_pred             HHHhcCcHHHHHHHHHHHHhccCCcHhHH--HHHHH-----------------HHHHHHHHHcCccCCHHHHHHHHHCCc
Confidence            36899999999999999999999999877  33212                 8999998 7789999999999999999


Q ss_pred             eEECcEEec
Q 022999          273 LASLVQISA  281 (289)
Q Consensus       273 V~vn~~~~~  281 (289)
                      |.|||+.+.
T Consensus       120 V~VNgk~v~  128 (203)
T PRK05327        120 ILVNGKKVN  128 (203)
T ss_pred             EEECCEEEC
Confidence            999999765

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.48  E-value=2.6e-07  Score=64.11  Aligned_cols=36  Identities=25%  Similarity=0.334  Sum_probs=33.5

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      +|||.+++ .++..||++|+++|++|.|+|||+++..
T Consensus         1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~   37 (48)
T PF01479_consen    1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKD   37 (48)
T ss_dssp             EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESS
T ss_pred             CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcC
Confidence            69999999 8899999999999999999999997774

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=98.08  E-value=5.8e-06  Score=60.06  Aligned_cols=42  Identities=5%  Similarity=0.043  Sum_probs=35.8

Q ss_pred             eecccchHHHHHccccc--cHHHHHHHHHcCCeEECcEEe-ccccc
Q 022999          243 IEASLRVDALASAGFKL--SRSKLVNLIRYSSLASLVQIS-AKASA  285 (289)
Q Consensus       243 tVsSlRLDaVvs~~f~l--SRska~~lI~~GkV~vn~~~~-~~~~~  285 (289)
                      .....|||.+++.. ++  ||+.++.+|+.|.|+|||++. +++.-
T Consensus         5 ~~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~   49 (59)
T TIGR02988         5 FTEYITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKK   49 (59)
T ss_pred             cchHHHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCC
Confidence            34668999999998 88  999999999999999999976 44443

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>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 []

Probab=97.66  E-value=8.5e-05  Score=56.44  Aligned_cols=60  Identities=25%  Similarity=0.339  Sum_probs=43.3

Q ss_pred             CCCCchhhHHHHHh-CCCCCCccccEEEecCCeEEEEecchHHHHHHHhhc--hhcceEEEEEE
Q 022999          164 QPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLE--KVGNVSVSCTR  224 (289)
Q Consensus       164 ~~LsHRD~LGaLmg-LGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLt--KIgr~~V~v~e  224 (289)
                      +.++++|++|+|.+ .||.++.||+|-+.+ +..+|-|.++.++-+++.|.  ++++.+|++++
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-~~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD-NFSFVEVPEEVAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S-S-EEEEE-TT-HHHHHHHHTT--SSS----EEE
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee-eEEEEEECHHHHHHHHHHhcCCCCCCeeEEEEE
Confidence            56799999999998 599999999998765 58999999999999999998  77888888864

; PDB: 2G0C_A 3MOJ_B.

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

Probab=97.29  E-value=0.00044  Score=48.89  Aligned_cols=39  Identities=18%  Similarity=0.188  Sum_probs=33.1

Q ss_pred             cchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEe-ccccc
Q 022999          247 LRVDALASAG-FKLSRSKLVNLIRYSSLASLVQIS-AKASA  285 (289)
Q Consensus       247 lRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~-~~~~~  285 (289)
                      +|||.++... +..||+.++.+|++|.|+|||+.. .++..
T Consensus         1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~   41 (70)
T cd00165           1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYK   41 (70)
T ss_pred             CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccC
Confidence            4899998877 678999999999999999999976 55443

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=97.13  E-value=0.00062  Score=57.96  Aligned_cols=43  Identities=19%  Similarity=0.147  Sum_probs=36.3

Q ss_pred             cccchHHH-HHccccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999          245 ASLRVDAL-ASAGFKLSRSKLVNLIRYSSLASLVQISAKASAIR  287 (289)
Q Consensus       245 sSlRLDaV-vs~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~~  287 (289)
                      .++|||.. .++.|=-||+.|+++|++|+|.|||+..+++.++.
T Consensus         7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~~Kps~~V~   50 (133)
T PRK10348          7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVE   50 (133)
T ss_pred             ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEECCCCCccC
Confidence            36799975 56789999999999999999999999977665543

>smart00363 S4 S4 RNA-binding domain

Probab=97.06  E-value=0.0011  Score=45.55  Aligned_cols=37  Identities=19%  Similarity=0.115  Sum_probs=32.1

Q ss_pred             cchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEe-ccc
Q 022999          247 LRVDALASAG-FKLSRSKLVNLIRYSSLASLVQIS-AKA  283 (289)
Q Consensus       247 lRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~-~~~  283 (289)
                      +|||.++... +..||+.++.+|++|.|.|||+.. .++
T Consensus         1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~   39 (60)
T smart00363        1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPS   39 (60)
T ss_pred             CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCC
Confidence            4899998876 679999999999999999999977 443

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=96.78  E-value=0.0015  Score=59.14  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=32.2

