Citrus Sinensis ID: 024057

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270---
Protein Sequence
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
Secondary Structure (PSIPRED)
cccccccccccccccccEEEcccccccccccccccccHHHHHHccccccccccccccccccHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHcccccccccccccccHHHHHHHHHcHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccccccccccccHHHHHHHHHHHHHHHEEEEccccEEEHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEEccccccccccccccccHHHccccccHHccccccccHcccccccHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccEEcHHHHHHccccccccccEEEccHHHHHHHHHHcHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHccccccEEEEHHHHHHcccEEEEEEcccc
Coil and Loop (DISEMBL)
maveatssflscsskthflfnlrassspsswkKFTQSANFaaknrhvcrnerpnvscsAAAFAVQETLEKTRESVMASSAKEmmpkidksgrfcsPRAARELALLVVYAACLEGSDPIRLFEKRLnsrrepgyefdksslleynhmsfggppvttetVEEADELLRSDEEESAIEAEvlsappklVYSKLLLRFTRKLLVAVVDKWDAHVHiidkvvppiwkdqpagrILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
Flexible Loop (DISEMBL)
maveatssflscssKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMassakemmpkidksGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIeaevlsappklvYSKLLLRFTRKLLVAVVDKWDAHVHIIDkvvppiwkdqpAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
Low Complexity Region (SEG)
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
Disordered region (IsUnstruct)
***************THFLFNL************************VC***********AAF******************************FCSPRAARELALLVVYAACLEGSDPIRLFEK*******************************************************LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCF*****
Disordered Region (DISOPRED)
************SSKTHFLFNLRASSSPS************************************************************SGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEAD*************AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSST*
Disordered Region (DISEMBL)
**********SCSSKTHFLFNLRAS*********TQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
Disordered Region (DISPRO)
***********C*SKTHFLFNLRA***********QS***************PNVS*********************************SGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSS**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIVCFSSSTI
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

No hits with e-value below 0.001 by BLAST

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	273
225435806	288	PREDICTED: uncharacterized protein LOC10	0.827	0.784	0.680	1e-89
224073118	218	predicted protein [Populus trichocarpa]	0.637	0.798	0.890	1e-87
255564810	309	RNA binding protein, putative [Ricinus c	0.695	0.614	0.785	2e-86
297746508	218	unnamed protein product [Vitis vinifera]	0.637	0.798	0.856	8e-86
449463840	378	PREDICTED: uncharacterized protein LOC10	0.641	0.462	0.805	2e-81
18416739	301	antitermination NusB domain-containing p	0.633	0.574	0.815	1e-73
388512429	288	unknown [Lotus japonicus]	0.725	0.687	0.675	1e-73
2982469	286	putative protein [Arabidopsis thaliana]	0.670	0.639	0.777	1e-73
297799366	300	antitermination NusB domain-containing p	0.670	0.61	0.771	2e-73
363807164	289	uncharacterized protein LOC100809333 [Gl	0.772	0.730	0.622	4e-67

>gi|225435806|ref|XP_002285757.1| PREDICTED: uncharacterized protein LOC100265613 [Vitis vinifera]

 Score =  335 bits (860), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 168/247 (68%), Positives = 193/247 (78%), Gaps = 21/247 (8%)

Query: 15  KTHFLFNLRASSS-----PSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLE 69
           K HF+FN   SSS     P   K    S   ++          P  S   +A  V++ L+
Sbjct: 14  KPHFIFNFNHSSSCQFLTPLPTKLLINSKLLSS----------PRTSLRTSALTVEKPLD 63

Query: 70  KTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRR 129
           K       S  +EM+P+IDKSGRFCSPRAARELALL+ YAACLEGSDP+RLFE+R+N+RR
Sbjct: 64  K------PSEPREMLPRIDKSGRFCSPRAARELALLIAYAACLEGSDPVRLFERRMNARR 117

Query: 130 EPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSK 189
           EPGYEFDK SLLEYNHMSFGGPPVTTETVEEADELLR++E+ESAIEAEVLSAPPKLVY K
Sbjct: 118 EPGYEFDKDSLLEYNHMSFGGPPVTTETVEEADELLRNNEKESAIEAEVLSAPPKLVYGK 177

Query: 190 LLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRH 249
           L+LRFTRKLLVAVVDKW++HV +IDKV PP WK++PAGRILEL ILHLAMSEI V+GTRH
Sbjct: 178 LILRFTRKLLVAVVDKWNSHVLVIDKVAPPNWKNEPAGRILELCILHLAMSEIAVLGTRH 237

Query: 250 QIVINEA 256
           QIVINEA
Sbjct: 238 QIVINEA 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073118|ref|XP_002303980.1| predicted protein [Populus trichocarpa] gi|222841412|gb|EEE78959.1| predicted protein [Populus trichocarpa]

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 155/174 (89%), Positives = 167/174 (95%)

Query: 83  MMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLE 142
           MMPKIDKSGRFCSPRAARELALL++YAACLEGSDPIRLFEKR+N+RREPGYEFDK+SLLE
Sbjct: 1   MMPKIDKSGRFCSPRAARELALLIIYAACLEGSDPIRLFEKRMNARREPGYEFDKASLLE 60

Query: 143 YNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 202
           YNHMSFGGPPVTTETVEEADEL  SDE+ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV
Sbjct: 61  YNHMSFGGPPVTTETVEEADELQLSDEKESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 120

Query: 203 VDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA 256
           VDKWD+HV +IDKV PP WK++PAGRILE  ILH+AMSEITV+GTRHQIVINEA
Sbjct: 121 VDKWDSHVLVIDKVSPPNWKNEPAGRILEFCILHMAMSEITVLGTRHQIVINEA 174

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564810|ref|XP_002523399.1| RNA binding protein, putative [Ricinus communis] gi|223537349|gb|EEF38978.1| RNA binding protein, putative [Ricinus communis]

 Score =  325 bits (832), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 154/196 (78%), Positives = 173/196 (88%), Gaps = 6/196 (3%)

Query: 60  AAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIR 119
           +AF V+++ E +      +  KEMMPKIDKSGRFCSPRAARELAL+++YAACLEGSDP+R
Sbjct: 84  SAFVVEKSAENS------TKDKEMMPKIDKSGRFCSPRAARELALMMIYAACLEGSDPVR 137

Query: 120 LFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVL 179
           LFEKR+N+RRE GYEFDK+SLLEYNHMSFGGPPVTT+T+EEAD+LL SDE ESA+EAEVL
Sbjct: 138 LFEKRINARREAGYEFDKTSLLEYNHMSFGGPPVTTDTIEEADKLLSSDEIESALEAEVL 197

Query: 180 SAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAM 239
           SAPPKLVYSKLLLRFTRKLL AVV+KWD+HV IIDKV PP WK QP GRILE  ILHLAM
Sbjct: 198 SAPPKLVYSKLLLRFTRKLLAAVVEKWDSHVLIIDKVAPPNWKSQPGGRILEFCILHLAM 257

Query: 240 SEITVVGTRHQIVINE 255
           SEI VVGTRHQIVINE
Sbjct: 258 SEIAVVGTRHQIVINE 273

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746508|emb|CBI16564.3| unnamed protein product [Vitis vinifera]

 Score =  322 bits (826), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 149/174 (85%), Positives = 166/174 (95%)

Query: 83  MMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLE 142
           M+P+IDKSGRFCSPRAARELALL+ YAACLEGSDP+RLFE+R+N+RREPGYEFDK SLLE
Sbjct: 1   MLPRIDKSGRFCSPRAARELALLIAYAACLEGSDPVRLFERRMNARREPGYEFDKDSLLE 60

Query: 143 YNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAV 202
           YNHMSFGGPPVTTETVEEADELLR++E+ESAIEAEVLSAPPKLVY KL+LRFTRKLLVAV
Sbjct: 61  YNHMSFGGPPVTTETVEEADELLRNNEKESAIEAEVLSAPPKLVYGKLILRFTRKLLVAV 120

Query: 203 VDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA 256
           VDKW++HV +IDKV PP WK++PAGRILEL ILHLAMSEI V+GTRHQIVINEA
Sbjct: 121 VDKWNSHVLVIDKVAPPNWKNEPAGRILELCILHLAMSEIAVLGTRHQIVINEA 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463840|ref|XP_004149639.1| PREDICTED: uncharacterized protein LOC101216754 [Cucumis sativus]

 Score =  308 bits (789), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 141/175 (80%), Positives = 161/175 (92%)

Query: 82  EMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLL 141
           EM+PK+DKSG+FCSPRAARELAL +VYAACLEGSDP+RLFEKRLN+RRE GYEFDK+SL+
Sbjct: 166 EMIPKVDKSGKFCSPRAARELALSIVYAACLEGSDPVRLFEKRLNARRESGYEFDKTSLM 225

