Citrus Sinensis ID: 028198

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--
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIFKHHTDKRAPLQPPIRKALAVFSGRRNPNDNHYSHPKH
cccccccccccccccccccHHHHHHHHccccccEEEEEccHHHHHHHHHHHccEEEccccccEEEEEEEEEEcccccEEcccccccccccccccccEEEEEEEEccccEEEEEccccccccccccccccccccccccccccEEcccccHHccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccccccccccccccccccHHHHHHccccccEEEEEHHHHHHHHHHHHcccEEccccHHHHHHHHHHHEHHHHHHcccccccEccccccccccEEEEEEEEccccEEEEEEcccEcccccEEEcccccccccccccccEEccccHHHHHHHHHHHHccccccccccccccccEcccccccccccccccccEcccccccccccccccccc
meissknneivdvsyvddecseqswMLRSLSESTVACITGDYAMQNVILQMGLRllapggmqIRQLHRWILKCHACYTITAEIgrifcpkcgnggtlRKVAVTVGENgivlasrrpritlrgtkfslpmpqggrdaiTKNLIlredqlpqkylyprnkkkvnkegdnfvtsddifkhhtdkraplqppIRKALAVFsgrrnpndnhyshpkh
meissknneivdvsyVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVgengivlasrrpritlrgtkfslpmpqggrDAITKNLIlredqlpqkylyprnkkkvnkegdNFVTSDDIFKhhtdkraplqppIRKALAVFSgrrnpndnhyshpkh
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIFKHHTDKRAPLQPPIRKALAVFSGRRNPNDNHYSHPKH
*********IVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLP*****RDAITKNLILREDQLPQKYLY**********************************************************
****************************SLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFS**************LILRED***********************TSDDIF*************************************
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIFKHHTDKRAPLQPPIRKALAVFSGRRNP**********
******************ECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKV*KEGDNFVTSDDIFKH***********************************
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MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIFKHHTDKRAPLQPPIRKALAVFSGRRNPNDNHYSHPKH
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 ?
Query212 2.2.26 [Sep-21-2011]
Q5RBB3411 RNA-binding protein NOB1 yes no 0.778 0.401 0.412 3e-27
Q9ULX3412 RNA-binding protein NOB1 yes no 0.778 0.400 0.406 5e-27
Q3T042413 RNA-binding protein NOB1 yes no 0.768 0.394 0.412 6e-27
Q4R537412 RNA-binding protein NOB1 N/A no 0.778 0.400 0.401 7e-27
Q6VEU1410 RNA-binding protein NOB1 yes no 0.778 0.402 0.389 2e-26
Q8BW10403 RNA-binding protein NOB1 yes no 0.778 0.409 0.389 5e-26
Q9UTK0388 20S-pre-rRNA D-site endon yes no 0.75 0.409 0.352 4e-21
Q08444459 20S-pre-rRNA D-site endon yes no 0.547 0.252 0.352 1e-11
O29862166 Putative ribonuclease Vap yes no 0.292 0.373 0.358 5e-05
>sp|Q5RBB3|NOB1_PONAB RNA-binding protein NOB1 OS=Pongo abelii GN=NOB1 PE=2 SV=1 Back     alignment and function desciption
 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 73/177 (41%), Positives = 110/177 (62%), Gaps = 12/177 (6%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94
           V C+T D+AMQNV+LQMGL +LA  GM IR+   +IL+CH C+  T+++ R+FC  CGN 
Sbjct: 231 VGCVTTDFAMQNVLLQMGLHVLAVNGMLIREARSYILRCHGCFKTTSDMSRVFCSHCGN- 289

Query: 95  GTLRKVAVTVGENGIVLA--SRRPRI-TLRGTKFSLPMPQGGRDAITKNLILREDQ-LPQ 150
            TL+KV+VTV ++G +    SR P++   RG ++SLP P+GG+ AI  +L   EDQ  PQ
Sbjct: 290 KTLKKVSVTVSDDGTLHMHFSRNPKVLNPRGLRYSLPTPKGGKYAINPHLT--EDQRFPQ 347

