Citrus Sinensis ID: 028677

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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-----
Protein Sequence
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHccHHHHHcccccccHHHHHHHHHHHHHHHHccccEEEEccccHHHHHHHHHHHHcccccEEEEEcccccccEEEEEEEcccccccccccEEEEEEEccccccccccHHHHHHHHHccccccccccEEEEccEEEEEEEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHcHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccEEcccccHHHHHHHHHHHHcccccEEEEccccccHHHEEEEEccccccccccccEEEEEEEcccccccccHHHHHHHHHHccccHcHccEEEEEcccEEEEcEEEEEc
Coil and Loop (DISEMBL)
MAAISLAAPWILRRAVrtfslpqpllhlnpgscfhgthrpftfptslrhtASGIRHLIQAVKGNFDDLlkgvgdknAIEEVKHILEMARRASSRRevlhsdfltppvLKESMMALEKLADVKAvaqggypqaercrlsvghpealtsdpDIVAALSitgnfgfqpcshgdflGSILGTGIAREKIGDIIlqnkgflcsgclqytl
Flexible Loop (DISEMBL)
maaislaapwILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIIlqnkgflcsgclqytl
Low Complexity Region (SEG)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
Disordered region (IsUnstruct)
***ISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMA********VLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQY**
Disordered Region (DISOPRED)
****S*AAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
Disordered Region (DISEMBL)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
Disordered Region (DISPRO)
****SLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLCSGCLQYTL
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	205	2.2.26 [Sep-21-2011]
P71020	257	Putative RNA-binding prot	yes	no	0.512	0.408	0.313	3e-05

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

 Score = 48.5 bits (114), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 10/115 (8%)

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

Query: 139 VGHPEALT---SDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIIL 190
           +  PE +T   SD ++  A ++     F    H   LG+++G G+ R+K GDI+ 
Sbjct: 72  ILFPEYITPEESDFEL-QAFNVRYADKFVSVDHRSLLGALMGIGLKRQKFGDIVF 125

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	205
225461477	321	PREDICTED: putative RNA-binding protein	0.936	0.598	0.678	2e-69
9454543	773	Unknown protein [Arabidopsis thaliana]	0.951	0.252	0.636	1e-65
297847696	759	hypothetical protein ARALYDRAFT_314636 [	0.956	0.258	0.61	2e-65
359807576	324	uncharacterized protein LOC100793767 [Gl	0.917	0.580	0.631	3e-64
18404337	320	RNA-binding S4 domain-containing protein	0.926	0.593	0.639	1e-63
449457021	319	PREDICTED: putative RNA-binding protein	0.902	0.579	0.661	6e-63
255586534	231	RNA binding protein, putative [Ricinus c	0.697	0.619	0.797	6e-62
147798253	269	hypothetical protein VITISV_010260 [Viti	0.673	0.513	0.804	5e-60
357452969	325	hypothetical protein MTR_2g085340 [Medic	0.926	0.584	0.608	5e-60
217074322	325	unknown [Medicago truncatula]	0.926	0.584	0.608	7e-60

>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 =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 131/193 (67%), Positives = 154/193 (79%), Gaps = 1/193 (0%)

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

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

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

Query: 181 AREKIGDIILQNK 193
           AREK+GDIILQ +
Sbjct: 180 AREKLGDIILQGE 192

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9454543|gb|AAF87866.1|AC022520_10 Unknown protein [Arabidopsis thaliana]

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 128/201 (63%), Positives = 153/201 (76%), Gaps = 6/201 (2%)

Query: 1   MAAISLAAPW-ILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQ 59
           MA  SLA PW ILR A R+ +     LH N  +       P +FP  LR +A    +  +
Sbjct: 453 MAVTSLAPPWVILRLAFRSVA-ASSCLHTNQKTLITNLSIPTSFP--LRQSALRRCYSAE 509

Query: 60  AVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLA 119
           A+KG+ D LLKGVGD+   +EVK ILEMARRASS+REVLH+DFLTPP++KES+  LEK A
Sbjct: 510 AIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREVLHTDFLTPPIVKESVSLLEKFA 569

