Psyllid ID: psy4748

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------
MTSEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
ccccccccccccccccccccccccccccEEEEccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHcccccccccccccccccEEEEEEHHccccccccEEEEcccc
cccccccccccHHcccccccccccccccEEEEccccccccHHHccccEEEEEEcccccccccEEEEEEEcccccHHccccccEEEccccccccccccccEEEccccccccccEEEEEEEEEccccccEEEEEcccc
mtsegyfnvesefcskcgtilplfdfkgdvkcyvcktsygtqeqqplllgpdilfLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEkekqkdkteiadgpiverkckrcnndtMSYATLQLRSADEGQTIFFTCTKC
MTSEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTsygtqeqqpllLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFntvekekqkdkteiadgpiverkckrcnNDTMSYATlqlrsadegqtIFFTCTKC
MTSEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
*****YFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVE************GPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTC***
******F*VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLF*****************************ADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
MTSEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
******FNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDK*EIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTSEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC
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 ?
Query136 2.2.26 [Sep-21-2011]
Q1XHV8126 DNA-directed RNA polymera yes N/A 0.779 0.841 0.323 1e-13
Q9P1U0126 DNA-directed RNA polymera yes N/A 0.779 0.841 0.323 1e-13
Q5TM50126 DNA-directed RNA polymera yes N/A 0.779 0.841 0.323 1e-13
Q1RMP0123 DNA-directed RNA polymera yes N/A 0.779 0.861 0.315 3e-13
Q6MFY5123 DNA-directed RNA polymera yes N/A 0.779 0.861 0.307 2e-12
Q791N7123 DNA-directed RNA polymera yes N/A 0.779 0.861 0.315 3e-12
P32529125 DNA-directed RNA polymera yes N/A 0.330 0.36 0.577 6e-10
O94703119 DNA-directed RNA polymera yes N/A 0.757 0.865 0.314 4e-09
Q56254110 DNA-directed RNA polymera N/A N/A 0.279 0.345 0.447 0.0006
>sp|Q1XHV8|RPA12_PANTR DNA-directed RNA polymerase I subunit RPA12 OS=Pan troglodytes GN=ZNRD1 PE=3 SV=1 Back     alignment and function desciption
 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/130 (32%), Positives = 67/130 (51%), Gaps = 24/130 (18%)

Query: 7   FNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLF 66
           F  + +FCS CG++LPL   +  V C  C  +               + ++ F+G     
Sbjct: 13  FQSDLDFCSDCGSVLPLPGAQDTVTCIRCGFN---------------INVRDFEGKVVKT 57

Query: 67  LAVFEEIKAEYTIHFNTVEKEKQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEG 126
             VF ++     +   +VE+  +        GP+V+R+C RC ++ M+Y T Q+RSADEG
Sbjct: 58  SVVFHQLGTAMPM---SVEEGPE------CQGPVVDRRCPRCGHEGMAYHTRQMRSADEG 108

Query: 127 QTIFFTCTKC 136
           QT+F+TCT C
Sbjct: 109 QTVFYTCTNC 118
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.
Pan troglodytes (taxid: 9598)
>sp|Q9P1U0|RPA12_HUMAN DNA-directed RNA polymerase I subunit RPA12 OS=Homo sapiens GN=ZNRD1 PE=1 SV=1 Back     alignment and function description
>sp|Q5TM50|RPA12_MACMU DNA-directed RNA polymerase I subunit RPA12 OS=Macaca mulatta GN=ZNRD1 PE=3 SV=1 Back     alignment and function description
>sp|Q1RMP0|RPA12_BOVIN DNA-directed RNA polymerase I subunit RPA12 OS=Bos taurus GN=ZNRD1 PE=2 SV=1 Back     alignment and function description
>sp|Q6MFY5|RPA12_RAT DNA-directed RNA polymerase I subunit RPA12 OS=Rattus norvegicus GN=Znrd1 PE=3 SV=1 Back     alignment and function description
>sp|Q791N7|RPA12_MOUSE DNA-directed RNA polymerase I subunit RPA12 OS=Mus musculus GN=Znrd1 PE=2 SV=1 Back     alignment and function description
>sp|P32529|RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPA12 PE=1 SV=1 Back     alignment and function description
>sp|O94703|RPA12_SCHPO DNA-directed RNA polymerase I subunit RPA12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpa12 PE=3 SV=1 Back     alignment and function description
>sp|Q56254|RPOM_THECE DNA-directed RNA polymerase subunit M OS=Thermococcus celer GN=rpoM PE=1 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 ?
Query136
383855900125 PREDICTED: DNA-directed RNA polymerase I 0.720 0.784 0.507 2e-25
380030611123 PREDICTED: DNA-directed RNA polymerase I 0.720 0.796 0.488 1e-24
328778973110 PREDICTED: DNA-directed RNA polymerase I 0.720 0.890 0.488 2e-24
357617341120 transcription-associated zinc ribbon pro 0.808 0.916 0.456 7e-24
321470559122 hypothetical protein DAPPUDRAFT_303407 [ 0.808 0.901 0.421 1e-23
312379327114 hypothetical protein AND_26701 [Anophele 0.794 0.947 0.446 2e-23
350407595123 PREDICTED: DNA-directed RNA polymerase I 0.772 0.853 0.474 3e-23
340717534123 PREDICTED: DNA-directed RNA polymerase I 0.772 0.853 0.467 3e-23
157126224124 DNA-directed RNA polymerase I, 12kD-subu 0.757 0.830 0.462 4e-23
157126222121 DNA-directed RNA polymerase I, 12kD-subu 0.757 0.851 0.462 5e-23
>gi|383855900|ref|XP_003703448.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like [Megachile rotundata] Back     alignment and taxonomy information
 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 65/128 (50%), Positives = 76/128 (59%), Gaps = 30/128 (23%)

