Citrus Sinensis ID: 027155

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-------
MASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
ccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccccHHHHHHHHcccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccccccccc
ccccHHHHccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccccEEcHHHHHHccccccccccEEEccHHHHHHHHHccHHHcHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcccccHEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccccccc
massakemmpkidksgrfcsPRAARELALLVVYAACLEGSDPIRLFEKRLnsrrepgyefdksslleynhmsfggppvttetVEEADELLRSDEEESAIEAEvlsappklVYSKLLLRFTRKLLVAVVDKWDAHVHiidkvvppiwkdqpagrILELSILHLAMSEITVVGTRHQIVINEAVDLAKrfcdgaapriiNGCLRTFVRNLEGtanieaskaskevpsev
massakemmpkidksgrfcSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIeaevlsappklvYSKLLLRFTRKLLVAVVDKWDAHVHIIDkvvppiwkdqpAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGtanieaskaskevpsev
MASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
******************CSPRAARELALLVVYAACLEGSDPIRLFEK*******************************************************LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT****************
****************RFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHM*F****VTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF***********************
*************KSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIE************
**************SGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE******************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
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 ?
Query227 2.2.26 [Sep-21-2011]
A7GWZ7131 N utilization substance p yes no 0.281 0.488 0.393 7e-07
Q5N1J7213 N utilization substance p yes no 0.295 0.314 0.420 1e-06
Q8GIR7213 N utilization substance p yes no 0.295 0.314 0.420 1e-06
B1WXY6209 N utilization substance p yes no 0.299 0.325 0.4 3e-06
B8HYJ8209 N utilization substance p yes no 0.352 0.382 0.365 3e-06
Q18B61169 N utilization substance p yes no 0.299 0.402 0.385 3e-06
B2J3F1213 N utilization substance p yes no 0.352 0.375 0.348 4e-06
Q8RAD1140 N utilization substance p yes no 0.352 0.571 0.376 5e-06
B7K4P4211 N utilization substance p yes no 0.334 0.360 0.346 7e-06
Q7MAE9135 N utilization substance p yes no 0.303 0.511 0.380 2e-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 = 54.3 bits (129), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 2/66 (3%)

Query: 138 IDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPR 195
           +D+++ P  K++   RI  +EL+IL L + E+   GT   ++INEA++LAK     +AP+
Sbjct: 59  LDEILKPYLKEKDIERIGIVELAILRLGVYEMKFTGTDKAVIINEAIELAKELGGDSAPK 118

Query: 196 IINGCL 201
            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|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|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|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|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|Q7MAE9|NUSB_WOLSU N utilization substance protein B homolog OS=Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) 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 ?
Query227
225435806288 PREDICTED: uncharacterized protein LOC10 0.982 0.774 0.825 1e-106
297746508218 unnamed protein product [Vitis vinifera] 0.960 1.0 0.834 1e-105
224073118218 predicted protein [Populus trichocarpa] 0.951 0.990 0.842 1e-105
449463840 378 PREDICTED: uncharacterized protein LOC10 0.894 0.537 0.812 4e-97
18416739301 antitermination NusB domain-containing p 0.947 0.714 0.781 4e-90
2982469286 putative protein [Arabidopsis thaliana] 0.947 0.751 0.781 5e-90
297799366300 antitermination NusB domain-containing p 0.947 0.716 0.776 6e-90
388512429288 unknown [Lotus japonicus] 0.903 0.711 0.736 4e-87
255564810309 RNA binding protein, putative [Ricinus c 0.814 0.598 0.816 1e-85
363807164289 uncharacterized protein LOC100809333 [Gl 0.911 0.716 0.748 2e-83
>gi|225435806|ref|XP_002285757.1| PREDICTED: uncharacterized protein LOC100265613 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 184/223 (82%), Positives = 207/223 (92%)

Query: 3   SSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDK 62
           S  +EM+P+IDKSGRFCSPRAARELALL+ YAACLEGSDP+RLFE+R+N+RREPGYEFDK
Sbjct: 66  SEPREMLPRIDKSGRFCSPRAARELALLIAYAACLEGSDPVRLFERRMNARREPGYEFDK 125