Q ss_pred             cchHHHH-HccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          247 LRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       247 lRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      +|||.++ ..+|..||+.|.++|..|+|.|||+++..
T Consensus        89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~  125 (201)
T CHL00113         89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDI  125 (201)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecC
Confidence            7999999 46778999999999999999999997644

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]

Probab=96.73  E-value=0.0015  Score=53.07  Aligned_cols=43  Identities=19%  Similarity=0.166  Sum_probs=36.6

Q ss_pred             cccchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999          245 ASLRVDALASAG-FKLSRSKLVNLIRYSSLASLVQISAKASAIR  287 (289)
Q Consensus       245 sSlRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~~~~~~~~  287 (289)
                      .-+|||.-+-.. |=-+|+-|++++++|+|+|||+.++++.++.
T Consensus         7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~aKpS~~VK   50 (100)
T COG1188           7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRAKPSKEVK   50 (100)
T ss_pred             cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEcccccccC
Confidence            358999987654 7789999999999999999999998877654

>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=96.32  E-value=0.0073  Score=52.00  Aligned_cols=34  Identities=35%  Similarity=0.382  Sum_probs=31.6

Q ss_pred             cccchHHHHHccccccHHHHHHHHHcCCeEECcE
Q 022999          245 ASLRVDALASAGFKLSRSKLVNLIRYSSLASLVQ  278 (289)
Q Consensus       245 sSlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~  278 (289)
                      .++|||++++..+++||++.+.++++|.+..+-.
T Consensus       101 ~~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~~  134 (142)
T PF06353_consen  101 FPLRLDRLLARQLGLSRSRLKRLIEQGLIRSDPD  134 (142)
T ss_pred             CCccHHHHHHHHhCcCHHHHHHHHHCCCEEecCc
Confidence            5799999999999999999999999999998843

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=96.13  E-value=0.0061  Score=58.25  Aligned_cols=38  Identities=18%  Similarity=0.177  Sum_probs=33.9

Q ss_pred             ecccchHHHHHccc-cccHHHHHHHHHcCCeEECcEEec
Q 022999          244 EASLRVDALASAGF-KLSRSKLVNLIRYSSLASLVQISA  281 (289)
Q Consensus       244 VsSlRLDaVvs~~f-~lSRska~~lI~~GkV~vn~~~~~  281 (289)
                      -+++|||.+++..| ..||+.++.+|++|+|+|||+.+.
T Consensus        15 ~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~   53 (325)
T PRK11180         15 QLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVIN   53 (325)
T ss_pred             cCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEcc
Confidence            35789999999987 589999999999999999999653

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=95.89  E-value=0.017  Score=55.06  Aligned_cols=49  Identities=14%  Similarity=0.162  Sum_probs=39.1

Q ss_pred             CeeEEEEe--ecccchHHHHHccc-cccHHHHHHHHHcCCeEECcEEecccc
Q 022999          236 RTKSFKTI--EASLRVDALASAGF-KLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       236 ~~ke~~~t--VsSlRLDaVvs~~f-~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      ..+++.+.  -++.|||.+++..+ ++||+.++.+|++|+|+|||+.+.++.
T Consensus         7 ~~~~~~v~~~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v~~~~   58 (317)
T PRK11025          7 SVKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEY   58 (317)
T ss_pred             ccEEEEECcccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEcCccc
Confidence            34444444  36799999999777 689999999999999999999775543

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.85  E-value=0.014  Score=52.16  Aligned_cols=77  Identities=21%  Similarity=0.230  Sum_probs=55.3

Q ss_pred             chHHHHHHHhhchhcceEEEEEEecCCcccC----CCCCee--EEEEe---ecccchHHHHHccccccHHHHHHHHHcCC
Q 022999          202 PELADYLITSLEKVGNVSVSCTRIPLLALEY----EPPRTK--SFKTI---EASLRVDALASAGFKLSRSKLVNLIRYSS  272 (289)
Q Consensus       202 ~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~----~~~~~k--e~~~t---VsSlRLDaVvs~~f~lSRska~~lI~~Gk  272 (289)
                      ++.+.+..-++.-+++..-++++.|.-.++.    ....++  |..+.   -+|+|||+++++-+|+|||..|.+|+.|+
T Consensus        85 a~larr~afdla~lRr~~~r~~g~pd~~i~krilge~~~~~~vel~l~~~~p~qlrl~~Ll~seL~LSrS~lq~lie~g~  164 (203)
T COG4332          85 AALARRFAFDLAILRRNNARLSGFPDFHIQKRILGEIASHAAVELSLRISRPFQLRLDRLLASELGLSRSELQRLIETGQ  164 (203)
T ss_pred             HHHHHHHHhhHHHHHhccccccCCCchhhhhheecCcccceeEEEEEcccCcchhHHHHHHHHHhCcCHHHHHHHHHcCc
Confidence            5677777778888887776776666533221    111222  22222   36899999999999999999999999999


Q ss_pred             eEECcE
Q 022999          273 LASLVQ  278 (289)
Q Consensus       273 V~vn~~  278 (289)
                      +..+-.
T Consensus       165 Irgdtd  170 (203)
T COG4332         165 IRGDTD  170 (203)
T ss_pred             eeecch
Confidence            998754