Query: 13  FCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEE 72
           FCS CG+ILPL   KGDVKCY CK ++G +                           F +
Sbjct: 16  FCSDCGSILPLLGEKGDVKCYACKRTWGPE--------------------------AFGD 49

Query: 73  IKAEYTIHFN---TVEKEKQKDKTEI-ADGPIVERKCKRCNNDTMSYATLQLRSADEGQT 128
           +   YTIHFN     E  KQKD  E  A+GP+VERKC +C ND MSYATLQLRSADEGQT
Sbjct: 50  MYMNYTIHFNKKDAYESSKQKDDDEDEAEGPVVERKCPQCQNDKMSYATLQLRSADEGQT 109

Query: 129 IFFTCTKC 136
           +F+TCTKC
Sbjct: 110 VFYTCTKC 117

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|380030611|ref|XP_003698937.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like [Apis florea] Back     alignment and taxonomy information
>gi|328778973|ref|XP_003249576.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like, partial [Apis mellifera] Back     alignment and taxonomy information
>gi|357617341|gb|EHJ70731.1| transcription-associated zinc ribbon protein [Danaus plexippus] Back     alignment and taxonomy information
>gi|321470559|gb|EFX81535.1| hypothetical protein DAPPUDRAFT_303407 [Daphnia pulex] Back     alignment and taxonomy information
>gi|312379327|gb|EFR25638.1| hypothetical protein AND_26701 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|350407595|ref|XP_003488137.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|340717534|ref|XP_003397236.1| PREDICTED: DNA-directed RNA polymerase I subunit RPA12-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|157126224|ref|XP_001660857.1| DNA-directed RNA polymerase I, 12kD-subunit, putative [Aedes aegypti] gi|108873328|gb|EAT37553.1| AAEL010468-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|157126222|ref|XP_001660856.1| DNA-directed RNA polymerase I, 12kD-subunit, putative [Aedes aegypti] gi|108873327|gb|EAT37552.1| AAEL010468-PB [Aedes aegypti] 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 ?
Query136
FB|FBgn0038903120 RpI12 "RpI12" [Drosophila mela 0.5 0.566 0.616 9.2e-20
CGD|CAL0006382123 RPA12 [Candida albicans (taxid 0.389 0.430 0.518 9.8e-17
UNIPROTKB|B6ICU4123 ZNRD1 "DNA-directed RNA polyme 0.286 0.317 0.615 9.8e-17
UNIPROTKB|F1PIF7126 ZNRD1 "DNA-directed RNA polyme 0.338 0.365 0.531 2.5e-16
MGI|MGI:1913386123 Znrd1 "zinc ribbon domain cont 0.286 0.317 0.564 4.1e-16
RGD|1303114123 Znrd1 "zinc ribbon domain cont 0.338 0.373 0.521 6.6e-16
WB|WBGene00007616119 rpoa-12 [Caenorhabditis elegan 0.419 0.478 0.448 7.2e-15
SGD|S000003824125 RPA12 "RNA polymerase I subuni 0.389 0.424 0.537 4.9e-14
POMBASE|SPCC1259.03119 rpa12 "DNA-directed RNA polyme 0.352 0.403 0.471 1.1e-12
TAIR|locus:2092185119 AT3G25940 [Arabidopsis thalian 0.338 0.386 0.425 7.4e-12
FB|FBgn0038903 RpI12 "RpI12" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 45/73 (61%), Positives = 56/73 (76%)