Query: 63  SSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRK 122
            SLLEYNHMSFGGPPVTTETVEEADELLR++E+ESAIEAEVLSAPPKLVY KL+LRFTRK
Sbjct: 126 DSLLEYNHMSFGGPPVTTETVEEADELLRNNEKESAIEAEVLSAPPKLVYGKLILRFTRK 185

Query: 123 LLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAV 182
           LLVAVVDKW++HV +IDKV PP WK++PAGRILEL ILHLAMSEI V+GTRHQIVINEAV
Sbjct: 186 LLVAVVDKWNSHVLVIDKVAPPNWKNEPAGRILELCILHLAMSEIAVLGTRHQIVINEAV 245

Query: 183 DLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPS 225
           DLAKRFCDGAAPRIINGCLRTFV++LEGT    AS+ ++EV S
Sbjct: 246 DLAKRFCDGAAPRIINGCLRTFVKDLEGTGITRASETTQEVVS 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|2982469|emb|CAA18233.1| putative protein [Arabidopsis thaliana] gi|7269489|emb|CAB79492.1| putative 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|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 ?
Query227
TAIR|locus:2131428301 AT4G26370 [Arabidopsis thalian 0.977 0.737 0.762 1.4e-87
UNIPROTKB|P65582140 nusB "N utilization substance 0.229 0.371 0.423 1.8e-05
UNIPROTKB|Q9KPU5156 nusB "N utilization substance 0.519 0.756 0.309 3.9e-05
TIGR_CMR|VC_2267156 VC_2267 "N utilization substan 0.519 0.756 0.309 3.9e-05
TIGR_CMR|CJE_0431132 CJE_0431 "transcription antite 0.370 0.636 0.3 0.00011
TIGR_CMR|CPS_1532138 CPS_1532 "transcription termin 0.299 0.492 0.333 0.00017
TIGR_CMR|GSU_1692138 GSU_1692 "N utilization substa 0.299 0.492 0.352 0.00019
TAIR|locus:2131428 AT4G26370 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 875 (313.1 bits), Expect = 1.4e-87, P = 1.4e-87
 Identities = 170/223 (76%), Positives = 193/223 (86%)

Query:     2 ASSAKEM-MPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEF 60
             A   K++ MPKIDKSGR  SPRAARELAL+++YAACLEGSDPIRLFEKR+N+RREPGYEF
Sbjct:    77 AEEVKDVPMPKIDKSGRLSSPRAARELALVILYAACLEGSDPIRLFEKRINARREPGYEF 136

Query:    61 DKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFT 120
             DKSSLLEYNHMSFGGPPV TET EE DEL+R DE+ES IEAEVLSAPPKLVYSKL+LRF 
Sbjct:   137 DKSSLLEYNHMSFGGPPVKTETKEEEDELVRHDEKESKIEAEVLSAPPKLVYSKLVLRFA 196

Query:   121 RKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINE 180
             +KLL AVVDKWD+HV II+K+ PP WK  PAGRILE SILHLAMSE+ V+ TRH IVINE
Sbjct:   197 KKLLAAVVDKWDSHVVIIEKISPPDWKSAPAGRILEFSILHLAMSEVAVLETRHPIVINE 256

Query:   181 AVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEV 223
             AVDLAKRFCDG+APRIINGCLRTFV++   T+  +A +  +EV
Sbjct:   257 AVDLAKRFCDGSAPRIINGCLRTFVKDRATTSTPQALELKQEV 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 ?
Query227
cd00619130 cd00619, Terminator_NusB, Transcription terminatio 4e-28
cd00447129 cd00447, NusB_Sun, RNA binding domain of NusB (N p 1e-20
TIGR01951129 TIGR01951, nusB, transcription antitermination fac 4e-10
pfam01029126 pfam01029, NusB, NusB family 4e-09
PRK00202137 PRK00202, nusB, transcription antitermination prot 2e-08
PRK09634207 PRK09634, nusB, transcription antitermination prot 4e-08
COG0781151 COG0781, NusB, Transcription termination factor [T 3e-06
PRK14902 444 PRK14902, PRK14902, 16S rRNA methyltransferase B; 4e-04
>gnl|CDD|238342 cd00619, Terminator_NusB, Transcription termination factor NusB (N protein-Utilization Substance B) Back     alignment and domain information 
 Score =  103 bits (258), Expect = 4e-28
 Identities = 43/131 (32%), Positives = 68/131 (51%), Gaps = 4/131 (3%)

