Citrus Sinensis ID: 026574

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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------
Protein Sequence
MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
Secondary Structure (PSIPRED)
cHHHHHccccEEEEccccHHHHHHHHHHHccccccEEEEEccccccEEEEEEEEcccccccccccEEEEEEEcccccccccccHHHHHHHHccccccccccEEEEcccEEEEEEcHHHHHHHHHcccccccEEEEEEEEcccccccccccEEEEEEEEcHHHHHHHHHccccccHHHHHHHHHcccEEEccEEEcccccccccccEEEEEEccEEEEEEEEcccccEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcccEccccccHHHHHHHHHHHHccccEEEEEcccccHHHHHEEEEccccccccccccEEEEEEEcccccccccHHHHHHHHHHccccHcccccEEEccccEEEEEEcHHHHHHHHHHHHHccccEEEEEEEcHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEcccccEEccccEEEEEcccEEEEEEEcccccccEEEEEEEEc
Coil and Loop (DISEMBL)
marrassrrevlhsdfltppvLKESMMALEKLADVKAvaqggypqaercrlsvghpealtsdpDIVAALSitgnfgfqpcshgdflGSILGTGIAREKIGDIilqgekgaqflvVPELADYLITSLEkvgnvsvsctripllaleyepprtksfktIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTtvtkngttlrtgdivsvsgkgrikigeinstrkGKFAVELIQYL
Flexible Loop (DISEMBL)
marrassrrevlhsdfltppvLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSlekvgnvsvSCTRIPLlaleyepprtksfKTIEASLRVDALASAGFklsrsklvnlisngdvrvnwttvtkngttlrtgdivsvsgkgrikigeinstrkgkfAVELIQYL
Low Complexity Region (SEG)
MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
Disordered region (IsUnstruct)
*************************MMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI***
Disordered Region (DISOPRED)
MARRA*SRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
Disordered Region (DISEMBL)
***********LHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
Disordered Region (DISPRO)
MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL
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	236	2.2.26 [Sep-21-2011]
P71020	257	Putative RNA-binding prot	yes	no	0.894	0.821	0.322	1e-20

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

 Score =  100 bits (248), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/223 (32%), Positives = 115/223 (51%), Gaps = 12/223 (5%)

Query: 14  SDFLTPPVLKESMM--ALEKLADVKAVAQGGYPQAERCRLSVGHPEALT---SDPDIVAA 68
           +DFL P   +E ++  A+   ADV     GGY +AER R ++  PE +T   SD ++  A
Sbjct: 35  TDFLDP---REQVILSAVTGQADVGLAFSGGYDRAERKR-AILFPEYITPEESDFEL-QA 89

Query: 69  LSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK 128
            ++     F    H   LG+++G G+ R+K GDI+   E   Q +V  + AD++   L +
Sbjct: 90  FNVRYADKFVSVDHRSLLGALMGIGLKRQKFGDIVF-SETAVQLIVSADTADFVAAQLTQ 148

Query: 129 VGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVR 188
            G  +VS  +I L  L       +      +SLR+DA+ ++  + SR K   L+ NG V+
Sbjct: 149 AGKAAVSLEKIDLSDLNIPAVDVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVK 208

Query: 189 VNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN-STRKGKFAV 230
           VNW  V      +  GD++S+ G GR  + +I   T+K K+ V
Sbjct: 209 VNWKVVEDPSYIVAEGDMLSIRGFGRCSLTKIEGKTKKDKWRV 251

Bacillus subtilis (strain 168) (taxid: 224308)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	236
147798253	269	hypothetical protein VITISV_010260 [Viti	1.0	0.877	0.855	1e-117
225461477	321	PREDICTED: putative RNA-binding protein	1.0	0.735	0.855	1e-117
224114944	268	predicted protein [Populus trichocarpa]	1.0	0.880	0.834	1e-113
359807576	324	uncharacterized protein LOC100793767 [Gl	1.0	0.728	0.809	1e-113
449457021	319	PREDICTED: putative RNA-binding protein	1.0	0.739	0.805	1e-112
18404337	320	RNA-binding S4 domain-containing protein	1.0	0.737	0.788	1e-112
357452969	325	hypothetical protein MTR_2g085340 [Medic	1.0	0.726	0.766	1e-110
217074322	325	unknown [Medicago truncatula]	1.0	0.726	0.766	1e-109
242054411	304	hypothetical protein SORBIDRAFT_03g03447	1.0	0.776	0.762	1e-106
212274707	304	uncharacterized protein LOC100191195 [Ze	1.0	0.776	0.762	1e-106

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

 Score =  428 bits (1100), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 202/236 (85%), Positives = 225/236 (95%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA+RAS+RREVLH+DFLTPPVLKESM+ LEKLAD+KAVAQGGYPQAERCRLSVGH E LT
Sbjct: 34  MAKRASARREVLHTDFLTPPVLKESMIVLEKLADMKAVAQGGYPQAERCRLSVGHSEVLT 93

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           + PDIVAAL ITGNFGFQ CSHGDFLG+ILGTGIAREK+GDIILQGEKGAQ L+VPEL D
Sbjct: 94  TAPDIVAALRITGNFGFQSCSHGDFLGAILGTGIAREKLGDIILQGEKGAQVLIVPELVD 153

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L++SLEKVGNVSVSCT++PLLALEYE PRT +FKTIE SLRVDALASAGFKLSRSKLV+
Sbjct: 154 FLVSSLEKVGNVSVSCTKMPLLALEYEEPRTTTFKTIELSLRVDALASAGFKLSRSKLVD 213

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LISNGDVRVNWTTVTKNGTTL+TGD+VSVSGKGR+KIGEINST+KGK+AVELI++L
Sbjct: 214 LISNGDVRVNWTTVTKNGTTLKTGDVVSVSGKGRLKIGEINSTKKGKYAVELIRFL 269

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  427 bits (1099), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 202/236 (85%), Positives = 225/236 (95%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA+RAS+RREVLH+DFLTPPVLKESM+ LEKLAD+KAVAQGGYPQAERCRLSVGH E LT
Sbjct: 86  MAKRASARREVLHTDFLTPPVLKESMIVLEKLADMKAVAQGGYPQAERCRLSVGHSEVLT 145

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           + PDIVAAL ITGNFGFQ CSHGDFLG+ILGTGIAREK+GDIILQGEKGAQ L+VPEL D
Sbjct: 146 TAPDIVAALRITGNFGFQSCSHGDFLGAILGTGIAREKLGDIILQGEKGAQVLIVPELVD 205

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L++SLEKVGNVSVSCT++PLLALEYE PRT +FKTIE SLRVDALASAGFKLSRSKLV+
Sbjct: 206 FLVSSLEKVGNVSVSCTKMPLLALEYEEPRTTTFKTIELSLRVDALASAGFKLSRSKLVD 265

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LISNGDVRVNWTTVTKNGTTL+TGD+VSVSGKGR+KIGEINST+KGK+AVELI++L
Sbjct: 266 LISNGDVRVNWTTVTKNGTTLKTGDVVSVSGKGRLKIGEINSTKKGKYAVELIRFL 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 197/236 (83%), Positives = 219/236 (92%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MARRAS RREVLH+DFLTPP LKES+  LEKLADVKA+AQGGYPQAERCRLSVGHPE LT
Sbjct: 33  MARRASLRREVLHTDFLTPPTLKESLHVLEKLADVKAIAQGGYPQAERCRLSVGHPETLT 92

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPDIVAALSITGNFGFQ CSHGDFLG+ILGTGIAR K+GDII+ G K AQ L+VP+L D
Sbjct: 93  SDPDIVAALSITGNFGFQLCSHGDFLGAILGTGIARNKLGDIIVLGGKRAQVLLVPDLVD 152

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           Y+++SL+KVG+VSVSCT IPL A+EYEPPRTKSFKT+EASLRVDALASAGFK+SRSKLV+
Sbjct: 153 YIVSSLDKVGDVSVSCTPIPLHAIEYEPPRTKSFKTVEASLRVDALASAGFKISRSKLVD 212

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LISN DVRVNWTT+TKN TTL+TGD+VSVSGKGR+KIGEIN+TRKGKFAVELI YL
Sbjct: 213 LISNKDVRVNWTTITKNNTTLKTGDVVSVSGKGRLKIGEINTTRKGKFAVELIHYL 268

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 191/236 (80%), Positives = 221/236 (93%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MARRAS +RE+LH+DFLTPPVLKESM  LEKLADVKA+AQGGYPQAERCR+SVGHPE LT
Sbjct: 89  MARRASLKREILHTDFLTPPVLKESMQVLEKLADVKAIAQGGYPQAERCRISVGHPEELT 148

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPDI++ALSITGNF F+PCSHGDFLGSILGTGI REK+GDIILQGE+GAQ +VVPEL +
Sbjct: 149 SDPDIISALSITGNFQFEPCSHGDFLGSILGTGIVREKLGDIILQGEQGAQIIVVPELVE 208

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L+++L KV NV VSCT+IPL++L+YEPPRTKSFKTIEASLRVDALASAGFK+SRSKLV+
Sbjct: 209 FLMSTLVKVRNVPVSCTKIPLISLDYEPPRTKSFKTIEASLRVDALASAGFKVSRSKLVD 268

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           +ISNGDVR+NW  VT  GTTL++GDIVS+SGKGR+KIGEINST+KGKFAVELI+YL
Sbjct: 269 MISNGDVRINWIPVTTKGTTLKSGDIVSISGKGRLKIGEINSTKKGKFAVELIRYL 324

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 =  410 bits (1055), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 190/236 (80%), Positives = 224/236 (94%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA+R+ SRREVLH++FLTPPV+KESM+A++KLADVKA+AQGGYP+AERCR+SVGH + LT
Sbjct: 84  MAKRSLSRREVLHTNFLTPPVVKESMLAIQKLADVKAIAQGGYPEAERCRISVGHADELT 143

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPDI++ALSITGNF F PCSHGDFLGSILGTGIAREK+GDI+LQ E GAQ ++VPEL D
Sbjct: 144 SDPDIISALSITGNFTFHPCSHGDFLGSILGTGIAREKLGDIMLQEETGAQVVIVPELVD 203

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +LI+SL KVGNV+VSCTRIPL ALEYEPP+TK+FKTIEASLRVDA+ASAGFK+SRSKLV+
Sbjct: 204 FLISSLRKVGNVTVSCTRIPLTALEYEPPKTKTFKTIEASLRVDAIASAGFKISRSKLVD 263

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LIS+GDVRVNWT++TKNGT L+TGDIVSVSGKGR+KIGEINST+KGKFAVELI+Y+
Sbjct: 264 LISSGDVRVNWTSITKNGTILKTGDIVSVSGKGRLKIGEINSTKKGKFAVELIRYV 319

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  409 bits (1050), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 186/236 (78%), Positives = 222/236 (94%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MARRASS+REVLH+DFLTPP++KES+  LEK ADVK VAQGGYP+AERCR+S+GHP+ LT
Sbjct: 85  MARRASSKREVLHTDFLTPPIVKESVSLLEKFADVKIVAQGGYPEAERCRISIGHPDVLT 144

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPDIVAALSITGNFGFQPCSHGDFLG+ILGTGI+REK+GDI++Q EKGAQ L+VPEL D
Sbjct: 145 SDPDIVAALSITGNFGFQPCSHGDFLGAILGTGISREKLGDILIQEEKGAQVLIVPELVD 204

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +++T+L+KVGNV V+C++IPLLALEYEPPRT SFKT+EASLR+DA+ASAGFK+SRSKLV+
Sbjct: 205 FVVTALDKVGNVGVTCSKIPLLALEYEPPRTNSFKTVEASLRIDAVASAGFKISRSKLVD 264

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LIS+ DVRVNW TVTKNGT ++TGD+VSVSGKGR+KIGEIN T+KGKFAVE+I+YL
Sbjct: 265 LISSKDVRVNWATVTKNGTIVKTGDVVSVSGKGRLKIGEINETKKGKFAVEIIRYL 320

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  402 bits (1032), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 181/236 (76%), Positives = 221/236 (93%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MARRAS +RE+LH++FLTPPVLKESM  LEKLAD+KA+AQGGYPQAERCR+SVGHP+ LT
Sbjct: 90  MARRASLKREILHTNFLTPPVLKESMQVLEKLADIKALAQGGYPQAERCRISVGHPDELT 149

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPD+++ALSITGNF F+PCSHGDFLGSILGTGIAREK+GDIILQGE+GAQ +VVPEL +
Sbjct: 150 SDPDVISALSITGNFQFEPCSHGDFLGSILGTGIAREKVGDIILQGEQGAQIIVVPELVE 209

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L ++L+KV NV V+CT+IPL++L+YEPPRTKSFKTIEASLRVDA+ASAGFK+SRSKLV+
Sbjct: 210 FLTSALDKVRNVPVTCTKIPLISLDYEPPRTKSFKTIEASLRVDAVASAGFKISRSKLVD 269

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           +ISNGDVR+NW  +T  GTT+++GD+VSVSG GR+KIGE+N+T+KGKFAVELI+YL
Sbjct: 270 MISNGDVRINWIPITTKGTTVKSGDLVSVSGLGRLKIGEVNTTKKGKFAVELIRYL 325

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 =  400 bits (1029), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 181/236 (76%), Positives = 221/236 (93%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MARRAS +RE+LH++FLTPPVLKESM  LEKLAD+KA+AQGGYPQAERCR+SVGHP+ LT
Sbjct: 90  MARRASLKREILHTNFLTPPVLKESMRVLEKLADIKALAQGGYPQAERCRISVGHPDELT 149

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           SDPD+++ALSITGNF F+PCSHGDFLGSILGTGIAREK+GDIILQGE+GAQ +VVPEL +
Sbjct: 150 SDPDVISALSITGNFQFEPCSHGDFLGSILGTGIAREKVGDIILQGEQGAQIIVVPELVE 209

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L ++L+KV NV V+CT+IPL++L+YEPPRTKSFKTIEASLRVDA+ASAGFK+SRSKLV+
Sbjct: 210 FLTSALDKVRNVPVTCTKIPLISLDYEPPRTKSFKTIEASLRVDAVASAGFKISRSKLVD 269

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           +ISNGDVR+NW  +T  GTT+++GD+VSVSG GR+KIGE+N+T+KGKFAVELI+YL
Sbjct: 270 MISNGDVRINWIPITTKGTTVKSGDLVSVSGLGRLKIGEVNTTKKGKFAVELIRYL 325

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242054411|ref|XP_002456351.1| hypothetical protein SORBIDRAFT_03g034470 [Sorghum bicolor] gi|241928326|gb|EES01471.1| hypothetical protein SORBIDRAFT_03g034470 [Sorghum bicolor]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 180/236 (76%), Positives = 217/236 (91%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA+RAS RR+V H++FLTPP++KE+M+A+EKLAD+KAVAQGGYPQAERCR+SVGHP+ +T
Sbjct: 69  MAQRASQRRDVFHTNFLTPPIVKEAMLAVEKLADIKAVAQGGYPQAERCRISVGHPDFMT 128