Query: 151 KYLYPRNKKKVNKEGDNFVTSDDIFKHH--TDKRAPLQPPIRKALAVFSGRRNPNDN 205
             L  + ++K N    ++V     F  +  + + A LQ  +R + ++ +GRR  N N
Sbjct: 348 LRLSRKARQKTNVFAPDYVAGVSPFVENDISSRSATLQ--VRDS-SLGAGRRRLNPN 401
May play a role in mRNA degradation.
Pongo abelii (taxid: 9601)
>sp|Q9ULX3|NOB1_HUMAN RNA-binding protein NOB1 OS=Homo sapiens GN=NOB1 PE=1 SV=1 Back     alignment and function description
>sp|Q3T042|NOB1_BOVIN RNA-binding protein NOB1 OS=Bos taurus GN=NOB1 PE=2 SV=1 Back     alignment and function description
>sp|Q4R537|NOB1_MACFA RNA-binding protein NOB1 OS=Macaca fascicularis GN=NOB1 PE=2 SV=1 Back     alignment and function description
>sp|Q6VEU1|NOB1_RAT RNA-binding protein NOB1 OS=Rattus norvegicus GN=Nob1 PE=2 SV=1 Back     alignment and function description
>sp|Q8BW10|NOB1_MOUSE RNA-binding protein NOB1 OS=Mus musculus GN=Nob1 PE=1 SV=1 Back     alignment and function description
>sp|Q9UTK0|NOB1_SCHPO 20S-pre-rRNA D-site endonuclease nob1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=nob1 PE=3 SV=1 Back     alignment and function description
>sp|Q08444|NOB1_YEAST 20S-pre-rRNA D-site endonuclease NOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NOB1 PE=1 SV=1 Back     alignment and function description
>sp|O29862|VAPC8_ARCFU Putative ribonuclease VapC8 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=vapC8 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 ?
Query212
255537423 628 RNA-binding protein nob1, putative [Rici 1.0 0.337 0.839 1e-106
449452344 617 PREDICTED: RNA-binding protein NOB1-like 1.0 0.343 0.826 1e-105
449495836 617 PREDICTED: LOW QUALITY PROTEIN: RNA-bind 1.0 0.343 0.826 1e-105
224071796 588 predicted protein [Populus trichocarpa] 1.0 0.360 0.816 1e-102
356513405 632 PREDICTED: uncharacterized protein LOC10 0.990 0.332 0.781 1e-99
356528162 634 PREDICTED: uncharacterized protein LOC10 0.995 0.332 0.764 9e-99
359474015 633 PREDICTED: RNA-binding protein NOB1-like 0.995 0.333 0.777 2e-98
297742539 560 unnamed protein product [Vitis vinifera] 0.995 0.376 0.777 2e-98
147800398 621 hypothetical protein VITISV_020978 [Viti 0.995 0.339 0.777 2e-98
357520491 613 RNA-binding protein NOB1 [Medicago trunc 0.981 0.339 0.752 1e-95
>gi|255537423|ref|XP_002509778.1| RNA-binding protein nob1, putative [Ricinus communis] gi|223549677|gb|EEF51165.1| RNA-binding protein nob1, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 178/212 (83%), Positives = 195/212 (91%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ++I S+  E VDVS+ DD+ SEQSWMLRSLSES+VAC+T DYAMQNV+LQMGLRLLAPGG
Sbjct: 417 LDILSETTETVDVSHGDDDASEQSWMLRSLSESSVACVTSDYAMQNVLLQMGLRLLAPGG 476

Query: 61  MQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITL 120
           MQIRQLHRWILKCHACYT+TAEIGRIFCPKCGNGGTLRKVA+TVGENGIVLA  RPRI+L
Sbjct: 477 MQIRQLHRWILKCHACYTVTAEIGRIFCPKCGNGGTLRKVAITVGENGIVLADCRPRISL 536

Query: 121 RGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIFKHHTD 180
           RGTKFSLP+PQGGRDAITKNLILREDQLPQK LYP+ KKKVNK+GD+F   DDIF HHTD
Sbjct: 537 RGTKFSLPLPQGGRDAITKNLILREDQLPQKLLYPKTKKKVNKQGDDFFAVDDIFSHHTD 596

Query: 181 KRAPLQPPIRKALAVFSGRRNPNDNHYSHPKH 212
           KRAP +PPIRKALAVFSGRRNPNDNHYS PK+
Sbjct: 597 KRAPFRPPIRKALAVFSGRRNPNDNHYSRPKN 628