Query: 142 EYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVA 201
           EYNHMSFGGPPVT ET+EEADELLR DE +S IEAE+L+APPK+VYSKL+LRFTRKLLVA
Sbjct: 226 EYNHMSFGGPPVTVETIEEADELLRKDERDSTIEAEILAAPPKIVYSKLILRFTRKLLVA 285

Query: 202 VVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA 256
           V D WD+    I+KV+PP WK++PAGRILEL ILHLAMSEITV+GTRHQIVINEA
Sbjct: 286 VGDGWDSRALKIEKVIPPTWKNKPAGRILELCILHLAMSEITVIGTRHQIVINEA 340

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416739|ref|NP_567745.1| antitermination NusB domain-containing protein [Arabidopsis thaliana] gi|15450968|gb|AAK96755.1| putative protein [Arabidopsis thaliana] gi|30984514|gb|AAP42720.1| At4g26370 [Arabidopsis thaliana] gi|332659789|gb|AEE85189.1| antitermination NusB domain-containing protein [Arabidopsis thaliana]

 Score =  282 bits (722), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 141/173 (81%), Positives = 155/173 (89%)

Query: 84  MPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEY 143
           MPKIDKSGR  SPRAARELAL+++YAACLEGSDPIRLFEKR+N+RREPGYEFDKSSLLEY
Sbjct: 85  MPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPGYEFDKSSLLEY 144

Query: 144 NHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVV 203
           NHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+LRF +KLL AVV
Sbjct: 145 NHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVLRFAKKLLAAVV 204

Query: 204 DKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA 256
           DKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IVINEA
Sbjct: 205 DKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIVINEA 257

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512429|gb|AFK44276.1| unknown [Lotus japonicus]

 Score =  282 bits (721), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 135/200 (67%), Positives = 165/200 (82%), Gaps = 2/200 (1%)

Query: 57  CSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSD 116
           CS A+ AV   +++   S +       +PK+DK+GRFCSPRAARELAL ++YA+CLEG D
Sbjct: 58  CSVASSAV--AVDRDEASGLGKPDTVGLPKVDKTGRFCSPRAARELALSIIYASCLEGLD 115

Query: 117 PIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEA 176
           P+RLFEKRLN RRE GY+FD+  LLEYN MSF GPPVT ++ EEA+ELLR+ E+ES +EA
Sbjct: 116 PVRLFEKRLNERREAGYQFDQRKLLEYNPMSFAGPPVTVQSEEEANELLRNIEKESDLEA 175

Query: 177 EVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILH 236
           E+LSAPPKLVY+KL+LRFTRKLLVAV D WD+HV +I+KVVPP WKD+PAG+ILELSILH
Sbjct: 176 EILSAPPKLVYNKLILRFTRKLLVAVRDSWDSHVLVINKVVPPTWKDEPAGKILELSILH 235

Query: 237 LAMSEITVVGTRHQIVINEA 256
           LAMSE+T + T HQIVINEA
Sbjct: 236 LAMSEMTKLETIHQIVINEA 255

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2982469|emb|CAA18233.1| putative protein [Arabidopsis thaliana] gi|7269489|emb|CAB79492.1| putative protein [Arabidopsis thaliana]

 Score =  282 bits (721), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 143/184 (77%), Positives = 161/184 (87%), Gaps = 1/184 (0%)

Query: 74  SVMASSAKEM-MPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPG 132
           ++ A   K++ MPKIDKSGR  SPRAARELAL+++YAACLEGSDPIRLFEKR+N+RREPG
Sbjct: 59  TISAEEVKDVPMPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPG 118

Query: 133 YEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLL 192
           YEFDKSSLLEYNHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+L
Sbjct: 119 YEFDKSSLLEYNHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVL 178

Query: 193 RFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIV 252
           RF +KLL AVVDKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IV
Sbjct: 179 RFAKKLLAAVVDKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIV 238

Query: 253 INEA 256
           INEA
Sbjct: 239 INEA 242

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297799366|ref|XP_002867567.1| antitermination NusB domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297313403|gb|EFH43826.1| antitermination NusB domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 142/184 (77%), Positives = 161/184 (87%), Gaps = 1/184 (0%)

Query: 74  SVMASSAKEM-MPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPG 132
           ++ A   K++ MPKIDKSGR  SPRAARELAL+++YAACLEGSDPIRLFEKR+N+RREPG
Sbjct: 73  TISAEEVKDVPMPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPG 132

Query: 133 YEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLL 192
           YEFDK+SLLEYNHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+L
Sbjct: 133 YEFDKTSLLEYNHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVL 192

Query: 193 RFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIV 252
           RF +KLL AVVDKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IV
Sbjct: 193 RFAKKLLAAVVDKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIV 252

Query: 253 INEA 256
           INEA
Sbjct: 253 INEA 256

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807164|ref|NP_001242346.1| uncharacterized protein LOC100809333 [Glycine max] gi|255636077|gb|ACU18383.1| unknown [Glycine max]

 Score =  260 bits (665), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 140/225 (62%), Positives = 175/225 (77%), Gaps = 14/225 (6%)

Query: 34  FTQSANFAAKNRHVCRNERPNVSCSAAAFAVQE--TLEKTRESVMASSAKEMMPKIDKSG 91
           F+Q+A F+ +N         ++  S  A A  E   L K   +   +++   +PKIDK+G
Sbjct: 41  FSQNAAFSLRN---------SLRTSTFALAQHEAPVLGKPDNN---NNSSPYLPKIDKTG 88

Query: 92  RFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGP 151
           RFCSPRAARELAL ++YAACLEG DP+RLFEKR+N+RRE GY+F++  LLEYNHMSFGGP
Sbjct: 89  RFCSPRAARELALSIIYAACLEGMDPVRLFEKRMNARREAGYKFNEERLLEYNHMSFGGP 148

Query: 152 PVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVH 211
           PVT  + EEA+ELLR  EEESAIEAEVL+APPKLVY+KL+LRFT+KLLVAV D WD+HV 
Sbjct: 149 PVTVGSDEEANELLRHIEEESAIEAEVLTAPPKLVYNKLILRFTKKLLVAVRDTWDSHVL 208

Query: 212 IIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA 256
           +I+K+ P  WK++PA +ILELSILHLAMSE+ V+ TRHQIVINEA
Sbjct: 209 VINKIAPQNWKNEPAAKILELSILHLAMSEMEVLETRHQIVINEA 253

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	273
TAIR|locus:2131428	301	AT4G26370 [Arabidopsis thalian	0.926	0.840	0.616	1.9e-74

TAIR|locus:2131428 AT4G26370 [Arabidopsis thaliana (taxid:3702)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 159/258 (61%), Positives = 187/258 (72%)

Query:     3 VEATSSFLSCSSKTHFLFNLRASSSPSSWKK--FTQSANFAAKNRHVCRNERPNVSCSAA 60
             +E T S L   S ++  +   ++ SP S +   FT   +    N    R      S S+ 
Sbjct:     1 MEGTFSPLCLRSSSNLCY-FSSNVSPDSHRSIGFTLVDSLRPTNLVSLRTGNKRSSSSSL 59

Query:    61 AFAVQETLEKTRE-SVMASSAKEM-MPKIDKSGRFCSPRAARELALLVVYAACLEGSDPI 118
                +  T    R  ++ A   K++ MPKIDKSGR  SPRAARELAL+++YAACLEGSDPI
Sbjct:    60 RLFLSPTRSALRTPTISAEEVKDVPMPKIDKSGRLSSPRAARELALVILYAACLEGSDPI 119

Query:   119 RLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178
             RLFEKR+N+RREPGYEFDKSSLLEYNHMSFGGPPV TET EE DEL+R DE+ES IEAEV
Sbjct:   120 RLFEKRINARREPGYEFDKSSLLEYNHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEV 179

Query:   179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLA 238
             LSAPPKLVYSKL+LRF +KLL AVVDKWD+HV II+K+ PP WK  PAGRILE SILHLA
Sbjct:   180 LSAPPKLVYSKLVLRFAKKLLAAVVDKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLA 239

Query:   239 MSEITVVGTRHQIVINEA 256
             MSE+ V+ TRH IVINEA
Sbjct:   240 MSEVAVLETRHPIVINEA 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        0.319   0.130   0.375    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      273       273    0.0010  114 3  11 22  0.47    33
                                                     32  0.40    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  616 (65 KB)
  Total size of DFA:  195 KB (2110 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:  25.63u 0.09s 25.72t   Elapsed:  00:00:02
  Total cpu time:  25.63u 0.09s 25.72t   Elapsed:  00:00:02
  Start:  Sat May 11 08:56:46 2013   End:  Sat May 11 08:56:48 2013

