Citrus Sinensis ID: 021860

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------
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
cccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccccccccccccccc
cccccccccccccccccEEEEccccccccccccccccHHHccccccHHccccccccHcccccccHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccEcHHHHHHccccccccccEEEccHHHHHHHHHccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHccccccccHHHHHHHHHHHHHHHHHHHHcccccHEEHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccccccccccc
maveatssflscsskthflfnlrassspsswkKFTQSANFaaknrhvcrnerpnvscsAAAFAVQETLEKTRESVMASSAKEmmpkidksgrfcsPRAARELALLVVYAACLEGSDPIRLFEKRLnsrrepgyefdksslleynhmsfggppvttetVEEADELLRSDEEESAIEAEvlsappklVYSKLLLRFTRKLLVAVVDKWDAhvhiidkvvppiwkvwkmdqpagrILELSILHLAMSEITVVGTRHQIVINEAVDLAKrfcdgaapriiNGCLRTFVRNLEGtanieaskaskevpsev
maveatssflscssKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMassakemmpkidksGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIeaevlsappklvYSKLLLRFTRKLLVAVVDKWDAHVhiidkvvppiwKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGtanieaskaskevpsev
MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
***************THFLFNL************************VC***********AAF******************************FCSPRAARELALLVVYAACLEGSDPIRLFEK*******************************************************LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT****************
*************SKTHFLFNLRASSSPS**************************************************************RFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF***********************
**********SCSSKTHFLFNLRAS*********TQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIE************
***********C*SKTHFLFNLRAS****S****TQSA**A****H***NERPNVS*********************************SGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE******************
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAVEATSSFLSCSSKTHFLFNLRASSSPSSWKKFTQSANFAAKNRHVCRNERPNVSCSAAAFAVQETLEKTRESVMASSAKEMMPKIDKSGRFCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPSEV
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 ?
Query306 2.2.26 [Sep-21-2011]
B1WXY6209 N utilization substance p yes no 0.225 0.330 0.394 6e-07
Q18B61169 N utilization substance p yes no 0.228 0.414 0.388 1e-06
Q5N1J7213 N utilization substance p yes no 0.225 0.323 0.394 2e-06
Q8GIR7213 N utilization substance p yes no 0.225 0.323 0.394 2e-06
B8HYJ8209 N utilization substance p yes no 0.267 0.392 0.357 2e-06
B5YE05144 N utilization substance p yes no 0.254 0.541 0.358 3e-06
B2J3F1213 N utilization substance p yes no 0.267 0.384 0.340 4e-06
A7GWZ7131 N utilization substance p yes no 0.215 0.503 0.367 4e-06
B7K4P4211 N utilization substance p yes no 0.254 0.369 0.325 6e-06
A7GSK0130 N utilization substance p yes no 0.274 0.646 0.344 1e-05
>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 desciption
 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 213 IDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 272
           ID+ +  + K W++ + A   ++  IL LA++EI  +    ++ INEAV+LAKR+ D   
Sbjct: 134 IDEQLEAVLKDWQLKRLAK--IDQDILRLAVAEILFLDVPEKVSINEAVELAKRYSDDDG 191

Query: 273 PRIINGCLRTF 283
            R ING LR F
Sbjct: 192 YRFINGVLRRF 202
Involved in the transcription termination process.
Cyanothece sp. (strain ATCC 51142) (taxid: 43989)
>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|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|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|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
>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|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 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|A7GSK0|NUSB_BACCN N utilization substance protein B homolog OS=Bacillus cereus subsp. cytotoxis (strain NVH 391-98) 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 ?
Query306
225435806288 PREDICTED: uncharacterized protein LOC10 0.882 0.937 0.681 1e-108
297746508218 unnamed protein product [Vitis vinifera] 0.712 1.0 0.819 1e-104
224073118218 predicted protein [Populus trichocarpa] 0.705 0.990 0.827 1e-103
449463840378 PREDICTED: uncharacterized protein LOC10 0.686 0.555 0.775 4e-96
18416739301 antitermination NusB domain-containing p 0.702 0.714 0.767 6e-89
2982469286 putative protein [Arabidopsis thaliana] 0.702 0.751 0.767 9e-89
297799366300 antitermination NusB domain-containing p 0.702 0.716 0.762 1e-88
388512429288 unknown [Lotus japonicus] 0.849 0.902 0.605 2e-86
255564810309 RNA binding protein, putative [Ricinus c 0.620 0.614 0.77 2e-84
363807164289 uncharacterized protein LOC100809333 [Gl 0.781 0.826 0.645 5e-82
>gi|225435806|ref|XP_002285757.1| PREDICTED: uncharacterized protein LOC100265613 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  397 bits (1019), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 201/295 (68%), Positives = 231/295 (78%), Gaps = 25/295 (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 LLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV 249
           L+LRFTRKLLVAVVDKW++HV +IDKV PP WK    ++PAGRILEL ILHLAMSEI V+
Sbjct: 178 LILRFTRKLLVAVVDKWNSHVLVIDKVAPPNWK----NEPAGRILELCILHLAMSEIAVL 233

