Citrus Sinensis ID: 022136

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300--
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
cccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccccccc
cccccccccccccccccEEEEccccccccccccccccHHHccccccHHccccccccHcccccccHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccEcHHHHHHcccccccccccEcccHHHHHHHHHccHHccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcccccHEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccccccc
maveatssflscsskthflfnlrassspsswkKFTQSANFaaknrhvcrnerpnvscsAAAFAVQETLEKTRESVMASSAKEmmpkidksgrfcsPRAARELALLVVYAACLEGSDPIRLFEKRLnsrrepgyefdksslleynhmsfggppvttetVEEADELLRSDEEESAIEAEvlsappklVYSKLLLRFTRKLLVAVVDKWDAHVHiidkvvppiwkdqpagrILELSILHLAMSEITVVGTRHQIVINEAVDLAKrfcdgaapriiNGCLRTFVRNLEGtanieaskaskevpsev
maveatssflscssKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMassakemmpkidksGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIeaevlsappklvYSKLLLRFTRKLLVAVVDKWDAHVHIIDkvvppiwkdqpAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGtanieaskaskevpsev
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
***************THFLFNL************************VC***********AAF******************************FCSPRAARELALLVVYAACLEGSDPIRLFEK*******************************************************LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT****************
********FLSCSSKTHFLFNLRASSSP****************************************************************FCSPRAARELALLVVYAACLE**D***LFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF***********************
**********SCSSKTHFLFNLRAS*********TQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIE************
***********C*SKTHFLFNLRAS****S****TQSA**A****H***NERPNVS*********************************SGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE******************
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query302 2.2.26 [Sep-21-2011]
A7GWZ7131 N utilization substance p yes no 0.211 0.488 0.393 6e-07
Q5N1J7213 N utilization substance p yes no 0.221 0.314 0.420 1e-06
Q8GIR7213 N utilization substance p yes no 0.221 0.314 0.420 1e-06
B1WXY6209 N utilization substance p yes no 0.221 0.320 0.405 2e-06
Q18B61169 N utilization substance p yes no 0.225 0.402 0.385 5e-06
B2J3F1213 N utilization substance p yes no 0.264 0.375 0.348 5e-06
B8HYJ8209 N utilization substance p yes no 0.264 0.382 0.365 6e-06
B7K4P4211 N utilization substance p yes no 0.251 0.360 0.346 8e-06
Q8RAD1140 N utilization substance p yes no 0.264 0.571 0.376 1e-05
B5YE05144 N utilization substance p yes no 0.208 0.437 0.430 3e-05
>sp|A7GWZ7|NUSB_CAMC5 N utilization substance protein B homolog OS=Campylobacter curvus (strain 525.92) GN=nusB PE=3 SV=1 Back     alignment and function desciption
 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 213 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 270
           +D+++ P  K++   RI  +EL+IL L + E+   GT   ++INEA++LAK     +AP+
Sbjct: 59  LDEILKPYLKEKDIERIGIVELAILRLGVYEMKFTGTDKAVIINEAIELAKELGGDSAPK 118