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

---

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	273
cd00619	130	cd00619, Terminator_NusB, Transcription terminatio	3e-15
cd00447	129	cd00447, NusB_Sun, RNA binding domain of NusB (N p	1e-08

>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B)

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 34/104 (32%), Positives = 52/104 (50%), Gaps = 4/104 (3%)

Query: 155 TETVEEADELLRSDEEESAIEAEVLSAPPKLVY-SKLLLRFTRKLLVAVVDKWDAHVHII 213
               E A + L + E    I AEV+S    L Y SK +L F  KL+  V++  +    +I
Sbjct: 2   RRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELI 61

Query: 214 DKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 256
           +K +     D+    I+E +IL LA+ E+  +    H +VINEA
Sbjct: 62  EKHLRNWSLDR--LAIVERAILRLAVYELLFLPDVPHPVVINEA 103

NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. Length = 130

>gnl|CDD|238253 cd00447, NusB_Sun, RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins

 Score = 52.4 bits (126), Expect = 1e-08
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 5/102 (4%)

Query: 159 EEADELLRSDE-EESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVV 217
           E A + L   E         VLSA  KL  +K    F  +L+  V+        II  ++
Sbjct: 4   EIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLL 63

Query: 218 PPIWKDQPAGRILELSILHLAMSEI--TVVGTRHQIVINEAR 257
                D+     ++ +IL L + E+   +      + INEA 
Sbjct: 64  KKWLLDR--LDKVDRAILRLLLYELYQLLYDVPPPVAINEAV 103

This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB. Length = 129

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	273
COG0781	151	NusB Transcription termination factor [Transcripti	99.95
PF01029	134	NusB: NusB family; InterPro: IPR006027 This domain	99.9
PRK00202	137	nusB transcription antitermination protein NusB; R	99.86
cd00619	130	Terminator_NusB Transcription termination factor N	99.86
TIGR01951	129	nusB transcription antitermination factor NusB. A	99.83
cd00620	126	Methyltransferase_Sun N-terminal RNA binding domai	99.79
PRK09634	207	nusB transcription antitermination protein NusB; P	99.76
cd00447	129	NusB_Sun RNA binding domain of NusB (N protein-Uti	99.76
PRK10901	427	16S rRNA methyltransferase B; Provisional	99.71
PRK14901	434	16S rRNA methyltransferase B; Provisional	99.69
PRK14904	445	16S rRNA methyltransferase B; Provisional	99.69
PRK14902	444	16S rRNA methyltransferase B; Provisional	99.67
TIGR00563	426	rsmB ribosomal RNA small subunit methyltransferase	99.53
PRK14903	431	16S rRNA methyltransferase B; Provisional	99.4

>COG0781 NusB Transcription termination factor [Transcription]

Probab=99.95  E-value=1.4e-27  Score=202.73  Aligned_cols=119  Identities=26%  Similarity=0.265  Sum_probs=94.8

Q ss_pred             CCCChHHHHHHHHHHHHHHHhcCC-ChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhH
Q 024057           92 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE  170 (273)
Q Consensus        92 Rf~srR~ARElALQvLYa~dl~g~-dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~  170 (273)
                      +-.+||+||++|+|+||+|+++|. ++..+++....   .    |.+                          - +++..
T Consensus         6 ~~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~---~----~~~--------------------------~-d~~~~   51 (151)
T COG0781           6 PKLTRRQARELAVQALYQWELSGSVSAEDILEDIEE---E----FVE--------------------------N-ELDIE   51 (151)
T ss_pred             ccchHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHH---H----Hhh--------------------------c-ccchh
Confidence            346899999999999999999886 33344433211   0    100                          0 00000


Q ss_pred             HHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCc
Q 024057          171 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRH  249 (273)
Q Consensus       171 ~s~~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~  249 (273)
                                        ..+..|+.+|+.||.+|..++|+.|..++ .+|+++||+. |||+|||+|+|||+| .|||+
T Consensus        52 ------------------~~~~~~~~~lv~gv~~~~~~iD~~I~~~L-~~w~~~rL~~-verAILRla~yEl~~~~dvP~  111 (151)
T COG0781          52 ------------------LADSEYFRSLVKGVLENQEELDELISPHL-KKWSLERLDL-VERAILRLALYELLFRDDVPY  111 (151)
T ss_pred             ------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCCHHHhhH-HHHHHHHHHHHHHHhcCCCCC
Confidence                              13579999999999999999999999999 4699999998 799999999999999 56999


Q ss_pred             cchHhHHHHHHHHHh
Q 024057          250 QIVINEARLTLHFLF  264 (273)
Q Consensus       250 kVaINEAVELAK~f~  264 (273)
                      +|+|||||||||+|+
T Consensus       112 ~VvInEaielaK~f~  126 (151)
T COG0781         112 KVVINEAIELAKKFS  126 (151)
T ss_pred             cchHHHHHHHHHHhC
Confidence            999999999999996

>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site

Probab=99.90  E-value=2.4e-23  Score=166.71  Aligned_cols=74  Identities=22%  Similarity=0.224  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHhHHHHHHHHHh
Q 024057          189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEARLTLHFLF  264 (273)
Q Consensus       189 ~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaINEAVELAK~f~  264 (273)
                      ..+..|+++|+.|+..++..+|..|+++ .++|+++||+. ++++|||||+|||+|. ++|++|+|||||||||+|+
T Consensus        43 ~~d~~~~~~lv~gv~~~~~~ld~~i~~~-~~~~~~~rl~~-~~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~  117 (134)
T PF01029_consen   43 EEDRAFARELVYGVLRNKEELDALISKL-LKNWPLERLPP-VDRAILRLAIYELLFLDDIPPHVAINEAVELAKKYG  117 (134)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHT-STSSTGGGSGH-HHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-hccCCccccCH-HHHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhC
Confidence            4578999999999999999999999996 48999999998 7999999999999996 9999999999999999994

Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....

>PRK00202 nusB transcription antitermination protein NusB; Reviewed

Probab=99.86  E-value=2.5e-21  Score=157.19  Aligned_cols=111  Identities=27%  Similarity=0.312  Sum_probs=97.0

Q ss_pred             ChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHH
Q 024057           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (273)
Q Consensus        95 srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~  174 (273)
                      +||.+|++|+|+||++...|....+++++.+.   ..  +.                                       
T Consensus         2 ~r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~~--~~---------------------------------------   37 (137)
T PRK00202          2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLL---EE--QY---------------------------------------   37 (137)
T ss_pred             chHHHHHHHHHHHHHHHccCCCHHHHHHHHHH---hc--cc---------------------------------------
Confidence            68999999999999999999998888887443   00  00                                       


Q ss_pred             HHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchH
Q 024057          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI  253 (273)
Q Consensus       175 ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaI  253 (273)
                                   +..+..|+++|+.|+..++..+|..|++.+ ++|+.++|+. ++++|||+|+|||+|. ++|+.++|
T Consensus        38 -------------~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l-~~~~~~~l~~-~~~~iLr~a~~Ell~~~~~p~~~vi  102 (137)
T PRK00202         38 -------------DKADPAYFRSLVRGVVENQAELDELISPYL-KDWTLERLDP-VERAILRLALYELLFRDDVPYKVVI  102 (137)
T ss_pred             -------------chhhHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchH
Confidence                         123579999999999999999999999998 5699999998 7999999999999996 89999999


Q ss_pred             hHHHHHHHHHh
Q 024057          254 NEARLTLHFLF  264 (273)
Q Consensus       254 NEAVELAK~f~  264 (273)
                      ||||||||+|+
T Consensus       103 nEaV~lak~~~  113 (137)
T PRK00202        103 NEAIELAKKFG  113 (137)
T ss_pred             HHHHHHHHHHC
Confidence            99999999875

>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B)

Probab=99.86  E-value=2.6e-21  Score=154.95  Aligned_cols=110  Identities=28%  Similarity=0.255  Sum_probs=94.5

Q ss_pred             hHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHH
Q 024057           96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE  175 (273)
Q Consensus        96 rR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~e  175 (273)
                      ||.+|+.|+|+||++...|.+..+++++.+.   .    .+                                       
T Consensus         1 r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~----~~---------------------------------------   34 (130)
T cd00619           1 RRRARELAVQALYAWELAPEILAEVVSLLEL---L----QY---------------------------------------   34 (130)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----cc---------------------------------------
Confidence            6789999999999999999888777765332   0    00                                       


Q ss_pred             HhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccC-CCccchHh
Q 024057          176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVIN  254 (273)
Q Consensus       176 a~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~D-vP~kVaIN  254 (273)
                           .      ++.+..|+.+|+.|+..++..+|..|++++ ++|+.++++. ++++|||+|+|||+|.+ +|+.|+||
T Consensus        35 -----~------~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l-~~~~~~~l~~-~~~~iLria~~el~~~~~~p~~~vin  101 (130)
T cd00619          35 -----K------SKKVLPFALKLVRGVLENIEEIDELIEKHL-RNWSLDRLAI-VERAILRLAVYELLFLPDVPHPVVIN  101 (130)
T ss_pred             -----c------chhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchHH
Confidence                 0      022579999999999999999999999998 6999889998 69999999999999965 99999999


Q ss_pred             HHHHHHHHHh
Q 024057          255 EARLTLHFLF  264 (273)
Q Consensus       255 EAVELAK~f~  264 (273)
                      |||||||+|+
T Consensus       102 EaV~lak~~~  111 (130)
T cd00619         102 EAIELAKRFG  111 (130)
T ss_pred             HHHHHHHHHC
Confidence            9999999985

NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.