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449452344|ref|XP_004143919.1| PREDICTED: RNA-binding protein NOB1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449495836|ref|XP_004159959.1| PREDICTED: LOW QUALITY PROTEIN: RNA-binding protein NOB1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224071796|ref|XP_002303575.1| predicted protein [Populus trichocarpa] gi|222841007|gb|EEE78554.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356513405|ref|XP_003525404.1| PREDICTED: uncharacterized protein LOC100800291 [Glycine max] Back     alignment and taxonomy information
>gi|356528162|ref|XP_003532674.1| PREDICTED: uncharacterized protein LOC100785714 [Glycine max] Back     alignment and taxonomy information
>gi|359474015|ref|XP_002269627.2| PREDICTED: RNA-binding protein NOB1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|297742539|emb|CBI34688.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|147800398|emb|CAN66411.1| hypothetical protein VITISV_020978 [Vitis vinifera] Back     alignment and taxonomy information
>gi|357520491|ref|XP_003630534.1| RNA-binding protein NOB1 [Medicago truncatula] gi|355524556|gb|AET05010.1| RNA-binding protein NOB1 [Medicago truncatula] 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 ?
Query212
TAIR|locus:2163071602 NOB1 [Arabidopsis thaliana (ta 1.0 0.352 0.733 2e-86
UNIPROTKB|Q9ULX3412 NOB1 "RNA-binding protein NOB1 0.768 0.395 0.412 1e-27
UNIPROTKB|Q3T042413 NOB1 "RNA-binding protein NOB1 0.768 0.394 0.412 2.2e-27
RGD|735222410 Nob1 "NIN1/RPN12 binding prote 0.768 0.397 0.395 2.2e-27
MGI|MGI:1914869403 Nob1 "NIN1/RPN12 binding prote 0.768 0.404 0.395 5.7e-27
POMBASE|SPAC1486.09388 SPAC1486.09 "ribosome biogenes 0.75 0.409 0.346 2.6e-21
FB|FBgn0030177472 CG2972 [Drosophila melanogaste 0.584 0.262 0.454 4.4e-21
WB|WBGene00021843364 Y54E10BR.4 [Caenorhabditis ele 0.542 0.315 0.388 7.8e-16
UNIPROTKB|G4MQ79467 MGG_09254 "20S-pre-rRNA D-site 0.523 0.237 0.357 2.1e-14
ASPGD|ASPL0000014547431 AN8253 [Emericella nidulans (t 0.617 0.303 0.342 4.7e-14
TAIR|locus:2163071 NOB1 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 864 (309.2 bits), Expect = 2.0e-86, P = 2.0e-86
 Identities = 157/214 (73%), Positives = 187/214 (87%)

Query:     1 MEISSKNNEIVDVSYV-DDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPG 59
             +EI+S+  +  + S + DD  SEQSW LR+LSES+VACITGDYAMQNVILQMGLRLLAPG
Sbjct:   389 LEIASEAEDTFEASSIGDDGSSEQSWSLRALSESSVACITGDYAMQNVILQMGLRLLAPG 448

Query:    60 GMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRIT 119
             GMQIRQLHRWILKCHACYT+T EIGRIFCPKCGNGGTLRKVAVT+G NG ++A+ +PRIT
Sbjct:   449 GMQIRQLHRWILKCHACYTVTPEIGRIFCPKCGNGGTLRKVAVTIGANGAIIAACKPRIT 508

Query:   120 LRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKKVNKEGDNFVTSDDIF-KHH 178
             LRGT++S+PMP+GGR+AITKNLILREDQLPQK L+PR KKK +K GD +  SDD+F  HH
Sbjct:   509 LRGTQYSIPMPKGGREAITKNLILREDQLPQKLLHPRTKKKASKPGDEYFVSDDVFLNHH 568