Query: 271 IINGCL 276
            ING L
Sbjct: 119 FINGVL 124
Involved in the transcription termination process.
Campylobacter curvus (strain 525.92) (taxid: 360105)
>sp|Q5N1J7|NUSB_SYNP6 N utilization substance protein B homolog OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|Q8GIR7|NUSB_SYNE7 N utilization substance protein B homolog OS=Synechococcus elongatus (strain PCC 7942) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|B1WXY6|NUSB_CYAA5 N utilization substance protein B homolog OS=Cyanothece sp. (strain ATCC 51142) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|Q18B61|NUSB_CLOD6 N utilization substance protein B homolog OS=Clostridium difficile (strain 630) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|B2J3F1|NUSB_NOSP7 N utilization substance protein B homolog OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|B8HYJ8|NUSB_CYAP4 N utilization substance protein B homolog OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|B7K4P4|NUSB_CYAP8 N utilization substance protein B homolog OS=Cyanothece sp. (strain PCC 8801) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|Q8RAD1|NUSB_THETN N utilization substance protein B homolog OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=nusB PE=3 SV=1 Back     alignment and function description
>sp|B5YE05|NUSB_DICT6 N utilization substance protein B homolog OS=Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) GN=nusB PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query302
225435806288 PREDICTED: uncharacterized protein LOC10 0.894 0.937 0.690 1e-110
297746508218 unnamed protein product [Vitis vinifera] 0.721 1.0 0.834 1e-106
224073118218 predicted protein [Populus trichocarpa] 0.715 0.990 0.842 1e-105
449463840378 PREDICTED: uncharacterized protein LOC10 0.695 0.555 0.790 7e-98
18416739301 antitermination NusB domain-containing p 0.711 0.714 0.781 1e-90
297799366300 antitermination NusB domain-containing p 0.711 0.716 0.776 1e-90
2982469286 putative protein [Arabidopsis thaliana] 0.711 0.751 0.781 2e-90
388512429288 unknown [Lotus japonicus] 0.860 0.902 0.614 3e-88
255564810309 RNA binding protein, putative [Ricinus c 0.629 0.614 0.785 3e-86
363807164289 uncharacterized protein LOC100809333 [Gl 0.791 0.826 0.656 7e-84
>gi|225435806|ref|XP_002285757.1| PREDICTED: uncharacterized protein LOC100265613 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 201/291 (69%), Positives = 231/291 (79%), Gaps = 21/291 (7%)

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 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPS 300
           QIVINEAVDLAKRFCDGAAPRIINGCLRTFV++LEGT    AS+ ++EV S
Sbjct: 238 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVKDLEGTGITRASETTQEVVS 288

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297746508|emb|CBI16564.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224073118|ref|XP_002303980.1| predicted protein [Populus trichocarpa] gi|222841412|gb|EEE78959.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449463840|ref|XP_004149639.1| PREDICTED: uncharacterized protein LOC101216754 [Cucumis sativus] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>gi|2982469|emb|CAA18233.1| putative protein [Arabidopsis thaliana] gi|7269489|emb|CAB79492.1| putative protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388512429|gb|AFK44276.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|255564810|ref|XP_002523399.1| RNA binding protein, putative [Ricinus communis] gi|223537349|gb|EEF38978.1| RNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|363807164|ref|NP_001242346.1| uncharacterized protein LOC100809333 [Glycine max] gi|255636077|gb|ACU18383.1| unknown [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query302
TAIR|locus:2131428301 AT4G26370 [Arabidopsis thalian 0.976 0.980 0.62 2.8e-89
UNIPROTKB|P65582140 nusB "N utilization substance 0.172 0.371 0.423 3.4e-05
UNIPROTKB|Q9KPU5156 nusB "N utilization substance 0.390 0.756 0.309 7.7e-05
TIGR_CMR|VC_2267156 VC_2267 "N utilization substan 0.390 0.756 0.309 7.7e-05
TIGR_CMR|CJE_0431132 CJE_0431 "transcription antite 0.278 0.636 0.3 0.0002
TIGR_CMR|CPS_1532138 CPS_1532 "transcription termin 0.225 0.492 0.333 0.00048
TIGR_CMR|GSU_1692138 GSU_1692 "N utilization substa 0.225 0.492 0.352 0.00054
TAIR|locus:2131428 AT4G26370 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 891 (318.7 bits), Expect = 2.8e-89, P = 2.8e-89
 Identities = 186/300 (62%), Positives = 221/300 (73%)

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 MSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 298
             MSE+ V+ TRH IVINEAVDLAKRFCDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct:   240 MSEVAVLETRHPIVINEAVDLAKRFCDGSAPRIINGCLRTFVKDRATTSTPQALELKQEV 299
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
UNIPROTKB|P65582 nusB "N utilization substance protein B homolog" [Streptococcus pneumoniae TIGR4 (taxid:170187)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KPU5 nusB "N utilization substance protein B homolog" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_2267 VC_2267 "N utilization substance protein B" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|CJE_0431 CJE_0431 "transcription antitermination factor NusB" [Campylobacter jejuni RM1221 (taxid:195099)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_1532 CPS_1532 "transcription termination/antitermination factor NusB" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_1692 GSU_1692 "N utilization substance protein B" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00024846001
SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (288 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query302
cd00619130 cd00619, Terminator_NusB, Transcription terminatio 2e-28
cd00447129 cd00447, NusB_Sun, RNA binding domain of NusB (N p 9e-21
TIGR01951129 TIGR01951, nusB, transcription antitermination fac 2e-10
pfam01029126 pfam01029, NusB, NusB family 2e-09
PRK00202137 PRK00202, nusB, transcription antitermination prot 1e-08
PRK09634207 PRK09634, nusB, transcription antitermination prot 5e-08
COG0781151 COG0781, NusB, Transcription termination factor [T 1e-06
PRK14902 444 PRK14902, PRK14902, 16S rRNA methyltransferase B; 5e-04
>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B) Back     alignment and domain information 
 Score =  105 bits (264), Expect = 2e-28
 Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 4/131 (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-TRHQIVINEAVDLAKRFCDGAAPRII 272
           +K +     D+    I+E +IL LA+ E+  +    H +VINEA++LAKRF    + + +
Sbjct: 62  EKHLRNWSLDR--LAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFV 119