Query:    69 VFEEIKAEYTIHFNTVEKEKQKDKTEI-----ADGPIVERKCKRCNNDTMSYATLQLRSA 123
             V+   K+E+TIHFNT +  K  ++T+      ADGP+VERKC +CN+D MSYATLQLRSA
Sbjct:    40 VYSGEKSEFTIHFNTYDPSKVFNRTKRESESDADGPVVERKCPKCNHDKMSYATLQLRSA 99

Query:   124 DEGQTIFFTCTKC 136
             DEGQT+FFTC KC
Sbjct:   100 DEGQTVFFTCLKC 112
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS
GO:0005736 "DNA-directed RNA polymerase I complex" evidence=ISS;NAS
GO:0006360 "transcription from RNA polymerase I promoter" evidence=NAS
GO:0003676 "nucleic acid binding" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
CGD|CAL0006382 RPA12 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
UNIPROTKB|B6ICU4 ZNRD1 "DNA-directed RNA polymerase subunit" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|F1PIF7 ZNRD1 "DNA-directed RNA polymerase subunit" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1913386 Znrd1 "zinc ribbon domain containing, 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1303114 Znrd1 "zinc ribbon domain containing 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
WB|WBGene00007616 rpoa-12 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
SGD|S000003824 RPA12 "RNA polymerase I subunit A12.2" [Saccharomyces cerevisiae (taxid:4932)] Back     alignment and assigned GO terms
POMBASE|SPCC1259.03 rpa12 "DNA-directed RNA polymerase complex I subunit Rpa12" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
TAIR|locus:2092185 AT3G25940 [Arabidopsis thaliana (taxid:3702)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
O94703RPA12_SCHPONo assigned EC number0.31450.75730.8655yesN/A
Q5TM50RPA12_MACMUNo assigned EC number0.32300.77940.8412yesN/A
Q6MFY5RPA12_RATNo assigned EC number0.30760.77940.8617yesN/A
Q9P1U0RPA12_HUMANNo assigned EC number0.32300.77940.8412yesN/A
Q791N7RPA12_MOUSENo assigned EC number0.31530.77940.8617yesN/A
Q1XHV8RPA12_PANTRNo assigned EC number0.32300.77940.8412yesN/A
Q1RMP0RPA12_BOVINNo assigned EC number0.31530.77940.8617yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query136
COG1594113 COG1594, RPB9, DNA-directed RNA polymerase, subuni 1e-12
pfam0109639 pfam01096, TFIIS_C, Transcription factor S-II (TFI 3e-11
smart0044040 smart00440, ZnF_C2C2, C2C2 Zinc finger 8e-09
TIGR01384104 TIGR01384, TFS_arch, transcription factor S, archa 3e-06
TIGR01385299 TIGR01385, TFSII, transcription elongation factor 1e-04
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information 
 Score = 59.8 bits (145), Expect = 1e-12
 Identities = 31/135 (22%), Positives = 49/135 (36%), Gaps = 41/135 (30%)

Query: 12  EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFE 71
            FC KCG++L       +    VC+                                 +E
Sbjct: 3   RFCPKCGSLL-YPKKDDEGGKLVCRKCG------------------------------YE 31

Query: 72  EIKAEYTIHFNTVEKEKQKDKTEIADG----------PIVERKCKRCNNDTMSYATLQLR 121
           E  +   ++  +V++  +K K  +             P  + KC +C N    Y  LQ R
Sbjct: 32  EEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGNKEAYYWQLQTR 91

Query: 122 SADEGQTIFFTCTKC 136
           SADE +T F+ CT+C
Sbjct: 92  SADEPETRFYKCTRC 106

Length = 113
>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS) Back     alignment and domain information
>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger Back     alignment and domain information
>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal Back     alignment and domain information
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 136
KOG2906|consensus105 100.0
KOG2907|consensus116 99.98
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 99.96
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 99.96
KOG2691|consensus113 99.94
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 99.82
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 99.78
PHA02998195 RNA polymerase subunit; Provisional 99.67
TIGR01385299 TFSII transcription elongation factor S-II. This m 99.4
PF0215035 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I 99.12
smart0066152 RPOL9 RNA polymerase subunit 9. 98.54
KOG1105|consensus296 98.19
PRK0043250 30S ribosomal protein S27ae; Validated 97.81
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 97.21
COG199851 RPS31 Ribosomal protein S27AE [Translation, riboso 96.43
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 96.41
PRK03564309 formate dehydrogenase accessory protein FdhE; Prov 96.06
TIGR01562305 FdhE formate dehydrogenase accessory protein FdhE. 95.96
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 95.86
PF1277350 DZR: Double zinc ribbon 95.23
PHA0062659 hypothetical protein 94.99
PF0775424 DUF1610: Domain of unknown function (DUF1610); Int 94.84
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 94.6
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 94.57
PF1324023 zinc_ribbon_2: zinc-ribbon domain 94.51
PF1324826 zf-ribbon_3: zinc-ribbon domain 94.3
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 94.22
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 93.46
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 93.41
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 93.25
TIGR00595 505 priA primosomal protein N'. All proteins in this f 93.18
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 92.76
PF1371937 zinc_ribbon_5: zinc-ribbon domain 92.74
PF0030147 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred 92.72
cd0073050 rubredoxin Rubredoxin; nonheme iron binding domain 92.61
COG2816279 NPY1 NTP pyrophosphohydrolases containing a Zn-fin 92.6
PRK00241256 nudC NADH pyrophosphatase; Reviewed 92.43
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 92.07
COG1198 730 PriA Primosomal protein N' (replication factor Y) 91.97
cd0072934 rubredoxin_SM Rubredoxin, Small Modular nonheme ir 91.97
PF0139639 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc 91.95
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 91.93
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 91.86
TIGR0105331 LSD1 zinc finger domain, LSD1 subclass. This model 91.84
PRK14973 936 DNA topoisomerase I; Provisional 91.6
PF1178136 RRN7: RNA polymerase I-specific transcription init 91.33
COG1592166 Rubrerythrin [Energy production and conversion] 91.32
PRK04023 1121 DNA polymerase II large subunit; Validated 91.25
TIGR0120654 lysW lysine biosynthesis protein LysW. This very s 90.92
PRK14559 645 putative protein serine/threonine phosphatase; Pro 90.87
PHA0062659 hypothetical protein 90.64
COG177355 Rubredoxin [Energy production and conversion] 90.57
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 90.52
PRK05580 679 primosome assembly protein PriA; Validated 90.51
PRK14873 665 primosome assembly protein PriA; Provisional 90.37
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 90.22
PRK14714 1337 DNA polymerase II large subunit; Provisional 90.19
COG283560 Uncharacterized conserved protein [Function unknow 89.59
PRK1228657 rpmF 50S ribosomal protein L32; Reviewed 89.58
COG1645131 Uncharacterized Zn-finger containing protein [Gene 89.09
PF0877273 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik 88.6
PRK10220111 hypothetical protein; Provisional 88.43
TIGR00686109 phnA alkylphosphonate utilization operon protein P 88.23
PF0178090 Ribosomal_L37ae: Ribosomal L37ae protein family; I 88.07
PRK07220740 DNA topoisomerase I; Validated 88.01
smart0064764 IBR In Between Ring fingers. the domains occurs be 87.59
PF0694325 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin 87.56
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 87.45
PF0148564 IBR: IBR domain; InterPro: IPR002867 Zinc finger ( 87.4
PF0879233 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I 87.21
PF1371736 zinc_ribbon_4: zinc-ribbon domain 86.88
PRK05452479 anaerobic nitric oxide reductase flavorubredoxin; 86.79
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 86.75
PRK1182760 hypothetical protein; Provisional 86.57
PF0908268 DUF1922: Domain of unknown function (DUF1922); Int 86.07
PF1345341 zf-TFIIB: Transcription factor zinc-finger 85.85
TIGR0103155 rpmF_bact ribosomal protein L32. This protein desc 85.6
PF0311928 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f 85.34
COG199649 RPC10 DNA-directed RNA polymerase, subunit RPC10 ( 85.29
TIGR00515 285 accD acetyl-CoA carboxylase, carboxyl transferase, 84.73
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 84.43
PF0667741 Auto_anti-p27: Sjogren's syndrome/scleroderma auto 84.39
COG1499 355 NMD3 NMD protein affecting ribosome stability and 84.36
PF0381136 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0 84.2
smart0083441 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C 84.17
COG2023105 RPR2 RNase P subunit RPR2 [Translation, ribosomal 84.02
CHL00174 296 accD acetyl-CoA carboxylase beta subunit; Reviewed 83.65
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 83.29
KOG3507|consensus62 83.27
PF07295146 DUF1451: Protein of unknown function (DUF1451); In 83.1
PRK05654 292 acetyl-CoA carboxylase subunit beta; Validated 82.76
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 82.09
TIGR0028091 L37a ribosomal protein L37a. This model finds euka 81.74
PF1012251 Mu-like_Com: Mu-like prophage protein Com; InterPr 81.7
KOG3084|consensus345 81.54
PRK00423 310 tfb transcription initiation factor IIB; Reviewed 81.52
COG0777 294 AccD Acetyl-CoA carboxylase beta subunit [Lipid me 81.45
PF1444654 Prok-RING_1: Prokaryotic RING finger family 1 81.44
PF0952671 DUF2387: Probable metal-binding protein (DUF2387); 81.43
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 81.38
PRK11032160 hypothetical protein; Provisional 81.38
PRK1489299 putative transcription elongation factor Elf1; Pro 80.62
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 80.57
COG347868 Predicted nucleic-acid-binding protein containing 80.54
PTZ0025590 60S ribosomal protein L37a; Provisional 80.2
PRK00420112 hypothetical protein; Validated 80.02
>KOG2906|consensus Back     alignment and domain information 
Probab=100.00  E-value=5.2e-34  Score=199.68  Aligned_cols=96  Identities=24%  Similarity=0.445  Sum_probs=81.1