Query:   179 TDKRAPLQPPIRKALAVFSGRRNPNDNHYSHPKH 212
             +D++APLQPP+RKA++VFS +RNPNDNHYS   H
Sbjct:   569 SDRKAPLQPPVRKAMSVFSQKRNPNDNHYSRSMH 602
GO:0005634 "nucleus" evidence=ISM
GO:0006606 "protein import into nucleus" evidence=RCA
GO:0000469 "cleavage involved in rRNA processing" evidence=IDA
GO:0004521 "endoribonuclease activity" evidence=IDA
GO:0005737 "cytoplasm" evidence=IDA
GO:0006364 "rRNA processing" evidence=IMP
GO:0009553 "embryo sac development" evidence=IMP
GO:0009555 "pollen development" evidence=IMP
UNIPROTKB|Q9ULX3 NOB1 "RNA-binding protein NOB1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q3T042 NOB1 "RNA-binding protein NOB1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
RGD|735222 Nob1 "NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
MGI|MGI:1914869 Nob1 "NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
POMBASE|SPAC1486.09 SPAC1486.09 "ribosome biogenesis protein Nob1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
FB|FBgn0030177 CG2972 [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
WB|WBGene00021843 Y54E10BR.4 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|G4MQ79 MGG_09254 "20S-pre-rRNA D-site endonuclease NOB1" [Magnaporthe oryzae 70-15 (taxid:242507)] Back     alignment and assigned GO terms
ASPGD|ASPL0000014547 AN8253 [Emericella nidulans (taxid:162425)] 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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query212
pfam0877273 pfam08772, NOB1_Zn_bind, Nin one binding (NOB1) Zn 7e-31
COG1439177 COG1439, COG1439, Predicted nucleic acid-binding p 6e-12
>gnl|CDD|192150 pfam08772, NOB1_Zn_bind, Nin one binding (NOB1) Zn-ribbon like Back     alignment and domain information 
 Score =  107 bits (270), Expect = 7e-31
 Identities = 36/74 (48%), Positives = 52/74 (70%), Gaps = 3/74 (4%)

Query: 62  QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENG--IVLASRRPRIT 119
           +I+QL RWIL+CHAC+  T ++ + FCPKCGN  TLR+VAV+V E+G   +   +  +  
Sbjct: 1   RIKQLRRWILRCHACFKTTPDMTKQFCPKCGN-ATLRRVAVSVDEDGEIKLHLKKNFQWN 59

Query: 120 LRGTKFSLPMPQGG 133
            RGT +S+P P+GG
Sbjct: 60  TRGTIYSIPKPKGG 73

This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding). Length = 73
>gnl|CDD|224356 COG1439, COG1439, Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 212
KOG2463376 consensus Predicted RNA-binding protein Nob1p invo 100.0
PF0877273 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik 99.98
COG1439177 Predicted nucleic acid-binding protein, consists o 99.88
PRK12496164 hypothetical protein; Provisional 99.74
TIGR03875206 RNA_lig_partner RNA ligase partner, MJ_0950 family 97.7
PRK04358217 hypothetical protein; Provisional 97.54
PF0972342 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134 96.38
smart0083441 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C 96.15
TIGR0260552 CxxC_CxxC_SSSS putative regulatory protein, FmdB f 96.06
PF1324826 zf-ribbon_3: zinc-ribbon domain 95.62
PF08745205 UPF0278: UPF0278 family; InterPro: IPR022785 This 95.53
PF1324023 zinc_ribbon_2: zinc-ribbon domain 94.47
COG1545140 Predicted nucleic-acid-binding protein containing 94.24
PF1217237 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35 94.15
PRK03681114 hypA hydrogenase nickel incorporation protein; Val 94.02
PRK00564117 hypA hydrogenase nickel incorporation protein; Pro 93.99
TIGR00100115 hypA hydrogenase nickel insertion protein HypA. In 93.94
PRK12380113 hydrogenase nickel incorporation protein HybF; Pro 93.83
PRK1313056 H/ACA RNA-protein complex component Nop10p; Review 93.45
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 93.45
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 93.33
PRK03824135 hypA hydrogenase nickel incorporation protein; Pro 92.97
PF01155113 HypA: Hydrogenase expression/synthesis hypA family 92.94
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 92.29
COG3364112 Zn-ribbon containing protein [General function pre 92.16
PF09845131 DUF2072: Zn-ribbon containing protein (DUF2072); I 91.96
cd0072934 rubredoxin_SM Rubredoxin, Small Modular nonheme ir 91.72
COG1579239 Zn-ribbon protein, possibly nucleic acid-binding [ 91.47
PF10263157 SprT-like: SprT-like family; InterPro: IPR006640 T 91.34
COG199649 RPC10 DNA-directed RNA polymerase, subunit RPC10 ( 91.32
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 91.17
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 90.79
COG1592166 Rubrerythrin [Energy production and conversion] 90.76
PF0413553 Nop10p: Nucleolar RNA-binding protein, Nop10p fami 90.71
PRK04351149 hypothetical protein; Provisional 89.62
COG209364 DNA-directed RNA polymerase, subunit E'' [Transcri 89.5
COG1645131 Uncharacterized Zn-finger containing protein [Gene 89.23
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 88.88
PRK0639364 rpoE DNA-directed RNA polymerase subunit E''; Vali 88.27
PRK07591 421 threonine synthase; Validated 88.19
TIGR03844 398 cysteate_syn cysteate synthase. Members of this fa 88.18
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 87.5
COG226059 Predicted Zn-ribbon RNA-binding protein [Translati 87.46
PRK0835161 DNA-directed RNA polymerase subunit E''; Validated 87.42
PF11023114 DUF2614: Protein of unknown function (DUF2614); In 87.38
COG1198 730 PriA Primosomal protein N' (replication factor Y) 87.33
COG233182 Uncharacterized protein conserved in bacteria [Fun 86.86
PRK00762124 hypA hydrogenase nickel incorporation protein; Pro 86.81
TIGR02300129 FYDLN_acid conserved hypothetical protein TIGR0230 86.37
PRK00241256 nudC NADH pyrophosphatase; Reviewed 86.0
TIGR00595 505 priA primosomal protein N'. All proteins in this f 85.8
COG5257 415 GCD11 Translation initiation factor 2, gamma subun 85.79
PRK06450 338 threonine synthase; Validated 85.63
PRK14714 1337 DNA polymerase II large subunit; Provisional 85.56
PF07295146 DUF1451: Protein of unknown function (DUF1451); In 84.93
PRK06260 397 threonine synthase; Validated 84.41
PF0519136 ADK_lid: Adenylate kinase, active site lid; InterP 84.18
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 84.09
PRK00420112 hypothetical protein; Validated 83.86
COG026750 RpmG Ribosomal protein L33 [Translation, ribosomal 83.38
PRK11032160 hypothetical protein; Provisional 83.19
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 83.11
smart00731146 SprT SprT homologues. Predicted to have roles in t 82.94
PRK14559 645 putative protein serine/threonine phosphatase; Pro 82.61
PF1277350 DZR: Double zinc ribbon 82.39
PF1277350 DZR: Double zinc ribbon 82.38
COG0375115 HybF Zn finger protein HypA/HybF (possibly regulat 81.89
PF1420555 Cys_rich_KTR: Cysteine-rich KTR 81.72
PF0215035 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I 81.05
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information 
Probab=100.00  E-value=1.5e-61  Score=438.64  Aligned_cols=181  Identities=41%  Similarity=0.721  Sum_probs=156.0