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           S+PD+VAALSI+GNF  +PCSHGDFLG+ILGTGI REK+GDI+LQGE+GAQ LV P L D
Sbjct: 129 SNPDVVAALSISGNFRLEPCSHGDFLGAILGTGITREKVGDILLQGERGAQVLVDPGLVD 188

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           YLI++LEKVG V VSCT+IPLLALEYEPPRT SFKT+E+SLRVDALASAGFK+SR+KL +
Sbjct: 189 YLISTLEKVGKVGVSCTQIPLLALEYEPPRTNSFKTVESSLRVDALASAGFKISRTKLAS 248

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LIS+GDVRVNWT  TKNG TL++GD+VSVSG GR+KIGEI +TRKGK+AVELI+YL
Sbjct: 249 LISSGDVRVNWTPTTKNGVTLKSGDVVSVSGMGRLKIGEIVTTRKGKYAVELIRYL 304

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|212274707|ref|NP_001130102.1| uncharacterized protein LOC100191195 [Zea mays] gi|194688290|gb|ACF78229.1| unknown [Zea mays] gi|223975061|gb|ACN31718.1| unknown [Zea mays] gi|414880496|tpg|DAA57627.1| TPA: RNA-binding S4 isoform 1 [Zea mays] gi|414880497|tpg|DAA57628.1| TPA: RNA-binding S4 isoform 2 [Zea mays] gi|414880498|tpg|DAA57629.1| TPA: RNA-binding S4 isoform 3 [Zea mays]

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 180/236 (76%), Positives = 213/236 (90%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA RAS RR V H++FLTPP++KE+M+ALEK AD KAVAQGGYPQAERCR+SVGHP+ +T
Sbjct: 69  MAERASQRRNVFHTNFLTPPIVKEAMLALEKFADTKAVAQGGYPQAERCRISVGHPDVMT 128

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           S+PD+VAALSI+GNF  + CSHGDFLG+ILGTGI REK+GDI+LQGE+GAQ LV PEL D
Sbjct: 129 SNPDVVAALSISGNFRLESCSHGDFLGAILGTGITREKVGDILLQGERGAQVLVDPELVD 188

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           YLI++LEKVG V VSCT+IPLLALEYEPPRT SFKT+E+SLRVDALASAGFK+SR+KL +
Sbjct: 189 YLISTLEKVGKVGVSCTQIPLLALEYEPPRTNSFKTVESSLRVDALASAGFKISRTKLAS 248

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LIS+GDVRVNWT  TKNG TL++GD+VSVSG GR+KIGEI +TRKGK+AVELI+YL
Sbjct: 249 LISSGDVRVNWTPTTKNGVTLKSGDVVSVSGMGRLKIGEIVTTRKGKYAVELIRYL 304

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

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	236
TAIR|locus:2037048	320	AT1G53120 [Arabidopsis thalian	1.0	0.737	0.788	6.9e-102
UNIPROTKB|P74082	259	sll1252 "Sll1252 protein" [Syn	0.995	0.907	0.470	2.6e-54
UNIPROTKB|Q3AAH6	246	CHY_2039 "S4 domain protein" [	0.974	0.934	0.364	5.2e-33
TIGR_CMR|CHY_2039	246	CHY_2039 "S4 domain protein" [	0.974	0.934	0.364	5.2e-33
UNIPROTKB|Q81WE2	255	BAS3748 "S4 domain protein" [B	0.949	0.878	0.297	6.3e-21
TIGR_CMR|BA_4036	255	BA_4036 "S4 domain protein" [B	0.949	0.878	0.297	6.3e-21
UNIPROTKB|Q71XY5	258	LMOf2365_2060 "S4 domain prote	0.932	0.852	0.300	1.5e-19

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

 Score = 1010 (360.6 bits), Expect = 6.9e-102, P = 6.9e-102
 Identities = 186/236 (78%), Positives = 222/236 (94%)

Query:     1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
             MARRASS+REVLH+DFLTPP++KES+  LEK ADVK VAQGGYP+AERCR+S+GHP+ LT
Sbjct:    85 MARRASSKREVLHTDFLTPPIVKESVSLLEKFADVKIVAQGGYPEAERCRISIGHPDVLT 144

Query:    61 SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
             SDPDIVAALSITGNFGFQPCSHGDFLG+ILGTGI+REK+GDI++Q EKGAQ L+VPEL D
Sbjct:   145 SDPDIVAALSITGNFGFQPCSHGDFLGAILGTGISREKLGDILIQEEKGAQVLIVPELVD 204

Query:   121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
             +++T+L+KVGNV V+C++IPLLALEYEPPRT SFKT+EASLR+DA+ASAGFK+SRSKLV+
Sbjct:   205 FVVTALDKVGNVGVTCSKIPLLALEYEPPRTNSFKTVEASLRIDAVASAGFKISRSKLVD 264

Query:   181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
             LIS+ DVRVNW TVTKNGT ++TGD+VSVSGKGR+KIGEIN T+KGKFAVE+I+YL
Sbjct:   265 LISSKDVRVNWATVTKNGTIVKTGDVVSVSGKGRLKIGEINETKKGKFAVEIIRYL 320

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

UNIPROTKB|P74082 sll1252 "Sll1252 protein" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 561 (202.5 bits), Expect = 2.6e-54, P = 2.6e-54
 Identities = 111/236 (47%), Positives = 160/236 (67%)

Query:     2 ARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEA-LT 60
             A +A    EV+ SDF  PP++ E     + L ++  +  GGYPQAER RL++   E  L 
Sbjct:    24 AEQALRTWEVVVSDFCAPPLIAEIQTRFDSLTELHFLPWGGYPQAERQRLAIARAEIPLE 83

Query:    61 SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
             ++   + AL + GNF F P SH DFLG++LGTG+ REK+GDIIL GE+GAQ +VVPE+A+
Sbjct:    84 TEQIPLTALDVAGNFLFDPASHRDFLGALLGTGLVREKVGDIILLGERGAQAIVVPEVAE 143

Query:   121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
             ++   L +V  V V    I L  L+  PP+TK   T+EASLR+DA+ASAGF LSRSK+ +
Sbjct:   144 FISLHLTQVRTVPVKAKAIALEELKIRPPKTKEMTTVEASLRLDAIASAGFGLSRSKMAD 203

Query:   181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
              ++ G+V+VNW  VT++   L+ GD+V+  GKGR++IGEI  T+K ++ ++L +YL
Sbjct:   204 AVTQGNVQVNWKPVTQSSYALKAGDLVTYRGKGRLEIGEITVTKKERYRIQLTRYL 259

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

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

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 85/233 (36%), Positives = 128/233 (54%)

Query:     6 SSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDI 65
             +++ +++ +DFL P     +   L    +V     GGYP AE+ R +         D ++
Sbjct:    15 AAKGQIVLTDFLDPAAASLTRDLLRNYPEVNYKVDGGYPNAEKVRFAFYPIYVFPEDVEL 74

Query:    66 -VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLIT 124
              +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL    G Q +V  +L  YLI 
Sbjct:    75 NLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILI-PNGCQVVVDRDLVPYLIQ 133

Query:   125 SLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISN 184
              L+KV  V V+   I    L     +T+       SLR+D++ ++GF +SRS++V  I  
Sbjct:   134 QLDKVHRVGVTVKEIVREELLLPEAKTREVVAFVKSLRLDSVGASGFGISRSQMVKEIEG 193

Query:   185 GDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRK-GKFAVELIQYL 236
               VRVNW    K    +  GD++S+ G+GR+++ EI    K G+  V L +YL
Sbjct:   194 QKVRVNWKLQVKPSYEVAPGDVISLRGRGRVEVLEIAGVSKSGRNKVILRRYL 246

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 = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 85/233 (36%), Positives = 128/233 (54%)

Query:     6 SSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDI 65
             +++ +++ +DFL P     +   L    +V     GGYP AE+ R +         D ++
Sbjct:    15 AAKGQIVLTDFLDPAAASLTRDLLRNYPEVNYKVDGGYPNAEKVRFAFYPIYVFPEDVEL 74

Query:    66 -VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLIT 124
              +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL    G Q +V  +L  YLI 
Sbjct:    75 NLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILI-PNGCQVVVDRDLVPYLIQ 133

Query:   125 SLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISN 184
              L+KV  V V+   I    L     +T+       SLR+D++ ++GF +SRS++V  I  
Sbjct:   134 QLDKVHRVGVTVKEIVREELLLPEAKTREVVAFVKSLRLDSVGASGFGISRSQMVKEIEG 193

Query:   185 GDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRK-GKFAVELIQYL 236
               VRVNW    K    +  GD++S+ G+GR+++ EI    K G+  V L +YL
Sbjct:   194 QKVRVNWKLQVKPSYEVAPGDVISLRGRGRVEVLEIAGVSKSGRNKVILRRYL 246

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 69/232 (29%), Positives = 117/232 (50%)

Query:     3 RRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSD 62
             ++A+   +V  +DFL P   +   M + +  D+     G   +AER R  + +P+ L  +
Sbjct:    22 KQAAEYHQVKLTDFLDPRQQQIVTMVIGQ-GDIAVQFDGATSRAERKRALI-YPDYLVVN 79

Query:    63 PDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
              +   V  L I     F    H   LG+ +  G+ REK GDI+LQ ++ AQ +V  E+  
Sbjct:    80 EEEFQVEGLEIDYPSKFYTLEHRQILGTFMSLGLTREKCGDILLQEDR-AQIVVAKEVVS 138

Query:   121 YLITSLEKVGNVSVSCTRIP-LLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLV 179
             Y+  +L+ +G V VS + +     L+ +    +   T+ +SLR+D + +    +SR K+ 
Sbjct:   139 YIEMNLQSIGKVKVSLSPVKGEKILQIQETWGEKSGTV-SSLRLDVMLAEMLHISRQKVQ 197

Query:   180 NLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINS-TRKGKFAV 230
               I NG V+VNW TV +       GD+ SV G GR K+  +   T++ K+ +
Sbjct:   198 PFIKNGLVKVNWKTVEQTSYECYPGDVFSVRGYGRSKLFSVEGRTKRDKWRI 249

GO:0008150 "biological_process" evidence=ND

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

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 69/232 (29%), Positives = 117/232 (50%)

Query:     3 RRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSD 62
             ++A+   +V  +DFL P   +   M + +  D+     G   +AER R  + +P+ L  +
Sbjct:    22 KQAAEYHQVKLTDFLDPRQQQIVTMVIGQ-GDIAVQFDGATSRAERKRALI-YPDYLVVN 79

Query:    63 PDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
              +   V  L I     F    H   LG+ +  G+ REK GDI+LQ ++ AQ +V  E+  
Sbjct:    80 EEEFQVEGLEIDYPSKFYTLEHRQILGTFMSLGLTREKCGDILLQEDR-AQIVVAKEVVS 138

Query:   121 YLITSLEKVGNVSVSCTRIP-LLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLV 179
             Y+  +L+ +G V VS + +     L+ +    +   T+ +SLR+D + +    +SR K+ 
Sbjct:   139 YIEMNLQSIGKVKVSLSPVKGEKILQIQETWGEKSGTV-SSLRLDVMLAEMLHISRQKVQ 197

Query:   180 NLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINS-TRKGKFAV 230
               I NG V+VNW TV +       GD+ SV G GR K+  +   T++ K+ +
Sbjct:   198 PFIKNGLVKVNWKTVEQTSYECYPGDVFSVRGYGRSKLFSVEGRTKRDKWRI 249

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 = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 68/226 (30%), Positives = 105/226 (46%)

Query:    14 SDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT-SDPDI-VAALSI 71
             +DFL P     +   +    ++     GG   AER R  + +P+  T ++ D  +A   I
Sbjct:    35 TDFLDPRQRFITETVIGGYDEINVQFFGGVAHAERRRALI-YPDYYTPTEADFEIALFHI 93

Query:    72 TGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGN 131
                  F   +H   LG+++  G+ R+  GDI+  G +  Q LV   + DYL   LEK+G 
Sbjct:    94 RYPVKFTTLTHQKILGTLMSLGMKRDIFGDILNNGTEW-QLLVESTMKDYLTLQLEKIGK 152

Query:   132 VSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNW 191
             V+V      L    Y P   +      +S+R+D + S    +SR K   L++ G V+VNW
Sbjct:   153 VNVMLEETDLANAVYAPVVWEEMGLTVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNW 212

Query:   192 TTVTKNGTTLRTGDIVSVSGKGRIKIGEINS-TRKGKFAVELIQYL 236
              TV          D++S  G GR+K+      T+K K  +E I YL
Sbjct:   213 KTVENPDFECEEEDVLSARGYGRVKVLSTGGRTKKDKIRIE-IGYL 257


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        0.317   0.135   0.378    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      236       236   0.00089  113 3  11 22  0.43    33
                                                     32  0.43    36


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:  580 (62 KB)
  Total size of DFA:  149 KB (2090 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:  19.41u 0.10s 19.51t   Elapsed:  00:00:01
  Total cpu time:  19.41u 0.10s 19.51t   Elapsed:  00:00:01
  Start:  Fri May 10 20:18:01 2013   End:  Fri May 10 20:18:02 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P71020	YLMH_BACSU	No assigned EC number	0.3228	0.8940	0.8210	yes	no

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	236
PLN00051	267	PLN00051, PLN00051, RNA-binding S4 domain-containi	1e-155
TIGR03069	257	TIGR03069, PS_II_S4, photosystem II S4 domain prot	1e-109
COG2302	257	COG2302, COG2302, Uncharacterized conserved protei	3e-63
cd00165	70	cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding d	4e-10
smart00363	60	smart00363, S4, S4 RNA-binding domain	8e-10
pfam01479	48	pfam01479, S4, S4 domain	5e-06

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

 Score =  431 bits (1111), Expect = e-155
 Identities = 175/236 (74%), Positives = 207/236 (87%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           MA RAS R EV H+DFLTPP++K+SM ALEKLADVKAVA GGY QAERCRLS+G PE LT
Sbjct: 32  MAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEVLT 91

Query: 61  SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELAD 120
           S PDIVAALS++GNF F P SHGDFLG+ILGTGI R+K+GDI++QGE+GAQ LVVPEL +
Sbjct: 92  SQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVE 151

Query: 121 YLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLVN 180
           +L +SL KV  V V C  IPL ALE EPPR +SFK++EASLR+DALASAGF++SRSKLV+
Sbjct: 152 FLSSSLTKVRTVPVECRAIPLSALEVEPPRVESFKSVEASLRLDALASAGFRMSRSKLVD 211

Query: 181 LISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL 236
           LIS+GDVRVNW  VTKNGTTL+TGD+VSVSGKGR+++GEIN+T+KGKFAVELI+YL
Sbjct: 212 LISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRLEVGEINTTKKGKFAVELIRYL 267