Query: 120 DVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTG 179
           DVK VAQGGYP+AERCR+S+GHP+ LTSDPDIVAALSITGNFGFQPCSHGDFLG+ILGTG
Sbjct: 570 DVKIVAQGGYPEAERCRISIGHPDVLTSDPDIVAALSITGNFGFQPCSHGDFLGAILGTG 629

Query: 180 IAREKIGDIILQ--NKGFLCS 198
           I+REK+GDI++Q  N G  CS
Sbjct: 630 ISREKLGDILIQVGNVGVTCS 650

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847696|ref|XP_002891729.1| hypothetical protein ARALYDRAFT_314636 [Arabidopsis lyrata subsp. lyrata] gi|297337571|gb|EFH67988.1| hypothetical protein ARALYDRAFT_314636 [Arabidopsis lyrata subsp. lyrata]

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 122/200 (61%), Positives = 151/200 (75%), Gaps = 4/200 (2%)

Query: 1   MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPFTFPTSLRHTASGIRHLIQA 60
           MA  SLA PWI+ R           LH N  +       P +FP  LRH+A    ++ +A
Sbjct: 439 MAVTSLAPPWIILRQTFRSVAASSYLHSNHKTLISNLSIPASFP--LRHSALRRCYIAEA 496

Query: 61  VKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLAD 120
           +KG+ D LLKGVGD+   +EVK ILEMARRA+S+REVLH+DFLTPP++KES++ L K AD
Sbjct: 497 IKGDVDFLLKGVGDQAVAKEVKQILEMARRAASKREVLHTDFLTPPIVKESVLVLGKFAD 556

Query: 121 VKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGI 180
           VK VAQGGYP+AERCR+S+GHP+ LT+DPDIVAALSITGNFGFQPCSHGDFLG+ILGTGI
Sbjct: 557 VKIVAQGGYPEAERCRISIGHPDVLTNDPDIVAALSITGNFGFQPCSHGDFLGAILGTGI 616

Query: 181 AREKIGDIILQ--NKGFLCS 198
           +REK+GDI++Q  N G  C+
Sbjct: 617 SREKLGDILIQVGNVGVTCT 636

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 125/198 (63%), Positives = 149/198 (75%), Gaps = 10/198 (5%)

Query: 1   MAAISLAAPWILRRAVRTFSLPQPLLHLNPGSCFHGTHRPF-----TFPTSLRHTASGIR 55
           + A S    W LRRA + F++     H+   +      R F     +  TSL   ASG+ 
Sbjct: 3   VTASSFGTTWCLRRAAQAFAISHS--HILRNNVKLSLQRNFCSHLLSVSTSL---ASGVS 57

Query: 56  HLIQAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMAL 115
             +QA+KG  D LLKGVG+++  +EVKHILEMARRAS +RE+LH+DFLTPPVLKESM  L
Sbjct: 58  QTVQALKGEVDLLLKGVGERSVTKEVKHILEMARRASLKREILHTDFLTPPVLKESMQVL 117

Query: 116 EKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSI 175
           EKLADVKA+AQGGYPQAERCR+SVGHPE LTSDPDI++ALSITGNF F+PCSHGDFLGSI
Sbjct: 118 EKLADVKAIAQGGYPQAERCRISVGHPEELTSDPDIISALSITGNFQFEPCSHGDFLGSI 177

Query: 176 LGTGIAREKIGDIILQNK 193
           LGTGI REK+GDIILQ +
Sbjct: 178 LGTGIVREKLGDIILQGE 195

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 124/194 (63%), Positives = 150/194 (77%), Gaps = 4/194 (2%)

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

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

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

Query: 180 IAREKIGDIILQNK 193
           I+REK+GDI++Q +
Sbjct: 178 ISREKLGDILIQEE 191

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  246 bits (627), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 127/192 (66%), Positives = 153/192 (79%), Gaps = 7/192 (3%)

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

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

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

Query: 182 REKIGDIILQNK 193
           REK+GDI+LQ +
Sbjct: 179 REKLGDIMLQEE 190

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  242 bits (618), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 114/143 (79%), Positives = 127/143 (88%)

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

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

Query: 171 FLGSILGTGIAREKIGDIILQNK 193
           FLGSILGTGI+REK+GDIILQ +
Sbjct: 133 FLGSILGTGISREKVGDIILQGE 155

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 125/138 (90%)