Q ss_pred             CcCCCCceeeec--------------CCCceeeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccccccc
Q 028198           18 DECSEQSWMLRS--------------LSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEI   83 (212)
Q Consensus        18 d~~s~~~Wi~~~--------------l~~~~vac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~   83 (212)
                      ||.++..||+++              ..++.|||+|+||||||||+||||+++++.|++|+++++|+|||||||+++++|
T Consensus       176 ed~DdDgwitp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iLRCh~Cfsit~~m  255 (376)
T KOG2463|consen  176 EDADDDGWITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYILRCHGCFSITSEM  255 (376)
T ss_pred             cccccccccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhheeEeeeeeEecCcc
Confidence            333344499977              146789999999999999999999999999999999999999999999999999


Q ss_pred             CccccCCCCCCCceeEEEEEeCCCceEEeec--CCccccccceeccCCCCCCCCCCCCCceecCCCCcccccchhhhcc-
Q 028198           84 GRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKK-  160 (212)
Q Consensus        84 ~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~--k~~~n~RG~~ySlPkpkgGk~~~~~~~IL~EDQ~~~~~~~~k~r~k-  160 (212)
                      ++.|||+||++ ||+||+|||++||+++.|.  +++||+||++||||+|||||+.  +|+||+|||+++++..+++|+| 
T Consensus       256 ~k~FCp~CG~~-TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~PkGgk~~--kN~~LrEDQ~~~q~~~~q~rkk~  332 (376)
T KOG2463|consen  256 PKDFCPSCGHK-TLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPKPKGGKVA--KNPILREDQPEPQRRYVQTRKKV  332 (376)
T ss_pred             chhcccccCCC-eeeEEEEEecCCCceeEEeecccccccCcceeecCCCCCCccc--cCccccccCchHHHHHHHHHHhh
Confidence            99999999999 9999999999999987665  5579999999999999999997  8999999998888888778887 