Length = 267

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

 Score =  314 bits (807), Expect = e-109
 Identities = 114/236 (48%), Positives = 155/236 (65%), Gaps = 4/236 (1%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
           +A +A    E + SDFL+ P+ +E +     L D+K +A GGYPQAER R++    +   
Sbjct: 22  LAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD-NP 80

Query: 61  SDPDI--VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPEL 118
            DPDI  +  L I GNF F P SH DF G++LGTGI REKIGDI + G++GAQ L  PEL
Sbjct: 81  LDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPEL 140

Query: 119 ADYLITSLEKVGNVSVSCTRIPLLALEYEPPRT-KSFKTIEASLRVDALASAGFKLSRSK 177
           A++L   L +V +V V C  IPL  L+   PRT K   T+EASLR+DA+ASAGF LSRSK
Sbjct: 141 AEFLQEKLGQVRDVEVKCKAIPLEELQIPAPRTPKELTTVEASLRIDAIASAGFGLSRSK 200

Query: 178 LVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI 233
           +V+ I  G +R+NW TVT+    L+ GD + + GKGR++I E+  T+K ++ VEL+
Sbjct: 201 IVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRLEILELEITKKERWRVELL 256

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 =  197 bits (503), Expect = 3e-63
 Identities = 92/238 (38%), Positives = 127/238 (53%), Gaps = 4/238 (1%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
             ++      V+ +DFL P      +  L  L DVK    GGYP+AER RL +       
Sbjct: 22  WIKQVEKTYTVVVTDFLDPREQAI-LKTLAGLEDVKVSFSGGYPRAERKRLILYPAYYPL 80

Query: 61  SDPDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELA 119
            + D  +  L I+    F   +H D LG++L  GI REK GDII++GE GAQ +V  ELA
Sbjct: 81  EESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEGE-GAQLIVATELA 139

Query: 120 DYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASAGFKLSRSKLV 179
           D+ +  L K+G   V    I L  L+    + K      +SLR+D + S GF LSR+K  
Sbjct: 140 DFFLLHLTKIGKAPVKLEEIDLEELKESTEKWKELDVTVSSLRLDVVISEGFGLSRAKAQ 199

Query: 180 NLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINS-TRKGKFAVELIQYL 236
            LI  G V+VNW  V K    ++ GD++S+ G GR+KI EIN  T+K KF + L +Y 
Sbjct: 200 QLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRLKILEINGVTKKDKFRITLRRYK 257

Length = 257

>gnl|CDD|238095 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

 Score = 53.8 bits (130), Expect = 4e-10
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 162 RVDA-LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIK 216
           R+D  LA  G   SRS+   LI +G V VN   VTK    ++ GD++ V GK   +
Sbjct: 2   RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEE 57

Length = 70

>gnl|CDD|214638 smart00363, S4, S4 RNA-binding domain

 Score = 53.0 bits (128), Expect = 8e-10
 Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 161 LRVD-ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR 214
            R+D  LA  G   SRS+   LI  G V+VN   VTK    ++ GD++SV GK  
Sbjct: 1   RRLDKFLARLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55

Length = 60

>gnl|CDD|201819 pfam01479, S4, S4 domain

 Score = 42.1 bits (100), Expect = 5e-06
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 161 LRVDA-LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV 207
           +R+D  LA  G   SRS+   LI +G VRVN   V      ++ GD++
Sbjct: 1   MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48

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 uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. Length = 48

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	236
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	99.81
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	99.32
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	99.27
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	99.2
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	99.14
COG1188	100	Ribosome-associated heat shock protein implicated	98.96
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	98.83
CHL00113	201	rps4 ribosomal protein S4; Reviewed	98.63
smart00363	60	S4 S4 RNA-binding domain.	98.63
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	98.6
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	98.45
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	98.29
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	98.28
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	98.28
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	98.18
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	98.13
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	98.05
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	97.97
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	97.96
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	97.94
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	97.85
PRK11507	70	ribosome-associated protein; Provisional	97.78
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	97.78
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	97.76
PF13275	65	S4_2: S4 domain; PDB: 1P9K_A.	97.55
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	97.43
PLN00189	194	40S ribosomal protein S9; Provisional	97.23
PTZ00155	181	40S ribosomal protein S9; Provisional	97.01
COG2501	73	S4-like RNA binding protein [Replication, recombin	96.66
COG4332	203	Uncharacterized protein conserved in bacteria [Fun	95.95
PF06353	142	DUF1062: Protein of unknown function (DUF1062); In	95.82
KOG4837	248	consensus Uncharacterized conserved protein [Funct	95.48
PRK13354	410	tyrosyl-tRNA synthetase; Provisional	94.02
PRK04313	237	30S ribosomal protein S4e; Validated	93.66
PTZ00223	273	40S ribosomal protein S4; Provisional	93.02
PLN00036	261	40S ribosomal protein S4; Provisional	92.96
PTZ00118	262	40S ribosomal protein S4; Provisional	92.96
PRK05912	408	tyrosyl-tRNA synthetase; Validated	92.7
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	91.54
COG1471	241	RPS4A Ribosomal protein S4E [Translation, ribosoma	90.09
PRK01777	95	hypothetical protein; Validated	88.35
COG0776	94	HimA Bacterial nucleoid DNA-binding protein [DNA r	84.92
KOG3301	183	consensus Ribosomal protein S4 [Translation, ribos	82.3

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

Probab=100.00  E-value=5.9e-74  Score=507.25  Aligned_cols=236  Identities=74%  Similarity=1.162  Sum_probs=221.9

Q ss_pred             ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCCccceEEEEeecCCCccCC
Q 026574            1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPC   80 (236)
Q Consensus         1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~~~~i~~l~i~~~~kf~~l   80 (236)
                      ++++|+++|.+++|+||||+++.++.+++++++++++.++|||++|||+|++|+|+++.+.+.+|+++++|++++||.+|
T Consensus        32 ~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~~~~~~f~i~~l~i~~~~kF~~l  111 (267)
T PLN00051         32 MAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEVLTSQPDIVAALSVSGNFMFDPA  111 (267)
T ss_pred             HHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHhccccCCcEEEEEEEcccCCCCC
Confidence            47899999999999999999999999999888899999999999999999999855444233369999999999999999


Q ss_pred             CccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccc
Q 026574           81 SHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEAS  160 (236)
Q Consensus        81 ~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s  160 (236)
                      +|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++|++++++++++.+|+++|++++.+++|
T Consensus       112 ~HrD~LGaLm~LGIkRe~iGDIlv~~~~~~~v~v~~~i~~fi~~nl~kIg~~~V~~~~~~~~~~~~~~~~~~e~~~~vas  191 (267)
T PLN00051        112 SHGDFLGAILGTGITRDKVGDILVQGERGAQVLVVPELVEFLSSSLTKVRTVPVECRAIPLSALEVEPPRVESFKSVEAS  191 (267)
T ss_pred             CHHHHHHHHHHcCCcHhhcCCEEEcCCCcEEEEEcHHHHHHHHHHhhhccceeEEEEEecHHHcCCCccceEEccCCcCc
Confidence            99999999999999999999999855546999999999999999999999999999999999988888899999999999


Q ss_pred             hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEEEeC
Q 026574          161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQYL  236 (236)
Q Consensus       161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r~~  236 (236)
                      +|||++++..+++||++++++|++|+|+|||+.+++|++.|++||+|||||+|||++.+++.|||||++|++++|+
T Consensus       192 ~RLD~vla~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~gD~isiRG~GR~~i~~~~~TKKgr~~i~i~ky~  267 (267)
T PLN00051        192 LRLDALASAGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTGDVVSVSGKGRLEVGEINTTKKGKFAVELIRYL  267 (267)
T ss_pred             ccHHHHHHHHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCCCEEEEeeCCEEEEEEEecccCCcEEEEEEecC
Confidence            9999999999999999999999999999999999999999999999999999999999988999999999999985

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=100.00  E-value=5.1e-71  Score=487.13  Aligned_cols=234  Identities=47%  Similarity=0.759  Sum_probs=216.8

Q ss_pred             ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCC-ccceEEEEeecCCCccC
Q 026574            1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSD-PDIVAALSITGNFGFQP   79 (236)
Q Consensus         1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~-~~~i~~l~i~~~~kf~~   79 (236)
                      ++++|+++|.+.+|+||||+|+.++.+++++.+++++.+||||++|||+|++|+|+++.+.. ++|+++++|+|++||.+
T Consensus        22 ~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~~~~~~~df~i~~l~i~~~~kF~~  101 (257)
T TIGR03069        22 LAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSDNPLDPDIIPIQGLLIEGNFLFDP  101 (257)
T ss_pred             HHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEecccccCCcccCceEEEEEEcccccCC
Confidence            47899999999999999999999999999888899999999999999999999744443222 35999999999999999


Q ss_pred             CCccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCc-eEEeeec
Q 026574           80 CSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRT-KSFKTIE  158 (236)
Q Consensus        80 l~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~-~~~~~~v  158 (236)
                      |+|||||||||||||+|+++|||++.++++||++|+++|++||++||+|||+++|++++++++++..|+++| +++..++
T Consensus       102 l~Hrd~LGalm~lGi~R~~iGDI~v~~~~~~~v~v~~~i~~~i~~~l~kIg~~~V~~~~~~~~~~~~~~~~~~~~~~~~v  181 (257)
T TIGR03069       102 ASHEDFRGALLGTGIVREKIGDIWVLGDRGAQALCTPELAEFLQEKLGQVRDVEVKCKAIPLEELQIPAPRTPKELTTVE  181 (257)
T ss_pred             CCHHHHHHHHHHcCCcHhhcCCEEEecCCcEEEEECHHHHHHHHHHhhhccceeEEEEEeCHHHcCCCCcccceEecCCC
Confidence            999999999999999999999998876656999999999999999999999999999999999876666656 9999999


Q ss_pred             cchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEEE
Q 026574          159 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELIQ  234 (236)
Q Consensus       159 ~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~r  234 (236)
                      +|+|||.+++..+++||++++++|++|+|+|||+.+++|++.|++||+|+++|+|||++.+++.|||||++|++.|
T Consensus       182 ~s~RLD~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~gD~IsvrG~Gr~~i~~~~~TKKgr~~i~i~~  257 (257)
T TIGR03069       182 ASLRIDAIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVGDRLQLRGKGRLEILELEITKKERWRVELLR  257 (257)
T ss_pred             ccccHHHHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCCCEEEEcCCceEEEEEeecCcCCcEEEEEeC
Confidence            9999999999999999999999999999999999998999999999999999999999999899999999999874

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=7e-70  Score=468.77  Aligned_cols=232  Identities=38%  Similarity=0.590  Sum_probs=219.7

Q ss_pred             hhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCC--CCccceEEEEeecCCCccC
Q 026574            2 ARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT--SDPDIVAALSITGNFGFQP   79 (236)
Q Consensus         2 ~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~--~~~~~i~~l~i~~~~kf~~   79 (236)
                      +++|+++|.+.+||||||+|+.+...+++ +.++++.+|||||+|||+|++++ |+|++  ..++++++++|.|++||.+
T Consensus        23 ~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l~-P~y~~~~~~df~l~l~eI~y~~kF~~  100 (257)
T COG2302          23 IKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLILY-PAYYPLEESDFELTLLEISYASKFVS  100 (257)
T ss_pred             HHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEEc-ccccChhhcccceEEEEEEccccccc
Confidence            57899999999999999999988877777 88999999999999999999997 66655  2234899999999999999


Q ss_pred             CCccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeecc
Q 026574           80 CSHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEA  159 (236)
Q Consensus        80 l~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~  159 (236)
                      ++|+||||+||||||+|+++|||++.+ ++||++|.+++++|+..+|++||+++|++++++++++..+.++|++.+.+++
T Consensus       101 l~H~~~LGtll~lGikRe~~GDIiv~~-~~aQliv~~~~~~f~~~~Ltkig~~~V~l~ei~~~~l~~~~~~~~e~~~~vs  179 (257)
T COG2302         101 LTHRDILGTLLSLGIKREKFGDIIVEG-EGAQLIVATELADFFLLHLTKIGKAPVKLEEIDLEELKESTEKWKELDVTVS  179 (257)
T ss_pred             ccHHHHHHHHHhccCcHHhhccEEEeC-CeeEEEEehhHHHHHHHHHHhhcCcceEEEEcCHHHcccCccceeEEeeeee
Confidence            999999999999999999999999976 5899999999999999999999999999999999999988889999999999


Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe-eccccccEEEEEEEeC
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-NSTRKGKFAVELIQYL  236 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~-~~TKKgr~~i~~~r~~  236 (236)
                      |+|||.+++.++++||++++++|.+|+|+|||++++++++.|++||.||+||+||+++.++ |.|||||+||++.+|+
T Consensus       180 SlRLD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~GDliSirG~GR~~i~~i~g~TKKdK~ri~l~~~~  257 (257)
T COG2302         180 SLRLDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGRLKILEINGVTKKDKFRITLRRYK  257 (257)
T ss_pred             hhhHHHHHHHHHhhhHHHHHHHHHcCceEEeeEEeccccceeccCCEEEEeccccEEEEeecCccccccEEEEEEEcC
Confidence            9999999999999999999999999999999999999999999999999999999999999 5999999999999985

>KOG4837 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.81  E-value=2.2e-21  Score=163.13  Aligned_cols=213  Identities=61%  Similarity=0.953  Sum_probs=178.3

Q ss_pred             ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCCCccceEEEEeecCCCccCC
Q 026574            1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPC   80 (236)
Q Consensus         1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~~~~~i~~l~i~~~~kf~~l   80 (236)
                      ||.++.......+|+||.|.       +.-.++++....-+||+.||+|++-|..|+-...+.+..+.+++..++.|++-
T Consensus        35 m~~~~~~~r~f~~t~~l~ps-------l~t~F~~v~s~~lpgl~~a~ec~~pi~~~~~~ts~k~~kksl~~td~~dsd~e  107 (248)
T KOG4837|consen   35 MARRASSKREFLHTDFLTPS-------LLTKFADVKSVALPGLPEAEECRIPIGHPDVLTSDKDIKKSLSITDNFDSDPE  107 (248)
T ss_pred             HHHHHHhhHHHHhhhhhCch-------hhhccccchhhhcCCCCCChheEeeccCccccccchhHHHHhhhccccCCCcc
Confidence            45667677778899999994       34456788888899999999999999988776666665688899999999999