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=95.64  E-value=0.015  Score=51.70  Aligned_cols=38  Identities=13%  Similarity=0.134  Sum_probs=33.0

Q ss_pred             chHHHH-HccccccHHHHHHHHHcCCeEECcEEeccccc
Q 022999          248 RVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKASA  285 (289)
Q Consensus       248 RLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~~~  285 (289)
                      |||.++ ..+|--||+.|+++|.+|+|.|||+++.+.|-
T Consensus       104 RLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~  142 (177)
T PRK04051        104 RLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY  142 (177)
T ss_pred             HHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCe
Confidence            999865 57999999999999999999999997666553

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=93.88  E-value=0.066  Score=48.76  Aligned_cols=35  Identities=17%  Similarity=0.199  Sum_probs=31.5

Q ss_pred             chHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          248 RVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       248 RLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      |||+||= .+|.-||..|.++|..|.|.|||+.+.-
T Consensus        95 RLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~i  130 (205)
T COG0522          95 RLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNI  130 (205)
T ss_pred             HHHHHHHHhcccccHHHHHHHhhcceEEECCEEecc
Confidence            8999986 6999999999999999999999995543

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

Probab=92.12  E-value=0.17  Score=44.48  Aligned_cols=42  Identities=12%  Similarity=0.005  Sum_probs=35.0

Q ss_pred             EEeecc---cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          241 KTIEAS---LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       241 ~~tVsS---lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      +++|++   -|||.|+- .+|--|...|.++|..|.|.|||+++..
T Consensus        95 ~Ltv~~~leRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~  140 (162)
T TIGR01018        95 GLTVEDFLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTS  140 (162)
T ss_pred             hccHHHHHHHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEecc
Confidence            455555   49999876 6899999999999999999999995544

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.

>PLN00189 40S ribosomal protein S9; Provisional

Probab=88.31  E-value=0.19  Score=45.44  Aligned_cols=42  Identities=21%  Similarity=0.120  Sum_probs=35.1

Q ss_pred             EEeecc---cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          241 KTIEAS---LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       241 ~~tVsS---lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      .++|++   -|||+|+- .+|--|+..|.++|..|.|.|||+++..
T Consensus       100 ~Ltvs~~leRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~  145 (194)
T PLN00189        100 ALTVENFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNV  145 (194)
T ss_pred             hccHHHHHHhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEec
Confidence            456666   69999875 6889999999999999999999995543

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=88.26  E-value=0.41  Score=42.86  Aligned_cols=36  Identities=22%  Similarity=0.092  Sum_probs=31.5

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      -|||+|+- .+|--|...|.++|..|.|.|||+++..
T Consensus       107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~  143 (181)
T PTZ00155        107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDI  143 (181)
T ss_pred             HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEecc
Confidence            38999886 5889999999999999999999996543

---

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	Length	Definition	E-value
Query	289
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	4e-43
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>2fph_X YLMH; division protein, bacteria, GRAM+, DNA binding protein; 1.70A {Streptococcus pneumoniae} Length = 165

 Score =  144 bits (364), Expect = 4e-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

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 37/290 (12%), Positives = 82/290 (28%), Gaps = 89/290 (30%)

Query: 35  HGTHRPFTFPTS-LRHTASGI-RHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRAS 92
           H  H    F T   ++    I      A   NFD               K + +M +   
Sbjct: 1   HHHHHHMDFETGEHQYQYKDILSVFEDAFVDNFD--------------CKDVQDMPKSIL 46

Query: 93  SRREVLHSDFLTPPVLKESMMALEKLAD---------VKAVAQGGYP-QAERCRLSVGHP 142
           S+ E+ H   ++   +  ++     L           V+ V +  Y       +     P
Sbjct: 47  SKEEIDHI-IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP 105

Query: 143 EALT-----------SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREK------- 184
             +T           +D  + A  +++                       R +       
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVS-----------------------RLQPYLKLRQ 142

Query: 185 -------IGDIILQGEKGA--QFLVVPELADYLITSLEKVGNV---SVSCTRIPLLALEY 232
                    ++++ G  G+   ++ +     Y +   +    +   ++     P   LE 
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC-KMDFKIFWLNLKNCNSPETVLE- 200

Query: 233 EPPRTKSFKTIEASLRVDALASAGFKLS----RSKLVNLIRYSSLA-SLV 277
                K    I+ +    +  S+  KL     +++L  L++       L+
Sbjct: 201 --MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.4 bits (96), Expect = 2e-04
 Identities = 49/296 (16%), Positives = 85/296 (28%), Gaps = 83/296 (28%)

Query: 8   APWILRRAVRTFSLPQPLLHLNPGS--CFHG------------------THRPFTFPT-- 45
           A + + R      L Q LL L P       G                        F    
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 46  -SLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLT 104
            +L++  S    +++ ++     LL  + D N      H   +  R  S +  L    L 
Sbjct: 187 LNLKNCNS-PETVLEMLQ----KLLYQI-DPNWTSRSDHSSNIKLRIHSIQAEL-RRLLK 239