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

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

Query: 176 LGTGIAREKIGDIILQNK 193
           LGTGIAREK+GDIILQ +
Sbjct: 123 LGTGIAREKLGDIILQGE 140

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 121/199 (60%), Positives = 144/199 (72%), Gaps = 9/199 (4%)

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

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

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

Query: 175 ILGTGIAREKIGDIILQNK 193
           ILGTGIAREK+GDIILQ +
Sbjct: 178 ILGTGIAREKVGDIILQGE 196

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 =  235 bits (600), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 121/199 (60%), Positives = 144/199 (72%), Gaps = 9/199 (4%)

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

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

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

Query: 175 ILGTGIAREKIGDIILQNK 193
           ILGTGIAREK+GDIILQ +
Sbjct: 178 ILGTGIAREKVGDIILQGE 196

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	205
TAIR|locus:2037048	320	AT1G53120 [Arabidopsis thalian	0.931	0.596	0.642	6.4e-60
UNIPROTKB|P74082	259	sll1252 "Sll1252 protein" [Syn	0.585	0.463	0.451	2.6e-22
UNIPROTKB|Q3AAH6	246	CHY_2039 "S4 domain protein" [	0.536	0.447	0.401	6.9e-15
TIGR_CMR|CHY_2039	246	CHY_2039 "S4 domain protein" [	0.536	0.447	0.401	6.9e-15

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

 Score = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 126/196 (64%), Positives = 151/196 (77%)

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

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

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

Query:   180 IAREKIGDIILQN-KG 194
             I+REK+GDI++Q  KG
Sbjct:   178 ISREKLGDILIQEEKG 193

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 = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 56/124 (45%), Positives = 77/124 (62%)

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

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

Query:   187 DIIL 190
             DIIL
Sbjct:   124 DIIL 127

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

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

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 45/112 (40%), Positives = 62/112 (55%)

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

Query:   144 ALTSDPDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKG 194
                 D ++ +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL   G
Sbjct:    67 VFPEDVELNLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILIPNG 118

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 = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 45/112 (40%), Positives = 62/112 (55%)

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

Query:   144 ALTSDPDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKG 194
                 D ++ +  + ITGNF FQ  +H DFLG+ILGTGI REK+GD+IL   G
Sbjct:    67 VFPEDVELNLGFIEITGNFKFQAVTHRDFLGAILGTGIKREKVGDLILIPNG 118


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        0.323   0.138   0.419    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      205       205   0.00096  111 3  11 22  0.45    32
                                                     31  0.47    35


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:  4
  No. of states in DFA:  591 (63 KB)
  Total size of DFA:  159 KB (2095 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:  20.01u 0.17s 20.18t   Elapsed:  00:00:01
  Total cpu time:  20.01u 0.17s 20.18t   Elapsed:  00:00:01
  Start:  Sat May 11 06:53:58 2013   End:  Sat May 11 06:53:59 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	205
PLN00051	267	PLN00051, PLN00051, RNA-binding S4 domain-containi	2e-79
TIGR03069	257	TIGR03069, PS_II_S4, photosystem II S4 domain prot	7e-48
COG2302	257	COG2302, COG2302, Uncharacterized conserved protei	2e-20
PRK15378	564	PRK15378, PRK15378, inositol phosphate phosphatase	0.004

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

 Score =  237 bits (607), Expect = 2e-79
 Identities = 94/136 (69%), Positives = 107/136 (78%)

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

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

Query: 176 LGTGIAREKIGDIILQ 191
           LGTGI R+K+GDI++Q
Sbjct: 121 LGTGITRDKVGDILVQ 136

Length = 267

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

 Score =  157 bits (398), Expect = 7e-48
 Identities = 57/127 (44%), Positives = 78/127 (61%), Gaps = 6/127 (4%)

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

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

Query: 185 IGDIILQ 191
           IGDI + 
Sbjct: 121 IGDIWVL 127

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 = 85.8 bits (213), Expect = 2e-20
 Identities = 41/116 (35%), Positives = 60/116 (51%), Gaps = 4/116 (3%)