Q ss_pred             CccchHHHHHcCCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccc
Q 026574           81 SHGDFLGSILGTGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEAS  160 (236)
Q Consensus        81 ~Hrd~LGalm~lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s  160 (236)
                      +|-||||+++     ||+.|||.+..+   ++...+++.+|-.+-|.|+| ..|....+++.-.... ++.-.....-.|
T Consensus       108 sh~Df~~e~~-----~e~~~D~~Vvk~---~~~i~~~v~sfr~d~llK~G-lgv~rnKVel~fye~e-~R~N~~Kl~kkS  177 (248)
T KOG4837|consen  108 SHGDFLGEIL-----REKLGDILVVKE---KVLIVPEVVSFRVDALLKVG-LGVTRNKVELLFYEYE-PRTNSFKLVKKS  177 (248)
T ss_pred             cchhHHHHHH-----HHhcCCceeeeh---hhhhhhHHHHHHHHHHHHhc-cccccchhhHhhhhcc-cccCcccccccc
Confidence            9999999998     999999998754   47788999999999999999 8888877775433322 344444556679


Q ss_pred             hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEeeccccccEEEEEE
Q 026574          161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEINSTRKGKFAVELI  233 (236)
Q Consensus       161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~~TKKgr~~i~~~  233 (236)
                      .|+|.--+..+.++|+  ..++.+..+.|||..+.+.+..++.||++..||++ +++.++..|||||+.+++.
T Consensus       178 ~~i~vgds~d~~ig~~--~~~~s~~~~rV~~~tV~~~~t~~e~~~Vvlrr~Ks-Lki~~~r~tk~~k~a~~i~  247 (248)
T KOG4837|consen  178 LRIDVGDSADFKIGRS--VDLISSKDVRVNWATVTKNGTIVETGDVVLRRGKS-LKIGEIRETKKGKFAVEII  247 (248)
T ss_pred             eeeecccccceeeecc--cccCCcceEEEeeeeecccceEeecceEEEEeccc-cccccccccccccchhhhc
Confidence            9999877777778887  77889999999999999999999999999999999 9999999999999988764

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=99.32  E-value=1.5e-12  Score=111.33  Aligned_cols=86  Identities=26%  Similarity=0.335  Sum_probs=76.3

Q ss_pred             eEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccchHHHHHHH-hCCCcCHHHHHHHHHCCcE
Q 026574          109 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALAS-AGFKLSRSKLVNLISNGDV  187 (236)
Q Consensus       109 ~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~ils-~~~~~SR~~a~~lI~~G~V  187 (236)
                      .+|.++.+++.+|+..++.++|++.+.+  +.+.+                 +|||.++. ..+..||+.|+++|.+|+|
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  22111                 89999995 5568899999999999999


Q ss_pred             EECCEEecCCCcccCCCCEEEEeeCC
Q 026574          188 RVNWTTVTKNGTTLRTGDIVSVSGKG  213 (236)
Q Consensus       188 ~VNg~~~~~~~~~v~~GD~Isvrg~G  213 (236)
                      .|||+.++.|++.|++||.|+|+|.-
T Consensus       118 ~VNgk~v~~ps~~V~~GD~I~V~~~~  143 (200)
T TIGR01017       118 LVNGKKVDIPSYQVRPGDIISIKEKS  143 (200)
T ss_pred             EECCEEeCCCCCCCCCCCEEEEeeCc
Confidence            99999999999999999999999864

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=99.27  E-value=2.4e-12  Score=110.36  Aligned_cols=87  Identities=23%  Similarity=0.385  Sum_probs=76.7

Q ss_pred             eEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccchHHHHHH-HhCCCcCHHHHHHHHHCCcE
Q 026574          109 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALA-SAGFKLSRSKLVNLISNGDV  187 (236)
Q Consensus       109 ~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~il-s~~~~~SR~~a~~lI~~G~V  187 (236)
                      .+|.++.+++.+|+..+++++|++++.+  +.+.|                 +|||.++ +..+..||++|+++|.+|.|
T Consensus        60 ~~Y~~~e~q~~~~~~~a~~~~g~t~~~l--l~~lE-----------------~RLD~iL~~~g~~~SR~~arqlI~~G~V  120 (203)
T PRK05327         60 RIYGVLEKQFRRYFKEAARRKGNTGENL--LQLLE-----------------SRLDNVVYRLGFAPTRRQARQLVSHGHI  120 (203)
T ss_pred             HHhcCcHHHHHHHHHHHHhccCCcHhHH--HHHHH-----------------HHHHHHHHHcCccCCHHHHHHHHHCCcE
Confidence            6899999999999999999999998876  22211                 8999998 45668999999999999999


Q ss_pred             EECCEEecCCCcccCCCCEEEEeeCCe
Q 026574          188 RVNWTTVTKNGTTLRTGDIVSVSGKGR  214 (236)
Q Consensus       188 ~VNg~~~~~~~~~v~~GD~Isvrg~Gr  214 (236)
                      .|||+.++.|++.|++||.|+|++.-|
T Consensus       121 ~VNgk~v~~ps~~v~~GD~I~v~~~sr  147 (203)
T PRK05327        121 LVNGKKVNIPSYRVKPGDVIEVREKSK  147 (203)
T ss_pred             EECCEEECCCCcCCCCCCEEEECCcCc
Confidence            999999988999999999999998643

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

Probab=99.20  E-value=3.8e-11  Score=79.44  Aligned_cols=47  Identities=34%  Similarity=0.543  Sum_probs=44.0

Q ss_pred             hHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 026574          161 LRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV  207 (236)
Q Consensus       161 ~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~I  207 (236)
                      ||||.+|+ ..+..||+.|+++|++|.|+|||+.+++|++.|++||+|
T Consensus         1 ~RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~d~I   48 (48)
T PF01479_consen    1 MRLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPGDVI   48 (48)
T ss_dssp             EBHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTTEEE
T ss_pred             CCHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCcCCC
Confidence            69999998 556889999999999999999999999999999999986

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=99.14  E-value=1.6e-10  Score=79.95  Aligned_cols=51  Identities=18%  Similarity=0.280  Sum_probs=47.2

Q ss_pred             ccchHHHHHHHhCCCc--CHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574          158 EASLRVDALASAGFKL--SRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV  209 (236)
Q Consensus       158 v~s~RLD~ils~~~~~--SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv  209 (236)
                      .+.+|||.+|+.. ++  ||+.++.+|++|.|+|||+.+++|++.|++||.|.|
T Consensus         6 ~~~~rLd~~L~~~-~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~Gd~v~i   58 (59)
T TIGR02988         6 TEYITLGQLLKEL-GIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEI   58 (59)
T ss_pred             chHHHHHHHHHHc-CCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCCCEEEe
Confidence            3669999999987 67  999999999999999999999889999999999986

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.

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

Probab=98.96  E-value=2.3e-09  Score=81.50  Aligned_cols=61  Identities=25%  Similarity=0.316  Sum_probs=54.2

Q ss_pred             cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574          159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~  220 (236)
                      ..||||.||. ..+--+|+.|++++++|+|.|||..+ +|++.|++||+|.|+-..+.....|
T Consensus         7 ~~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~GD~l~i~~~~~~~~v~V   68 (100)
T COG1188           7 DRMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVGDILTIRFGNKEFTVKV   68 (100)
T ss_pred             cceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCCCEEEEEeCCcEEEEEE
Confidence            5799999986 44788999999999999999999999 7999999999999998887765555

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=98.83  E-value=2.1e-08  Score=80.44  Aligned_cols=67  Identities=15%  Similarity=0.199  Sum_probs=57.4

Q ss_pred             cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe-e-ccccc
Q 026574          159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-N-STRKG  226 (236)
Q Consensus       159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~-~-~TKKg  226 (236)
                      .++|||.+|. ..+--||+.|+++|.+|+|.|||+. .+|+..|++||.|.|+-.++.....| . ..+.|
T Consensus         7 ~~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~gd~l~v~~~~~~~~v~Vl~l~~~R~   76 (133)
T PRK10348          7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELNATLTLRQGNDERTVIVKAITEQRR   76 (133)
T ss_pred             ccccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCCCEEEEEECCEEEEEEEeECccccC
Confidence            4689999975 6678999999999999999999999 58999999999999988887777666 3 45444

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=98.63  E-value=7.5e-08  Score=82.46  Aligned_cols=55  Identities=20%  Similarity=0.265  Sum_probs=50.0

Q ss_pred             chHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCe
Q 026574          160 SLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR  214 (236)
Q Consensus       160 s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr  214 (236)
                      .+|||.+|... +..||+.|+++|.+|.|.|||+.++.|++.|++||.|+|++..+
T Consensus        88 E~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~GD~I~V~~~~~  143 (201)
T CHL00113         88 EMRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPKDIITVKDKQK  143 (201)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCCCEEEEccccc
Confidence            48999999654 57899999999999999999999999999999999999998654

>smart00363 S4 S4 RNA-binding domain

Probab=98.63  E-value=1.1e-07  Score=63.56  Aligned_cols=51  Identities=37%  Similarity=0.510  Sum_probs=46.6

Q ss_pred             hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      +|||.++... +..||+.++.++++|.|+|||+.+.+++..+++||.|++.+
T Consensus         1 ~rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~gd~i~~~~   52 (60)
T smart00363        1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRG   52 (60)
T ss_pred             CcHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCCCEEEEcc
Confidence            5899999876 47999999999999999999999977999999999999876

>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=98.60  E-value=1.2e-07  Score=65.08  Aligned_cols=52  Identities=37%  Similarity=0.526  Sum_probs=47.2

Q ss_pred             hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      +|||.++++. +..||+.+++++++|.|+|||+.++++++.+++||.|++.+.
T Consensus         1 ~rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~d~i~i~~~   53 (70)
T cd00165           1 MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGK   53 (70)
T ss_pred             CcHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCCCEEEEcCC
Confidence            5899999876 578999999999999999999999789999999999998764

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

Probab=98.45  E-value=3.4e-07  Score=78.57  Aligned_cols=59  Identities=29%  Similarity=0.386  Sum_probs=52.5

Q ss_pred             cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574          159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI  217 (236)
Q Consensus       159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~  217 (236)
                      -..|||+++- .+|..||.+|+++|.+|.|.|||+.++.|++.|++||.++|+-+-+-.+
T Consensus        92 LErRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~gdei~V~~k~~s~~  151 (205)
T COG0522          92 LERRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPGDEISVREKSKSPI  151 (205)
T ss_pred             HHHHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCCCEEEeeecccchh
Confidence            3579999985 5679999999999999999999999999999999999999997765443

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=98.29  E-value=1.5e-06  Score=78.44  Aligned_cols=54  Identities=28%  Similarity=0.397  Sum_probs=49.6

Q ss_pred             eccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          157 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       157 ~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      +.+++|||.+|+....+||+.+.++|.+|+|+|||+.+ .+++.|.+||.|.|.|
T Consensus         3 ~~~~~RL~k~La~~g~~SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~gD~V~v~g   56 (290)
T PRK10475          3 TDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRA-TIGDQVKAGDVVKVNG   56 (290)
T ss_pred             cchHHHHHHHHHhCCCCCHHHHHHHHHCCcEEECCEEc-cCCCCcCCCCEEEECC
Confidence            45789999999987678999999999999999999998 6999999999999986

>TIGR00478 tly hemolysin TlyA family protein

Probab=98.28  E-value=1.2e-06  Score=76.36  Aligned_cols=52  Identities=27%  Similarity=0.202  Sum_probs=47.2

Q ss_pred             HHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574          162 RVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG  213 (236)
Q Consensus       162 RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G  213 (236)
                      |||.+|... +..||++|+++|++|+|+|||+.+++|++.|.+||.|++.+.-
T Consensus         1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~d~I~v~~~~   53 (228)
T TIGR00478         1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFDAKIELLQNP   53 (228)
T ss_pred             CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCCCEEeccCcc
Confidence            899998765 4789999999999999999999999999999999999998753

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=98.28  E-value=1.6e-06  Score=75.41  Aligned_cols=51  Identities=22%  Similarity=0.232  Sum_probs=47.5

Q ss_pred             hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      +|||.+++..+.+||+.+++++++|+|+|||+.+.++++.|++||.|++.+
T Consensus         1 ~rld~~L~~~~~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~gd~I~l~~   51 (232)
T PRK10839          1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDG   51 (232)
T ss_pred             CcHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeccCCcCcCCCCEEEECC
Confidence            589999998889999999999999999999999866999999999999975

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=98.18  E-value=3.7e-06  Score=75.53  Aligned_cols=55  Identities=31%  Similarity=0.462  Sum_probs=49.4

Q ss_pred             ccchHHHHHHHhCCC-cCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          158 EASLRVDALASAGFK-LSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       158 v~s~RLD~ils~~~~-~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      .+++|||.+++..+. +||+.++++|++|.|+|||+.+.++++.|++||.|++.+.
T Consensus         3 ~~g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~gd~I~i~~~   58 (299)
T TIGR00005         3 QAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVP   58 (299)
T ss_pred             ccchhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCCCEEEEecC
Confidence            368999999998885 9999999999999999999766679999999999999654

modifies uracil-65 in transfer RNAs to pseudouridine.