Q ss_pred             ccccccCCCccccCCCC--CeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecceeec-
Q psy4748          11 SEFCSKCGTILPLFDFK--GDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKE-   87 (136)
Q Consensus        11 ~~FCp~CgnlL~~~~~~--~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~-   87 (136)
                      |.|||.|||||...++.  ..+.|++|+|..++..                              +|..++.+..++.+ 
T Consensus         1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~------------------------------ei~~r~~~~~Kevd~   50 (105)
T KOG2906|consen    1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFPISR------------------------------EISSRKYPKLKEVDD   50 (105)
T ss_pred             CcccCCCCCEEEEecCCeEeeEEcCCCCceeeEee------------------------------eeeccccCchhhhhh
Confidence            68999999999999763  6899999999999842                              24445555556655 


Q ss_pred             cccccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748          88 KQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC  136 (136)
Q Consensus        88 ~~~~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C  136 (136)
                      +++.+++++....+++.||+|||++|||+|+|+||||||||+||+|.+|
T Consensus        51 vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C   99 (105)
T KOG2906|consen   51 VLGGDEAWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKC   99 (105)
T ss_pred             hcCCcccccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcc
Confidence            5556667888888999999999999999999999999999999999998

>KOG2907|consensus Back     alignment and domain information
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal Back     alignment and domain information
>KOG2691|consensus Back     alignment and domain information
>smart00440 ZnF_C2C2 C2C2 Zinc finger Back     alignment and domain information
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PHA02998 RNA polymerase subunit; Provisional Back     alignment and domain information
>TIGR01385 TFSII transcription elongation factor S-II 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
>smart00661 RPOL9 RNA polymerase subunit 9 Back     alignment and domain information
>KOG1105|consensus Back     alignment and domain information
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains Back     alignment and domain information
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Back     alignment and domain information
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE Back     alignment and domain information
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex [] Back     alignment and domain information
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species 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
>PF13240 zinc_ribbon_2: zinc-ribbon domain Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain 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
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins Back     alignment and domain information
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues Back     alignment and domain information
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>TIGR00595 priA primosomal protein N' Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier [] Back     alignment and domain information
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center Back     alignment and domain information
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00241 nudC NADH pyrophosphatase; Reviewed Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] 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
>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
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i Back     alignment and domain information
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins Back     alignment and domain information
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass Back     alignment and domain information
>PRK14973 DNA topoisomerase I; Provisional Back     alignment and domain information
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[] Back     alignment and domain information
>COG1592 Rubrerythrin [Energy production and conversion] Back     alignment and domain information
>PRK04023 DNA polymerase II large subunit; Validated Back     alignment and domain information
>TIGR01206 lysW lysine biosynthesis protein LysW Back     alignment and domain information
>PRK14559 putative protein serine/threonine phosphatase; Provisional Back     alignment and domain information
>PHA00626 hypothetical protein Back     alignment and domain information
>COG1773 Rubredoxin [Energy production and conversion] Back     alignment and domain information
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc Back     alignment and domain information
>PRK05580 primosome assembly protein PriA; Validated Back     alignment and domain information
>PRK14873 primosome assembly protein PriA; Provisional Back     alignment and domain information
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Back     alignment and domain information
>PRK14714 DNA polymerase II large subunit; Provisional Back     alignment and domain information
>COG2835 Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Back     alignment and domain information
>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
>PRK10220 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA Back     alignment and domain information
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>smart00647 IBR In Between Ring fingers Back     alignment and domain information
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [] Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional Back     alignment and domain information
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information
>PRK11827 hypothetical protein; Provisional Back     alignment and domain information
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus Back     alignment and domain information
>PF13453 zf-TFIIB: Transcription factor zinc-finger Back     alignment and domain information
>TIGR01031 rpmF_bact ribosomal protein L32 Back     alignment and domain information
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Back     alignment and domain information
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit Back     alignment and domain information
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr Back     alignment and domain information
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) Back     alignment and domain information
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases Back     alignment and domain information
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein Back     alignment and domain information
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed 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
>KOG3507|consensus 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
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family Back     alignment and domain information
>TIGR00280 L37a ribosomal protein L37a Back     alignment and domain information
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ] Back     alignment and domain information
>KOG3084|consensus Back     alignment and domain information
>PRK00423 tfb transcription initiation factor IIB; Reviewed Back     alignment and domain information
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism] Back     alignment and domain information
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1 Back     alignment and domain information
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC Back     alignment and domain information
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc Back     alignment and domain information
>PRK11032 hypothetical protein; Provisional Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional 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
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only] Back     alignment and domain information
>PTZ00255 60S ribosomal protein L37a; Provisional Back     alignment and domain information
>PRK00420 hypothetical protein; Validated 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 ?
Query136
1qyp_A57 Thermococcus Celer Rpb9, Nmr, 25 Structures Length 4e-05
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures Length = 57 Back     alignment and structure 
Iteration: 1