Query: 250 GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKEVPS 304
           GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV++LEGT    AS+ ++EV S
Sbjct: 234 GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVKDLEGTGITRASETTQEVVS 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 ?
Query306
TAIR|locus:2131428301 AT4G26370 [Arabidopsis thalian 0.964 0.980 0.611 1.1e-87
TIGR_CMR|BA_4406130 BA_4406 "N utilization substan 0.274 0.646 0.321 5.9e-06
UNIPROTKB|P65582140 nusB "N utilization substance 0.274 0.6 0.333 7.6e-06
TIGR_CMR|GSU_1692138 GSU_1692 "N utilization substa 0.228 0.507 0.356 0.00023
TIGR_CMR|DET_1278143 DET_1278 "N utilization substa 0.264 0.566 0.309 0.00023
TAIR|locus:2131428 AT4G26370 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 876 (313.4 bits), Expect = 1.1e-87, P = 1.1e-87
 Identities = 186/304 (61%), Positives = 221/304 (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 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSI 238
             LSAPPKLVYSKL+LRF +KLL AVVDKWD+HV II+K+ PP WK      PAGRILE SI
Sbjct:   180 LSAPPKLVYSKLVLRFAKKLLAAVVDKWDSHVVIIEKISPPDWK----SAPAGRILEFSI 235

Query:   239 LHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKA 298
             LHLAMSE+ V+ TRH IVINEAVDLAKRFCDG+APRIINGCLRTFV++   T+  +A + 
Sbjct:   236 LHLAMSEVAVLETRHPIVINEAVDLAKRFCDGSAPRIINGCLRTFVKDRATTSTPQALEL 295

Query:   299 SKEV 302
              +EV
Sbjct:   296 KQEV 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
TIGR_CMR|BA_4406 BA_4406 "N utilization substance protein B" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|P65582 nusB "N utilization substance protein B homolog" [Streptococcus pneumoniae TIGR4 (taxid:170187)] 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
TIGR_CMR|DET_1278 DET_1278 "N utilization substance protein B" [Dehalococcoides ethenogenes 195 (taxid:243164)] 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 ?
Query306
cd00619130 cd00619, Terminator_NusB, Transcription terminatio 3e-28
cd00447129 cd00447, NusB_Sun, RNA binding domain of NusB (N p 5e-20
TIGR01951129 TIGR01951, nusB, transcription antitermination fac 4e-11
pfam01029126 pfam01029, NusB, NusB family 4e-10
PRK00202137 PRK00202, nusB, transcription antitermination prot 3e-09
PRK09634207 PRK09634, nusB, transcription antitermination prot 4e-08
COG0781151 COG0781, NusB, Transcription termination factor [T 3e-07
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 = 3e-28
 Identities = 44/135 (32%), Positives = 70/135 (51%), Gaps = 8/135 (5%)

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 DKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAA 272
           +K +      W +D+    I+E +IL LA+ E+  +    H +VINEA++LAKRF    +
Sbjct: 62  EKHLRN----WSLDR--LAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDS 115

Query: 273 PRIINGCLRTFVRNL 287
            + +NG L    ++L
Sbjct: 116 HKFVNGVLDKIAKDL 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 306
COG0781151 NusB Transcription termination factor [Transcripti 99.97
PF01029134 NusB: NusB family; InterPro: IPR006027 This domain 99.97
PRK00202137 nusB transcription antitermination protein NusB; R 99.96
cd00619130 Terminator_NusB Transcription termination factor N 99.96
TIGR01951129 nusB transcription antitermination factor NusB. A 99.96
cd00620126 Methyltransferase_Sun N-terminal RNA binding domai 99.95
PRK09634207 nusB transcription antitermination protein NusB; P 99.92
cd00447129 NusB_Sun RNA binding domain of NusB (N protein-Uti 99.92
PRK10901 427 16S rRNA methyltransferase B; Provisional 99.91
PRK14904 445 16S rRNA methyltransferase B; Provisional 99.89
PRK14902 444 16S rRNA methyltransferase B; Provisional 99.89
PRK14901 434 16S rRNA methyltransferase B; Provisional 99.88
TIGR00563 426 rsmB ribosomal RNA small subunit methyltransferase 99.85
PRK14903 431 16S rRNA methyltransferase B; Provisional 99.83
>COG0781 NusB Transcription termination factor [Transcription] Back     alignment and domain information 
Probab=99.97  E-value=3e-30  Score=224.13  Aligned_cols=141  Identities=26%  Similarity=0.399  Sum_probs=113.7