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=98.13  E-value=5.7e-06  Score=75.53  Aligned_cols=56  Identities=23%  Similarity=0.306  Sum_probs=50.5

Q ss_pred             eccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          157 IEASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       157 ~v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ..+++|||.+++..+ ..||+.++++|++|+|+|||+.+.++++.|++||.|++.+.
T Consensus        14 ~~~g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~gD~I~v~~~   70 (325)
T PRK11180         14 SQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE   70 (325)
T ss_pred             ccCCccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCCCCEEEEeec
Confidence            346799999999876 68999999999999999999998779999999999999863

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=98.05  E-value=8.5e-06  Score=71.93  Aligned_cols=53  Identities=32%  Similarity=0.417  Sum_probs=48.8

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC-CEEEEeeC
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG-DIVSVSGK  212 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G-D~Isvrg~  212 (236)
                      ++||++++|+.-..||+.|.++|.+|+|+|||+++..+...+.++ |.|.+.|.
T Consensus         2 ~~RL~K~La~~G~~SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~~~i~v~g~   55 (248)
T COG1187           2 SMRLNKFLAEAGVGSRREAEKLIEEGRVTVNGKVATLGGVVVDPDDDVVEVDGK   55 (248)
T ss_pred             ccchHHHHHHcCCCCHHHHHHHHHcCCEEECCEEeccCCeEeCCCCcEEEECCE
Confidence            689999999988999999999999999999999999999999998 47777765

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=97.97  E-value=1.9e-05  Score=71.96  Aligned_cols=54  Identities=28%  Similarity=0.438  Sum_probs=48.6

Q ss_pred             eccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          157 IEASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       157 ~v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      ..+++|||.+|+..+ ++||+.++.++++|.|+|||+.+ ++++.|++||.|.+..
T Consensus        16 ~~~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~GD~I~i~~   70 (317)
T PRK11025         16 DEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAGDEVRIPP   70 (317)
T ss_pred             ccCCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCCCEEEeCC
Confidence            346899999999766 78999999999999999999998 6999999999999854

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=97.96  E-value=1.4e-05  Score=69.96  Aligned_cols=52  Identities=38%  Similarity=0.460  Sum_probs=47.9

Q ss_pred             chHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          160 SLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      -||||.+|.+ .+.-||++|+.+|.+|.|.|||+.+.+|+..|..++.|.|.+
T Consensus         2 k~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~~~i~v~~   54 (245)
T COG1189           2 KMRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKG   54 (245)
T ss_pred             cchHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCCceEEEcc
Confidence            4899999764 578999999999999999999999999999999999999984

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=97.94  E-value=1.7e-05  Score=71.48  Aligned_cols=55  Identities=35%  Similarity=0.477  Sum_probs=49.1

Q ss_pred             eccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          157 IEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       157 ~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ..+++|||.+++..+.+||+.+++++++|.|+|||+.+. +++.|++||+|++.-.
T Consensus         9 ~~~g~rld~~L~~l~~~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~   63 (289)
T COG0564           9 EEAGQRLDKFLAKLLPISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLP   63 (289)
T ss_pred             hhcCCCHHHHHHHccCcCHHHHHHHHHCCCEEECCEEcc-CCeeeCCCCEEEEecc
Confidence            457899999999833399999999999999999999996 9999999999998653

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=97.85  E-value=3.1e-05  Score=69.83  Aligned_cols=51  Identities=18%  Similarity=0.235  Sum_probs=44.4

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEee
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg  211 (236)
                      ++|||.+|+....+||+.+.++|++|+|+|||+.+ .+.+.|.++  |.|.+.|
T Consensus         2 ~~RL~k~La~~g~~SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~~~~d~I~v~g   54 (289)
T PRK10700          2 SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIA-TLGDRVEVTPGLKIRIDG   54 (289)
T ss_pred             chhHHHHHHHCCCCCHHHHHHHHHcCCEEECCEec-cCCCEeCCCCCeEEEECC
Confidence            58999999986569999999999999999999988 699999887  5566654

>PRK11507 ribosome-associated protein; Provisional

Probab=97.78  E-value=6.6e-05  Score=53.77  Aligned_cols=52  Identities=23%  Similarity=0.344  Sum_probs=46.6

Q ss_pred             hHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          161 LRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       161 ~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      .+||.+|+. .+--|=..|+.+|.+|.|+|||.+.+.-..++.+||+|++.|.
T Consensus        12 I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~GD~V~~~g~   64 (70)
T PRK11507         12 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH   64 (70)
T ss_pred             EEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCCCEEEECCE
Confidence            579999974 3466888999999999999999999999999999999999885

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=97.78  E-value=6.2e-05  Score=63.30  Aligned_cols=53  Identities=17%  Similarity=0.267  Sum_probs=45.8

Q ss_pred             chHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEeeC
Q 026574          160 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSGK  212 (236)
Q Consensus       160 s~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg~  212 (236)
                      ..|||.++ ...+.-||++|+++|.+|.|.|||+.+++|++.|.++  |.|+....
T Consensus       102 erRLd~il~r~gla~S~~~Ar~lI~hGhV~V~g~~V~~Ps~~V~~~~ed~I~~~~~  157 (177)
T PRK04051        102 ERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSYLVSVEEEDLIDYYPT  157 (177)
T ss_pred             HhHHHHHHHHccCcCCHHHHHHHHHcCCEEECCEEeCCCCeECCCCCcceEEEeCC
Confidence            46999986 4667899999999999999999999999999999998  56665443

>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=97.76  E-value=4.5e-05  Score=55.01  Aligned_cols=62  Identities=24%  Similarity=0.305  Sum_probs=43.9

Q ss_pred             CccCCCccchHHHHHc-CCCCccccccEEEecCCeEEEEechhhHHHHHhccc--eecceEEEEEE
Q 026574           76 GFQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLE--KVGNVSVSCTR  138 (236)
Q Consensus        76 kf~~l~Hrd~LGalm~-lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~--kI~~~~V~~~~  138 (236)
                      +-+.++++|++|+|.+ .||+++.||+|-+.+ +.++|-|.++.++-+.+.|.  ++++-+|+++.
T Consensus         9 r~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~-~~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve~   73 (74)
T PF03880_consen    9 RKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD-NFSFVEVPEEVAEKVLEALNGKKIKGKKVRVER   73 (74)
T ss_dssp             GGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S-S-EEEEE-TT-HHHHHHHHTT--SSS----EEE
T ss_pred             cccCCCHHHHHHHHHhccCCCHHhEEEEEEee-eEEEEEECHHHHHHHHHHhcCCCCCCeeEEEEE
Confidence            3367899999999999 599999999998865 48999999999999999998  77777887764

; PDB: 2G0C_A 3MOJ_B.

>PF13275 S4_2: S4 domain; PDB: 1P9K_A

Probab=97.55  E-value=2.2e-05  Score=55.49  Aligned_cols=58  Identities=28%  Similarity=0.461  Sum_probs=38.1

Q ss_pred             cchHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574          159 ASLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI  217 (236)
Q Consensus       159 ~s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~  217 (236)
                      ...+|+.+|.. .+--|=..|+.+|.+|.|+|||...+..+..+.+||+|++ ..+.+++
T Consensus         6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~GD~V~~-~~~~~~V   64 (65)
T PF13275_consen    6 EYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPGDVVEI-DGEEYRV   64 (65)
T ss_dssp             S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SSEEEEE-TTEEEEE
T ss_pred             CcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCCCEEEE-CCEEEEE
Confidence            45779999974 3455777999999999999999999999999999999999 4445554

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

Probab=97.43  E-value=0.00027  Score=58.65  Aligned_cols=51  Identities=18%  Similarity=0.236  Sum_probs=45.1

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEe
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVS  210 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvr  210 (236)
                      ..|||.++- ..+.-|..+|+++|.+|.|.||++.++.|++.|..|  |.|+.-
T Consensus       103 eRRL~~vv~r~g~a~s~~~ArqlI~hgHI~V~~~~V~~Ps~~V~~~~Ed~I~~~  156 (162)
T TIGR01018       103 ERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSYIVRREEEKKIDFA  156 (162)
T ss_pred             HHhHhhHhhhccCcCCHHHHHHHhhCCCeeECCEEeccCceEecCCCCCeeeee
Confidence            479999975 567899999999999999999999999999999998  666653

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

>PLN00189 40S ribosomal protein S9; Provisional

Probab=97.23  E-value=0.00023  Score=60.57  Aligned_cols=54  Identities=19%  Similarity=0.129  Sum_probs=47.7

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG  213 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G  213 (236)
                      ..|||.++. ..+.-|..+|+++|.+|.|.||++.++.|++.|..||...|....
T Consensus       108 eRRL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~~e~~Itw~~  162 (194)
T PLN00189        108 ERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVDSQKHIDFSL  162 (194)
T ss_pred             HhhhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecCCEEEEEEec
Confidence            479999875 567889999999999999999999999999999999888876543

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=97.01  E-value=0.00066  Score=57.31  Aligned_cols=51  Identities=18%  Similarity=0.131  Sum_probs=44.1

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS  210 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr  210 (236)
                      ..|||.++. ..+.-|...|+++|.+|.|.|||+.++.|++.|..||.=.|.
T Consensus       106 eRRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~~Ed~I~  157 (181)
T PTZ00155        106 ERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVDSEKHID  157 (181)
T ss_pred             HHhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccCccCcee
Confidence            579999975 457889999999999999999999999999999998654333

>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]

Probab=96.66  E-value=0.0066  Score=43.83  Aligned_cols=53  Identities=28%  Similarity=0.490  Sum_probs=46.1

Q ss_pred             hHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCC
Q 026574          161 LRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKG  213 (236)
Q Consensus       161 ~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~G  213 (236)
                      ..|+.+|... .--|=.+|+.++.+|.|+|||++.+.-...+..||+|.+.+..
T Consensus        12 I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr~gd~V~i~~~~   65 (73)
T COG2501          12 ITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLRDGDVVEIPGQR   65 (73)
T ss_pred             EEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEeecCCEEEECCEE
Confidence            4588888753 4567789999999999999999999999999999999998874

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.95  E-value=0.013  Score=49.16  Aligned_cols=96  Identities=22%  Similarity=0.240  Sum_probs=67.3

Q ss_pred             hhhHHHHHhccceecceEEEEEEecCcccc----cCCCCceEEe--eec---cchHHHHHHHhCCCcCHHHHHHHHHCCc
Q 026574          116 PELADYLITSLEKVGNVSVSCTRIPLLALE----YEPPRTKSFK--TIE---ASLRVDALASAGFKLSRSKLVNLISNGD  186 (236)
Q Consensus       116 ~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~----~~~~~~~~~~--~~v---~s~RLD~ils~~~~~SR~~a~~lI~~G~  186 (236)
                      ++.+.+..-|+.-+++.+-++++.|.-.++    -...++...+  ..+   +++|||+++++.+++||+..+.++..|.
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            567777777888888877777776653322    1222343322  222   4799999999999999999999999999


Q ss_pred             EEECCEEecCCCcccCCCCEEEEee
Q 026574          187 VRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       187 V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      +..+-.........+..|-.|.+.-
T Consensus       165 Irgdtd~~~l~rkrlr~~~~i~Id~  189 (203)
T COG4332         165 IRGDTDKMLLLRKRLRAGYDIQIDV  189 (203)
T ss_pred             eeecchHHHHhhhhhhcCcEEEEEc
Confidence            9987665434556777777766643

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

Probab=95.82  E-value=0.015  Score=47.28  Aligned_cols=33  Identities=39%  Similarity=0.527  Sum_probs=30.5

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCE
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWT  192 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~  192 (236)
                      +.|||++|++.+++||+.+++++.+|.+..+-.
T Consensus       102 ~~Rld~lLa~~L~lSrs~l~~l~~~G~I~~~~~  134 (142)
T PF06353_consen  102 PLRLDRLLARQLGLSRSRLKRLIEQGLIRSDPD  134 (142)
T ss_pred             CccHHHHHHHHhCcCHHHHHHHHHCCCEEecCc
Confidence            799999999999999999999999999987643

>KOG4837 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.48  E-value=0.021  Score=49.03  Aligned_cols=86  Identities=24%  Similarity=0.255  Sum_probs=67.7

Q ss_pred             CceEEeeeccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe-eC---------CeEEEEE
Q 026574          150 RTKSFKTIEASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS-GK---------GRIKIGE  219 (236)
Q Consensus       150 ~~~~~~~~v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr-g~---------Gr~~~~~  219 (236)
                      +++.+...+.|.|.|.++..++++.|+++.-+.-.+..++|+....+.+.++..||.+-+. |.         -|+-...
T Consensus       129 ~~~~i~~~v~sfr~d~llK~Glgv~rnKVel~fye~e~R~N~~Kl~kkS~~i~vgds~d~~ig~~~~~~s~~~~rV~~~t  208 (248)
T KOG4837|consen  129 EKVLIVPEVVSFRVDALLKVGLGVTRNKVELLFYEYEPRTNSFKLVKKSLRIDVGDSADFKIGRSVDLISSKDVRVNWAT  208 (248)
T ss_pred             hhhhhhhHHHHHHHHHHHHhccccccchhhHhhhhcccccCcccccccceeeecccccceeeecccccCCcceEEEeeee
Confidence            4555666788999999999999999999999999999999999998999999999998874 31         1444444


Q ss_pred             e--eccccccEEEEEEEe
Q 026574          220 I--NSTRKGKFAVELIQY  235 (236)
Q Consensus       220 ~--~~TKKgr~~i~~~r~  235 (236)
                      +  +.|.-..+.|.+.||
T Consensus       209 V~~~~t~~e~~~Vvlrr~  226 (248)
T KOG4837|consen  209 VTKNGTIVETGDVVLRRG  226 (248)
T ss_pred             ecccceEeecceEEEEec
Confidence            4  245555666666665

>PRK13354 tyrosyl-tRNA synthetase; Provisional

Probab=94.02  E-value=0.16  Score=48.14  Aligned_cols=45  Identities=29%  Similarity=0.434  Sum_probs=38.6

Q ss_pred             HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 026574          163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV  207 (236)
Q Consensus       163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~I  207 (236)
                      +|.+++..+.-|++.|+++|++|.|+|||..+.++.+.+.++|.+
T Consensus       346 ~~~l~~~~~~~S~~earrli~~ggv~in~~~v~~~~~~~~~~~~l  390 (410)
T PRK13354        346 VDLLVDLGLEPSKREARRLIQNGAIKINGEKVTDVDAIINPEDAF  390 (410)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEccCcccccChhhhc
Confidence            455556778899999999999999999999998898888887753

>PRK04313 30S ribosomal protein S4e; Validated

Probab=93.66  E-value=0.2  Score=44.11  Aligned_cols=62  Identities=18%  Similarity=0.205  Sum_probs=50.3

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  ..+++.|+..+.+|.|+|||++.+++.+.+---|+||+..           .|||.+.++
T Consensus        36 ~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I  110 (237)
T PRK04313         36 ESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPI  110 (237)
T ss_pred             cccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCceeEEEEccCCCeEEEEECCCCcEEEEEC
Confidence            4566777777655  5788999999999999999999999999998889999943           567766555

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=93.02  E-value=0.26  Score=44.17  Aligned_cols=62  Identities=16%  Similarity=0.192  Sum_probs=50.3

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  -.+.+.|+..+.+|.|+|||++.+++.+.+---|+|+|..           .|||.+.++
T Consensus        37 esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I  111 (273)
T PTZ00223         37 ECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKV  111 (273)
T ss_pred             cccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEc
Confidence            4566777777655  4677899999999999999999998988888889999954           677777666

>PLN00036 40S ribosomal protein S4; Provisional

Probab=92.96  E-value=0.28  Score=43.70  Aligned_cols=62  Identities=18%  Similarity=0.264  Sum_probs=49.9

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  -.+.+.|+..+.+|.|+|||++.+++.+.+---|+|++..           .|||.+.++
T Consensus        40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I  114 (261)
T PLN00036         40 ECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRI  114 (261)
T ss_pred             cccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEc
Confidence            4566777777655  5677899999999999999999998888888789999954           667766655

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=92.96  E-value=0.28  Score=43.80  Aligned_cols=62  Identities=21%  Similarity=0.198  Sum_probs=49.8

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  ..+.+.|+..+.+|.|+|||++.++..+.+---|+|++..           .|||.+.++
T Consensus        40 eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I  114 (262)
T PTZ00118         40 ECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKI  114 (262)
T ss_pred             cccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEc
Confidence            4566667777655  5677899999999999999999998888888889999953           667666555

>PRK05912 tyrosyl-tRNA synthetase; Validated

Probab=92.70  E-value=0.45  Score=45.05  Aligned_cols=42  Identities=29%  Similarity=0.404  Sum_probs=35.6

Q ss_pred             HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC
Q 026574          163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG  204 (236)
Q Consensus       163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G  204 (236)
                      +|.++...+.-|++.|+++|++|.|+||++.+.+++..+.+.
T Consensus       346 ~~~l~~~~~~~S~~earr~i~~g~v~in~~~v~~~~~~~~~~  387 (408)
T PRK05912        346 LALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYVLTAD  387 (408)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHcCCEEECCEEecCcccccccc
Confidence            455566677899999999999999999999998888777763