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

Query: 141 HPEALTSD-PDI-VAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKG 194
           +P     +  D  +  L I+    F   +H D LG++L  GI REK GDII++ +G
Sbjct: 74  YPAYYPLEESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEGEG 129

Length = 257

>gnl|CDD|237953 PRK15378, PRK15378, inositol phosphate phosphatase SopB; Provisional

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 28/122 (22%), Positives = 47/122 (38%), Gaps = 16/122 (13%)

Query: 52  SGIRHLIQAVKGNFDDLLKGVGDKNAIEEV--------KHILEMARRASSRREVLHS-DF 102
            GIRH + +     + LL+ VG +N  +EV          +L  A    +    L S   
Sbjct: 247 CGIRHGVLSPYHEKNPLLRAVGAENKAKEVLTAALFSKPELLNQALEGEAVSLKLVSVSL 306

Query: 103 LTPPVL--KESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTSDPDIVAALSITGN 160
           LT   +  KE  M  +++   +++ Q G     + R   G  + +    D+        N
Sbjct: 307 LTASNIFGKEGTMLEDQMRAWQSLTQPGKMIHLKIRNKDGDLQTVKVKLDVA-----AFN 361

Query: 161 FG 162
           FG
Sbjct: 362 FG 363

Length = 564

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	205
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	99.42
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.82
cd02644	67	R3H_jag R3H domain found in proteins homologous to	87.27

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

Probab=100.00  E-value=1e-36  Score=269.09  Aligned_cols=127  Identities=70%  Similarity=1.062  Sum_probs=114.7

Q ss_pred             HHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCCCC
Q 028677           66 DDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEAL  145 (205)
Q Consensus        66 ~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe~~  145 (205)
                      ..+++|+. ++++.++++++|++++|.+++.+++|+||||+||.+++++++++.++++.++|||++|||+|++|.|+++.
T Consensus        12 ~~i~~h~~-~ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~~   90 (267)
T PLN00051         12 SALLGVVD-PAHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEVL   90 (267)
T ss_pred             hHHHhhcC-hhhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHhc
Confidence            46889977 56699999999999999999999999999999999999999888899999999999999999998666554


Q ss_pred             CCCcCceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCC
Q 028677          146 TSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNK  193 (205)
Q Consensus       146 ~~~~~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~  193 (205)
                      +.++.+|++++|++++||.+++|||||||||||||+||+||||++.++
T Consensus        91 ~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~  138 (267)
T PLN00051         91 TSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGE  138 (267)
T ss_pred             cccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCC
Confidence            222357999999999999999999999999999999999999999654

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=100.00  E-value=1.8e-36  Score=265.87  Aligned_cols=128  Identities=40%  Similarity=0.637  Sum_probs=114.6

Q ss_pred             chHHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCC
Q 028677           64 NFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE  143 (205)
Q Consensus        64 ~~~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe  143 (205)
                      +++++++++.++|+   +++++||+++|.++|++++|+||||+|+.++++++++.+++++.++|||++|||+|+++.|++
T Consensus         2 ~~~~~~~~~~~~ee---~~~~~d~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~   78 (257)
T TIGR03069         2 PREELLKGANYPEE---LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD   78 (257)
T ss_pred             ChHHHHHhCCCHHH---HHHHHHHHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEeccc
Confidence            57889999886453   999999999999999999999999999999999998888999999999999999999986554


Q ss_pred             CCCCCc-CceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCe
Q 028677          144 ALTSDP-DIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKG  194 (205)
Q Consensus       144 ~~~~~~-~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~  194 (205)
                      +.++.+ .+|++++|+++++|.+++|||||||||||||+||++|||++.+++
T Consensus        79 ~~~~~~df~i~~l~i~~~~kF~~l~Hrd~LGalm~lGi~R~~iGDI~v~~~~  130 (257)
T TIGR03069        79 NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDR  130 (257)
T ss_pred             ccCCcccCceEEEEEEcccccCCCCHHHHHHHHHHcCCcHhhcCCEEEecCC
Confidence            443332 479999999999999999999999999999999999999887653

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=8.3e-34  Score=247.61  Aligned_cols=126  Identities=32%  Similarity=0.479  Sum_probs=114.8