Query: 80  TETVEEADELLRSDEEESAIEAEVLSAPPKLVY-SKLLLRFTRKLLVAVVDKWDAHVHII 138
               E A + L + E    I AEV+S    L Y SK +L F  KL+  V++  +    +I
Sbjct: 2   RRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELI 61

Query: 139 DKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRII 197
           +K +     D+    I+E +IL LA+ E+  +    H +VINEA++LAKRF    + + +
Sbjct: 62  EKHLRNWSLDR--LAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFV 119

Query: 198 NGCLRTFVRNL 208
           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 227
COG0781151 NusB Transcription termination factor [Transcripti 100.0
PF01029134 NusB: NusB family; InterPro: IPR006027 This domain 100.0
PRK00202137 nusB transcription antitermination protein NusB; R 100.0
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 99.97
cd00447129 NusB_Sun RNA binding domain of NusB (N protein-Uti 99.95
PRK09634207 nusB transcription antitermination protein NusB; P 99.95
PRK10901 427 16S rRNA methyltransferase B; Provisional 99.93
PRK14904 445 16S rRNA methyltransferase B; Provisional 99.92
PRK14901 434 16S rRNA methyltransferase B; Provisional 99.92
PRK14902 444 16S rRNA methyltransferase B; Provisional 99.92
TIGR00563 426 rsmB ribosomal RNA small subunit methyltransferase 99.89
PRK14903 431 16S rRNA methyltransferase B; Provisional 99.87
PF09185140 DUF1948: Domain of unknown function (DUF1948); Int 82.86
>COG0781 NusB Transcription termination factor [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=4e-33  Score=231.25  Aligned_cols=142  Identities=25%  Similarity=0.363  Sum_probs=117.5

Q ss_pred             CCCccHHHHHHHHHHHHHHHhcCC-ChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhH
Q 027155           17 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE   95 (227)
Q Consensus        17 ~~~~R~~aRe~Avq~Lyq~~~~~~-~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~   95 (227)
                      +..+|+++|++|+|+||||++++. ++.++++....               .|..+   +.                   
T Consensus         6 ~~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~---------------~~~~~---d~-------------------   48 (151)
T COG0781           6 PKLTRRQARELAVQALYQWELSGSVSAEDILEDIEE---------------EFVEN---EL-------------------   48 (151)
T ss_pred             ccchHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHH---------------HHhhc---cc-------------------
Confidence            567899999999999999999765 45555543322               00000   00                   


Q ss_pred             HHHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcC-Cch
Q 027155           96 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRH  174 (227)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~-iP~  174 (227)
                            +         ....+..|+..|+.||.+|+..||.+|.++++ +|+++||+.+ ||+|||+|+|||+|.+ +|.
T Consensus        49 ------~---------~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L~-~w~~~rL~~v-erAILRla~yEl~~~~dvP~  111 (151)
T COG0781          49 ------D---------IELADSEYFRSLVKGVLENQEELDELISPHLK-KWSLERLDLV-ERAILRLALYELLFRDDVPY  111 (151)
T ss_pred             ------c---------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHc-cCCHHHhhHH-HHHHHHHHHHHHHhcCCCCC
Confidence                  0         01147899999999999999999999999994 6999999997 9999999999999975 999