Query: 105 PPVLKESMMALEKLADVKAVAQGGYPQA--ERCRLSVGHPEALTSDPDIVAALSITGNFG 162
               +  ++ L  + + KA        A    C++ +      T    +           
Sbjct: 240 SKPYENCLLVLLNVQNAKAW------NAFNLSCKILL-----TTRFKQVT---------- 278

Query: 163 FQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSC 222
                  DFL +   T I+ +     +   E  +          YL    + +       
Sbjct: 279 -------DFLSAATTTHISLDHHSMTLTPDEVKSLL------LKYLDCRPQDLP--REVL 323

Query: 223 TRIPL-LALEYEPPRTKSFKTIEASLRVDALASAGFK-LSRSKLVNLIRYSSLASL 276
           T  P  L++            I  S+R        +K ++  KL  +I  SSL  L
Sbjct: 324 TTNPRRLSI------------IAESIRDGLATWDNWKHVNCDKLTTIIE-SSLNVL 366

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	289
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	100.0
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	98.08
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	97.74
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	97.74
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	97.65
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	97.49
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	97.41
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	97.35
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	97.29
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	97.28
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	97.25
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	96.61
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	94.92
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	94.29
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	88.78
2ktl_A	164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	82.18

>2fph_X YLMH; division protein, bacteria, GRAM+, DNA binding protein; 1.70A {Streptococcus pneumoniae}

Probab=100.00  E-value=7e-49  Score=339.80  Aligned_cols=160  Identities=16%  Similarity=0.245  Sum_probs=145.9

Q ss_pred             HhccCCCcchHHHHHHHHHHHHHHhcCCCeEEecCCCHHHHHHHHHHHhccCCeeEEEeCCCcccceeEEEeeCCCCCCC
Q 022999           68 LLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTS  147 (289)
Q Consensus        68 ll~~~~~~e~k~~v~ri~D~~~~a~~~~~~~~TdFLdP~e~~i~~~il~~~~~v~~~~~GGy~~AERkrl~i~~p~y~~~  147 (289)
                      +++|+. ++++++++|++||+++|.++|.+++|+||||+||+++.+++++. ++++.++|||++|||||++|+|+++..+
T Consensus         2 ~~~hf~-~~e~~~i~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~i~~~~-~~~~~~~GGy~~AER~r~~i~p~~~~~~   79 (165)
T 2fph_X            2 IYQHFS-IEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTY-GLACSSSGEFVSSEYVRVLLYPDYFQPE   79 (165)
T ss_dssp             CCCCCC-GGGHHHHHHHHHHHHHHHHHTSCEECCCBCHHHHHHHHHHHHHT-TCEEEEGGGTSCCSSBCEEEECTTCCCC
T ss_pred             hhhhcC-hhhHHHHHHHHHHHHHHHHhCCEEECCCCCHHHHHHHHHHHhcc-CcEEEEeCCCcHHheeEEEEecccccCc
Confidence            577877 56679999999999999999999999999999999999998876 7999999999999999999985544322


Q ss_pred             -CcCceEEEEEecCCCCCCCCchhhHHHHHh-CCCCCCccccEEEecCCeEEEEecchHHHHHHHhhchhcceEEEEEEe
Q 022999          148 -DPDIVAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRI  225 (289)
Q Consensus       148 -~~~~i~~L~I~~~~kF~~LsHRD~LGaLmg-LGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei  225 (289)
                       .++++++++|++|+||.+++|||||||||| |||+|+++|||++.+ ++||++|+++|++||.+||+|||+++|+++++
T Consensus        80 ~~d~~i~~l~i~~~~kF~~l~Hrd~LGaLm~~LGI~Re~iGDI~v~~-~~~qv~v~~~i~~~i~~nl~kIg~~~V~~~~i  158 (165)
T 2fph_X           80 FSDFEISLQEIVYSNKFEYLTHAKILGTVINQLGIERKLFGDILVDE-ERAQIMINQQFLLLFQDGLKKIGRIPVSLEER  158 (165)
T ss_dssp             GGGGCEEEEEEESCCCCHHHHHHHHHSCSSSCCCCCGGGEEEEECSS-SCCEEEEEGGGHHHHHHHCCEETTEECEEEEC
T ss_pred             ccCCceEEEEEecccccccCCHHHHHHHHHHhcCCCHhhcCCEEEEC-CEEEEEEcHHHHHHHHHHHhhccCeeEEEEEe
Confidence             234799999999999999999999999999 999999999999876 58999999999999999999999999999999


Q ss_pred             cCCcc
Q 022999          226 PLLAL  230 (289)
Q Consensus       226 ~~~~l  230 (289)
                      +++++
T Consensus       159 ~~~~l  163 (165)
T 2fph_X          159 PFTEK  163 (165)
T ss_dssp             CGGGC
T ss_pred             CHHHc
Confidence            98776

>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* ...