Q ss_pred             HHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCCCCC
Q 028677           67 DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT  146 (205)
Q Consensus        67 ~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe~~~  146 (205)
                      .+.+|+. .|++++++|++||+++|+++|.+++||||||+|+.+++.+++ +.|+++.++||||+|||+|+++ +|+|++
T Consensus         3 ~iyqhf~-~eer~fidr~l~~~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l-~P~y~~   79 (257)
T COG2302           3 GIYQHFR-AEERPFIDRVLEWIKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLIL-YPAYYP   79 (257)
T ss_pred             cHhhhcC-chhHHHHHHHHHHHHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEE-cccccC
Confidence            4677766 789999999999999999999999999999999999988888 7899999999999999999988 565654


Q ss_pred             -CCcC-ceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCeE
Q 028677          147 -SDPD-IVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGF  195 (205)
Q Consensus       147 -~~~~-~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~~  195 (205)
                       ++.| ++++++|.+++||.+++|+||||+||||||+||++|||++.++++
T Consensus        80 ~~~~df~l~l~eI~y~~kF~~l~H~~~LGtll~lGikRe~~GDIiv~~~~a  130 (257)
T COG2302          80 LEESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEGEGA  130 (257)
T ss_pred             hhhcccceEEEEEEcccccccccHHHHHHHHHhccCcHHhhccEEEeCCee
Confidence             3334 599999999999999999999999999999999999999998874

>KOG4837 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.42  E-value=4.3e-14  Score=121.51  Aligned_cols=127  Identities=62%  Similarity=0.966  Sum_probs=114.1

Q ss_pred             HhhccchHHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEE
Q 028677           59 QAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS  138 (205)
Q Consensus        59 ~~~~~~~~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~  138 (205)
                      .++|++.+.+++++.+.-.-..+.++++++..+.......+|+||.|       +....++|+.....|||+.||++++-
T Consensus         7 ~~i~g~~~~~~~~vg~~~v~k~~~~~~~m~~~~~~~r~f~~t~~l~p-------sl~t~F~~v~s~~lpgl~~a~ec~~p   79 (248)
T KOG4837|consen    7 EAIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREFLHTDFLTP-------SLLTKFADVKSVALPGLPEAEECRIP   79 (248)
T ss_pred             hHhhhhhhhhhhcccHHHHHhhcHHHHHHHHHHHhhHHHHhhhhhCc-------hhhhccccchhhhcCCCCCChheEee
Confidence            78899999999999998888889999999999999999999999999       44457789999999999999999999


Q ss_pred             eeCCCCCCCCcCceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCeEEe
Q 028677          139 VGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLC  197 (205)
Q Consensus       139 i~~pe~~~~~~~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~~~~  197 (205)
                      |.+|+-.....+..+.++++.|+.|++.+|.||+|+++     ||+.|||.+..+.+.+
T Consensus        80 i~~~~~~ts~k~~kksl~~td~~dsd~esh~Df~~e~~-----~e~~~D~~Vvk~~~~i  133 (248)
T KOG4837|consen   80 IGHPDVLTSDKDIKKSLSITDNFDSDPESHGDFLGEIL-----REKLGDILVVKEKVLI  133 (248)
T ss_pred             ccCccccccchhHHHHhhhccccCCCcccchhHHHHHH-----HHhcCCceeeehhhhh
Confidence            99997776666668899999999999999999999998     9999999998876544

>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=93.82  E-value=0.057  Score=38.81  Aligned_cols=31  Identities=26%  Similarity=0.372  Sum_probs=24.0

Q ss_pred             CCCChhhHHHHHHcC-CCCCCCcccEEEeCCe
Q 028677          164 QPCSHGDFLGSILGT-GIAREKIGDIILQNKG  194 (205)
Q Consensus       164 ~~lsHRDfLGALmgL-GIkREkIGDIlv~~~~  194 (205)
                      +.++++|++|+|.+. ||+++.||+|-+.++.
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~   42 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDNF   42 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeeeE
Confidence            568999999999985 9999999999988875

; PDB: 2G0C_A 3MOJ_B.