 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 99  PIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
           P  +  C +C NDT  +  +Q R+ DE  TIF+ CTKC
Sbjct: 12  PTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC 49

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query136
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 3e-11
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 4e-11
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 5e-11
1tfi_A50 Transcriptional elongation factor SII; transcripti 3e-08
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 4e-08
3po3_S178 Transcription elongation factor S-II; RNA polymera 6e-08
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 8e-07
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Length = 57 Back     alignment and structure
 Score = 54.1 bits (130), Expect = 3e-11
 Identities = 17/45 (37%), Positives = 26/45 (57%)

Query: 92  KTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
           + ++   P  +  C +C NDT  +  +Q R+ DE  TIF+ CTKC
Sbjct: 5   EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC 49
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 113 Back     alignment and structure
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Length = 133 Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50 Back     alignment and structure
>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ... Length = 122 Back     alignment and structure
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178 Back     alignment and structure
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query136
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 100.0
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 100.0
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 99.97
1tfi_A50 Transcriptional elongation factor SII; transcripti 99.82
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 99.81
3po3_S178 Transcription elongation factor S-II; RNA polymera 99.6
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 99.49
2k4x_A55 30S ribosomal protein S27AE; metal-binding, ribonu 98.05
3j20_Y50 30S ribosomal protein S27AE; archaea, archaeal, KI 97.26
2fiy_A309 Protein FDHE homolog; FDHE protein, structural gen 96.46
6rxn_A46 Rubredoxin; electron transfer(iron-sulfur protein) 94.87
1dl6_A58 Transcription factor II B (TFIIB); zinc ribbon, ge 94.82
1yk4_A52 Rubredoxin, RD; electron transport; 0.69A {Pyrococ 94.71
2jr6_A68 UPF0434 protein NMA0874; solution, structural geno 94.56
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 94.5
2v3b_B55 Rubredoxin 2, rubredoxin; alkane degradation, iron 94.48
2kn9_A81 Rubredoxin; metalloprotein, ssgcid, structural gen 94.47
2pk7_A69 Uncharacterized protein; NESG, PLR1, putative tetr 94.27
2js4_A70 UPF0434 protein BB2007; NESG, northeast structural 94.15
1gh9_A71 8.3 kDa protein (gene MTH1184); beta+alpha complex 94.09
4rxn_A54 Rubredoxin; electron transfer(iron-sulfur protein) 94.02
1e8j_A52 Rubredoxin; iron-sulfur-protein, zinc-substitution 93.97
2hf1_A68 Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A 93.96
1dx8_A70 Rubredoxin; electron transport, zinc-substitution; 93.91
2jny_A67 Uncharacterized BCR; structure, CGR1, NESG, struct 93.86
1s24_A87 Rubredoxin 2; electron transport; NMR {Pseudomonas 93.45
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 92.27
3a43_A139 HYPD, hydrogenase nickel incorporation protein HYP 92.0
2ct7_A86 Ring finger protein 31; IBR, structural genomics, 91.94
3cng_A189 Nudix hydrolase; structural genomics, APC7497, PSI 91.9
3j21_g51 50S ribosomal protein L40E; archaea, archaeal, KIN 91.03
2kdx_A119 HYPA, hydrogenase/urease nickel incorporation prot 90.99
1vk6_A269 NADH pyrophosphatase; 1790429, structural genomics 90.46
1lko_A191 Rubrerythrin all-iron(II) form; reduced form, DIIR 89.84
2fnf_X72 Putative RAS effector NORE1; zinc, signal transduc 89.45
3pwf_A170 Rubrerythrin; non heme iron peroxidases, oxidative 89.38
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 88.68
2kpi_A56 Uncharacterized protein SCO3027; zinc finger, PSI- 88.17
1rfh_A59 RAS association (ralgds/AF-6) domain family 5; zin 87.97
2con_A79 RUH-035 protein, NIN one binding protein; ribosome 86.75
1yuz_A202 Nigerythrin; rubrythrin, rubredoxin, hemerythrin, 86.54
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 86.19
3jyw_972 60S ribosomal protein L43; eukaryotic ribosome, RA 85.28
3j21_i83 50S ribosomal protein L37AE; archaea, archaeal, KI 84.98
3cc2_Z116 50S ribosomal protein L37AE, 50S ribosomal protein 84.22
1x0t_A120 Ribonuclease P protein component 4; pyrococcus hor 83.85
3izc_m92 60S ribosomal protein RPL43 (L37AE); eukaryotic ri 83.72
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 83.38
2k3r_A123 Ribonuclease P protein component 4; PFU RPP21, RNA 81.85
1ffk_W73 Ribosomal protein L37AE; ribosome assembly, RNA-RN 81.77
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 80.97
1faq_A52 RAF-1; transferase, serine/threonine-protein kinas 80.37
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
Probab=100.00  E-value=1.5e-33  Score=201.90  Aligned_cols=99  Identities=19%  Similarity=0.422  Sum_probs=78.1