Q ss_pred             cCCCCCCccCCCCcccc--CCCccccCCchhhhhceeccccCCCCCCCCCC
Q 028198          161 VNKEGDNFVTSDDIFKH--HTDKRAPLQPPIRKALAVFSGRRNPNDNHYSH  209 (212)
Q Consensus       161 ~~~~d~dy~~~~~~f~~--~~~k~a~l~~~~~~~~~~~~grrNPN~~~~~~  209 (212)
                      .+++++ |    .||+.  ..+++|.++  +|+.+.+|. |||||++|+++
T Consensus       333 ~~~~~~-y----gpf~~~d~~s~~a~~~--v~~~~~~~k-~rnpN~skr~~  375 (376)
T KOG2463|consen  333 KKPLNE-Y----GPFSGHDVTSRSAILG--VRQHVRIGK-RRNPNESKRKS  375 (376)
T ss_pred             hccccc-c----CCcccccccccccccc--hhhhhhhhc-cCCCchhcccc
Confidence            577776 7    38953  367777776  455565665 78999999875

>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 Back     alignment and domain information
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only] Back     alignment and domain information
>PRK12496 hypothetical protein; Provisional Back     alignment and domain information
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family Back     alignment and domain information
>PRK04358 hypothetical protein; Provisional Back     alignment and domain information
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria Back     alignment and domain information
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein Back     alignment and domain information
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains Back     alignment and domain information
>PF13240 zinc_ribbon_2: zinc-ribbon domain Back     alignment and domain information
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only] Back     alignment and domain information
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins Back     alignment and domain information
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated Back     alignment and domain information
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional Back     alignment and domain information
>TIGR00100 hypA hydrogenase nickel insertion protein HypA Back     alignment and domain information
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional Back     alignment and domain information
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed Back     alignment and domain information
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Back     alignment and domain information
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional Back     alignment and domain information
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation Back     alignment and domain information
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>COG3364 Zn-ribbon containing protein [General function prediction only] Back     alignment and domain information
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function Back     alignment and domain information
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase Back     alignment and domain information
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only] Back     alignment and domain information
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT) Back     alignment and domain information
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Back     alignment and domain information
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center Back     alignment and domain information
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues Back     alignment and domain information
>COG1592 Rubrerythrin [Energy production and conversion] Back     alignment and domain information
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs Back     alignment and domain information
>PRK04351 hypothetical protein; Provisional Back     alignment and domain information
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription] Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>PRK07591 threonine synthase; Validated Back     alignment and domain information
>TIGR03844 cysteate_syn cysteate synthase Back     alignment and domain information
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates Back     alignment and domain information
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins Back     alignment and domain information
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair] Back     alignment and domain information
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional Back     alignment and domain information
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300 Back     alignment and domain information
>PRK00241 nudC NADH pyrophosphatase; Reviewed Back     alignment and domain information
>TIGR00595 priA primosomal protein N' Back     alignment and domain information
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK06450 threonine synthase; Validated Back     alignment and domain information
>PRK14714 DNA polymerase II large subunit; Provisional Back     alignment and domain information
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length Back     alignment and domain information
>PRK06260 threonine synthase; Validated Back     alignment and domain information
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2 Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>PRK00420 hypothetical protein; Validated Back     alignment and domain information
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK11032 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>smart00731 SprT SprT homologues Back     alignment and domain information
>PRK14559 putative protein serine/threonine phosphatase; Provisional Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only] Back     alignment and domain information
>PF14205 Cys_rich_KTR: Cysteine-rich KTR Back     alignment and domain information
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2 Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query212
2con_A79 Solution Structure Of Rsgi Ruh-035, A Zn-Ribbon Mod 8e-09
>pdb|2CON|A Chain A, Solution Structure Of Rsgi Ruh-035, A Zn-Ribbon Module In Mouse Cdna Length = 79 Back     alignment and structure 
Iteration: 1

 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 47/73 (64%), Gaps = 4/73 (5%)
Query: 57  APGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLA--SR 114
           + G   +R+   +IL+CH C+  T+++ R+FC  CGN  TL+KV+VT+ ++G +    SR
Sbjct: 2   SSGSSGVREARSYILRCHGCFKTTSDMNRVFCGHCGN-KTLKKVSVTINDDGTLHMHFSR 60
Query: 115 RPRI-TLRGTKFS 126
            P++   RG ++S
Sbjct: 61  NPKVLNPRGLRYS 73

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query212
2con_A79 RUH-035 protein, NIN one binding protein; ribosome 3e-30
2lcq_A165 Putative toxin VAPC6; PIN domain, Zn ribbon domain 2e-19
>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1 Length = 79 Back     alignment and structure
 Score =  105 bits (265), Expect = 3e-30
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 5/80 (6%)