Probab=98.08  E-value=3.3e-07  Score=81.71  Aligned_cols=68  Identities=15%  Similarity=0.105  Sum_probs=57.8

Q ss_pred             eEEEEecchHHHHHHHhhchhcceEEEEEEecCCcccCCCCCeeEEEEeecccchHHHHH-ccccccHHHHHHHHHcCCe
Q 022999          195 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALAS-AGFKLSRSKLVNLIRYSSL  273 (289)
Q Consensus       195 ~aqv~v~~eia~fi~~nLtKIgr~~V~v~ei~~~~l~~~~~~~ke~~~tVsSlRLDaVvs-~~f~lSRska~~lI~~GkV  273 (289)
                      ..|.++.+++.+|+..+..++|++.+.+.                   ....+|||.+++ .+++.||++|+++|.+|+|
T Consensus        66 ~~Yg~~e~q~~~y~~~a~~~~g~t~~~l~-------------------~~le~RLD~~L~~~g~~~SR~~arqLI~~G~V  126 (209)
T 2vqe_D           66 RIYGISERQFRNLFEEASKKKGVTGSVFL-------------------GLLESRLDNVVYRLGFAVSRRQARQLVRHGHI  126 (209)
T ss_dssp             HHHTCCHHHHHHHHHHHHHSSSCHHHHHH-------------------HHHHTBHHHHHHHTTSSSSHHHHHHHHHTTCE
T ss_pred             HHhCccHHHHHHHHHHHHHccCCcchHHH-------------------HhHHHHHHHHHHHhcCcCCHHHHHHHHHCCCE
Confidence            46778899999999999999999886541                   123489999997 5789999999999999999


Q ss_pred             EECcEEec
Q 022999          274 ASLVQISA  281 (289)
Q Consensus       274 ~vn~~~~~  281 (289)
                      .|||+++.
T Consensus       127 ~VNG~~v~  134 (209)
T 2vqe_D          127 TVNGRRVD  134 (209)
T ss_dssp             EETTEECC
T ss_pred             EECCEEeC
Confidence            99999775

>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

Probab=97.74  E-value=2.8e-05  Score=64.43  Aligned_cols=43  Identities=19%  Similarity=0.140  Sum_probs=36.4

Q ss_pred             ecccchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEecccccc
Q 022999          244 EASLRVDALASAG-FKLSRSKLVNLIRYSSLASLVQISAKASAI  286 (289)
Q Consensus       244 VsSlRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~~~~~~~  286 (289)
                      -+++|||.+++.. +..||+.++++|++|+|+|||+.++++..+
T Consensus         6 ~~~~RLDk~L~~~~~~~SRs~a~~li~~G~V~VNG~~vk~s~~V   49 (133)
T 1dm9_A            6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIV   49 (133)
T ss_dssp             TTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCTTCBC
T ss_pred             ccchhHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEcCCCCEe
Confidence            3579999999875 668999999999999999999987665444

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.74  E-value=2.3e-05  Score=58.45  Aligned_cols=38  Identities=5%  Similarity=0.047  Sum_probs=31.9

Q ss_pred             cchHHHH-HccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          247 LRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       247 lRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      .|||.++ ..+|--||++|+++|.+|+|+|||+++.+.|
T Consensus         8 ~RLD~~l~~~gla~SR~~A~~lI~~G~V~Vng~~v~kps   46 (71)
T 2cqj_A            8 RRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPA   46 (71)
T ss_dssp             EEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTT
T ss_pred             HHHHHHHHHhCCcCCHHHHHHHHHCCcEEECCEEECCCC
Confidence            4999765 5688889999999999999999999665544

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D

Probab=97.65  E-value=2.2e-05  Score=68.56  Aligned_cols=41  Identities=15%  Similarity=0.011  Sum_probs=35.5

Q ss_pred             ecccchHHHH-HccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          244 EASLRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       244 VsSlRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      .-++|||.++ ..+|..||++|+++|++|.|.|||+++.+.|
T Consensus       104 ~le~RLD~vL~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps  145 (181)
T 2xzm_D          104 LMERRLQTRVFKLNLANSIHHSRVLIRQRHIKVGKNLVNVPS  145 (181)
T ss_dssp             HHTTBHHHHHHHTTCSSSTTHHHHHTTTTCCEETTEECCCSC
T ss_pred             hhccchhHHHHhccccCCHHHHHHHHHCCEEEECCEEECCCC
Confidence            4457999999 7899999999999999999999999665443

>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

Probab=97.49  E-value=1.1e-05  Score=60.60  Aligned_cols=37  Identities=8%  Similarity=-0.021  Sum_probs=31.1

Q ss_pred             cccchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEec
Q 022999          245 ASLRVDALASAG-FKLSRSKLVNLIRYSSLASLVQISA  281 (289)
Q Consensus       245 sSlRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~~  281 (289)
                      ..+|||.+++.. +..||++|+.+|++|.|+|||++..
T Consensus        19 ~~~RLdk~L~~~g~~~SR~~a~~lI~~G~V~VNG~~v~   56 (79)
T 1p9k_A           19 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVET   56 (79)
T ss_dssp             SCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCC
T ss_pred             CCchHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEec
Confidence            448999998864 3349999999999999999999653