>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ

Probab=87.27  E-value=5.4  Score=28.47  Aligned_cols=58  Identities=12%  Similarity=0.039  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677           78 IEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL  137 (205)
Q Consensus        78 ~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri  137 (205)
                      ..+.....++++++.+++.++.-+=+++.|..++-.++++++++.-...|  ++..|..+
T Consensus         6 ~~L~~~A~~~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G--~~~~R~vv   63 (67)
T cd02644           6 ETLIRLAERAAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEG--EGPYRRVV   63 (67)
T ss_pred             HHHHHHHHHHHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeec--CCCCeEEE
Confidence            34566777888889999999999999999999999999988889888887  33355554

SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.

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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	205
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	2e-29

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

 Score =  106 bits (266), Expect = 2e-29
 Identities = 21/122 (17%), Positives = 46/122 (37%), Gaps = 3/122 (2%)

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

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

Query: 193 KG 194
           + 
Sbjct: 127 ER 128

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	205
2fph_X	165	YLMH; division protein, bacteria, GRAM+, DNA bindi	100.0
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	84.56

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

Probab=100.00  E-value=1.2e-39  Score=267.63  Aligned_cols=125  Identities=14%  Similarity=0.204  Sum_probs=112.7

Q ss_pred             HhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCCCCCC
Q 028677           68 LLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALTS  147 (205)
Q Consensus        68 ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe~~~~  147 (205)
                      +++|+. ++++++++|++||+++|.++|++++|+||||+||+++++++++. ++++.++|||++|||+|++++|+++..+
T Consensus         2 ~~~hf~-~~e~~~i~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~i~~~~-~~~~~~~GGy~~AER~r~~i~p~~~~~~   79 (165)
T 2fph_X            2 IYQHFS-IEDRPFLDKGMEWIKKVEDSYAPFLTPFINPHQEKLLKILAKTY-GLACSSSGEFVSSEYVRVLLYPDYFQPE   79 (165)
T ss_dssp             CCCCCC-GGGHHHHHHHHHHHHHHHHHTSCEECCCBCHHHHHHHHHHHHHT-TCEEEEGGGTSCCSSBCEEEECTTCCCC
T ss_pred             hhhhcC-hhhHHHHHHHHHHHHHHHHhCCEEECCCCCHHHHHHHHHHHhcc-CcEEEEeCCCcHHheeEEEEecccccCc
Confidence            578877 56779999999999999999999999999999999999999886 7999999999999999998855444323


Q ss_pred             Cc-CceEEEEeecCCCCCCCChhhHHHHHHc-CCCCCCCcccEEEeCCe
Q 028677          148 DP-DIVAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQNKG  194 (205)
Q Consensus       148 ~~-~~I~~L~I~~n~kF~~lsHRDfLGALmg-LGIkREkIGDIlv~~~~  194 (205)
                      .. .+|++++|++|++|.+++|||||||||| |||+||++|||++++++
T Consensus        80 ~~d~~i~~l~i~~~~kF~~l~Hrd~LGaLm~~LGI~Re~iGDI~v~~~~  128 (165)
T 2fph_X           80 FSDFEISLQEIVYSNKFEYLTHAKILGTVINQLGIERKLFGDILVDEER  128 (165)
T ss_dssp             GGGGCEEEEEEESCCCCHHHHHHHHHSCSSSCCCCCGGGEEEEECSSSC
T ss_pred             ccCCceEEEEEecccccccCCHHHHHHHHHHhcCCCHhhcCCEEEECCE
Confidence            33 4699999999999999999999999999 99999999999999887

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

Probab=84.56  E-value=0.51  Score=32.36  Aligned_cols=31  Identities=26%  Similarity=0.514  Sum_probs=24.7

Q ss_pred             CCCChhhHHHHHHc-CCCCCCCcccEEEeCCe
Q 028677          164 QPCSHGDFLGSILG-TGIAREKIGDIILQNKG  194 (205)
Q Consensus       164 ~~lsHRDfLGALmg-LGIkREkIGDIlv~~~~  194 (205)
                      +.+..+|++|+|-+ .||.++.||+|-+.++.
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~~   42 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMDNA   42 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECSSC
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeCCc
Confidence            56789999999997 79999999999888775

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00