Query: 273 NGCLRTFVRNL 283
           NG L    ++L
Sbjct: 120 NGVLDKIAKDL 130

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 Back     alignment and domain information
>gnl|CDD|233652 TIGR01951, nusB, transcription antitermination factor NusB Back     alignment and domain information
>gnl|CDD|216253 pfam01029, NusB, NusB family Back     alignment and domain information
>gnl|CDD|234686 PRK00202, nusB, transcription antitermination protein NusB; Reviewed Back     alignment and domain information
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB; Provisional Back     alignment and domain information
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription] Back     alignment and domain information
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 302
PF01029134 NusB: NusB family; InterPro: IPR006027 This domain 99.98
COG0781151 NusB Transcription termination factor [Transcripti 99.97
PRK00202137 nusB transcription antitermination protein NusB; R 99.97
cd00619130 Terminator_NusB Transcription termination factor N 99.97
TIGR01951129 nusB transcription antitermination factor NusB. A 99.97
cd00620126 Methyltransferase_Sun N-terminal RNA binding domai 99.96
cd00447129 NusB_Sun RNA binding domain of NusB (N protein-Uti 99.94
PRK09634207 nusB transcription antitermination protein NusB; P 99.94
PRK10901 427 16S rRNA methyltransferase B; Provisional 99.93
PRK14904 445 16S rRNA methyltransferase B; Provisional 99.91
PRK14901 434 16S rRNA methyltransferase B; Provisional 99.91
PRK14902 444 16S rRNA methyltransferase B; Provisional 99.9
TIGR00563 426 rsmB ribosomal RNA small subunit methyltransferase 99.87
PRK14903 431 16S rRNA methyltransferase B; Provisional 99.86
>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 Back     alignment and domain information 
Probab=99.98  E-value=9e-32  Score=223.02  Aligned_cols=93  Identities=28%  Similarity=0.432  Sum_probs=88.2

Q ss_pred             ccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHHHHHHHHHHhhCC
Q 022136          187 YSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCD  265 (302)
Q Consensus       187 ~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaINEAVELAKky~~  265 (302)
                      .+..|++|+++|++|+++|+..||++|++++ ++|+++|++++ +++|||+|+|||+|+ ++|++++|||||++||+|++
T Consensus        41 ~~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~~~~rl~~~-~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~~  118 (134)
T PF01029_consen   41 LSEEDRAFARELVYGVLRNKEELDALISKLL-KNWPLERLPPV-DRAILRLAIYELLFLDDIPPHVAINEAVELAKKYGD  118 (134)
T ss_dssp             STHHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSSTGGGSGHH-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccccCHH-HHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCC
Confidence            4578999999999999999999999999988 68999999999 799999999999999 89999999999999999999


Q ss_pred             CCCCCchhHHHhHHHh
Q 022136          266 GAAPRIINGCLRTFVR  281 (302)
Q Consensus       266 ~~s~gFVNAVLrkI~R  281 (302)
                      ++++||||||||+++|
T Consensus       119 ~~~~~fVNaVL~~~~R  134 (134)
T PF01029_consen  119 EKSAGFVNAVLRRIAR  134 (134)
T ss_dssp             TTHHHHHHHHHHHHHH
T ss_pred             CCcchhHHHHHHHhhC
Confidence            9999999999999986