>TIGR01951 nusB transcription antitermination factor NusB

Probab=99.83  E-value=2.9e-20  Score=148.42  Aligned_cols=110  Identities=25%  Similarity=0.258  Sum_probs=95.1

Q ss_pred             hHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHH
Q 024057           96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE  175 (273)
Q Consensus        96 rR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~e  175 (273)
                      ||.+|+.|+|+||++...|....+++++.+.   .    +                                        
T Consensus         1 ~~~~R~~a~~~l~~~~~~~~~~~~~l~~~~~---~----~----------------------------------------   33 (129)
T TIGR01951         1 RRKARELALQALYQWELSGNDVEEIIEEFLE---E----R----------------------------------------   33 (129)
T ss_pred             ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHH---h----c----------------------------------------
Confidence            5789999999999999999988888876432   0    0                                        


Q ss_pred             HhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHh
Q 024057          176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVIN  254 (273)
Q Consensus       176 a~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaIN  254 (273)
                          ..+      ..+..|+++|+.|+..++..+|..|+++++ +|+.++++. ++++|||+|+|||+|. ++|+.++||
T Consensus        34 ----~l~------~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~-~~~~iLr~a~~el~~~~~~p~~avin  101 (129)
T TIGR01951        34 ----ELD------EEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDP-VDRAILRLAAYELLYRPDVPYKVVIN  101 (129)
T ss_pred             ----ccc------hhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchHH
Confidence                001      225799999999999999999999999985 899999998 6999999999999996 799999999


Q ss_pred             HHHHHHHHHh
Q 024057          255 EARLTLHFLF  264 (273)
Q Consensus       255 EAVELAK~f~  264 (273)
                      |||||||+++
T Consensus       102 eaV~lak~~~  111 (129)
T TIGR01951       102 EAVELAKKFG  111 (129)
T ss_pred             HHHHHHHHHC
Confidence            9999999975

A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.

>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun

Probab=99.79  E-value=9.3e-19  Score=140.42  Aligned_cols=105  Identities=10%  Similarity=0.014  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057           99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV  178 (273)
Q Consensus        99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v  178 (273)
                      +|+.|+|+||++...|....+++.+.+.   .    .                                           
T Consensus         3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~---~----~-------------------------------------------   32 (126)
T cd00620           3 ARSTAAEVLRDVLQRGASLNAVLSALQK---K----D-------------------------------------------   32 (126)
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHH---h----c-------------------------------------------
Confidence            6999999999999999988888876332   0    0                                           


Q ss_pred             hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHHH
Q 024057          179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARL  258 (273)
Q Consensus       179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAVE  258 (273)
                        .+      ..+..|+.+|+.|+..++.++|..|++++ ..|. .+++. ++++|||+|+|||+|.++|+.++||||||
T Consensus        33 --~~------~~d~~~~~~lv~g~~r~~~~ld~~i~~~l-~~~~-~~~~~-~~~~iLr~a~~el~~~~~p~~avvneaVe  101 (126)
T cd00620          33 --KS------DRDRGLATELVYGTLRWLALLDWIINPLL-KKPD-VGKDP-DVRNLLRLGLYQLLYLDVPPHAAVDETVE  101 (126)
T ss_pred             --CC------HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-CCCc-cccCH-HHHHHHHHHHHHHHhcCCCchHHHHHHHH
Confidence              01      12579999999999999999999999998 3444 48888 69999999999999977999999999999


Q ss_pred             HHHHHh
Q 024057          259 TLHFLF  264 (273)
Q Consensus       259 LAK~f~  264 (273)
                      |||+++
T Consensus       102 lak~~~  107 (126)
T cd00620         102 IAKIRK  107 (126)
T ss_pred             HHHHhC
Confidence            999985

The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.

>PRK09634 nusB transcription antitermination protein NusB; Provisional

Probab=99.76  E-value=1.2e-18  Score=155.09  Aligned_cols=74  Identities=23%  Similarity=0.276  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHHHHHHHHh
Q 024057          189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLF  264 (273)
Q Consensus       189 ~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAVELAK~f~  264 (273)
                      +.+..|+.+|+.||..++..+|..|++++ ++|++.|+++ +|++|||||+|||+|.++|+.|+|||||||||+|+
T Consensus       110 ~~~r~~a~~Lv~gvlr~~~~LD~iI~~~l-~~W~l~rL~~-idr~ILRlavyELl~l~~P~~vaINEAVeLAK~~~  183 (207)
T PRK09634        110 EEVREYALERIGAVIRNRKEIDQLLDTVM-VGWQLKRLPR-IDRDILRLAVVEILFLNTPAAVAINEAVELAKRYS  183 (207)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-ccccccCCCH-HHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHhC
Confidence            55789999999999999999999999998 7999999999 69999999999999989999999999999999986

>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins

Probab=99.76  E-value=8.3e-18  Score=133.65  Aligned_cols=72  Identities=19%  Similarity=0.212  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc--CCCccchHhHHHHHHHHHh
Q 024057          191 LLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV--GTRHQIVINEARLTLHFLF  264 (273)
Q Consensus       191 ~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~--DvP~kVaINEAVELAK~f~  264 (273)
                      +..|+.+|+.|+.+++..+|..|++++ ++|..+||+. +|+.||||+++||.+.  ++|+.++|||||||||+++
T Consensus        37 d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~-~~~~il~l~~~el~~~~~~~p~~~vineaVelak~~~  110 (129)
T cd00447          37 DRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDK-VDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFG  110 (129)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhH-HHHHHHHHHHHHHHhCcCCCCchhHHHHHHHHHHHHC
Confidence            579999999999999999999999998 7999999999 6999999999999974  6899999999999999985

This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the

>PRK10901 16S rRNA methyltransferase B; Provisional

Probab=99.71  E-value=6.2e-17  Score=153.27  Aligned_cols=105  Identities=11%  Similarity=0.083  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057           98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE  177 (273)
Q Consensus        98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~  177 (273)
                      .+|+.|+|+||++..+|.....++.+.++   .    +                                          
T Consensus         3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~----l------------------------------------------   33 (427)
T PRK10901          3 NLRALAAAAILQVVDQGQSLSAALPALQQ---K----V------------------------------------------   33 (427)
T ss_pred             hHHHHHHHHHHHHHHcCCcHHHHHHHHHh---h----C------------------------------------------
Confidence            47999999999999999988887766221   0    0                                          


Q ss_pred             hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHH
Q 024057          178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAR  257 (273)
Q Consensus       178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAV  257 (273)
                                .+.+..|+.+||.||+.++..+|.+|++++  +|+.++++. ++|+|||||+|||+|.++|+.++|||||
T Consensus        34 ----------~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~-~~r~iLrla~yell~~~iP~~a~vneaV  100 (427)
T PRK10901         34 ----------SDKDRALLQELCYGVLRRLPRLEWLIAQLL--AKPLKGKQR-IVHALLLVGLYQLLYTRIPAHAAVDETV  100 (427)
T ss_pred             ----------CHHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCH-HHHHHHHHHHHHHhccCCCcchHHHHHH
Confidence                      123579999999999999999999999987  678889998 7999999999999997799999999999


Q ss_pred             HHHHHHh
Q 024057          258 LTLHFLF  264 (273)
Q Consensus       258 ELAK~f~  264 (273)
                      ||||+|+
T Consensus       101 elak~~~  107 (427)
T PRK10901        101 EAAKALK  107 (427)
T ss_pred             HHHHhcC
Confidence            9999985