Q ss_pred             CCCCchHHHHHHHHHHHHHHhcCC-ChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhH
Q 021860           92 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE  170 (306)
Q Consensus        92 ~~~~Rr~ARe~Avq~LYq~e~~g~-~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~  170 (306)
                      .+..||++|++|||+||||++++. +++++++....               .|.+.   +.                   
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            345789999999999999999765 45555553322               11000   00                   


Q ss_pred             HHHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-
Q 021860          171 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-  249 (306)
Q Consensus       171 ~~~~~~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-  249 (306)
                            +         ....+..|+..|+.||.+|+.+||.+|.++|++ |+   +++++  .|||+|||+|+|||+|. 
T Consensus        49 ------~---------~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L~~-w~---~~rL~--~verAILRla~yEl~~~~  107 (151)
T COG0781          49 ------D---------IELADSEYFRSLVKGVLENQEELDELISPHLKK-WS---LERLD--LVERAILRLALYELLFRD  107 (151)
T ss_pred             ------c---------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHcc-CC---HHHhh--HHHHHHHHHHHHHHHhcC
Confidence                  0         011478999999999999999999999999976 65   56665  69999999999999997 


Q ss_pred             CCChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhcc
Q 021860          250 GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT  290 (306)
Q Consensus       250 diP~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~~  290 (306)
                      ++|.+|+|||||+|||.|+++++++|||||||++++..+..
T Consensus       108 dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~  148 (151)
T COG0781         108 DVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPK  148 (151)
T ss_pred             CCCCcchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhh
Confidence            59999999999999999999999999999999999876543

>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
>PRK09634 nusB transcription antitermination protein NusB; Provisional 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
>PRK10901 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14904 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14902 16S rRNA methyltransferase B; Provisional Back     alignment and domain information
>PRK14901 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 ?
Query306
3r2d_A149 Protein NUSB, N utilization substance protein B; c 1e-11
3d3b_A141 Protein NUSB, N utilization substance protein B; N 1e-10
1tzv_A142 NUSB protein, N utilization substance protein B ho 1e-10
1eyv_A156 NUSB protein, N-utilizing substance protein B homo 2e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
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 = 60.8 bits (148), Expect = 1e-11
 Identities = 24/109 (22%), Positives = 48/109 (44%), Gaps = 7/109 (6%)

Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRH 253
           + +KL+   V   +     ID ++    K W +D+     +E + L L ++E+  + ++ 
Sbjct: 47  YAKKLVDTAVRHIEE----IDSIIEKHLKGWSIDRLG--YVERNALRLGVAELIFLKSKE 100

Query: 254 -QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASKE 301
              V  + VDL K++ D  A + +NG L    +    ++  E      E
Sbjct: 101 PGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEKPSLKSE 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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 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 ?
Query306
3r2d_A149 Protein NUSB, N utilization substance protein B; c 100.0
1tzv_A142 NUSB protein, N utilization substance protein B ho 99.98
3d3b_A141 Protein NUSB, N utilization substance protein B; N 99.98
1eyv_A156 NUSB protein, N-utilizing substance protein B homo 99.97
1sqg_A 429 SUN protein, FMU protein; rossmann-fold, mixed bet 99.89
2yxl_A 450 PH0851 protein, 450AA long hypothetical FMU protei 99.88
>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=1.6e-33  Score=240.68  Aligned_cols=141  Identities=25%  Similarity=0.415  Sum_probs=115.1

Q ss_pred             CCCchHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHH
Q 021860           93 FCSPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEES  172 (306)
Q Consensus        93 ~~~Rr~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~  172 (306)
                      |+.|+.+|+.|+|+||+++.+|.+++++++.++....                                           
T Consensus         2 m~~R~~aR~~A~q~L~~~~~~~~~~~~~l~~~~~~~~-------------------------------------------   38 (149)
T 3r2d_A            2 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKN-------------------------------------------   38 (149)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHT-------------------------------------------
T ss_pred             CccHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcc-------------------------------------------
Confidence            5678999999999999999999999999887654100                                           


Q ss_pred             HHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CC
Q 021860          173 AIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GT  251 (306)
Q Consensus       173 ~~~~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-di  251 (306)
                                   ..++.|++|+++|++||++|+..||++|++++ ++|+   +++++  +++++|||+|+|||+|+ ++
T Consensus        39 -------------~~~~~dr~~~~~lv~gvl~~~~~lD~~i~~~l-~~w~---~~rl~--~~~r~iLrla~yEl~~~~~i   99 (149)
T 3r2d_A           39 -------------IKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL-KGWS---IDRLG--YVERNALRLGVAELIFLKSK   99 (149)
T ss_dssp             -------------CCCHHHHHHHHHHHHHHHHTHHHHHHHHHTTC----C---GGGSC--HHHHHHHHHHHHHHTTSCCS
T ss_pred             -------------cCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCC---ccccC--HHHHHHHHHHHHHHHHcCCC
Confidence                         02456899999999999999999999999998 4554   45554  58899999999999997 89