>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

Probab=97.41  E-value=0.00012  Score=62.40  Aligned_cols=37  Identities=16%  Similarity=0.133  Sum_probs=32.8

Q ss_pred             cccchHHHHH-ccccccHHHHHHHHHcCCeEECcEEec
Q 022999          245 ASLRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISA  281 (289)
Q Consensus       245 sSlRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~  281 (289)
                      -.+|||.+++ .++..||++|+++|++|.|.|||+++.
T Consensus        49 le~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VNG~~v~   86 (159)
T 1c05_A           49 LESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVN   86 (159)
T ss_dssp             HHHBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTEECC
T ss_pred             HHHHHHHHHHHcCCcCCHHHHHHHHHCCCEEECCEEeC
Confidence            4679999987 467899999999999999999999774

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=97.35  E-value=9.8e-05  Score=64.49  Aligned_cols=37  Identities=16%  Similarity=0.157  Sum_probs=33.0

Q ss_pred             cchHHHH-HccccccHHHHHHHHHcCCeEECcEEeccc
Q 022999          247 LRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKA  283 (289)
Q Consensus       247 lRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~  283 (289)
                      +|||.++ ..+|.-||++|+++|++|+|+|||+++.+.
T Consensus       103 ~RLD~~L~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~P  140 (180)
T 3j20_D          103 RRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSP  140 (180)
T ss_dssp             TSHHHHHHHHTSSSSHHHHHHHHHHTCCEESSSBCCCS
T ss_pred             hhhhheeecCcccCcHHHHHHHHHcCCeEECCEEeCCC
Confidence            5999988 689999999999999999999999976543

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

Probab=97.28  E-value=3.2e-05  Score=59.40  Aligned_cols=39  Identities=8%  Similarity=0.063  Sum_probs=32.5

Q ss_pred             cchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEeccccc
Q 022999          247 LRVDALASAG-FKLSRSKLVNLIRYSSLASLVQISAKASA  285 (289)
Q Consensus       247 lRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~~~~~~  285 (289)
                      +|||.+++.. +..||++++++|++|+|+|||++.+++..
T Consensus         1 ~RLD~~L~~~~~~~sR~~~~~li~~G~V~VNg~~~~~~~~   40 (92)
T 2k6p_A            1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAKASKE   40 (92)
T ss_dssp             CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECCTTCB
T ss_pred             ChHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEcCCCCC
Confidence            5999999875 34599999999999999999998755433

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=97.25  E-value=9.3e-05  Score=65.64  Aligned_cols=39  Identities=13%  Similarity=0.089  Sum_probs=33.5

Q ss_pred             ecccchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          244 EASLRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       244 VsSlRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      .-++|||.+++ .+|..||+.|+++|+.|.|.|||+++.+
T Consensus        86 ~Le~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VNG~~V~~  125 (201)
T 3bbn_D           86 LLEMRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDI  125 (201)
T ss_dssp             HHHSBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCC
T ss_pred             HHHHHHHHHHHHcCCcCCHHHHHHHHhCCcEEeCCEEEee
Confidence            44679999995 5778899999999999999999997643

>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*

Probab=96.61  E-value=0.00094  Score=59.05  Aligned_cols=37  Identities=22%  Similarity=0.109  Sum_probs=32.0

Q ss_pred             cchHHHH-HccccccHHHHHHHHHcCCeEECcEEeccc
Q 022999          247 LRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKA  283 (289)
Q Consensus       247 lRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~  283 (289)
                      .|||.++ ..+|--||++|.++|.+|+|+|||+++.+.
T Consensus       107 ~RLD~~L~r~G~a~Sr~~ArqLI~~GhV~VNG~~V~~P  144 (197)
T 3u5c_J          107 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIP  144 (197)
T ss_dssp             TSHHHHHHHSSTTSSHHHHHHHHHTSCCBSSSCBCCCT
T ss_pred             HHHHHHHHHccccCCHHHHHHHHHcCCEEECCEEeCCC
Confidence            4899976 478989999999999999999999966543

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=94.92  E-value=0.032  Score=40.83  Aligned_cols=59  Identities=15%  Similarity=0.302  Sum_probs=45.1

Q ss_pred             CCCCchhhHHHHHh-CCCCCCccccEEEecCCeEEEEecchHHHHHHHhhch--hcceEEEEE
Q 022999          164 QPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK--VGNVSVSCT  223 (289)
Q Consensus       164 ~~LsHRD~LGaLmg-LGI~RekiGDIiv~~~~~aqv~v~~eia~fi~~nLtK--Igr~~V~v~  223 (289)
                      +.+.-+|++|+|.+ .||.++.||+|-+.+ +..+|=+.+++++-+...|.+  +.+.+++++
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d-~~s~v~v~~~~~~~~~~~l~~~~i~g~~~~v~   72 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMD-NASYVEILNGKGPHVLKVMKNTTVKGKQLKVN   72 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECS-SCEEEEECTTCHHHHHHHHTTCCC---CCCEE
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeC-CcEEEEECHHHHHHHHHHhccccCcCceEEEE
Confidence            56789999999998 899999999998765 589999999999999999875  455555554