>PRK14901 16S rRNA methyltransferase B; Provisional

Probab=99.69  E-value=1.6e-16  Score=150.84  Aligned_cols=105  Identities=15%  Similarity=0.062  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057           99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV  178 (273)
Q Consensus        99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v  178 (273)
                      +|+.|+|+||+++. |.+..+++++.+...+     +                                           
T Consensus         3 ~R~~A~~~L~~i~~-~~~~~~~l~~~~~~~~-----l-------------------------------------------   33 (434)
T PRK14901          3 ARQLAWEILQAVAR-GAYADVALERVLRKYP-----L-------------------------------------------   33 (434)
T ss_pred             HHHHHHHHHHHHHc-CCchHHHHHHHHHhcC-----C-------------------------------------------
Confidence            79999999999988 7777777776443000     1                                           


Q ss_pred             hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHhHHH
Q 024057          179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAR  257 (273)
Q Consensus       179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaINEAV  257 (273)
                               +..+..|+.+||.||+.++..+|..|++++  +|...+|+. ++|+|||||+|||+|. ++|+.++|||||
T Consensus        34 ---------~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~~l~~-~~r~iLrla~yel~~~~~~p~~aavneaV  101 (434)
T PRK14901         34 ---------SGADRALVTELVYGCIRRRRTLDAWIDQLG--KKPAHKQPP-DLRWLLHLGLYQLRYMDRIPASAAVNTTV  101 (434)
T ss_pred             ---------ChhHHHHHHHHHHHHHHhHHHHHHHHHHhc--CCChhhcCH-HHHHHHHHHHHHHHhCccCCcHHHHHHHH
Confidence                     122579999999999999999999999985  566678998 7999999999999994 689999999999


Q ss_pred             HHHHHHh
Q 024057          258 LTLHFLF  264 (273)
Q Consensus       258 ELAK~f~  264 (273)
                      ||||+|+
T Consensus       102 elak~~~  108 (434)
T PRK14901        102 ELAKQNG  108 (434)
T ss_pred             HHHHHcC
Confidence            9999985

>PRK14904 16S rRNA methyltransferase B; Provisional

Probab=99.69  E-value=1.5e-16  Score=151.43  Aligned_cols=107  Identities=18%  Similarity=0.091  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057           98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE  177 (273)
Q Consensus        98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~  177 (273)
                      .+|++|+|+||+++..|.....++.+.+.   .    +                                          
T Consensus         3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~---~----~------------------------------------------   33 (445)
T PRK14904          3 TARELALQVLQELETGERKSDTLLHRMLE---R----S------------------------------------------   33 (445)
T ss_pred             hHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----c------------------------------------------
Confidence            58999999999999999888888876442   0    0                                          


Q ss_pred             hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHH
Q 024057          178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEA  256 (273)
Q Consensus       178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEA  256 (273)
                         .     +++.+..|+.+||.||+.++..+|..|++++  +|+..+|+. ++|+|||+|+|||+| .++|+.|+||||
T Consensus        34 ---~-----l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~rl~~-~~r~iLrla~~ell~~~~~p~~a~vnea  102 (445)
T PRK14904         34 ---S-----LERNDRALATELVNGVLRYRLQLDFIISRFY--HHDLEKAAP-VLKNILRLGVYQLLFLDRVPRWAAVNEC  102 (445)
T ss_pred             ---C-----CChHHHHHHHHHHHHHHHHHHHHHHHHHHHc--CCChhhCCH-HHHHHHHHHHHHHHhCCCCCCeeeHHHH
Confidence               0     0123579999999999999999999999997  588889998 799999999999999 568999999999


Q ss_pred             HHHHHHHh
Q 024057          257 RLTLHFLF  264 (273)
Q Consensus       257 VELAK~f~  264 (273)
                      |||||+|+
T Consensus       103 Velak~~~  110 (445)
T PRK14904        103 VKLARKYK  110 (445)
T ss_pred             HHHHHHhC
Confidence            99999984

>PRK14902 16S rRNA methyltransferase B; Provisional

Probab=99.67  E-value=3.7e-16  Score=148.24  Aligned_cols=106  Identities=15%  Similarity=0.065  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057           98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE  177 (273)
Q Consensus        98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~  177 (273)
                      .|||.|+|+||+++..|.++.+++++.+.   .    .                                          
T Consensus         4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~---~----~------------------------------------------   34 (444)
T PRK14902          4 NARELALEVLIKVENNGAYSNIALNKVLK---K----S------------------------------------------   34 (444)
T ss_pred             cHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----c------------------------------------------
Confidence            68999999999999999999888887543   1    0                                          


Q ss_pred             hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHH
Q 024057          178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEA  256 (273)
Q Consensus       178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEA  256 (273)
                         .     .+..+..|+.+||.|++.++..+|.+|++++. +  .+||+. ++|+|||||+|||+| +++|+.|+||||
T Consensus        35 ---~-----l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~-~--~~~l~~-~~r~iLrla~~el~~~~~~p~~~~inea  102 (444)
T PRK14902         35 ---E-----LSDKDKALLTELVYGTIQRKLTLDYYLAPFIK-K--RKKLDP-WVRNLLRMSLYQLLYLDKVPDHAAVNEA  102 (444)
T ss_pred             ---C-----CChHHHHHHHHHHHHHHHhHHHHHHHHHHHhh-h--hhhCCH-HHHHHHHHHHHHHHhccCCCCceeHHHH
Confidence               0     01235799999999999999999999999983 3  778998 799999999999998 569999999999


Q ss_pred             HHHHHHHh
Q 024057          257 RLTLHFLF  264 (273)
Q Consensus       257 VELAK~f~  264 (273)
                      |||||+|+
T Consensus       103 v~lak~~~  110 (444)
T PRK14902        103 VEIAKKRG  110 (444)
T ss_pred             HHHHHHhC
Confidence            99999984

>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB

Probab=99.53  E-value=3.2e-14  Score=134.64  Aligned_cols=70  Identities=11%  Similarity=-0.038  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHHHHHHHHHh
Q 024057          191 LLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEARLTLHFLF  264 (273)
Q Consensus       191 ~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEAVELAK~f~  264 (273)
                      +.+|+++||.||++++.++|..|++++  +|+..+++. +.+ |||+++||+++ .++|+.|+|||||||||+|+
T Consensus        32 d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~-~~~-~L~~~~~e~l~~~~~p~~aainEaVelaK~~~  102 (426)
T TIGR00563        32 DRALLQELCFGVLRTLSQLDWLIKKLM--DRPMKGKPR-TVH-YLILVGLYQLLYTRIPAHAAVAETVEGAKAIK  102 (426)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCH-HHH-HHHHHHHHHHhcCCCCCEehHHHHHHHHHhcC
Confidence            579999999999999999999999986  577777886 455 99999999986 68999999999999999985

The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.

>PRK14903 16S rRNA methyltransferase B; Provisional

Probab=99.40  E-value=2e-12  Score=123.85  Aligned_cols=101  Identities=14%  Similarity=0.002  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057           99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV  178 (273)
Q Consensus        99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v  178 (273)
                      +|++|+.+|+++.-.|.....++++.+.   .                                                
T Consensus         5 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~---~------------------------------------------------   33 (431)
T PRK14903          5 VRLLAYRLLRKYEKEKFIFREDVDSVLS---F------------------------------------------------   33 (431)
T ss_pred             HHHHHHHHHHHHHhCCCchHHHHHHHHH---h------------------------------------------------
Confidence            6999999999998888766666654221   0                                                


Q ss_pred             hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccC-CCccchHhHHH
Q 024057          179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEAR  257 (273)
Q Consensus       179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~D-vP~kVaINEAV  257 (273)
                              ++..+..|+.+||.||.+++..+|..|++++ .+|   +|+. ++|+|||+|+|||+|.+ +|+.++|||||
T Consensus        34 --------l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~-~~~---~l~~-~~r~iLr~~~yel~~~~~~p~~aavneaV  100 (431)
T PRK14903         34 --------LDDKDRRFFKELVWGVVRKEELLDWYINQLL-KKK---DIPP-AVRVALRMGAYQLLFMNSVPDYAAVSETV  100 (431)
T ss_pred             --------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC---CCCH-HHHHHHHHHHHHHHhccCCCcceeHHHHH
Confidence                    1134679999999999999999999999987 677   5887 69999999999999965 69999999999


Q ss_pred             HHHHHH
Q 024057          258 LTLHFL  263 (273)
Q Consensus       258 ELAK~f  263 (273)
                      ||||+.
T Consensus       101 ~lak~~  106 (431)
T PRK14903        101 KLVKNE  106 (431)
T ss_pred             HHHhcc
Confidence            999975