Query: 57  APGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIV---LAS 113
           + G   +R+   +IL+CH C+  T+++ R+FC  CGN  TL+KV+VT+ ++G +    + 
Sbjct: 2   SSGSSGVREARSYILRCHGCFKTTSDMNRVFCGHCGN-KTLKKVSVTINDDGTLHMHFSR 60

Query: 114 RRPRITLRGTKFSLPMPQGG 133
               +  RG ++S   P  G
Sbjct: 61  NPKVLNPRGLRYS-SGPSSG 79
>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii} Length = 165 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query212
2con_A79 RUH-035 protein, NIN one binding protein; ribosome 100.0
2lcq_A165 Putative toxin VAPC6; PIN domain, Zn ribbon domain 99.64
3irb_A145 Uncharacterized protein from DUF35 family; 1381535 96.13
2gnr_A145 Conserved hypothetical protein; 13815350, structur 95.88
2kdx_A119 HYPA, hydrogenase/urease nickel incorporation prot 94.88
2aus_D60 NOP10, ribosome biogenesis protein NOP10; isomeras 93.41
2apo_B60 Ribosome biogenesis protein NOP10; protein-protein 93.37
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 92.83
4ayb_P48 DNA-directed RNA polymerase; transferase, multi-su 92.15
3a43_A139 HYPD, hydrogenase nickel incorporation protein HYP 91.98
3i8o_A142 KH domain-containing protein MJ1533; APC89320.5, m 91.82
3pwf_A170 Rubrerythrin; non heme iron peroxidases, oxidative 90.46
3ix7_A134 Uncharacterized protein TTHA0540; unknown function 89.6
6rxn_A46 Rubredoxin; electron transfer(iron-sulfur protein) 89.18
3na7_A256 HP0958; flagellar biogenesis, flagellum export, C4 87.2
1yuz_A202 Nigerythrin; rubrythrin, rubredoxin, hemerythrin, 86.9
1lko_A191 Rubrerythrin all-iron(II) form; reduced form, DIIR 86.45
3cng_A189 Nudix hydrolase; structural genomics, APC7497, PSI 83.58
1vk6_A269 NADH pyrophosphatase; 1790429, structural genomics 83.37
2jrp_A81 Putative cytoplasmic protein; two-zinc binding pro 83.19
3h0g_L63 DNA-directed RNA polymerases I, II, and III subuni 83.07
1yk4_A52 Rubredoxin, RD; electron transport; 0.69A {Pyrococ 82.56
1e8j_A52 Rubredoxin; iron-sulfur-protein, zinc-substitution 82.34
4rxn_A54 Rubredoxin; electron transfer(iron-sulfur protein) 82.17
2gmg_A105 Hypothetical protein PF0610; winged-helix like pro 80.79
1qxf_A66 GR2, 30S ribosomal protein S27E; structural genomi 80.77
>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1 Back     alignment and structure
Probab=100.00  E-value=2.1e-34  Score=214.70  Aligned_cols=75  Identities=35%  Similarity=0.821  Sum_probs=71.3