Q ss_pred             hhHHHHHHHHHHhhCCCCCCChhHHHHhHHHhhhhccc
Q 027155          175 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  212 (227)
Q Consensus       175 ~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r~~~~~e  212 (227)
                      .|+|||||+|||.||.+++++||||||+++++..++.+
T Consensus       112 ~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~~  149 (151)
T COG0781         112 KVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPKE  149 (151)
T ss_pred             cchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhhc
Confidence            99999999999999999999999999999998876543

>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
>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
>PF09185 DUF1948: Domain of unknown function (DUF1948); InterPro: IPR015268 Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold 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 ?
Query227
3r2d_A149 Protein NUSB, N utilization substance protein B; c 9e-11
3d3b_A141 Protein NUSB, N utilization substance protein B; N 4e-10
1eyv_A156 NUSB protein, N-utilizing substance protein B homo 4e-10
1tzv_A142 NUSB protein, N utilization substance protein B ho 6e-10
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed bet 3e-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 = 57.4 bits (139), Expect = 9e-11
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 7/107 (6%)

Query: 119 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-Q 175
           + +KL+   V   +     ID ++    K     R+  +E + L L ++E+  + ++   
Sbjct: 47  YAKKLVDTAVRHIEE----IDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPG 102

Query: 176 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKE 222
            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
>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
>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
>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 ?
Query227
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 99.91
2yxl_A 450 PH0851 protein, 450AA long hypothetical FMU protei 99.91
>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=4.6e-36  Score=245.90  Aligned_cols=140  Identities=25%  Similarity=0.402  Sum_probs=117.5

Q ss_pred             CccHHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHH
Q 027155           19 CSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESA   98 (227)
Q Consensus        19 ~~R~~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~   98 (227)
                      .+|+++|+.|+|+||+++.+|.++.++++.++....                                            
T Consensus         3 ~~R~~aR~~A~q~L~~~~~~~~~~~~~l~~~~~~~~--------------------------------------------   38 (149)
T 3r2d_A            3 RYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKN--------------------------------------------   38 (149)
T ss_dssp             THHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHT--------------------------------------------
T ss_pred             ccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcc--------------------------------------------
Confidence            468999999999999999999999999887654100                                            


Q ss_pred             HHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhH
Q 027155           99 IEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIV  177 (227)
Q Consensus        99 ~~~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~va  177 (227)
                                  ..+..|++|+++||+||++|+..||++|++++ ++|+++|++++ +++|||+|+|||+|+ ++|++|+
T Consensus        39 ------------~~~~~dr~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~~~rl~~~-~r~iLrla~yEl~~~~~iP~~va  104 (149)
T 3r2d_A           39 ------------IKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-KGWSIDRLGYV-ERNALRLGVAELIFLKSKEPGRV  104 (149)
T ss_dssp             ------------CCCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC----CGGGSCHH-HHHHHHHHHHHHTTSCCSCHHHH
T ss_pred             ------------cCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCccccCHH-HHHHHHHHHHHHHHcCCCCCeeh
Confidence                        01346899999999999999999999999999 68999999997 799999999999997 8999999


Q ss_pred             HHHHHHHHHhhCCCCCCChhHHHHhHHHhhhhccccccc
Q 027155          178 INEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEA  216 (227)
Q Consensus       178 InEaVeLAK~~g~~~s~~FVNaVLr~i~r~~~~~e~~~~  216 (227)
                      |||||++||.|+++++++|||||||++.|+.+..+.++.
T Consensus       105 InEaVelaK~~~~~~~~~fVNgVLr~i~r~~~~~~~~~~  143 (149)
T 3r2d_A          105 FIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEK  143 (149)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHC--------
T ss_pred             HHHHHHHHHHhCCCCccccchHHhhHHHHhhcccccccC
Confidence            999999999999999999999999999999988887764
>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 227
d1sqga1140 a.79.1.3 (A:5-144) Ribosomal RNA small subunit met 3e-09
d1ey1a_139 a.79.1.1 (A:) Antitermination factor NusB {Escheri 3e-09
d1tzva_141 a.79.1.1 (A:) Antitermination factor NusB {Thermot 3e-09
d1eyva_131 a.79.1.1 (A:) Antitermination factor NusB {Mycobac 5e-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 = 51.6 bits (123), Expect = 3e-09
 Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 3/91 (3%)