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=91.54  E-value=0.21  Score=36.77  Aligned_cols=44  Identities=23%  Similarity=0.293  Sum_probs=34.5

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      ...+..++.+ +|+.-+.+      |.|.|||+.+ .+++.+++||.|+|.-
T Consensus        32 ~~tvkd~IEs-LGVP~tEV------~~i~vNG~~v-~~~~~~~~Gd~v~V~P   75 (81)
T PF14451_consen   32 GATVKDVIES-LGVPHTEV------GLILVNGRPV-DFDYRLKDGDRVAVYP   75 (81)
T ss_pred             CCcHHHHHHH-cCCChHHe------EEEEECCEEC-CCcccCCCCCEEEEEe
Confidence            3456666654 67777654      8899999999 6999999999999853

>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]

Probab=90.09  E-value=0.88  Score=39.89  Aligned_cols=52  Identities=15%  Similarity=0.139  Sum_probs=37.0

Q ss_pred             chHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          160 SLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      |+-|-.++...+  --.-+.|+..|.+|.|+|||++.++..+.|--=|+|++.-
T Consensus        40 slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~vRkd~kfPVGlmDVisip~   93 (241)
T COG1471          40 SLPLLVIIRDYLKYADNAREARKILSEGKVLVDGKVRKDYKFPVGLMDVISIPK   93 (241)
T ss_pred             cccEEeeehhHHHhccchHHHHHHHhcCcEEECCEEeccccCCcceEEEEEECC
Confidence            344444444433  2345688999999999999999876666665559999973

>PRK01777 hypothetical protein; Validated

Probab=88.35  E-value=1.1  Score=34.00  Aligned_cols=59  Identities=19%  Similarity=0.098  Sum_probs=38.8

Q ss_pred             CceEEeeecc-chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEe
Q 026574          150 RTKSFKTIEA-SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS  210 (236)
Q Consensus       150 ~~~~~~~~v~-s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvr  210 (236)
                      ++......++ +.++-.++.+ .++....-.--+..+.|-|||+.+ ..++.|++||.|+|-
T Consensus        15 ~~~~~~l~vp~GtTv~dal~~-sgi~~~~pei~~~~~~vgI~Gk~v-~~d~~L~dGDRVeIy   74 (95)
T PRK01777         15 RQYLQRLTLQEGATVEEAIRA-SGLLELRTDIDLAKNKVGIYSRPA-KLTDVLRDGDRVEIY   74 (95)
T ss_pred             ceEEEEEEcCCCCcHHHHHHH-cCCCccCcccccccceEEEeCeEC-CCCCcCCCCCEEEEe
Confidence            3444555444 6666666654 355444111123468899999999 599999999999873

>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]

Probab=84.92  E-value=0.59  Score=35.42  Aligned_cols=47  Identities=17%  Similarity=0.244  Sum_probs=35.8

Q ss_pred             HHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEE
Q 026574          165 ALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE  219 (236)
Q Consensus       165 ~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~  219 (236)
                      ..++...++|+..+..++..        ....-...|..||.|+++|+|.|++.+
T Consensus         9 ~~ia~~~~l~k~~a~~~v~~--------~~~~i~~aL~~G~~V~l~gFG~F~v~~   55 (94)
T COG0776           9 DAIAEKAGLSKKDAEEAVDA--------FLEEITEALAKGERVELRGFGTFEVRE   55 (94)
T ss_pred             HHHHHHcCCCHHHHHHHHHH--------HHHHHHHHHHcCCeEEEeeeeeeEeec
Confidence            34555568999999998775        222334578899999999999999864

>KOG3301 consensus Ribosomal protein S4 [Translation, ribosomal structure and biogenesis]

Probab=82.30  E-value=1.6  Score=36.32  Aligned_cols=44  Identities=20%  Similarity=0.191  Sum_probs=38.2

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCC
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT  203 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~  203 (236)
                      .+||+..+- ..+..|=..|+.+|.++.|.||++.+.-|++.|+.
T Consensus        96 ErRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl  140 (183)
T KOG3301|consen   96 ERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL  140 (183)
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence            589998864 45677888999999999999999999999999974

---

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	236
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	1e-40
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	1e-05
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	2e-04
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	4e-04

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

 Score =  136 bits (343), Expect = 1e-40
 Identities = 29/143 (20%), Positives = 57/143 (39%), Gaps = 4/143 (2%)

Query: 1   MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 60
             ++         + F+ P   K  +  L K   +   + G +  +E  R+ +       
Sbjct: 20  WIKKVEDSYAPFLTPFINPHQEK-LLKILAKTYGLACSSSGEFVSSEYVRVLLYPDYFQP 78

Query: 61  SDPDI-VAALSITGNFGFQPCSHGDFLGSILGT-GIAREKIGDIILQGEKGAQFLVVPEL 118
              D  ++   I  +  F+  +H   LG+++   GI R+  GDI++  E  AQ ++  + 
Sbjct: 79  EFSDFEISLQEIVYSNKFEYLTHAKILGTVINQLGIERKLFGDILVDEE-RAQIMINQQF 137

Query: 119 ADYLITSLEKVGNVSVSCTRIPL 141
                  L+K+G + VS    P 
Sbjct: 138 LLLFQDGLKKIGRIPVSLEERPF 160

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325

 Score = 44.1 bits (105), Expect = 1e-05
 Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 158 EASLRVDALASAGFK-LSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVS 210
           +   R+D   +  F   SRS++   I +  V VN     K    +  G+ V+++
Sbjct: 14  QLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAIN 67

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Length = 243

 Score = 40.2 bits (95), Expect = 2e-04
 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 2/54 (3%)

Query: 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219
           +A     L+RS+    I    V++N   V      +   D +    +  +   E
Sbjct: 9   IAENVG-LTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDE-LLTWIE 60

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Length = 234

 Score = 39.4 bits (93), Expect = 4e-04
 Identities = 10/54 (18%), Positives = 16/54 (29%), Gaps = 2/54 (3%)

Query: 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGE 219
           +A     +SR+     I    V V+   V      L     V+  G   +    
Sbjct: 10  IAQQLG-VSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGN-PLAQQH 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	236
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	100.0
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	99.07
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	98.97
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	98.91
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	98.76
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	98.73
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	98.72
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	98.7
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	98.53
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	98.52
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	98.45
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	98.44
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	98.42
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	98.41
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	98.4
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	98.23
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	97.97
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	97.33
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	97.0
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	96.9
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	95.28
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	95.19
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	94.28
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	93.9
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	92.92
2ktl_A	164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	90.92
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	89.28
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	88.98
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	88.54

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

Probab=100.00  E-value=5.3e-47  Score=313.37  Aligned_cols=141  Identities=19%  Similarity=0.327  Sum_probs=129.5

Q ss_pred             ChhhhhcCCceEEecCCChHHHHHHHHHhcccCCeeEEEeCCCccceeeEEEeeCCCCCCC--CccceEEEEeecCCCcc
Q 026574            1 MARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTS--DPDIVAALSITGNFGFQ   78 (236)
Q Consensus         1 ~~~~~~~~~~~~~T~FL~p~~~~~~~~~~~~~~~~~~~~~GGy~~AER~~~~~~~~~~~~~--~~~~i~~l~i~~~~kf~   78 (236)
                      ++++|.++|.+++|+||||+++.++.+++++. ++++.+||||++|||+|++|+ |+|++.  .++|+++++|+||+||.
T Consensus        20 ~~~~a~~~~~~~~T~FL~p~e~~i~~~i~~~~-~~~~~~~GGy~~AER~r~~i~-p~~~~~~~~d~~i~~l~i~~~~kF~   97 (165)
T 2fph_X           20 WIKKVEDSYAPFLTPFINPHQEKLLKILAKTY-GLACSSSGEFVSSEYVRVLLY-PDYFQPEFSDFEISLQEIVYSNKFE   97 (165)
T ss_dssp             HHHHHHHHTSCEECCCBCHHHHHHHHHHHHHT-TCEEEEGGGTSCCSSBCEEEE-CTTCCCCGGGGCEEEEEEESCCCCH
T ss_pred             HHHHHHHhCCEEECCCCCHHHHHHHHHHHhcc-CcEEEEeCCCcHHheeEEEEe-cccccCcccCCceEEEEEecccccc
Confidence            37889999999999999999999999988876 799999999999999999997 666542  23489999999999999


Q ss_pred             CCCccchHHHHHc-CCCCccccccEEEecCCeEEEEechhhHHHHHhccceecceEEEEEEecCccc
Q 026574           79 PCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLAL  144 (236)
Q Consensus        79 ~l~Hrd~LGalm~-lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~  144 (236)
                      +|+|||||||||| |||+|+++|||++.++ +||++|+++|++||.+||+|||+++|++++++++++
T Consensus        98 ~l~Hrd~LGaLm~~LGI~Re~iGDI~v~~~-~~qv~v~~~i~~~i~~nl~kIg~~~V~~~~i~~~~l  163 (165)
T 2fph_X           98 YLTHAKILGTVINQLGIERKLFGDILVDEE-RAQIMINQQFLLLFQDGLKKIGRIPVSLEERPFTEK  163 (165)
T ss_dssp             HHHHHHHHSCSSSCCCCCGGGEEEEECSSS-CCEEEEEGGGHHHHHHHCCEETTEECEEEECCGGGC
T ss_pred             cCCHHHHHHHHHHhcCCCHhhcCCEEEECC-EEEEEEcHHHHHHHHHHHhhccCeeEEEEEeCHHHc
Confidence            9999999999999 9999999999999665 899999999999999999999999999999998775

>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=99.07  E-value=1.6e-11  Score=104.53  Aligned_cols=87  Identities=22%  Similarity=0.265  Sum_probs=75.1

Q ss_pred             eEEEEechhhHHHHHhccceecceEEEEEEecCcccccCCCCceEEeeeccchHHHHHHHh-CCCcCHHHHHHHHHCCcE
Q 026574          109 GAQFLVVPELADYLITSLEKVGNVSVSCTRIPLLALEYEPPRTKSFKTIEASLRVDALASA-GFKLSRSKLVNLISNGDV  187 (236)
Q Consensus       109 ~~~~~v~~~i~~~i~~~l~kI~~~~V~~~~~~~~~~~~~~~~~~~~~~~v~s~RLD~ils~-~~~~SR~~a~~lI~~G~V  187 (236)
                      ..|.++.+++.+|+..+++++|++++.+.                   ...++|||.+|++ .++.||+.|+++|.+|.|
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            45668899999999999999998877530                   1235899999975 468899999999999999


Q ss_pred             EECCEEecCCCcccCCCCEEEEeeCCe
Q 026574          188 RVNWTTVTKNGTTLRTGDIVSVSGKGR  214 (236)
Q Consensus       188 ~VNg~~~~~~~~~v~~GD~Isvrg~Gr  214 (236)
                      .|||+.+++|++.|++||.|+|++.++
T Consensus       127 ~VNG~~v~~ps~~V~~gD~I~V~~~~r  153 (209)
T 2vqe_D          127 TVNGRRVDLPSYRVRPGDEIAVAEKSR  153 (209)
T ss_dssp             EETTEECCCTTCBCCTTCEEEECGGGT
T ss_pred             EECCEEeCcCCcCcCCCCEEEEcCccc
Confidence            999999988999999999999998765

>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=98.97  E-value=2.2e-09  Score=85.11  Aligned_cols=62  Identities=16%  Similarity=0.186  Sum_probs=55.8

Q ss_pred             ccchHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574          158 EASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI  220 (236)
Q Consensus       158 v~s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~  220 (236)
                      .+++|||.||+.. +..||+.++.+|.+|+|+|||+.+ ++++.|++||.|+|...+.....++
T Consensus         6 ~~~~RLDk~L~~~~~~~SRs~a~~li~~G~V~VNG~~v-k~s~~V~~GD~I~I~~~~~~~~~~v   68 (133)
T 1dm9_A            6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRS-KPSKIVELNATLTLRQGNDERTVIV   68 (133)
T ss_dssp             TTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEEC-CTTCBCCTTCEEEEEETTEEEEEEE
T ss_pred             ccchhHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEc-CCCCEeCCCCEEEEEeCCceeeEEE
Confidence            4579999999875 567999999999999999999998 7999999999999999888776666

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

Probab=98.91  E-value=2.7e-10  Score=84.32  Aligned_cols=63  Identities=19%  Similarity=0.197  Sum_probs=55.6

Q ss_pred             hHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe-eccc
Q 026574          161 LRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI-NSTR  224 (236)
Q Consensus       161 ~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~-~~TK  224 (236)
                      +|||.+|+... ..||++++++|.+|.|+|||+.+ ++++.|++||.|+|...++....++ +.||
T Consensus         1 ~RLD~~L~~~~~~~sR~~~~~li~~G~V~VNg~~~-~~~~~v~~gd~I~v~~~~~~~~~~~~~~~~   65 (92)
T 2k6p_A            1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCA-KASKEVKAGDTISLHYLKGIEEYTILQIPA   65 (92)
T ss_dssp             CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEEC-CTTCBCCTTCEEEECCSSCCEEEEECCCCC
T ss_pred             ChHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEc-CCCCCcCCCCEEEEEeCCceEEEEEecccc
Confidence            58999998754 45999999999999999999998 7999999999999999998887776 5666

>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=98.76  E-value=1e-08  Score=83.52  Aligned_cols=56  Identities=21%  Similarity=0.332  Sum_probs=50.5

Q ss_pred             cchHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCe
Q 026574          159 ASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR  214 (236)
Q Consensus       159 ~s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr  214 (236)
                      -++|||.+|++. +..||+.|+++|.+|.|.|||+.+++|++.|++||.|+|++..+
T Consensus        49 le~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VNG~~v~~ps~~V~~gD~I~V~~~~~  105 (159)
T 1c05_A           49 LESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSR  105 (159)
T ss_dssp             HHHBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTEECCCSSCBCCTTCEEEECGGGS
T ss_pred             HHHHHHHHHHHcCCcCCHHHHHHHHHCCCEEECCEEeCcCCcEeCCCCEEEEeCcee
Confidence            478999999865 57899999999999999999999988999999999999987653

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

Probab=98.73  E-value=3.1e-09  Score=89.71  Aligned_cols=58  Identities=12%  Similarity=0.100  Sum_probs=52.3

Q ss_pred             cchHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEE
Q 026574          159 ASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIK  216 (236)
Q Consensus       159 ~s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~  216 (236)
                      -++|||.+|++. +..||+.|+++|.+|.|.|||+.++.|++.|++||.|+|++.++..
T Consensus        87 Le~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VNG~~V~~pS~~V~~gD~I~V~~~~r~~  145 (201)
T 3bbn_D           87 LEMRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQKSI  145 (201)
T ss_dssp             HHSBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSSTTSC
T ss_pred             HHHHHHHHHHHcCCcCCHHHHHHHHhCCcEEeCCEEEeecceecCCCCEEEEccccchH
Confidence            478999999654 5679999999999999999999998999999999999999988753