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=94.29  E-value=0.00079  Score=59.44  Aligned_cols=36  Identities=28%  Similarity=0.175  Sum_probs=31.2

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAK  282 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~  282 (289)
                      .|||.++. .+|.-||++|.++|.+|+|+|||+++.+
T Consensus       109 ~RLD~~L~r~G~a~SR~~ArqlI~~GhV~VNG~~V~~  145 (195)
T 3iz6_C          109 RRLQTLVFKAGMAKSIHHARVLIRQRHIRVGRQIVNI  145 (195)
T ss_dssp             SCCCSSCCCCCCHHHHSCTTSHHHHHSTTTSCCCCCC
T ss_pred             hhhhHHHHhccccCCHHHHHHHHHcCCEEECCEEeCC
Confidence            48999775 6888899999999999999999996654

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=88.78  E-value=0.08  Score=49.08  Aligned_cols=28  Identities=14%  Similarity=0.074  Sum_probs=0.0

Q ss_pred             ccccHHHHHHHHHcCCeEECcEE-ecccc
Q 022999          257 FKLSRSKLVNLIRYSSLASLVQI-SAKAS  284 (289)
Q Consensus       257 f~lSRska~~lI~~GkV~vn~~~-~~~~~  284 (289)
                      .+.||++++++|++|+|+|||++ .+++.
T Consensus        28 ~~~SR~~~~~lI~~G~V~VNG~~v~~~~~   56 (325)
T 1v9f_A           28 PDYSRSRIKEWILDQRVLVNGKVCDKPKE   56 (325)
T ss_dssp             -----------------------------
T ss_pred             cccCHHHHHHHHHCCCEEECCEEccCCCC
Confidence            38999999999999999999996 55543

>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}

Probab=82.18  E-value=0.77  Score=39.29  Aligned_cols=33  Identities=21%  Similarity=0.066  Sum_probs=30.3

Q ss_pred             chHHHHHccccccHHHHHHHHHcCCeEECcEEe
Q 022999          248 RVDALASAGFKLSRSKLVNLIRYSSLASLVQIS  280 (289)
Q Consensus       248 RLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~  280 (289)
                      =+|.++++++--|++.|..+|++|-|+|||+..
T Consensus        52 ivdlLv~aGLa~SKsEARRlI~qGGv~VNg~kv   84 (164)
T 2ktl_A           52 FSKVLWSAGLVASKSEGQRIINNNGAYVGSRPG   84 (164)
T ss_dssp             HHHHHHHHTSCSTHHHHHHHHHHTCEEEEECCS
T ss_pred             HHHHHHHhCcccCHHHHHHHHHhCCEEECCEec
Confidence            479999999999999999999999999999644

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	289
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.78
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.55
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	98.0
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	97.14
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	95.26
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	95.1
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	94.33
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	94.11
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	93.43

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

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=98.78  E-value=2.1e-09  Score=75.61  Aligned_cols=39  Identities=31%  Similarity=0.358  Sum_probs=36.1

Q ss_pred             ccchHHHHHccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          246 SLRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       246 SlRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      |||||.++|.....||++|+++|++|+|.|||+++.+.+
T Consensus         1 smRLD~~Ls~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~   39 (58)
T d1vioa2           1 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGS   39 (58)
T ss_dssp             CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTT
T ss_pred             CcHHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeCCCC
Confidence            799999999999999999999999999999999876544

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

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: Escherichia coli [TaxId: 562]

Probab=98.55  E-value=2.4e-08  Score=70.27  Aligned_cols=37  Identities=22%  Similarity=0.210  Sum_probs=34.3

Q ss_pred             cchHHHHHccccccHHHHHHHHHcCCeEECcEEeccc
Q 022999          247 LRVDALASAGFKLSRSKLVNLIRYSSLASLVQISAKA  283 (289)
Q Consensus       247 lRLDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~~~  283 (289)
                      ||||.++|....+||++|+++|++|+|+|||+++.+.
T Consensus         1 mRLdk~l~~~~~~SR~~a~~lI~~g~V~Vng~~v~~~   37 (59)
T d1kska3           1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNA   37 (59)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCT
T ss_pred             CcHHHHHHHcCCCCHHHHHHHHHcCcEEECCEEeecC
Confidence            7999999999999999999999999999999977553

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=98.00  E-value=3e-06  Score=66.00  Aligned_cols=43  Identities=19%  Similarity=0.166  Sum_probs=37.4

Q ss_pred             cccchHHHH-HccccccHHHHHHHHHcCCeEECcEEeccccccc
Q 022999          245 ASLRVDALA-SAGFKLSRSKLVNLIRYSSLASLVQISAKASAIR  287 (289)
Q Consensus       245 sSlRLDaVv-s~~f~lSRska~~lI~~GkV~vn~~~~~~~~~~~  287 (289)
                      +.+|||..+ ++.|--||+.|+++|++|+|+|||+.++++-.++
T Consensus         3 ~~mRlD~~L~~~r~~ktR~~A~~~i~~G~V~vNg~~vKps~~vk   46 (104)
T d1dm9a_           3 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVE   46 (104)
T ss_dssp             TCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCTTCBCC
T ss_pred             ccEeHHHHHHHhhhHhhHHHHHHHHHcCCeeeCCeeccccccCC
Confidence            469999988 5668889999999999999999999988776654