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	273
1tzv_A	142	NUSB protein, N utilization substance protein B ho	99.92
3r2d_A	149	Protein NUSB, N utilization substance protein B; c	99.92
3d3b_A	141	Protein NUSB, N utilization substance protein B; N	99.92
1eyv_A	156	NUSB protein, N-utilizing substance protein B homo	99.91
2yxl_A	450	PH0851 protein, 450AA long hypothetical FMU protei	99.7
1sqg_A	429	SUN protein, FMU protein; rossmann-fold, mixed bet	99.68

>1tzv_A NUSB protein, N utilization substance protein B homolog; RNA-protein interaction, transcriptional antitermination, transcription regulation; 1.35A {Thermotoga maritima} SCOP: a.79.1.1 PDB: 1tzu_A 1tzt_A 1tzw_A 1tzx_A*

Probab=99.92  E-value=3e-25  Score=180.90  Aligned_cols=111  Identities=14%  Similarity=0.182  Sum_probs=96.2

Q ss_pred             CChHHHHHHHHHHHHHHHhcCC-ChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHH
Q 024057           94 CSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEES  172 (273)
Q Consensus        94 ~srR~ARElALQvLYa~dl~g~-dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s  172 (273)
                      -+||.||+.|+|+||+++..|. +...++...++      ...                                     
T Consensus         3 ~~r~~aR~~A~~~L~~~~~~~~~~~~~~l~~~~~------~~l-------------------------------------   39 (142)
T 1tzv_A            3 TPRRRMRLAVFKALFQHEFRRDEDLEQILEEILD------ETY-------------------------------------   39 (142)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCTTSCHHHHHHHHCC------TTS-------------------------------------
T ss_pred             CchHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH------hcC-------------------------------------
Confidence            3689999999999999999998 88777765221      000                                     


Q ss_pred             HHHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccc
Q 024057          173 AIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQI  251 (273)
Q Consensus       173 ~~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kV  251 (273)
                                     ++.+..|+.+|+.||..++.++|..|++++ ++|+++||+. +|++|||||+|||+| +++|+.|
T Consensus        40 ---------------~~~d~~~~~~Lv~gvl~~~~~lD~~I~~~l-~~w~l~rl~~-~~r~iLrla~yEl~~~~~iP~~v  102 (142)
T 1tzv_A           40 ---------------DKKAKEDARRYIRGIKENLSMIDDLISRYL-EKWSLNRLSV-VDRNVLRLATYELLFEKDIPIEV  102 (142)
T ss_dssp             ---------------CHHHHHHHHHHHHHHHHTHHHHHHHHHTTC-SSSCGGGSCH-HHHHHHHHHHHHHHHCTTSCHHH
T ss_pred             ---------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCChHHCCH-HHHHHHHHHHHHHHhcCCCCchh
Confidence                           123679999999999999999999999998 5899999998 799999999999999 5899999


Q ss_pred             hHhHHHHHHHHHh
Q 024057          252 VINEARLTLHFLF  264 (273)
Q Consensus       252 aINEAVELAK~f~  264 (273)
                      +|||||||||+|+
T Consensus       103 aInEaVelaK~~~  115 (142)
T 1tzv_A          103 TIDEAIEIAKRYG  115 (142)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHC
Confidence            9999999999985

>3r2d_A Protein NUSB, N utilization substance protein B; cross species NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB: 2jr0_A 3r2c_A* 4eya_A

Probab=99.92  E-value=4.9e-25  Score=182.44  Aligned_cols=113  Identities=24%  Similarity=0.306  Sum_probs=95.8

Q ss_pred             CChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHH
Q 024057           94 CSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESA  173 (273)
Q Consensus        94 ~srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~  173 (273)
                      .+||.||++|+|+||+++..|.++.+++++.++   .      .                                    
T Consensus         3 ~~R~~aR~~A~q~L~~~~~~~~~~~~~l~~~~~---~------~------------------------------------   37 (149)
T 3r2d_A            3 RYRKGARDTAFLVLYRWDLRGENPGELFKEVVE---E------K------------------------------------   37 (149)
T ss_dssp             THHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH---H------H------------------------------------
T ss_pred             ccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h------c------------------------------------
Confidence            368999999999999999999999988877443   0      0                                    


Q ss_pred             HHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccch
Q 024057          174 IEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIV  252 (273)
Q Consensus       174 ~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVa  252 (273)
                            ...     +..+..|+.+|+.||+.++.++|..|++++ ++|+++||+. +|++|||||+|||+| +++|+.|+
T Consensus        38 ------~~~-----~~~dr~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~~~rl~~-~~r~iLrla~yEl~~~~~iP~~va  104 (149)
T 3r2d_A           38 ------NIK-----NKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-KGWSIDRLGY-VERNALRLGVAELIFLKSKEPGRV  104 (149)
T ss_dssp             ------TCC-----CHHHHHHHHHHHHHHHHTHHHHHHHHHTTC----CGGGSCH-HHHHHHHHHHHHHTTSCCSCHHHH
T ss_pred             ------ccC-----CHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCccccCH-HHHHHHHHHHHHHHHcCCCCCeeh
Confidence                  000     123679999999999999999999999998 7999999998 799999999999999 58999999


Q ss_pred             HhHHHHHHHHHh
Q 024057          253 INEARLTLHFLF  264 (273)
Q Consensus       253 INEAVELAK~f~  264 (273)
                      |||||||||+|+
T Consensus       105 InEaVelaK~~~  116 (149)
T 3r2d_A          105 FIDIVDLVKKYA  116 (149)
T ss_dssp             HHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhC
Confidence            999999999985

>3d3b_A Protein NUSB, N utilization substance protein B; NUSB, NUSE, NUT site, phage lambda, lambdan antitermina antitermination; HET: NHE; 1.30A {Escherichia coli} PDB: 3d3c_A 3imq_A 1ey1_A

Probab=99.92  E-value=6.6e-25  Score=178.74  Aligned_cols=110  Identities=21%  Similarity=0.196  Sum_probs=94.7

Q ss_pred             ChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHH
Q 024057           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (273)
Q Consensus        95 srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~  174 (273)
                      +||.||++|+|+||++++.|.+..+++...++   +    .                                       
T Consensus         7 ~R~~aR~~A~~~L~~~~~~~~~~~~~~~~~~~---~----~---------------------------------------   40 (141)
T 3d3b_A            7 ARRRARECAVQALYSWQLSQNDIADVEYQFLA---E----Q---------------------------------------   40 (141)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH---H----S---------------------------------------
T ss_pred             hHHHHHHHHHHHHHHHHccCCCHHHHHHHHHH---h----c---------------------------------------
Confidence            68999999999999999999888887755332   0    0                                       


Q ss_pred             HHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchH
Q 024057          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVI  253 (273)
Q Consensus       175 ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaI  253 (273)
                           ..+      +.+..|+.+|+.||+.++.++|..|++++.  |+++||+. +|++|||||+|||+| +++|+.|+|
T Consensus        41 -----~l~------~~d~~~~~~Lv~gvl~~~~~lD~~I~~~l~--~~l~rl~~-~~r~iLrla~yEll~~~~iP~~vaI  106 (141)
T 3d3b_A           41 -----DVK------DVDVLYFRELLAGVATNTAYLDGLMKPYLS--RLLEELGQ-VEKAVLRIALYELSKRSDVPYKVAI  106 (141)
T ss_dssp             -----CCT------TSCHHHHHHHHHHHHHTHHHHHHHHGGGGT--TCSSCCCH-HHHHHHHHHHHHHHHCTTSCHHHHH
T ss_pred             -----cCC------HHHHHHHHHHHHHHHHhHHHHHHHHHHHcC--CCHHHcCH-HHHHHHHHHHHHHHhCCCCCchhhH
Confidence                 000      114689999999999999999999999983  99999998 799999999999999 589999999


Q ss_pred             hHHHHHHHHHh
Q 024057          254 NEARLTLHFLF  264 (273)
Q Consensus       254 NEAVELAK~f~  264 (273)
                      ||||||||+|+
T Consensus       107 nEaVelaK~~~  117 (141)
T 3d3b_A          107 NEAIELAKSFG  117 (141)
T ss_dssp             HHHHHHHHHHS
T ss_pred             HHHHHHHHHHC
Confidence            99999999985

>1eyv_A NUSB protein, N-utilizing substance protein B homolog; helical bundle, structural genomics, PSI, protein structure initiative; 1.60A {Mycobacterium tuberculosis} SCOP: a.79.1.1

Probab=99.91  E-value=1.7e-24  Score=180.33  Aligned_cols=117  Identities=16%  Similarity=0.190  Sum_probs=95.3