Query: 119 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVI 178
             ++L   V+        +I+K++      +         ++ + + ++          +
Sbjct: 39  LLQELCFGVLRTLSQLDWLINKLMARPMTGKQR---TVHYLIMVGLYQLLYTRIPPHAAL 95

Query: 179 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 209
            E V+ A          +ING LR F R  E
Sbjct: 96  AETVEGAIAIKRPQLKGLINGVLRQFQRQQE 126
>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} Length = 139 Back     information, alignment and structure
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Length = 141 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 ?
Query227
d1tzva_141 Antitermination factor NusB {Thermotoga maritima [ 100.0
d1ey1a_139 Antitermination factor NusB {Escherichia coli [Tax 100.0
d1eyva_131 Antitermination factor NusB {Mycobacterium tubercu 99.98
d1sqga1140 Ribosomal RNA small subunit methyltransferase B, R 99.96
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
class: All alpha proteins
fold: NusB-like
superfamily: NusB-like
family: Antitermination factor NusB
domain: Antitermination factor NusB
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=4.1e-34  Score=227.75  Aligned_cols=136  Identities=16%  Similarity=0.295  Sum_probs=118.0

Q ss_pred             CCccHHHHHHHHHHHHHHHhcCCC-hHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHH
Q 027155           18 FCSPRAARELALLVVYAACLEGSD-PIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEE   96 (227)
Q Consensus        18 ~~~R~~aRe~Avq~Lyq~~~~~~~-~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~   96 (227)
                      ..+|+.+|++|+|+|||+++++.. .+.+++.+...                   .                        
T Consensus         2 k~pR~~aR~~a~q~Ly~~~~~~~~~~~~~~~~~~~~-------------------~------------------------   38 (141)
T d1tzva_           2 KTPRRRMRLAVFKALFQHEFRRDEDLEQILEEILDE-------------------T------------------------   38 (141)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCTTSCHHHHHHHHCCT-------------------T------------------------
T ss_pred             CChhHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHh-------------------c------------------------
Confidence            357899999999999999998654 44444332220                   0                        


Q ss_pred             HHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchh
Q 027155           97 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQ  175 (227)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~  175 (227)
                                     .+..|++|++.|++||++++..||++|.+++ ++|+++|++++ +++|||+|+|||+|. ++|++
T Consensus        39 ---------------~~~~d~~~~~~lv~g~~~~~~~id~~I~~~~-~~~~~~rl~~~-~~~iLr~a~~El~~~~~~p~~  101 (141)
T d1tzva_          39 ---------------YDKKAKEDARRYIRGIKENLSMIDDLISRYL-EKWSLNRLSVV-DRNVLRLATYELLFEKDIPIE  101 (141)
T ss_dssp             ---------------SCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC-SSSCGGGSCHH-HHHHHHHHHHHHHHCTTSCHH
T ss_pred             ---------------cchhHHHHHHHHHHHHHHhHHHHHHHHHHhc-ccCChHHHHHH-HHHHHHHHHHHHHhccccchh
Confidence                           2456899999999999999999999999998 68999999997 799999999999995 79999


Q ss_pred             hHHHHHHHHHHhhCCCCCCChhHHHHhHHHhhhhcccc
Q 027155          176 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTAN  213 (227)
Q Consensus       176 vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r~~~~~e~  213 (227)
                      |+|||||++||.||+++++||||||||+++|+.++.|-
T Consensus       102 v~InEaVelak~~~~~~~~~fVNaVL~~i~r~~~~~e~  139 (141)
T d1tzva_         102 VTIDEAIEIAKRYGTENSGKFVNGILDRIAKEHAPKEK  139 (141)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHCCGGG
T ss_pred             HHHHHHHHHHHHhCCCcccchHHHHHHHHHHHcCchhc
Confidence            99999999999999999999999999999999887664
>d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]} 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