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=97.14  E-value=1.9e-05  Score=58.24  Aligned_cols=43  Identities=12%  Similarity=0.025  Sum_probs=34.9

Q ss_pred             ecccchHHHHHcc-ccccHHHHHHHHHcCCeEECcEEe-cccccc
Q 022999          244 EASLRVDALASAG-FKLSRSKLVNLIRYSSLASLVQIS-AKASAI  286 (289)
Q Consensus       244 VsSlRLDaVvs~~-f~lSRska~~lI~~GkV~vn~~~~-~~~~~~  286 (289)
                      .+.+|||-+++.. +--||++|+++|++|+|+|||+++ +++-.+
T Consensus        18 ~~~irL~k~L~~~gl~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V   62 (79)
T d1p9ka_          18 HPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKI   62 (79)
T ss_dssp             CSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCC
T ss_pred             CCcEEHHHHHHHCCCccCHHHHHHHHHhCCcccCCEEeccccccC
Confidence            3458999999865 667999999999999999999966 454433

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.26  E-value=0.0079  Score=49.38  Aligned_cols=38  Identities=18%  Similarity=0.141  Sum_probs=33.3

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      .|||+|+= .+|-.||..|.++|.-|.|.|||+.+...|
T Consensus        51 ~RlD~vv~r~gfa~t~~~arQ~v~Hghi~vNgk~v~iPS   89 (159)
T d1c06a_          51 SRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPS   89 (159)
T ss_dssp             HCHHHHHHHHTSSSSHHHHHHHHHTSCEEETTEECCCSS
T ss_pred             HHhhhhhccCcccCCHHHHHHHHHhcceEccceEEEecc
Confidence            48999986 799999999999999999999999665433

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=95.10  E-value=0.0097  Score=50.83  Aligned_cols=38  Identities=24%  Similarity=0.286  Sum_probs=33.1

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      .|||+|+= .+|-.||..|.++|.-|.|.|||+.+...|
T Consensus        98 ~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i~vNg~~v~ips  136 (208)
T d2uubd1          98 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPS  136 (208)
T ss_dssp             TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTT
T ss_pred             HHHHHHHHhccccccHHHHHHHHHhcCeecCCeEEEecc
Confidence            48999884 799999999999999999999999665433

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.33  E-value=0.022  Score=42.57  Aligned_cols=33  Identities=21%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             hHHHHHccccccHHHHHHHHHcCCeEECcEEec
Q 022999          249 VDALASAGFKLSRSKLVNLIRYSSLASLVQISA  281 (289)
Q Consensus       249 LDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~  281 (289)
                      +|.++..++--||+.|..+|++|-|+|||+.+.
T Consensus        35 ~~ll~~~~l~~S~seaRrlI~~ggv~iN~~kv~   67 (99)
T d1jh3a_          35 VELLVSAGISPSKRQAREDIQNGAIYVNGERLQ   67 (99)
T ss_dssp             HHHHHHHTSCCSHHHHHHHHHSTTEEETTEECC
T ss_pred             HHHHHHcCCCcCHHHHHHHHHcCCEEECCEEec
Confidence            699999999999999999999999999999654

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=94.11  E-value=0.017  Score=49.12  Aligned_cols=38  Identities=21%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             cchHHHHH-ccccccHHHHHHHHHcCCeEECcEEecccc
Q 022999          247 LRVDALAS-AGFKLSRSKLVNLIRYSSLASLVQISAKAS  284 (289)
Q Consensus       247 lRLDaVvs-~~f~lSRska~~lI~~GkV~vn~~~~~~~~  284 (289)
                      .|||+|+= .+|--||..|.++|.-|.|.|||+.+...|
T Consensus        94 ~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk~VnIPS  132 (204)
T d2gy9d1          94 GRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIAS  132 (204)
T ss_dssp             TBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSSBCCCTT
T ss_pred             HHHHHHHhhccccccHHHHHHHHHhcceecCCEEEEecc
Confidence            48999885 799999999999999999999999665433

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.43  E-value=0.041  Score=39.70  Aligned_cols=33  Identities=18%  Similarity=0.158  Sum_probs=30.0

Q ss_pred             hHHHHHccccccHHHHHHHHHcCCeEECcEEec
Q 022999          249 VDALASAGFKLSRSKLVNLIRYSSLASLVQISA  281 (289)
Q Consensus       249 LDaVvs~~f~lSRska~~lI~~GkV~vn~~~~~  281 (289)
                      +|.++..++--|++.|..+|++|-|+|||+.+.
T Consensus        21 ~~ll~~~gl~~S~searRlI~~g~V~iN~~ki~   53 (81)
T d1h3fa2          21 ARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLT   53 (81)
T ss_dssp             HHHHHHTTSSSSHHHHHHHHHTTCEEETTEECC
T ss_pred             HHHHHHcCCCcCHHHHHHHHHcCCEEECCEEec
Confidence            488888999999999999999999999999653