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 ....
>COG0781 NusB Transcription termination factor [Transcription] Back     alignment and domain information
>PRK00202 nusB transcription antitermination protein NusB; Reviewed Back     alignment and domain information
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B) Back     alignment and domain information
>TIGR01951 nusB transcription antitermination factor NusB Back     alignment and domain information
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun Back     alignment and domain information
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins Back     alignment and domain information
>PRK09634 nusB transcription antitermination protein NusB; Provisional Back     alignment and domain information
>PRK10901 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14904 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14901 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14902 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB Back     alignment and domain information
>PRK14903 16S rRNA methyltransferase B; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query302
3r2d_A149 Protein NUSB, N utilization substance protein B; c 5e-11
3d3b_A141 Protein NUSB, N utilization substance protein B; N 2e-10
1tzv_A142 NUSB protein, N utilization substance protein B ho 3e-10
1eyv_A156 NUSB protein, N-utilizing substance protein B homo 3e-10
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed bet 4e-04
>3r2d_A Protein NUSB, N utilization substance protein B; cross species NUSB-NUSE-RNA interaction; 2.20A {Aquifex aeolicus} PDB: 2jr0_A 3r2c_A* Length = 149 Back     alignment and structure
 Score = 58.9 bits (143), Expect = 5e-11
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 7/107 (6%)

Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-Q 250
           + +KL+   V   +     ID ++    K     R+  +E + L L ++E+  + ++   
Sbjct: 47  YAKKLVDTAVRHIEE----IDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPG 102

Query: 251 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKE 297
            V  + VDL K++ D  A + +NG L    +    ++  E      E
Sbjct: 103 RVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEKPSLKSE 149
>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 Length = 141 Back     alignment and structure
>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* Length = 142 Back     alignment and structure
>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 Length = 156 Back     alignment and structure
>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 Length = 429 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query302
3r2d_A149 Protein NUSB, N utilization substance protein B; c 100.0
1tzv_A142 NUSB protein, N utilization substance protein B ho 100.0
3d3b_A141 Protein NUSB, N utilization substance protein B; N 100.0
1eyv_A156 NUSB protein, N-utilizing substance protein B homo 100.0
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed bet 99.9
2yxl_A 450 PH0851 protein, 450AA long hypothetical FMU protei 99.89
>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 Back     alignment and structure
Probab=100.00  E-value=9.8e-35  Score=247.66  Aligned_cols=138  Identities=25%  Similarity=0.416  Sum_probs=117.4

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHH
Q 022136           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (302)
Q Consensus        95 ~R~~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~  174 (302)
                      .|+++|++|+|+||+++.+|.+++++++.++...                  .                           
T Consensus         4 ~R~~aR~~A~q~L~~~~~~~~~~~~~l~~~~~~~------------------~---------------------------   38 (149)
T 3r2d_A            4 YRKGARDTAFLVLYRWDLRGENPGELFKEVVEEK------------------N---------------------------   38 (149)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH------------------T---------------------------
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc------------------c---------------------------
Confidence            6899999999999999999999999988766410                  0                           


Q ss_pred             HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHH
Q 022136          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI  253 (302)
Q Consensus       175 ~~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaI  253 (302)
                                 ..+..|++|+++||+||++|+..||++|++++ ++|+++||+++ +++|||+|+|||+|+ ++|++|+|
T Consensus        39 -----------~~~~~dr~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~~~rl~~~-~r~iLrla~yEl~~~~~iP~~vaI  105 (149)
T 3r2d_A           39 -----------IKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-KGWSIDRLGYV-ERNALRLGVAELIFLKSKEPGRVF  105 (149)
T ss_dssp             -----------CCCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC----CGGGSCHH-HHHHHHHHHHHHTTSCCSCHHHHH
T ss_pred             -----------cCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCccccCHH-HHHHHHHHHHHHHHcCCCCCeehH
Confidence                       02357899999999999999999999999999 68999999999 799999999999998 79999999