>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=98.70  E-value=1.2e-09  Score=78.73  Aligned_cols=55  Identities=20%  Similarity=0.283  Sum_probs=47.7

Q ss_pred             ccchHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          158 EASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       158 v~s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ...+|||.+|+.. +..||+.|+++|++|.|+|||+.+.++++.|.+||.|.+.|.
T Consensus        18 ~~~~RLdk~L~~~g~~~SR~~a~~lI~~G~V~VNG~~v~~~~~~v~~gd~I~v~~~   73 (79)
T 1p9k_A           18 HPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH   73 (79)
T ss_dssp             CSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETTE
T ss_pred             CCCchHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEecCCCCCCCCCCEEEECCE
Confidence            3458999999864 235999999999999999999998889999999999888654

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

Probab=98.53  E-value=3.2e-08  Score=70.18  Aligned_cols=51  Identities=20%  Similarity=0.202  Sum_probs=45.1

Q ss_pred             chHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCC--CCEEEEe
Q 026574          160 SLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRT--GDIVSVS  210 (236)
Q Consensus       160 s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~--GD~Isvr  210 (236)
                      ..|||.+|.+ .+.-||++|+++|.+|+|+|||+.+++|++.|.+  +|.|++.
T Consensus         7 ~~RLD~~l~~~gla~SR~~A~~lI~~G~V~Vng~~v~kps~~V~~~~~d~I~~~   60 (71)
T 2cqj_A            7 GRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWV   60 (71)
T ss_dssp             EEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEES
T ss_pred             HHHHHHHHHHhCCcCCHHHHHHHHHCCcEEECCEEECCCCCCCCCCCCcEEEEE
Confidence            4699999865 4567999999999999999999999999999998  7888864

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=98.52  E-value=5.5e-08  Score=83.28  Aligned_cols=53  Identities=21%  Similarity=0.228  Sum_probs=48.9

Q ss_pred             cchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          159 ASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       159 ~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      +++|||.+|+....+||+.++++|++|+|+|||+.++++++.|++||.|++.+
T Consensus         2 ~~~RLd~~L~~~~~~SR~~~~~li~~G~V~VNG~~v~~~~~~v~~gD~I~v~~   54 (234)
T 1ksk_A            2 SHMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDG   54 (234)
T ss_dssp             CCEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETT
T ss_pred             CcccHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeCCCCCCCCCCCEEEEeC
Confidence            47899999987778999999999999999999999977999999999999974

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}

Probab=98.45  E-value=9.8e-08  Score=84.79  Aligned_cols=54  Identities=24%  Similarity=0.259  Sum_probs=48.7

Q ss_pred             cchHHHHHHHh-CCCcCHHHHHHHHHCCcEEECC-E-EecCCCcccCCCCEEEEeeC
Q 026574          159 ASLRVDALASA-GFKLSRSKLVNLISNGDVRVNW-T-TVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       159 ~s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg-~-~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ..+|||.+|++ .+..||++|+++|++|+|+||| + .+.+|++.|.+||.|+|+|.
T Consensus         5 ~~~RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~~~v~kp~~~V~~~d~I~v~g~   61 (291)
T 3hp7_A            5 PKERVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDGTELKLKGE   61 (291)
T ss_dssp             CEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEETTC
T ss_pred             chhhHHHHHHHcCCcccHHHHHHHHHCCeEEECCeEEEEccCCCCCCCCCEEEEccc
Confidence            46899999975 4678999999999999999999 8 78899999999999999875

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=98.44  E-value=1.6e-07  Score=83.37  Aligned_cols=53  Identities=28%  Similarity=0.416  Sum_probs=49.4

Q ss_pred             ccchHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          158 EASLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       158 v~s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      .+++|||.||+....+||+.++++|.+|+|+|||+.+ ++++.|.+||.|+|.+
T Consensus         4 ~~g~RLdk~La~~g~~SR~~a~~lI~~G~V~VNG~~v-~~~~~V~~gD~I~v~~   56 (290)
T 3dh3_A            4 DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRA-TIGDQVKPGDVVKVNG   56 (290)
T ss_dssp             CCCEEHHHHHHTTTSSCHHHHHHHHHTTCEEETTEEC-CTTCEECTTCCEEETT
T ss_pred             ccchHHHHHHHhCCCCCHHHHHHHHHCCCEEECCEEc-cCCcCcCCCCEEEecc
Confidence            3689999999987778999999999999999999999 7999999999999976

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

Probab=98.42  E-value=5.9e-08  Score=80.50  Aligned_cols=55  Identities=15%  Similarity=0.244  Sum_probs=49.7

Q ss_pred             chHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEeeCCe
Q 026574          160 SLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSGKGR  214 (236)
Q Consensus       160 s~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg~Gr  214 (236)
                      .+|||.+| ...+.-||+.|+++|.+|+|.|||+.+++|++.|.+|  |.|++.+.-.
T Consensus       102 e~RLD~~L~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~~eD~I~v~~~s~  159 (180)
T 3j20_D          102 ERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKEEEDTITYARTSP  159 (180)
T ss_dssp             HTSHHHHHHHHTSSSSHHHHHHHHHHTCCEESSSBCCCSSCCCCTGGGGCEECSSCSS
T ss_pred             hhhhhheeecCcccCcHHHHHHHHHcCCeEECCEEeCCCCcccCCCCCCEEEEeCCCc
Confidence            68999998 4667889999999999999999999999999999999  9999976544

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=98.41  E-value=1.4e-07  Score=81.27  Aligned_cols=52  Identities=23%  Similarity=0.346  Sum_probs=47.8

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      ++|||.+|+....+||+.++++|++|+|+|||+.++++++.|++||.|.+.+
T Consensus         2 ~~RLd~~L~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~   53 (243)
T 1vio_A            2 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFED   53 (243)
T ss_dssp             CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETT
T ss_pred             CccHHHHHHHcCCCCHHHHHHHHHcCcEEECCEEeCCCCCCcCCCCEEEEec
Confidence            5899999987778999999999999999999999977999999999998864

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

Probab=98.40  E-value=1.4e-07  Score=78.48  Aligned_cols=52  Identities=15%  Similarity=0.085  Sum_probs=46.1

Q ss_pred             ccchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCC--EEEE
Q 026574          158 EASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGD--IVSV  209 (236)
Q Consensus       158 v~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD--~Isv  209 (236)
                      .-++|||.+|. ..+..||+.|+++|.+|.|.|||+.+++|++.|.+||  .|++
T Consensus       104 ~le~RLD~vL~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~d~~~I~v  158 (181)
T 2xzm_D          104 LMERRLQTRVFKLNLANSIHHSRVLIRQRHIKVGKNLVNVPSFMVRTDSEKSIDF  158 (181)
T ss_dssp             HHTTBHHHHHHHTTCSSSTTHHHHHTTTTCCEETTEECCCSCCBCCSTTSSCEEC
T ss_pred             hhccchhHHHHhccccCCHHHHHHHHHCCEEEECCEEECCCCcCCCCCCceEEEE
Confidence            34789999985 5667899999999999999999999999999999997  5665

>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=98.23  E-value=1.4e-07  Score=84.69  Aligned_cols=55  Identities=24%  Similarity=0.309  Sum_probs=0.0

Q ss_pred             ccchHHHHHHHhCC-CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          158 EASLRVDALASAGF-KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       158 v~s~RLD~ils~~~-~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      .+++|||.+|+..+ .+||+.++++|++|+|+|||+.+.++++.|++||.|++.+.
T Consensus        14 ~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~gD~I~v~~~   69 (325)
T 1v9f_A           14 QLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAE   69 (325)
T ss_dssp             --------------------------------------------------------
T ss_pred             cCCchHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCCCEEEEecc
Confidence            46899999999877 89999999999999999999985689999999999999764

>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=97.97  E-value=1.4e-06  Score=73.15  Aligned_cols=52  Identities=15%  Similarity=0.134  Sum_probs=45.8

Q ss_pred             chHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCC--CEEEEee
Q 026574          160 SLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTG--DIVSVSG  211 (236)
Q Consensus       160 s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~G--D~Isvrg  211 (236)
                      .+|||.+|.+ .+.-||++|+++|.+|+|.|||+.++.|++.|.+|  |.|++..
T Consensus       106 e~RLD~~L~r~G~a~Sr~~ArqLI~~GhV~VNG~~V~~Ps~~V~~g~ed~I~~~~  160 (197)
T 3u5c_J          106 ERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAP  160 (197)
T ss_dssp             TTSHHHHHHHSSTTSSHHHHHHHHHTSCCBSSSCBCCCTTCCCCSTTGGGCBCCS
T ss_pred             HHHHHHHHHHccccCCHHHHHHHHHcCCEEECCEEeCCCccccCCCCccEEEEcC
Confidence            5799999864 56779999999999999999999999999999999  5677653

>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=97.33  E-value=7.6e-07  Score=74.59  Aligned_cols=56  Identities=18%  Similarity=0.112  Sum_probs=48.4

Q ss_pred             cchHHHHHHHh-CCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCe
Q 026574          159 ASLRVDALASA-GFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGR  214 (236)
Q Consensus       159 ~s~RLD~ils~-~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr  214 (236)
                      -.+|||.+|.. .+.-||++|+++|.+|+|.|||+.++.|++.|.+||.+.|...+.
T Consensus       107 le~RLD~~L~r~G~a~SR~~ArqlI~~GhV~VNG~~V~~Ps~~V~~gde~~I~~~~~  163 (195)
T 3iz6_C          107 LARRLQTLVFKAGMAKSIHHARVLIRQRHIRVGRQIVNIPSFMVRVESEKHIDFSLT  163 (195)
T ss_dssp             TTSCCCSSCCCCCCHHHHSCTTSHHHHHSTTTSCCCCCCCCCCCSSSCSSSSCSSSC
T ss_pred             HHhhhhHHHHhccccCCHHHHHHHHHcCCEEECCEEeCCCCcCcCCCCEEEEEecCC
Confidence            35799999864 456699999999999999999999999999999999988875444

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=97.00  E-value=0.0014  Score=55.49  Aligned_cols=50  Identities=16%  Similarity=0.230  Sum_probs=43.5

Q ss_pred             chHHHHHHHhC--CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574          160 SLRVDALASAG--FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV  209 (236)
Q Consensus       160 s~RLD~ils~~--~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv  209 (236)
                      |+-|--+|...  +..+++.|++++.+|.|+|||+..+++++.+..+|+|++
T Consensus         7 slPL~i~LRdrLgyA~t~rEarkIv~~~~I~VDGKvr~d~~ypvG~mDVIsI   58 (213)
T 3kbg_A            7 SVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFMDVIEI   58 (213)
T ss_dssp             CEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEE
T ss_pred             ceeeHHHHhhhhcccccHHHHHHHHHCCCEEECCEEecccCCCccceeEEEe
Confidence            45566666643  467889999999999999999999999999999999999

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=96.90  E-value=0.0027  Score=54.73  Aligned_cols=53  Identities=11%  Similarity=0.117  Sum_probs=47.5

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      .|+-|--+|...+  ..+++.|++++.+|.|+|||+..+++++.+..+|+|++.-
T Consensus        41 ~~lPL~i~LRdrLgyA~t~rEar~Iv~~~~I~VdGKvr~d~~ypvG~mDVIsI~k   95 (243)
T 3j20_E           41 TSIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIMDVVSIPE   95 (243)
T ss_dssp             TCEEHHHHHHTTSCCCSSHHHHHHHHHHCSCEETTEECCCSSCEECTTCEEEETT
T ss_pred             cceeehhhhhhhhccccCHHHHHHHHHCCcEEECCEEeccccCCcccceEEEecc
Confidence            4677888888765  5788999999999999999999999999999999999975

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}

Probab=95.28  E-value=0.018  Score=53.49  Aligned_cols=45  Identities=27%  Similarity=0.327  Sum_probs=39.3

Q ss_pred             HHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCE
Q 026574          162 RVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDI  206 (236)
Q Consensus       162 RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~  206 (236)
                      -+|.++...+--|++.|+++|++|.|+|||..+++++..+.++|.
T Consensus       358 ~~~ll~~~gl~~S~~earr~i~~ggv~in~~~v~d~~~~~~~~~~  402 (432)
T 2jan_A          358 IVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF  402 (432)
T ss_dssp             HHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS
T ss_pred             HHHHHHHhCCcccHHHHHHHHHhCCEEECCEEccChhcccChhhc
Confidence            466667777889999999999999999999999999999987653

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

Probab=95.19  E-value=0.019  Score=40.00  Aligned_cols=59  Identities=15%  Similarity=0.280  Sum_probs=44.3

Q ss_pred             ccCCCccchHHHHHc-CCCCccccccEEEecCCeEEEEechhhHHHHHhccce--ecceEEEE
Q 026574           77 FQPCSHGDFLGSILG-TGIAREKIGDIILQGEKGAQFLVVPELADYLITSLEK--VGNVSVSC  136 (236)
Q Consensus        77 f~~l~Hrd~LGalm~-lGi~Re~iGDI~~~~~~~~~~~v~~~i~~~i~~~l~k--I~~~~V~~  136 (236)
                      =+.+..+|++|+|.+ .||.++.||+|-+.+ +..+|-+.+++++-+...|..  +..-++++
T Consensus        10 k~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d-~~s~v~v~~~~~~~~~~~l~~~~i~g~~~~v   71 (76)
T 2g0c_A           10 KKKIRAVDFVGTIAKIDGVSADDIGIITIMD-NASYVEILNGKGPHVLKVMKNTTVKGKQLKV   71 (76)
T ss_dssp             C----CHHHHHHHHTSTTCCGGGEEEEEECS-SCEEEEECTTCHHHHHHHHTTCCC---CCCE
T ss_pred             ccCCCHHHHHHHHHHccCCChhhccEEEEeC-CcEEEEECHHHHHHHHHHhccccCcCceEEE
Confidence            356788999999999 899999999998855 589999999999999988875  34444443

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*

Probab=94.28  E-value=0.14  Score=47.57  Aligned_cols=55  Identities=20%  Similarity=0.207  Sum_probs=42.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE-eeCCeEE
Q 026574          162 RVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV-SGKGRIK  216 (236)
Q Consensus       162 RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv-rg~Gr~~  216 (236)
                      -+|.+....+.-|++.|+++|++|.|+|||..+++++..+.+++.+.+ +|+-+|-
T Consensus       371 ~~~~l~~~~l~~S~~earr~i~~ggv~vn~~~v~d~~~~~~~~~~~~l~~GKk~~~  426 (432)
T 1h3f_A          371 VARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFV  426 (432)
T ss_dssp             HHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEEETTTEEE
T ss_pred             HHHHHHHhCCcccHHHHHHHHHhCCEEECCEEecCccceecCCCcEEEEeCCeeEE
Confidence            345555667889999999999999999999999999999987652222 3444443