Q ss_pred             cCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeec--CCc-cccccceeccCCCCC
Q 028198           57 APGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPR-ITLRGTKFSLPMPQG  132 (212)
Q Consensus        57 s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~--k~~-~n~RG~~ySlPkpkg  132 (212)
                      +++|++|+++++|+|||||||+++.+|+++|||+|||+ ||+||+|+||+||++++|.  +++ ||+||++||||+|+|
T Consensus         2 s~~G~~Ir~~k~~iLrC~aCf~~t~~~~k~FCp~CGn~-TL~Rvsvsvd~~G~~~~hl~~n~~~~n~RG~~ySlPkpkG   79 (79)
T 2con_A            2 SSGSSGVREARSYILRCHGCFKTTSDMNRVFCGHCGNK-TLKKVSVTINDDGTLHMHFSRNPKVLNPRGLRYSSGPSSG   79 (79)
T ss_dssp             CCCCCCCCCCCCEEEECSSSCCEESCSSCCSCSSSCCS-CCEEEECBCCSSCCCBCCCCCCCCCCCCCCCCCCCCCCCC
T ss_pred             CCCceEeeeeeeeeeEecccceECCCcccccccccCcc-cceEEEEEECCCCcEEEeccCCccccccCCCCccCCCCCC
Confidence            68999999999999999999999999999999999998 9999999999999987765  578 999999999999997
>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii} Back     alignment and structure
>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus} Back     alignment and structure
>2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} PDB: 3irb_A Back     alignment and structure
>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori} Back     alignment and structure
>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B Back     alignment and structure
>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A Back     alignment and structure
>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ... Back     alignment and structure
>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X Back     alignment and structure
>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A* Back     alignment and structure
>3i8o_A KH domain-containing protein MJ1533; APC89320.5, methanocaldococcus jannaschii DSM 2661, structural genomics, PSI-2; 2.64A {Methanocaldococcus jannaschii} Back     alignment and structure
>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A Back     alignment and structure
>3ix7_A Uncharacterized protein TTHA0540; unknown function, thermus thermophilus HB8, structural genom 2, protein structure initiative; HET: MSE; 2.15A {Thermus thermophilus} Back     alignment and structure
>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1 Back     alignment and structure
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori} Back     alignment and structure
>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A Back     alignment and structure
>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A Back     alignment and structure
>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718} Back     alignment and structure
>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A Back     alignment and structure
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ... Back     alignment and structure
>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A Back     alignment and structure
>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ... Back     alignment and structure
>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82 Back     alignment and structure
>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4 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 212
d2cona166 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin o 1e-25
>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]} Length = 66 Back     information, alignment and structure

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 92.5 bits (230), Expect = 1e-25
 Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 4/67 (5%)

Query: 63  IRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENG---IVLASRRPRIT 119
           +R+   +IL+CH C+  T+++ R+FC  CGN  TL+KV+VT+ ++G   +  +     + 
Sbjct: 1   VREARSYILRCHGCFKTTSDMNRVFCGHCGN-KTLKKVSVTINDDGTLHMHFSRNPKVLN 59

Query: 120 LRGTKFS 126
            RG ++S
Sbjct: 60  PRGLRYS 66

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query212
d2cona166 RNA-binding protein NOB1 (Nin one binding) {Mouse 99.94
d2gnra1137 Hypothetical protein SSO2064 {Sulfolobus solfatari 95.46
d2apob155 Ribosome biogenesis protein Nop10 {Archaeon Methan 93.47
d2ey4e152 Ribosome biogenesis protein Nop10 {Archaeon Pyroco 93.4
d1nnqa237 Rubrerythrin, C-terminal domain {Archaeon Pyrococc 93.37
d1yuza236 Nigerythrin, C-terminal domain {Desulfovibrio vulg 92.06
d1lkoa244 Rubrerythrin, C-terminal domain {Desulfovibrio vul 85.22
d2ak3a237 Microbial and mitochondrial ADK, insert "zinc fing 84.69
>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.94  E-value=3.6e-28  Score=173.99  Aligned_cols=63  Identities=38%  Similarity=0.936  Sum_probs=58.4

Q ss_pred             ceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeecC--Cc-cccccceec
Q 028198           63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRR--PR-ITLRGTKFS  126 (212)
Q Consensus        63 I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~k--~~-~n~RG~~yS  126 (212)
                      |+++++|+|||||||+++.+|++.|||+|||+ ||+||+|+||+||++++|.+  ++ ||+||++||
T Consensus         1 Ir~vr~~~LrC~aCf~~t~~~~k~FCpkCGn~-TL~rvsvsvd~~G~~~~h~~~~~k~~n~RG~~yS   66 (66)
T d2cona1           1 VREARSYILRCHGCFKTTSDMNRVFCGHCGNK-TLKKVSVTINDDGTLHMHFSRNPKVLNPRGLRYS   66 (66)
T ss_dssp             CCCCCCEEEECSSSCCEESCSSCCSCSSSCCS-CCEEEECBCCSSCCCBCCCCCCCCCCCCCCCCCC
T ss_pred             ChhhheeeeEeeecCcCcCCcccccCcccCCC-ceeEEEEEECCCCcEEEEecCCCceecCCccCCc
Confidence            78999999999999999999999999999998 99999999999999877654  35 899999998
>d2gnra1 b.40.4.15 (A:8-144) Hypothetical protein SSO2064 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2apob1 g.41.16.1 (B:403-457) Ribosome biogenesis protein Nop10 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2ey4e1 g.41.16.1 (E:4-55) Ribosome biogenesis protein Nop10 {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]} Back     information, alignment and structure