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHhHHHhhhhcccccc
Q 022136          254 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIE  290 (302)
Q Consensus       254 NEAVELAKky~~~~s~gFVNAVLrkI~R~l~~~e~~~  290 (302)
                      ||||+|||.|++++++||||||||++.++.++.+.+.
T Consensus       106 nEaVelaK~~~~~~~~~fVNgVLr~i~r~~~~~~~~~  142 (149)
T 3r2d_A          106 IDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEE  142 (149)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHhCCCCccccchHHhhHHHHhhccccccc
Confidence            9999999999999999999999999999998876643
>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* Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog, methyltransferase, structural genomics, NPPSFA; HET: SFG; 2.55A {Pyrococcus horikoshii} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 302
d1sqga1140 a.79.1.3 (A:5-144) Ribosomal RNA small subunit met 3e-09
d1tzva_141 a.79.1.1 (A:) Antitermination factor NusB {Thermot 4e-09
d1ey1a_139 a.79.1.1 (A:) Antitermination factor NusB {Escheri 4e-09
d1eyva_131 a.79.1.1 (A:) Antitermination factor NusB {Mycobac 4e-09
>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]} Length = 140 Back     information, alignment and structure

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]

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 3/91 (3%)

Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVI 253
             ++L   V+        +I+K++      +         ++ + + ++          +
Sbjct: 39  LLQELCFGVLRTLSQLDWLINKLMARPMTGKQR---TVHYLIMVGLYQLLYTRIPPHAAL 95

Query: 254 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 284
            E V+ A          +ING LR F R  E
Sbjct: 96  AETVEGAIAIKRPQLKGLINGVLRQFQRQQE 126
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Length = 141 Back     information, alignment and structure
>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Length = 139 Back     information, alignment and structure
>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 131 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query302
d1ey1a_139 Antitermination factor NusB {Escherichia coli [Tax 100.0
d1tzva_141 Antitermination factor NusB {Thermotoga maritima [ 99.98
d1eyva_131 Antitermination factor NusB {Mycobacterium tubercu 99.97
d1sqga1140 Ribosomal RNA small subunit methyltransferase B, R 99.96
>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.5e-33  Score=231.19  Aligned_cols=133  Identities=22%  Similarity=0.287  Sum_probs=119.6

Q ss_pred             CcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHH
Q 022136           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (302)
Q Consensus        95 ~R~~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~  174 (302)
                      +|+++|++|+|+|||+++++.++++++..++...                  .                           
T Consensus         5 ~R~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~------------------~---------------------------   39 (139)
T d1ey1a_           5 ARRRARECAVQALYSWQLSQNDIADVEYQFLAEQ------------------D---------------------------   39 (139)
T ss_dssp             CCCSHHHHHHHHHHHHHHHCCCSHHHHHHHHHTT------------------T---------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc------------------c---------------------------
Confidence            5678999999999999999999999988877520                  0                           


Q ss_pred             HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHH
Q 022136          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI  253 (302)
Q Consensus       175 ~~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaI  253 (302)
                                  +++.|+.|+++|++|+++|...||.+|+.++ + |+++|++++ +++|||+|+|||+|+ ++|++|+|
T Consensus        40 ------------~~~~d~~~~~~l~~gv~~~~~~id~~I~~~l-~-~~~~r~~~~-~~~ILr~a~~El~~~~~~p~~viI  104 (139)
T d1ey1a_          40 ------------VKDVDVLYFRELLAGVATNTAYLDGLMKPYL-S-RLLEELGQV-EKAVLRIALYELSKRSDVPYKVAI  104 (139)
T ss_dssp             ------------SSSCCCHHHHHHHHHHHHHHHHHHHHHTTCC-C-SCTTTSCHH-HHHHHHHHHHHHHSCSSCCSHHHH
T ss_pred             ------------cchhhHHHHHHHHHHHHHhHHHHHHHHHHHH-H-hhHHhcChH-HHHHHHHHHHHHHHccCCCceehH
Confidence                        1235789999999999999999999999999 3 679999999 799999999999997 69999999


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHhHHHhhhhccc
Q 022136          254 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  287 (302)
Q Consensus       254 NEAVELAKky~~~~s~gFVNAVLrkI~R~l~~~e  287 (302)
                      ||||+|||.|++++++||||||||++++++++.+
T Consensus       105 nE~Velak~~~~~~~~~fVNgVL~~i~k~~r~~e  138 (139)
T d1ey1a_         105 NEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNK  138 (139)
T ss_dssp             HHHHHHTTTTTCSSSSHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHhCCCCccchHHHHHHHHHHHhCccC
Confidence            9999999999999999999999999999988754
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1eyva_ a.79.1.1 (A:) Antitermination factor NusB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>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]} Back     information, alignment and structure