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*

Probab=93.90  E-value=0.01  Score=54.94  Aligned_cols=57  Identities=16%  Similarity=0.205  Sum_probs=0.0

Q ss_pred             hHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEee
Q 026574          161 LRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN  221 (236)
Q Consensus       161 ~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~  221 (236)
                      ..|..+| ...+--|++.|+++|++|.|+|||..+++++..+.+||.+    .|++.+...|
T Consensus       353 i~l~~lL~~agl~~SksEARRlI~~GgV~VNgekv~d~~~~l~~~dl~----~~~~~~l~~G  410 (420)
T 1jil_A          353 TNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI----DGEFTIIRRG  410 (420)
T ss_dssp             --------------------------------------------------------------
T ss_pred             ccHHHHHHHcCCccCHHHHHHHHHhCCEEECCEEecccccccCccccc----CCcEEEEEEC
Confidence            3555555 4556779999999999999999999999999999999876    4454443333

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A

Probab=92.92  E-value=0.018  Score=53.25  Aligned_cols=45  Identities=29%  Similarity=0.353  Sum_probs=0.0

Q ss_pred             HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEE
Q 026574          163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIV  207 (236)
Q Consensus       163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~I  207 (236)
                      +|.++...+--|++.|+++|++|.|+|||..+++++..+.++|.+
T Consensus       355 ~~~l~~~gl~~S~~earr~i~~ggv~in~~~v~d~~~~~~~~~~~  399 (419)
T 2ts1_A          355 VELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL  399 (419)
T ss_dssp             ---------------------------------------------
T ss_pred             HHHHHHhCCCCCHHHHHHHHHhCCEEECCEEecCcccccChhhcc
Confidence            444555667789999999999999999999999999999888765

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

Probab=90.92  E-value=0.15  Score=41.38  Aligned_cols=34  Identities=26%  Similarity=0.171  Sum_probs=29.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEec
Q 026574          162 RVDALASAGFKLSRSKLVNLISNGDVRVNWTTVT  195 (236)
Q Consensus       162 RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~  195 (236)
                      -+|.+++..+--|++.|+++|.+|.|+||+..+.
T Consensus        52 ivdlLv~aGLa~SKsEARRlI~qGGv~VNg~kv~   85 (164)
T 2ktl_A           52 FSKVLWSAGLVASKSEGQRIINNNGAYVGSRPGV   85 (164)
T ss_dssp             HHHHHHHHTSCSTHHHHHHHHHHTCEEEEECCSC
T ss_pred             HHHHHHHhCcccCHHHHHHHHHhCCEEECCEecc
Confidence            5677778888999999999999999999997763

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W

Probab=89.28  E-value=1.4  Score=38.14  Aligned_cols=62  Identities=19%  Similarity=0.295  Sum_probs=50.8

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHC--CcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISN--GDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~--G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  -.+.+.|+..+.+  |.|+|||++.++..+.+--=|+|||..           +|||.+..+
T Consensus        40 eslPL~i~LRd~LkyA~t~rEak~Il~q~~~~VkVDGkvr~D~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I  116 (260)
T 2xzm_W           40 ESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKVRRDKGYPTGLMDVVRIEKTDQSFRILYDTKGRFVLKSL  116 (260)
T ss_dssp             SCEEHHHHHTTTTCSCCSHHHHHHHTTSTTCCEEETTEECCCTTCEECTTCEEEEGGGTEEEEEEECSSSCEEEEEC
T ss_pred             eeehhHhhhhhhhccccchhHHHHHHhccCCeEEECCEEeccCCCCCcEEEEEeEcCCCCEEEEEEcCCccEEEEEc
Confidence            3566778887766  4788999999999  999999999988889998889999963           566666555

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E

Probab=88.98  E-value=0.39  Score=41.62  Aligned_cols=62  Identities=18%  Similarity=0.261  Sum_probs=51.3

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  -.+.+.|+..+.+|.|+|||++.++..+.+--=|+|||..           +|||.+..+
T Consensus        40 eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I  114 (261)
T 3u5c_E           40 ESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRI  114 (261)
T ss_dssp             GEEEHHHHHHHTTCCCSSSHHHHHHHTTTCEEETTBCCCCTTCEEETTCEEEETTTTEEEECCBCSSSCBCCEEC
T ss_pred             hheeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCceEEEEEEcCCCCEEEEEECCCCcEEEEEC
Confidence            4667888888766  4667899999999999999999999999998889999943           677776665

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=88.54  E-value=0.31  Score=42.32  Aligned_cols=62  Identities=16%  Similarity=0.268  Sum_probs=48.1

Q ss_pred             cchHHHHHHHhCC--CcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee-----------CCeEEEEEe
Q 026574          159 ASLRVDALASAGF--KLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG-----------KGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils~~~--~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg-----------~Gr~~~~~~  220 (236)
                      .|+-|--+|...+  -.+.+.|+..+.+|.|+|||++.++..+.+--=|+|||..           +|||.+..+
T Consensus        40 eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~MDVIsI~kt~e~fRll~D~kGrf~l~~I  114 (265)
T 3iz6_D           40 ECLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFMDVISIPKTGENYRLLYDTKGRFRLQSV  114 (265)
T ss_dssp             ---CHHHHHHHHHTTSSCSSSTHHHHHTTCCEETTEECCCTTCCCCTTCEEECCSSCCEEEEEECTTSCEEEEEE
T ss_pred             hheeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCcEEEEEEEcCCCCEEEEEECCCCcEEEEEC
Confidence            3566767776544  5667899999999999999999988888888889999954           677777666

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	236
d1vioa2	58	d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-te	7e-10
d1kska3	59	d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-te	2e-07
d1p9ka_	79	d.66.1.6 (A:) Hypothetical protein YbcJ {Escherich	2e-04

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58

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

 Score = 51.2 bits (123), Expect = 7e-10
 Identities = 12/53 (22%), Positives = 21/53 (39%)

Query: 160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212
           SLR+D   +    L+RS+    I    V++N   V      +   D +    +
Sbjct: 1   SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDE 53

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

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]

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 11/52 (21%), Positives = 18/52 (34%)

Query: 161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK 212
           +R+D   +    +SR+     I    V V+   V      L     V+  G 
Sbjct: 1   MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGN 52

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Length = 79

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]

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 166 LASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI 217
           L   G+  S ++    I+ G V+V+    T+    +  G  VS +G   +++
Sbjct: 27  LKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH-SVQV 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	236
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	99.43
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	99.36
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	99.19
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	98.76
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	98.74
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	98.62
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	98.6
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.52
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	97.34

>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=99.43  E-value=3.6e-14  Score=95.60  Aligned_cols=53  Identities=23%  Similarity=0.347  Sum_probs=50.3

Q ss_pred             chHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          160 SLRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       160 s~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      |||||.+|+....+||++|+++|++|+|+|||+.+.+|++.|++||.|+++|.
T Consensus         1 smRLD~~Ls~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~~~g~   53 (58)
T d1vioa2           1 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDE   53 (58)
T ss_dssp             CEEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEETTE
T ss_pred             CcHHHHHHHHcCCCCHHHHHHHHHcCeEEECCEEeCCCCCCCCCCCEEEECCE
Confidence            69999999998889999999999999999999999999999999999999763

>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=99.36  E-value=1.9e-13  Score=92.26  Aligned_cols=52  Identities=21%  Similarity=0.231  Sum_probs=49.7

Q ss_pred             hHHHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          161 LRVDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       161 ~RLD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ||||.||+....+||++|+++|++|+|+|||+.+.+|++.|.++|.|+++|.
T Consensus         1 mRLdk~l~~~~~~SR~~a~~lI~~g~V~Vng~~v~~~~~~V~~~d~I~~dg~   52 (59)
T d1kska3           1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGN   52 (59)
T ss_dssp             EEHHHHHHHHHTCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEETTE
T ss_pred             CcHHHHHHHcCCCCHHHHHHHHHcCcEEECCEEeecCCcCcCCCCEEEECCE
Confidence            7999999988899999999999999999999999999999999999999775

>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=99.19  E-value=3.8e-11  Score=89.70  Aligned_cols=61  Identities=16%  Similarity=0.181  Sum_probs=55.3

Q ss_pred             cchHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEe
Q 026574          159 ASLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEI  220 (236)
Q Consensus       159 ~s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~  220 (236)
                      +.||||.+|. ..+..||+.|+++|++|.|+|||+.+ +|++.|++||+|+|+..++.....+
T Consensus         3 ~~mRlD~~L~~~r~~ktR~~A~~~i~~G~V~vNg~~v-Kps~~vk~GDvI~i~~~~~~~~i~V   64 (104)
T d1dm9a_           3 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRS-KPSKIVELNATLTLRQGNDERTVIV   64 (104)
T ss_dssp             TCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEEC-CTTCBCCTTCEEEEEETTEEEEEEE
T ss_pred             ccEeHHHHHHHhhhHhhHHHHHHHHHcCCeeeCCeec-cccccCCCCCEEEEEeCCeEEEEEE
Confidence            4699999995 45788999999999999999999998 6999999999999999998887666

>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=98.76  E-value=5.3e-09  Score=83.28  Aligned_cols=53  Identities=23%  Similarity=0.392  Sum_probs=49.1

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ..|||+++- .+|..||..|++++.+|.|.|||+.++-||+.|++||+|+++-.
T Consensus        50 E~RlD~vv~r~gfa~t~~~arQ~v~Hghi~vNgk~v~iPSy~vk~GDvIsvkek  103 (159)
T d1c06a_          50 ESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREK  103 (159)
T ss_dssp             HHCHHHHHHHHTSSSSHHHHHHHHHTSCEEETTEECCCSSCCCCSSCEEEECGG
T ss_pred             HHHhhhhhccCcccCCHHHHHHHHHhcceEccceEEEecceeecCCcEEeeccc
Confidence            579999974 67899999999999999999999999999999999999999754

>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=98.74  E-value=2.6e-10  Score=81.00  Aligned_cols=58  Identities=19%  Similarity=0.310  Sum_probs=51.1

Q ss_pred             cchHHHHHHHhC-CCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEE
Q 026574          159 ASLRVDALASAG-FKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKI  217 (236)
Q Consensus       159 ~s~RLD~ils~~-~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~  217 (236)
                      +..|||.+|+.. +.-||++|+++|++|+|+|||+.+++|++.|.+||.|.+.|. ++++
T Consensus        19 ~~irL~k~L~~~gl~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V~~~d~I~vdG~-~i~i   77 (79)
T d1p9ka_          19 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGH-SVQV   77 (79)
T ss_dssp             SCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETTE-EEEE
T ss_pred             CcEEHHHHHHHCCCccCHHHHHHHHHhCCcccCCEEeccccccCCCCCEEEECCE-EEEE
Confidence            458999999865 456999999999999999999999999999999999999875 4544

>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=98.62  E-value=1.3e-08  Score=84.05  Aligned_cols=53  Identities=25%  Similarity=0.347  Sum_probs=49.1

Q ss_pred             cchHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEee
Q 026574          159 ASLRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSG  211 (236)
Q Consensus       159 ~s~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg  211 (236)
                      -..|||+++ ...|.-||..|+++|.+|.|.|||+.++-||+.|++||+|+|+-
T Consensus        92 LE~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk~VnIPSy~vk~GDvIsvke  145 (204)
T d2gy9d1          92 LEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIRE  145 (204)
T ss_dssp             HTTBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSSBCCCTTCBCCTTCBEEECT
T ss_pred             HHHHHHHHHhhccccccHHHHHHHHHhcceecCCEEEEeccEeecCCCEEEecc
Confidence            358999997 46789999999999999999999999999999999999999984

>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=98.60  E-value=3.2e-08  Score=81.78  Aligned_cols=53  Identities=30%  Similarity=0.468  Sum_probs=48.9

Q ss_pred             chHHHHHHH-hCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeC
Q 026574          160 SLRVDALAS-AGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGK  212 (236)
Q Consensus       160 s~RLD~ils-~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~  212 (236)
                      ..|||+++- ..|..||..|++++.+|.|.|||+.++.|++.|++||+|+++-.
T Consensus        97 E~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i~vNg~~v~ips~~~~~gd~I~vrek  150 (208)
T d2uubd1          97 ESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK  150 (208)
T ss_dssp             HTBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGG
T ss_pred             HHHHHHHHHhccccccHHHHHHHHHhcCeecCCeEEEeccEEecCCceeehhhc
Confidence            589999975 56789999999999999999999999999999999999999754

>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=97.52  E-value=0.00018  Score=50.11  Aligned_cols=49  Identities=20%  Similarity=0.181  Sum_probs=41.0

Q ss_pred             hHHHHHH-HhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEE
Q 026574          161 LRVDALA-SAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSV  209 (236)
Q Consensus       161 ~RLD~il-s~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isv  209 (236)
                      +.|..++ ...+--|++.|+++|++|.|+|||..++++++.+..++.+-+
T Consensus        18 i~l~~ll~~~gl~~S~searRlI~~g~V~iN~~ki~d~~~~l~~~~~~il   67 (81)
T d1h3fa2          18 IWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRIL   67 (81)
T ss_dssp             EEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEE
T ss_pred             ccHHHHHHHcCCCcCHHHHHHHHHcCCEEECCEEecCccceecCCCeEEE
Confidence            4565555 456778999999999999999999999999999988876555

>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=97.34  E-value=0.00024  Score=51.26  Aligned_cols=55  Identities=27%  Similarity=0.353  Sum_probs=43.5

Q ss_pred             HHHHHHhCCCcCHHHHHHHHHCCcEEECCEEecCCCcccCCCCEEEEeeCCeEEEEEee
Q 026574          163 VDALASAGFKLSRSKLVNLISNGDVRVNWTTVTKNGTTLRTGDIVSVSGKGRIKIGEIN  221 (236)
Q Consensus       163 LD~ils~~~~~SR~~a~~lI~~G~V~VNg~~~~~~~~~v~~GD~Isvrg~Gr~~~~~~~  221 (236)
                      +|.++...+..|++.|+++|++|.|+||++.++++++.+.++|.+    .|++.+...|
T Consensus        35 ~~ll~~~~l~~S~seaRrlI~~ggv~iN~~kv~d~~~~l~~~~~~----~~~~~ll~~G   89 (99)
T d1jh3a_          35 VELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL----EGRFTVIRRG   89 (99)
T ss_dssp             HHHHHHHTSCCSHHHHHHHHHSTTEEETTEECCSTTTCCSSTTTS----SSSEEEEEET
T ss_pred             HHHHHHcCCCcCHHHHHHHHHcCCEEECCEEecCcccccCHhHcc----CCCEEEEEec
Confidence            555566777889999999999999999999999999999988742    3454444333