Q ss_pred             CCCChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHH
Q 024057           92 RFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEE  171 (273)
Q Consensus        92 Rf~srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~  171 (273)
                      +..+||.||++|+|+||+++..|.+..+++.....                                     +... +. 
T Consensus         6 ~~~~R~~aR~~Alq~L~~~~~~~~~~~~~l~~~~~-------------------------------------l~~~-d~-   46 (156)
T 1eyv_A            6 PVRGRHQARKRAVALLFEAEVRGISAAEVVDTRAA-------------------------------------LAEA-KP-   46 (156)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHH-------------------------------------HHHH-CT-
T ss_pred             CccchHHHHHHHHHHHHHHHhcCCCHHHHHHHHHh-------------------------------------cccc-cc-
Confidence            34689999999999999999999888777654211                                     0000 00 


Q ss_pred             HHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCcc
Q 024057          172 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQ  250 (273)
Q Consensus       172 s~~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~k  250 (273)
                               ..+      .+..|+.+|+.||+.++.++|..|++++ ++|+++||+. +|++|||||+|||+| +++|+.
T Consensus        47 ---------~~~------~~~~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~l~rl~~-~~r~iLrla~yel~~~~~iP~~  109 (156)
T 1eyv_A           47 ---------DIA------RLHPYTAAVARGVSEHAAHIDDLITAHL-RGWTLDRLPA-VDRAILRVSVWELLHAADVPEP  109 (156)
T ss_dssp             ---------TSC------CCCHHHHHHHHHHHHTHHHHHHHHHTTS-TTCCGGGSCH-HHHHHHHHHHHHHHHCTTSCHH
T ss_pred             ---------ccH------HHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCChhhCCH-HHHHHHHHHHHHHHHcCCCCch
Confidence                     011      1358999999999999999999999998 7999999998 799999999999999 579999


Q ss_pred             chHhHHHHHHHHHh
Q 024057          251 IVINEARLTLHFLF  264 (273)
Q Consensus       251 VaINEAVELAK~f~  264 (273)
                      |+|||||||||+|+
T Consensus       110 v~InEaVelak~~~  123 (156)
T 1eyv_A          110 VVVDEAVQLAKELS  123 (156)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHhC
Confidence            99999999999985

>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii}

Probab=99.70  E-value=6.6e-17  Score=150.83  Aligned_cols=116  Identities=9%  Similarity=-0.024  Sum_probs=95.9

Q ss_pred             cccCCCCChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhh
Q 024057           88 DKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRS  167 (273)
Q Consensus        88 dk~gRf~srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q  167 (273)
                      ++..|+++++.||+.|+|+||+++..|.....++.+.++..+     +                                
T Consensus         2 ~~~~~~~~~~~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~~~-----l--------------------------------   44 (450)
T 2yxl_A            2 EAEKKKLSIPPKGIRAIIEAIRLGEIIKPSQYAKREAFKKHD-----V--------------------------------   44 (450)
T ss_dssp             ----CCBCCCHHHHHHHHHHHHHTTTSSSTHHHHHHHHHHTT-----C--------------------------------
T ss_pred             cccccccCcchHHHHHHHHHHHHHhcCCcHHHHHHHHHHhcc-----C--------------------------------
Confidence            456799999999999999999999999777777766543100     0                                


Q ss_pred             hhHHHHHHHhhhcCCChhhhhH-HHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccC
Q 024057          168 DEEESAIEAEVLSAPPKLVYSK-LLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG  246 (273)
Q Consensus       168 ~d~~s~~ea~vl~apPklvyn~-~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~D  246 (273)
                                          +. .+..|+.+||.||+.++..+|..|++.+. + ++++|+. ++++|||||+|||+| +
T Consensus        45 --------------------~~~~dr~~~~~lv~gvlr~~~~ld~~i~~~~~-~-~~~~~~~-~~~~iLrla~yell~-~  100 (450)
T 2yxl_A           45 --------------------EEAWLNRVLTMIFYDIMKKQGLIDKVIKEIVG-V-TPLILDP-WLRAALRVAVDIALF-H  100 (450)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S-CGGGSCH-HHHHHHHHHHHHHHH-S
T ss_pred             --------------------CcHHHHHHHHHHHHHHHHhHHHHHHHHHHhcc-C-ChhhcCH-HHHHHHHHHHHHHhc-C
Confidence                                01 36899999999999999999999999874 3 7778888 799999999999999 9


Q ss_pred             CCccchHh----HHHHHHHHHh
Q 024057          247 TRHQIVIN----EARLTLHFLF  264 (273)
Q Consensus       247 vP~kVaIN----EAVELAK~f~  264 (273)
                      +|..|+||    |||||||+|+
T Consensus       101 ip~~~ain~~~~eaVelak~~~  122 (450)
T 2yxl_A          101 DPSSQTIKNLRWKASDFISSRT  122 (450)
T ss_dssp             CBCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCchHHhccccHHHHHHHHhcc
Confidence            99999999    9999999984

>1sqg_A SUN protein, FMU protein; rossmann-fold, mixed beta sheet, methyltransferase-fold, RNA-binding domain; 1.65A {Escherichia coli} SCOP: a.79.1.3 c.66.1.38 PDB: 1sqf_A

Probab=99.68  E-value=2.1e-16  Score=146.02  Aligned_cols=105  Identities=10%  Similarity=0.053  Sum_probs=90.0

Q ss_pred             HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057           98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE  177 (273)
Q Consensus        98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~  177 (273)
                      .||+.|+|+||+++..|.+..+++.+...   .    .                                          
T Consensus         6 ~aR~~A~~~L~~~~~~~~~~~~~l~~~~~---~----~------------------------------------------   36 (429)
T 1sqg_A            6 NLRSMAAQAVEQVVEQGQSLSNILPPLQQ---K----V------------------------------------------   36 (429)
T ss_dssp             CHHHHHHHHHHHHHHHCCCHHHHHHHHHT---T----S------------------------------------------
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHh---h----C------------------------------------------
Confidence            59999999999999999888777654211   0    0                                          


Q ss_pred             hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHH
Q 024057          178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAR  257 (273)
Q Consensus       178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAV  257 (273)
                                +..+..|+.+||.||+.++..+|..|++.+. + ++++++. ++++|||||+|||+|.++|..|+|||||
T Consensus        37 ----------~~~dr~~~~~lv~gvlr~~~~ld~~i~~~~~-~-~~~~~~~-~~~~iLrl~~yel~~~~~p~~~~ineaV  103 (429)
T 1sqg_A           37 ----------SDKDKALLQELCFGVLRTLSQLDWLINKLMA-R-PMTGKQR-TVHYLIMVGLYQLLYTRIPPHAALAETV  103 (429)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-S-CCCGGGH-HHHHHHHHHHHHHHHCCSCHHHHHHHHH
T ss_pred             ----------CHHHHHHHHHHHHHHHHhHHHHHHHHHHhcC-C-ChhhcCH-HHHHHHHHHHHHHhhCCCCchHhhHHHH
Confidence                      1236899999999999999999999999874 4 7778988 7999999999999998999999999999


Q ss_pred             HHHHHHh
Q 024057          258 LTLHFLF  264 (273)
Q Consensus       258 ELAK~f~  264 (273)
                      ||||+|+
T Consensus       104 elak~~~  110 (429)
T 1sqg_A          104 EGAIAIK  110 (429)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHhc
Confidence            9999875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	273
d1eyva_	131	Antitermination factor NusB {Mycobacterium tubercu	99.92
d1tzva_	141	Antitermination factor NusB {Thermotoga maritima [	99.91
d1ey1a_	139	Antitermination factor NusB {Escherichia coli [Tax	99.91
d1sqga1	140	Ribosomal RNA small subunit methyltransferase B, R	99.75

>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.92  E-value=9.7e-26  Score=177.61  Aligned_cols=114  Identities=17%  Similarity=0.195  Sum_probs=97.5

Q ss_pred             ChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHH
Q 024057           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (273)
Q Consensus        95 srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~  174 (273)
                      .||+||++|+|+||+++++|.++.++++........                                            
T Consensus         1 gR~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------   36 (131)
T d1eyva_           1 GRHQARKRAVALLFEAEVRGISAAEVVDTRAALAEA--------------------------------------------   36 (131)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--------------------------------------------
T ss_pred             CcHHHHHHHHHHHHHHHhhCcCHHHHHHHHHHHHhh--------------------------------------------
Confidence            479999999999999999999999999874430000                                            