Q ss_pred             ChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhccccccc
Q 021860          252 RHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEA  295 (306)
Q Consensus       252 P~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~~e~~~~  295 (306)
                      |++|+|||||+|||.|+++++++|||||||++.++..+.+.+.+
T Consensus       100 P~~vaInEaVelaK~~~~~~~~~fVNgVLr~i~r~~~~~~~~~~  143 (149)
T 3r2d_A          100 EPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEK  143 (149)
T ss_dssp             CHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHC--------
T ss_pred             CCeehHHHHHHHHHHhCCCCccccchHHhhHHHHhhcccccccC
Confidence            99999999999999999999999999999999999887777644
>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 306
d1sqga1140 a.79.1.3 (A:5-144) Ribosomal RNA small subunit met 4e-09
d1ey1a_139 a.79.1.1 (A:) Antitermination factor NusB {Escheri 9e-09
d1eyva_131 a.79.1.1 (A:) Antitermination factor NusB {Mycobac 1e-08
d1tzva_141 a.79.1.1 (A:) Antitermination factor NusB {Thermot 1e-08
>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 = 52.0 bits (124), Expect = 4e-09
 Identities = 15/95 (15%), Positives = 32/95 (33%), Gaps = 7/95 (7%)

Query: 194 FTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRH 253
             ++L   V+        +I+K++       +            ++ + + ++       
Sbjct: 39  LLQELCFGVLRTLSQLDWLINKLMARPMTGKQRTV-------HYLIMVGLYQLLYTRIPP 91

Query: 254 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 288
              + E V+ A          +ING LR F R  E
Sbjct: 92  HAALAETVEGAIAIKRPQLKGLINGVLRQFQRQQE 126
>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
>d1tzva_ a.79.1.1 (A:) Antitermination factor NusB {Thermotoga maritima [TaxId: 2336]} Length = 141 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 ?
Query306
d1ey1a_139 Antitermination factor NusB {Escherichia coli [Tax 99.97
d1tzva_141 Antitermination factor NusB {Thermotoga maritima [ 99.97
d1eyva_131 Antitermination factor NusB {Mycobacterium tubercu 99.96
d1sqga1140 Ribosomal RNA small subunit methyltransferase B, R 99.95
>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=99.97  E-value=6.3e-32  Score=223.33  Aligned_cols=133  Identities=21%  Similarity=0.296  Sum_probs=115.8

Q ss_pred             CchHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHH
Q 021860           95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI  174 (306)
Q Consensus        95 ~Rr~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~  174 (306)
                      +||.+|++|+|+|||++++|.++++++..++...                  .                           
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            4788999999999999999999999988776520                  0                           


Q ss_pred             HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCCh
Q 021860          175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRH  253 (306)
Q Consensus       175 ~~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~  253 (306)
                                  +++.|+.|+++|++||++|+..||.+|+++++.+     +++++  +++++|||+|+|||+|. ++|+
T Consensus        40 ------------~~~~d~~~~~~l~~gv~~~~~~id~~I~~~l~~~-----~~r~~--~~~~~ILr~a~~El~~~~~~p~  100 (139)
T d1ey1a_          40 ------------VKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRL-----LEELG--QVEKAVLRIALYELSKRSDVPY  100 (139)
T ss_dssp             ------------SSSCCCHHHHHHHHHHHHHHHHHHHHHTTCCCSC-----TTTSC--HHHHHHHHHHHHHHHSCSSCCS
T ss_pred             ------------cchhhHHHHHHHHHHHHHhHHHHHHHHHHHHHhh-----HHhcC--hHHHHHHHHHHHHHHHccCCCc
Confidence                        1234789999999999999999999999998522     45665  58999999999999996 7999


Q ss_pred             hhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhccc
Q 021860          254 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA  291 (306)
Q Consensus       254 ~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~~e  291 (306)
                      +|+|||||+|||.|+++++++|||||||++++++++.+
T Consensus       101 ~viInE~Velak~~~~~~~~~fVNgVL~~i~k~~r~~e  138 (139)
T d1ey1a_         101 KVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNK  138 (139)
T ss_dssp             HHHHHHHHHHTTTTTCSSSSHHHHHHHHHHHHHHCTTC
T ss_pred             eehHHHHHHHHHHhCCCCccchHHHHHHHHHHHhCccC
Confidence            99999999999999999999999999999999887654
>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