Q ss_pred             cccccccCCCccccCCC----CCeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeeccee
Q psy4748          10 ESEFCSKCGTILPLFDF----KGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVE   85 (136)
Q Consensus        10 ~~~FCp~CgnlL~~~~~----~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e   85 (136)
                      +|.|||+|||||+++++    .+.++|++|+|.+++++.                       .+|+     ..+....++
T Consensus         3 ~m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~~~~~-----------------------~v~~-----~~~~~~~~e   54 (113)
T 3h0g_I            3 NFQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAATS-----------------------KVYR-----HELQSSNVE   54 (113)
T ss_dssp             CCCCCSSSCCCCEECCCTTTCCCCEECSSSCCEECCSCS-----------------------EEEE-----CCCCSCSCT
T ss_pred             cceeCcCCCCEeeEcccCCCCeeEEECCCCCCeEEcCCC-----------------------eEEE-----EEEeccccc
Confidence            58999999999999965    358999999999998531                       1221     111112223


Q ss_pred             ec-cccccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748          86 KE-KQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC  136 (136)
Q Consensus        86 ~~-~~~~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C  136 (136)
                      .+ ++.+...++++|+++..||+|||++|+|||+|+||||||||+||+|++|
T Consensus        55 ~~~v~~~~~~~~tlp~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C  106 (113)
T 3h0g_I           55 NTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHC  106 (113)
T ss_dssp             TCTTCTTSTTCSSSCBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSS
T ss_pred             ccceeccccccccCCCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCC
Confidence            22 4555667899999999999999999999999999999999999999988
>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ... Back     alignment and structure
>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Back     alignment and structure
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Back     alignment and structure
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Back     alignment and structure
>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8 Back     alignment and structure
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1 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
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A 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
>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis} Back     alignment and structure
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1 Back     alignment and structure
>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa} Back     alignment and structure
>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis} Back     alignment and structure
>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1 Back     alignment and structure
>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50} Back     alignment and structure
>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1 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
>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
>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1 Back     alignment and structure
>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A Back     alignment and structure
>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1 Back     alignment and structure
>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1 Back     alignment and structure
>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ... 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
>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 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
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>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
>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
>2fnf_X Putative RAS effector NORE1; zinc, signal transduction, apoptosis, cysteine rich domain; NMR {Mus musculus} 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
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Back     alignment and structure
>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor} Back     alignment and structure
>1rfh_A RAS association (ralgds/AF-6) domain family 5; zinc, signal transduction, apoptosis, cysteine rich domain, metal binding protein; NMR {Mus musculus} Back     alignment and structure
>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
>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
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} Back     alignment and structure
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z Back     alignment and structure
>1x0t_A Ribonuclease P protein component 4; pyrococcus horikoshii OT3, hydrolase; 1.60A {Pyrococcus horikoshii} PDB: 2zae_B Back     alignment and structure
>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5 Back     alignment and structure
>2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P, hydrolase, tRNA processing; NMR {Pyrococcus furiosus} PDB: 2ki7_B Back     alignment and structure
>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y* 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
>1faq_A RAF-1; transferase, serine/threonine-protein kinase, proto- oncogene, zinc, ATP-binding, phorbol-ester binding; NMR {Homo sapiens} SCOP: g.49.1.1 PDB: 1far_A 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 136
d1qypa_57 g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A 1e-11
d1twfi272 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase 5e-10
d1tfia_50 g.41.3.1 (A:) Transcriptional factor SII, C-termin 2e-09
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57 Back     information, alignment and structure