Q ss_pred             HHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchH
Q 024057          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVI  253 (273)
Q Consensus       175 ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaI  253 (273)
                             ++   ..+.+.+|+++|+.|+.+++..+|..|++++ ++|+.+|++. +|++|||+|+|||++ .++|.+|+|
T Consensus        37 -------~~---~~~~~~~~~~~l~~gv~~~~~~id~~I~~~l-~~~~~~~l~~-i~~~iLr~a~~El~~~~~~p~~viI  104 (131)
T d1eyva_          37 -------KP---DIARLHPYTAAVARGVSEHAAHIDDLITAHL-RGWTLDRLPA-VDRAILRVSVWELLHAADVPEPVVV  104 (131)
T ss_dssp             -------CT---TSCCCCHHHHHHHHHHHHTHHHHHHHHHTTS-TTCCGGGSCH-HHHHHHHHHHHHHHHCTTSCHHHHH
T ss_pred             -------hh---hhHHHHHHHHHHHHHHHHhHHHHHHHHHHhh-hhhHHHHhhH-HHHHHHHHHHHHHHhcccCCchhHH
Confidence                   00   0012358999999999999999999999998 6999999998 799999999999997 789999999


Q ss_pred             hHHHHHHHHHh
Q 024057          254 NEARLTLHFLF  264 (273)
Q Consensus       254 NEAVELAK~f~  264 (273)
                      ||||||||+|+
T Consensus       105 nE~V~lak~~~  115 (131)
T d1eyva_         105 DEAVQLAKELS  115 (131)
T ss_dssp             HHHHHHHHHHS
T ss_pred             HHHHHHHHHhC
Confidence            99999999986

>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.91  E-value=1e-24  Score=173.19  Aligned_cols=111  Identities=13%  Similarity=0.162  Sum_probs=95.7

Q ss_pred             ChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHH
Q 024057           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (273)
Q Consensus        95 srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~  174 (273)
                      .||+||++|+|+||++++.+..+.+.+.+...   .    ++                                      
T Consensus         4 pR~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~---~----~~--------------------------------------   38 (141)
T d1tzva_           4 PRRRMRLAVFKALFQHEFRRDEDLEQILEEIL---D----ET--------------------------------------   38 (141)
T ss_dssp             CHHHHHHHHHHHHHHHTTCTTSCHHHHHHHHC---C----TT--------------------------------------
T ss_pred             hhHHHHHHHHHHHHHHHhcCCccHHHHHHHHH---H----hc--------------------------------------
Confidence            47899999999999999998777776655332   0    00                                      


Q ss_pred             HHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchH
Q 024057          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVI  253 (273)
Q Consensus       175 ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaI  253 (273)
                                  .++.+..|+.+|+.|+..++..+|..|++++ .+|+.+|++. ++++|||+|+|||+| .++|++|+|
T Consensus        39 ------------~~~~d~~~~~~lv~g~~~~~~~id~~I~~~~-~~~~~~rl~~-~~~~iLr~a~~El~~~~~~p~~v~I  104 (141)
T d1tzva_          39 ------------YDKKAKEDARRYIRGIKENLSMIDDLISRYL-EKWSLNRLSV-VDRNVLRLATYELLFEKDIPIEVTI  104 (141)
T ss_dssp             ------------SCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC-SSSCGGGSCH-HHHHHHHHHHHHHHHCTTSCHHHHH
T ss_pred             ------------cchhHHHHHHHHHHHHHHhHHHHHHHHHHhc-ccCChHHHHH-HHHHHHHHHHHHHHhccccchhHHH
Confidence                        1134689999999999999999999999987 7999999998 799999999999998 789999999


Q ss_pred             hHHHHHHHHHh
Q 024057          254 NEARLTLHFLF  264 (273)
Q Consensus       254 NEAVELAK~f~  264 (273)
                      ||||||||+|+
T Consensus       105 nEaVelak~~~  115 (141)
T d1tzva_         105 DEAIEIAKRYG  115 (141)
T ss_dssp             HHHHHHHHHHS
T ss_pred             HHHHHHHHHhC
Confidence            99999999986

>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Escherichia coli [TaxId: 562]

Probab=99.91  E-value=8.3e-25  Score=173.75  Aligned_cols=111  Identities=21%  Similarity=0.205  Sum_probs=95.4

Q ss_pred             CChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHH
Q 024057           94 CSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESA  173 (273)
Q Consensus        94 ~srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~  173 (273)
                      .+||+||++|+|+||+++++|.++.+++.+.+.   +.  .+                                      
T Consensus         4 ~~R~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~---~~--~~--------------------------------------   40 (139)
T d1ey1a_           4 AARRRARECAVQALYSWQLSQNDIADVEYQFLA---EQ--DV--------------------------------------   40 (139)
T ss_dssp             TCCCSHHHHHHHHHHHHHHHCCCSHHHHHHHHH---TT--TS--------------------------------------
T ss_pred             cHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH---hc--cc--------------------------------------
Confidence            357899999999999999999999999988554   10  00                                      


Q ss_pred             HHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccch
Q 024057          174 IEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIV  252 (273)
Q Consensus       174 ~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVa  252 (273)
                                    ++.+..|+++|+.|+.++...+|..|++.+  .|+.+|++. +|++|||+|+|||++ .++|++|+
T Consensus        41 --------------~~~d~~~~~~l~~gv~~~~~~id~~I~~~l--~~~~~r~~~-~~~~ILr~a~~El~~~~~~p~~vi  103 (139)
T d1ey1a_          41 --------------KDVDVLYFRELLAGVATNTAYLDGLMKPYL--SRLLEELGQ-VEKAVLRIALYELSKRSDVPYKVA  103 (139)
T ss_dssp             --------------SSCCCHHHHHHHHHHHHHHHHHHHHHTTCC--CSCTTTSCH-HHHHHHHHHHHHHHSCSSCCSHHH
T ss_pred             --------------chhhHHHHHHHHHHHHHhHHHHHHHHHHHH--HhhHHhcCh-HHHHHHHHHHHHHHHccCCCceeh
Confidence                          012468999999999999999999999987  466889998 799999999999998 67999999


Q ss_pred             HhHHHHHHHHHh
Q 024057          253 INEARLTLHFLF  264 (273)
Q Consensus       253 INEAVELAK~f~  264 (273)
                      |||||||||.|+
T Consensus       104 InE~Velak~~~  115 (139)
T d1ey1a_         104 INEAIELAKSFG  115 (139)
T ss_dssp             HHHHHHHTTTTT
T ss_pred             HHHHHHHHHHhC
Confidence            999999999986

>d1sqga1 a.79.1.3 (A:5-144) Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: RmsB N-terminal domain-like
domain: Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.75  E-value=2.8e-18  Score=137.28  Aligned_cols=106  Identities=11%  Similarity=0.063  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHH
Q 024057           97 RAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEA  176 (273)
Q Consensus        97 R~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea  176 (273)
                      |.+|++|+|+||++...|.....++++..+   .    .                                         
T Consensus         1 r~~R~~A~q~L~~v~~~g~~l~~~l~~~~~---~----l-----------------------------------------   32 (140)
T d1sqga1           1 RNLRSMAAQAVEQVVEQGQSLSNILPPLQQ---K----V-----------------------------------------   32 (140)
T ss_dssp             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHT---T----S-----------------------------------------
T ss_pred             CCHHHHHHHHHHHHHHcCCCHHHHHHHHHH---h----C-----------------------------------------
Confidence            458999999999999999999999887432   0    1                                         


Q ss_pred             hhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHH
Q 024057          177 EVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEA  256 (273)
Q Consensus       177 ~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEA  256 (273)
                                 ++.+..|+++|+.||..++..+|..|+.++.. |. .++.. ++++|||+|+|||++.++|+.++||||
T Consensus        33 -----------~~~dr~~~~~lv~gvlr~~~~ld~~i~~~l~~-~~-~~~~~-~~~~iLr~a~~el~~~~~p~~avvnea   98 (140)
T d1sqga1          33 -----------SDKDKALLQELCFGVLRTLSQLDWLINKLMAR-PM-TGKQR-TVHYLIMVGLYQLLYTRIPPHAALAET   98 (140)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS-CC-CGGGH-HHHHHHHHHHHHHHHCCSCHHHHHHHH
T ss_pred             -----------CHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhc-cc-chhhH-HHHHHHHHHHHHHHcCCCCCccchHHH
Confidence                       12368999999999999999999999999854 42 46776 689999999999999999999999999


Q ss_pred             HHHHHHHh
Q 024057          257 RLTLHFLF  264 (273)
Q Consensus       257 VELAK~f~  264 (273)
                      ||+||+|+
T Consensus        99 V~lak~~~  106 (140)
T d1sqga1          99 VEGAIAIK  106 (140)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHHhC
Confidence            99999986