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

 Score = 53.6 bits (129), Expect = 1e-11
 Identities = 17/47 (36%), Positives = 26/47 (55%)

Query: 90  KDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
             + ++   P  +  C +C NDT  +  +Q R+ DE  TIF+ CTKC
Sbjct: 3   HMEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC 49
>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72 Back     information, alignment and structure
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50 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 ?
Query136
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 99.85
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.84
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 99.76
d1twfi149 RBP9 subunit of RNA polymerase II {Baker's yeast ( 99.1
d1lkoa244 Rubrerythrin, C-terminal domain {Desulfovibrio vul 95.51
d2k4xa155 Ribosomal protein S27ae {Thermoplasma acidophilum 95.23
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 95.18
d1dx8a_70 Rubredoxin {Guillardia theta [TaxId: 55529]} 95.14
d1yuza236 Nigerythrin, C-terminal domain {Desulfovibrio vulg 94.88
d6rxna_45 Rubredoxin {Desulfovibrio desulfuricans, strain 27 94.73
d1brfa_53 Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2 94.68
d2dsxa152 Rubredoxin {Desulfovibrio gigas [TaxId: 879]} 94.67
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 94.56
d2ct7a173 Ring finger protein 31 {Human (Homo sapiens) [TaxI 94.54
d1iroa_53 Rubredoxin {Clostridium pasteurianum [TaxId: 1501] 94.36
d1nnqa237 Rubrerythrin, C-terminal domain {Archaeon Pyrococc 93.92
d1s24a_56 Two-iron rubredoxin {Pseudomonas oleovorans [TaxId 93.91
d2jnya159 Uncharacterized protein Cgl1405/cg1592 {Corynebact 92.61
d1dl6a_58 Transcription initiation factor TFIIB, N-terminal 92.51
d2hf1a159 Hypothetical protein CV3345 {Chromobacterium viola 92.14
d2pk7a159 Uncharacterized protein PFL1779 {Pseudomonas fluor 91.89
d1pfta_50 Transcription initiation factor TFIIB, N-terminal 91.05
d2cona166 RNA-binding protein NOB1 (Nin one binding) {Mouse 90.29
d1vqoz173 Ribosomal protein L37ae {Archaeon Haloarcula maris 88.61
d1jj2y_73 Ribosomal protein L37ae {Archaeon Haloarcula maris 87.08
d2f9yb1 263 Acetyl-coenzyme A carboxylase carboxyl transferase 84.17
d1vk6a429 NADH pyrophosphatase intervening domain {Escherich 82.49
d2j015159 Ribosomal protein L32p {Thermus thermophilus [TaxI 80.34
d1pfva335 Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch 80.33
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Back     information, alignment and structure
class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=99.85  E-value=3.2e-22  Score=126.14  Aligned_cols=44  Identities=39%  Similarity=0.801  Sum_probs=41.5

Q ss_pred             ccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748          93 TEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC  136 (136)
Q Consensus        93 ~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C  136 (136)
                      ++..++|+++..||+|||++|+|+++|+||||||||+||+|.+|
T Consensus         6 ~~~~~~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~C   49 (57)
T d1qypa_           6 QDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKC   49 (57)
T ss_dssp             CCCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSS
T ss_pred             hccccCCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCC
Confidence            45678899999999999999999999999999999999999998
>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1twfi1 g.41.3.1 (I:1-49) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]} 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
>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]} Back     information, alignment and structure
>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure
>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]} 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
>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]} Back     information, alignment and structure
>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]} Back     information, alignment and structure
>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>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
>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vk6a4 g.41.14.1 (A:97-125) NADH pyrophosphatase intervening domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure