Psyllid ID: psy2244

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---
MGYSQVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
cccccccccccccccEEEEcccccccccccccccEEccccccEEEEEEcccEEEEEEccccccccccEEEEEc
ccccEEEEccccccccHEEEcccccccccccccccEEccccEEEEEEEcccEEEEEEcccccccccccEEEEc
mgysqvlvgkclpgdiEKYYLEChfeneirprdpircrecgyrimykkrTKRCIlyfkpqtggfpklkttvtv
MGYSQVLVGKCLPGDIEKYYLEChfeneirprdpircrECGYRIMYKKRTKRCIlyfkpqtggfpklkttvtv
MGYSQVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
****QVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGF*********
**************DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
MGYSQVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
*GYSQVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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MGYSQVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKPQTGGFPKLKTTVTV
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 ?
Query73 2.2.26 [Sep-21-2011]
Q6387158 DNA-directed RNA polymera no N/A 0.479 0.603 0.8 3e-10
P5380358 DNA-directed RNA polymera yes N/A 0.479 0.603 0.8 3e-10
Q3ZBC058 DNA-directed RNA polymera yes N/A 0.479 0.603 0.8 3e-10
Q54R6646 DNA-directed RNA polymera yes N/A 0.479 0.760 0.514 9e-05
P4801163 DNA-directed RNA polymera yes N/A 0.479 0.555 0.514 0.0003
>sp|Q63871|RPAB4_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus GN=Polr2k PE=2 SV=2 Back     alignment and function desciption
 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/35 (80%), Positives = 32/35 (91%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          ECH ENEI+ RDPIRCRECGYRIMYKKRTKR +++
Sbjct: 21 ECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVF 55
Factor that activates expression from a metal response element of the mouse metallothionein-I gene.
Mus musculus (taxid: 10090)
>sp|P53803|RPAB4_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens GN=POLR2K PE=2 SV=1 Back     alignment and function description
>sp|Q3ZBC0|RPAB4_BOVIN DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus GN=POLR2K PE=3 SV=1 Back     alignment and function description
>sp|Q54R66|RPAB4_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc4 OS=Dictyostelium discoideum GN=polr2k PE=3 SV=1 Back     alignment and function description
>sp|P48011|RPAB4_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc10 PE=1 SV=2 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 ?
Query73
221220904115 DNA-directed RNA polymerases I, II, and 0.465 0.295 0.911 1e-10
403183200 279 AAEL017317-PA [Aedes aegypti] 0.479 0.125 0.828 2e-10
24185365859 RNA polymerases I, II and III shared pol 0.479 0.593 0.885 6e-10
30720702338 DNA-directed RNA polymerases I, II, and 0.493 0.947 0.861 6e-10
43190176366 DNA-directed RNA polymerases I, II, and 0.465 0.515 0.911 7e-10
16107709257 Rpb12 [Drosophila melanogaster] gi|19488 0.479 0.614 0.828 8e-10
19502497457 GH20797 [Drosophila grimshawi] gi|195123 0.479 0.614 0.828 8e-10
34647028759 hypothetical protein [Amblyomma maculatu 0.479 0.593 0.885 8e-10
15713597258 RNA polymerase small Zn-binding subunit, 0.479 0.603 0.828 8e-10
35577986154 DNA-directed RNA polymerases I, II, and 0.465 0.629 0.911 8e-10
>gi|221220904|gb|ACM09113.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Salmo salar] Back     alignment and taxonomy information
 Score = 70.5 bits (171), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/34 (91%), Positives = 32/34 (94%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCIL 55
          ECH ENEI+ RDPIRCRECGYRIMYKKRTKRCIL
Sbjct: 51 ECHTENEIKARDPIRCRECGYRIMYKKRTKRCIL 84

Source: Salmo salar

Species: Salmo salar

Genus: Salmo

Family: Salmonidae

Order: Salmoniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota
>gi|403183200|gb|EJY57925.1| AAEL017317-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|241853658|ref|XP_002415907.1| RNA polymerases I, II and III shared polypeptide, putative [Ixodes scapularis] gi|215510121|gb|EEC19574.1| RNA polymerases I, II and III shared polypeptide, putative [Ixodes scapularis] Back     alignment and taxonomy information
>gi|307207023|gb|EFN84846.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Harpegnathos saltator] Back     alignment and taxonomy information
>gi|431901763|gb|ELK08640.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Pteropus alecto] Back     alignment and taxonomy information
>gi|161077092|ref|NP_001097319.1| Rpb12 [Drosophila melanogaster] gi|194882899|ref|XP_001975547.1| GG22374 [Drosophila erecta] gi|195334543|ref|XP_002033937.1| GM20158 [Drosophila sechellia] gi|195486190|ref|XP_002091399.1| GE12262 [Drosophila yakuba] gi|195583568|ref|XP_002081589.1| GD25636 [Drosophila simulans] gi|41617164|tpg|DAA02521.1| TPA_inf: HDC06513 [Drosophila melanogaster] gi|125660184|gb|ABN49320.1| IP17848p [Drosophila melanogaster] gi|157400336|gb|ABV53802.1| Rpb12 [Drosophila melanogaster] gi|190658734|gb|EDV55947.1| GG22374 [Drosophila erecta] gi|194125907|gb|EDW47950.1| GM20158 [Drosophila sechellia] gi|194177500|gb|EDW91111.1| GE12262 [Drosophila yakuba] gi|194193598|gb|EDX07174.1| GD25636 [Drosophila simulans] Back     alignment and taxonomy information
>gi|195024974|ref|XP_001985975.1| GH20797 [Drosophila grimshawi] gi|195123317|ref|XP_002006154.1| GI20882 [Drosophila mojavensis] gi|195154096|ref|XP_002017958.1| GL17021 [Drosophila persimilis] gi|195381935|ref|XP_002049688.1| GJ20617 [Drosophila virilis] gi|198458378|ref|XP_002138535.1| GA24334 [Drosophila pseudoobscura pseudoobscura] gi|193901975|gb|EDW00842.1| GH20797 [Drosophila grimshawi] gi|193911222|gb|EDW10089.1| GI20882 [Drosophila mojavensis] gi|194113754|gb|EDW35797.1| GL17021 [Drosophila persimilis] gi|194144485|gb|EDW60881.1| GJ20617 [Drosophila virilis] gi|198136322|gb|EDY69093.1| GA24334 [Drosophila pseudoobscura pseudoobscura] Back     alignment and taxonomy information
>gi|346470287|gb|AEO34988.1| hypothetical protein [Amblyomma maculatum] Back     alignment and taxonomy information
>gi|157135972|ref|XP_001663644.1| RNA polymerase small Zn-binding subunit, putative [Aedes aegypti] gi|170033365|ref|XP_001844548.1| RNA polymerase small Zn-binding subunit [Culex quinquefasciatus] gi|108870059|gb|EAT34284.1| AAEL013457-PA [Aedes aegypti] gi|167874286|gb|EDS37669.1| RNA polymerase small Zn-binding subunit [Culex quinquefasciatus] Back     alignment and taxonomy information
>gi|355779861|gb|EHH64337.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4, partial [Macaca fascicularis] 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 ?
Query73
UNIPROTKB|E1BU6558 E1BU65 "Uncharacterized protei 0.465 0.586 0.911 1.3e-13
UNIPROTKB|E5RGX267 POLR2K "DNA-directed RNA polym 0.465 0.507 0.911 1.3e-13
FB|FBgn026295457 Rpb12 "Rpb12" [Drosophila mela 0.479 0.614 0.828 2.1e-13
UNIPROTKB|E1BW7958 LOC771626 "Uncharacterized pro 0.479 0.603 0.8 1.9e-12
UNIPROTKB|Q3ZBC058 POLR2K "DNA-directed RNA polym 0.479 0.603 0.8 1.9e-12
UNIPROTKB|P5380358 POLR2K "DNA-directed RNA polym 0.479 0.603 0.8 1.9e-12
UNIPROTKB|I3LN5158 POLR2K "Uncharacterized protei 0.479 0.603 0.8 1.9e-12
RGD|231989587 LOC100361574 "mCG145114-like" 0.479 0.402 0.8 1.9e-12
UNIPROTKB|F1LTT488 LOC100361574 "Protein LOC10036 0.479 0.397 0.8 1.9e-12
ZFIN|ZDB-GENE-070820-1858 polr2k "polymerase (RNA) II (D 0.479 0.603 0.8 1.9e-12
UNIPROTKB|E1BU65 E1BU65 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
 Score = 177 (67.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 31/34 (91%), Positives = 32/34 (94%)

Query:    22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCIL 55
             ECH ENEI+ RDPIRCRECGYRIMYKKRTKRCIL
Sbjct:    21 ECHTENEIKARDPIRCRECGYRIMYKKRTKRCIL 54
GO:0003677 "DNA binding" evidence=IEA
GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA
GO:0006351 "transcription, DNA-dependent" evidence=IEA
UNIPROTKB|E5RGX2 POLR2K "DNA-directed RNA polymerases I, II, and III subunit RPABC4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
FB|FBgn0262954 Rpb12 "Rpb12" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
UNIPROTKB|E1BW79 LOC771626 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q3ZBC0 POLR2K "DNA-directed RNA polymerases I, II, and III subunit RPABC4" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P53803 POLR2K "DNA-directed RNA polymerases I, II, and III subunit RPABC4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|I3LN51 POLR2K "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
RGD|2319895 LOC100361574 "mCG145114-like" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1LTT4 LOC100361574 "Protein LOC100361574" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-070820-18 polr2k "polymerase (RNA) II (DNA directed) polypeptide K" [Danio rerio (taxid:7955)] 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) ?
P48011RPAB4_SCHPONo assigned EC number0.51420.47940.5555yesN/A
P53803RPAB4_HUMANNo assigned EC number0.80.47940.6034yesN/A
Q54R66RPAB4_DICDINo assigned EC number0.51420.47940.7608yesN/A
Q3ZBC0RPAB4_BOVINNo assigned EC number0.80.47940.6034yesN/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 ?
Query73
pfam0360432 pfam03604, DNA_RNApol_7kD, DNA directed RNA polyme 3e-10
smart0065944 smart00659, RPOLCX, RNA polymerase subunit CX 4e-10
>gnl|CDD|202700 pfam03604, DNA_RNApol_7kD, DNA directed RNA polymerase, 7 kDa subunit Back     alignment and domain information 
 Score = 49.2 bits (118), Expect = 3e-10
 Identities = 19/28 (67%), Positives = 24/28 (85%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKR 49
          EC  E E++P DPIRC+ECG+RI+YKKR
Sbjct: 5  ECGAEVELKPGDPIRCKECGHRILYKKR 32

Length = 32
>gnl|CDD|128906 smart00659, RPOLCX, RNA polymerase subunit CX Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 73
smart0065944 RPOLCX RNA polymerase subunit CX. present in RNA p 99.86
KOG3507|consensus62 99.86
PF0360432 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa 99.75
COG199649 RPC10 DNA-directed RNA polymerase, subunit RPC10 ( 99.66
PRK0039846 rpoP DNA-directed RNA polymerase subunit P; Provis 99.19
smart0083441 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C 97.47
TIGR0260552 CxxC_CxxC_SSSS putative regulatory protein, FmdB f 97.34
PF0972342 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134 97.26
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 97.23
smart00531147 TFIIE Transcription initiation factor IIE. 96.54
PF1371736 zinc_ribbon_4: zinc-ribbon domain 96.26
PRK03824135 hypA hydrogenase nickel incorporation protein; Pro 96.21
PF1324826 zf-ribbon_3: zinc-ribbon domain 96.18
PF1371937 zinc_ribbon_5: zinc-ribbon domain 96.11
PRK00564117 hypA hydrogenase nickel incorporation protein; Pro 96.03
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 95.89
PF1324023 zinc_ribbon_2: zinc-ribbon domain 95.84
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 95.83
PRK03681114 hypA hydrogenase nickel incorporation protein; Val 95.73
PF01155113 HypA: Hydrogenase expression/synthesis hypA family 95.66
COG1579239 Zn-ribbon protein, possibly nucleic acid-binding [ 95.63
cd0035033 rubredoxin_like Rubredoxin_like; nonheme iron bind 95.62
TIGR0120654 lysW lysine biosynthesis protein LysW. This very s 95.43
PF07295146 DUF1451: Protein of unknown function (DUF1451); In 95.31
PF09538108 FYDLN_acid: Protein of unknown function (FYDLN_aci 95.27
cd0072934 rubredoxin_SM Rubredoxin, Small Modular nonheme ir 95.22
PF0929732 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do 95.2
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 94.83
PRK12380113 hydrogenase nickel incorporation protein HybF; Pro 94.8
PF0827430 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01 94.63
TIGR00100115 hypA hydrogenase nickel insertion protein HypA. In 94.46
smart0066152 RPOL9 RNA polymerase subunit 9. 94.38
PF0775424 DUF1610: Domain of unknown function (DUF1610); Int 94.0
COG1439177 Predicted nucleic acid-binding protein, consists o 93.86
TIGR00373158 conserved hypothetical protein TIGR00373. This fam 93.84
PRK06266178 transcription initiation factor E subunit alpha; V 93.82
PF1005854 DUF2296: Predicted integral membrane metal-binding 93.66
PRK00762124 hypA hydrogenase nickel incorporation protein; Pro 93.65
PF14353128 CpXC: CpXC protein 93.32
PRK12496164 hypothetical protein; Provisional 93.25
TIGR02300129 FYDLN_acid conserved hypothetical protein TIGR0230 92.9
PF0827143 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013 92.53
PF1345149 zf-trcl: Probable zinc-binding domain 92.22
PF0139639 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc 92.19
PF1277350 DZR: Double zinc ribbon 92.13
PRK11032160 hypothetical protein; Provisional 91.96
PF10263157 SprT-like: SprT-like family; InterPro: IPR006640 T 91.53
PF0879233 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I 91.38
PF1277350 DZR: Double zinc ribbon 91.34
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 91.17
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 91.0
PRK0043250 30S ribosomal protein S27ae; Validated 90.92
COG1592166 Rubrerythrin [Energy production and conversion] 90.74
COG1096188 Predicted RNA-binding protein (consists of S1 doma 90.65
COG1571421 Predicted DNA-binding protein containing a Zn-ribb 90.59
PF0985564 DUF2082: Nucleic-acid-binding protein containing Z 90.45
PHA0062659 hypothetical protein 90.21
PRK14714 1337 DNA polymerase II large subunit; Provisional 89.68
PRK00420112 hypothetical protein; Validated 89.37
PF02318118 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 89.36
PRK06450 338 threonine synthase; Validated 89.18
COG335797 Predicted transcriptional regulator containing an 89.15
PF1444654 Prok-RING_1: Prokaryotic RING finger family 1 89.15
PRK07591 421 threonine synthase; Validated 88.97
TIGR00686109 phnA alkylphosphonate utilization operon protein P 88.79
smart00731146 SprT SprT homologues. Predicted to have roles in t 88.6
cd01675555 RNR_III Class III ribonucleotide reductase. Ribonu 88.29
PF1436935 zf-RING_3: zinc-finger 87.89
COG0375115 HybF Zn finger protein HypA/HybF (possibly regulat 87.76
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 87.64
COG1326 201 Uncharacterized archaeal Zn-finger protein [Genera 87.24
PF0719170 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 87.14
PF0908268 DUF1922: Domain of unknown function (DUF1922); Int 87.0
PF0519136 ADK_lid: Adenylate kinase, active site lid; InterP 86.83
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 86.58
PRK00464154 nrdR transcriptional regulator NrdR; Validated 86.42
PRK10220111 hypothetical protein; Provisional 86.41
COG1645131 Uncharacterized Zn-finger containing protein [Gene 86.37
PRK04351149 hypothetical protein; Provisional 86.22
PF1012251 Mu-like_Com: Mu-like prophage protein Com; InterPr 86.2
COG2816 279 NPY1 NTP pyrophosphohydrolases containing a Zn-fin 86.19
cd0073050 rubredoxin Rubredoxin; nonheme iron binding domain 85.88
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 85.78
PRK06260 397 threonine synthase; Validated 85.72
KOG2846|consensus328 85.45
PRK0041559 rps27e 30S ribosomal protein S27e; Reviewed 85.19
PF0259156 DUF164: Putative zinc ribbon domain; InterPro: IPR 85.06
PF1340858 Zn_ribbon_recom: Recombinase zinc beta ribbon doma 85.06
PRK04173 456 glycyl-tRNA synthetase; Provisional 84.8
PRK15103 419 paraquat-inducible membrane protein A; Provisional 84.75
COG3364112 Zn-ribbon containing protein [General function pre 84.69
PRK0413648 rpl40e 50S ribosomal protein L40e; Provisional 84.16
COG205167 RPS27A Ribosomal protein S27E [Translation, riboso 84.11
COG1379403 PHP family phosphoesterase with a Zn ribbon [Gener 84.05
PRK14559 645 putative protein serine/threonine phosphatase; Pro 83.72
PF1469047 zf-ISL3: zinc-finger of transposase IS204/IS1001/I 83.67
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 82.76
PF0215035 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I 82.17
COG1503411 eRF1 Peptide chain release factor 1 (eRF1) [Transl 81.9
smart00709160 Zpr1 Duplicated domain in the epidermal growth fac 81.16
PF14319111 Zn_Tnp_IS91: Transposase zinc-binding domain 81.11
PRK0835161 DNA-directed RNA polymerase subunit E''; Validated 80.75
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 80.5
PHA02942383 putative transposase; Provisional 80.18
PF03367161 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004 80.14
>smart00659 RPOLCX RNA polymerase subunit CX Back     alignment and domain information 
Probab=99.86  E-value=4.1e-22  Score=115.38  Aligned_cols=43  Identities=53%  Similarity=0.888  Sum_probs=41.4

Q ss_pred             eEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244          16 IEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFK   58 (73)
Q Consensus        16 v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~   58 (73)
                      |.|+|++||.+++++..++||||+||||||||+||++++||.+
T Consensus         1 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~A   43 (44)
T smart00659        1 MIYICGECGRENEIKSKDVVRCRECGYRILYKKRTKRLVEVKA   43 (44)
T ss_pred             CEEECCCCCCEeecCCCCceECCCCCceEEEEeCCCceEEEEc
Confidence            6799999999999999999999999999999999999999975

present in RNA polymerase I, II and III
>KOG3507|consensus 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
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Back     alignment and domain information
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional 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
>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
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PF13717 zinc_ribbon_4: zinc-ribbon domain Back     alignment and domain information
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional Back     alignment and domain information
>PF13248 zf-ribbon_3: zinc-ribbon domain Back     alignment and domain information
>PF13719 zinc_ribbon_5: zinc-ribbon domain Back     alignment and domain information
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional 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
>PF13240 zinc_ribbon_2: zinc-ribbon domain 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
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated 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
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only] 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
>TIGR01206 lysW lysine biosynthesis protein LysW 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
>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
>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
>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
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Back     alignment and domain information
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional 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
>TIGR00100 hypA hydrogenase nickel insertion protein HypA Back     alignment and domain information
>smart00661 RPOL9 RNA polymerase subunit 9 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
>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
>TIGR00373 conserved hypothetical protein TIGR00373 Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [] Back     alignment and domain information
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional Back     alignment and domain information
>PF14353 CpXC: CpXC protein Back     alignment and domain information
>PRK12496 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300 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
>PF13451 zf-trcl: Probable zinc-binding domain 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
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>PRK11032 hypothetical protein; Provisional 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
>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
>PF12773 DZR: Double zinc ribbon Back     alignment and domain information
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional 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
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>COG1592 Rubrerythrin [Energy production and conversion] Back     alignment and domain information
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only] 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
>PHA00626 hypothetical protein Back     alignment and domain information
>PRK14714 DNA polymerase II large subunit; Provisional Back     alignment and domain information
>PRK00420 hypothetical protein; Validated Back     alignment and domain information
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A Back     alignment and domain information
>PRK06450 threonine synthase; Validated Back     alignment and domain information
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription] Back     alignment and domain information
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1 Back     alignment and domain information
>PRK07591 threonine synthase; Validated Back     alignment and domain information
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA Back     alignment and domain information
>smart00731 SprT SprT homologues Back     alignment and domain information
>cd01675 RNR_III Class III ribonucleotide reductase Back     alignment and domain information
>PF14369 zf-RING_3: zinc-finger 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
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only] Back     alignment and domain information
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length 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
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2 Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal Back     alignment and domain information
>PRK00464 nrdR transcriptional regulator NrdR; Validated Back     alignment and domain information
>PRK10220 hypothetical protein; Provisional Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] Back     alignment and domain information
>PRK04351 hypothetical protein; Provisional 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
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center 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
>PRK06260 threonine synthase; Validated Back     alignment and domain information
>KOG2846|consensus Back     alignment and domain information
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Back     alignment and domain information
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function Back     alignment and domain information
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain Back     alignment and domain information
>PRK04173 glycyl-tRNA synthetase; Provisional Back     alignment and domain information
>PRK15103 paraquat-inducible membrane protein A; Provisional Back     alignment and domain information
>COG3364 Zn-ribbon containing protein [General function prediction only] Back     alignment and domain information
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional Back     alignment and domain information
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only] Back     alignment and domain information
>PRK14559 putative protein serine/threonine phosphatase; Provisional Back     alignment and domain information
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165 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
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2 Back     alignment and domain information
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1 Back     alignment and domain information
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain Back     alignment and domain information
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>PHA02942 putative transposase; Provisional Back     alignment and domain information
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query73
3h0g_L63 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 2e-05
>pdb|3H0G|L Chain L, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 63 Back     alignment and structure 
Iteration: 1

 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 18/35 (51%), Positives = 26/35 (74%)
Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          +C   N I+ ++ IRCRECG+R+MYK RTKR + +
Sbjct: 26 DCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQF 60

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query73
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 2e-16
3h0g_L63 DNA-directed RNA polymerases I, II, and III subuni 3e-16
>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* ... Length = 70 Back     alignment and structure
 Score = 65.7 bits (160), Expect = 2e-16
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          EC  +  +   D +RC++CG+RI+ K RTKR + +
Sbjct: 33 ECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQF 67
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 63 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query73
3h0g_L63 DNA-directed RNA polymerases I, II, and III subuni 99.87
1twf_L70 ABC10-alpha, DNA-directed RNA polymerases I, II, a 99.83
4ayb_P48 DNA-directed RNA polymerase; transferase, multi-su 99.31
2lcq_A165 Putative toxin VAPC6; PIN domain, Zn ribbon domain 97.49
2kdx_A119 HYPA, hydrogenase/urease nickel incorporation prot 97.01
2gmg_A105 Hypothetical protein PF0610; winged-helix like pro 96.16
3na7_A256 HP0958; flagellar biogenesis, flagellum export, C4 96.01
3a43_A139 HYPD, hydrogenase nickel incorporation protein HYP 95.6
3pwf_A170 Rubrerythrin; non heme iron peroxidases, oxidative 95.11
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 94.15
3j21_g51 50S ribosomal protein L40E; archaea, archaeal, KIN 93.32
1gh9_A71 8.3 kDa protein (gene MTH1184); beta+alpha complex 92.81
6rxn_A46 Rubredoxin; electron transfer(iron-sulfur protein) 92.79
2kn9_A81 Rubredoxin; metalloprotein, ssgcid, structural gen 92.0
1lko_A191 Rubrerythrin all-iron(II) form; reduced form, DIIR 91.75
1yuz_A202 Nigerythrin; rubrythrin, rubredoxin, hemerythrin, 90.36
2k4x_A55 30S ribosomal protein S27AE; metal-binding, ribonu 90.0
1dx8_A70 Rubredoxin; electron transport, zinc-substitution; 89.24
1pft_A50 TFIIB, PFTFIIBN; N-terminal domain, transcription 88.97
2jrp_A81 Putative cytoplasmic protein; two-zinc binding pro 88.27
3jyw_972 60S ribosomal protein L43; eukaryotic ribosome, RA 88.02
2ct7_A86 Ring finger protein 31; IBR, structural genomics, 87.81
2v3b_B55 Rubredoxin 2, rubredoxin; alkane degradation, iron 87.81
1e8j_A52 Rubredoxin; iron-sulfur-protein, zinc-substitution 87.08
1yk4_A52 Rubredoxin, RD; electron transport; 0.69A {Pyrococ 86.98
3uk3_C57 Zinc finger protein 217; transcription factor, DNA 86.19
1ltl_A279 DNA replication initiator (CDC21/CDC54); HET: DNA; 86.04
3j20_Y50 30S ribosomal protein S27AE; archaea, archaeal, KI 85.96
1x5w_A70 Zinc finger protein 64, isoforms 1; ZNF338, nuclea 85.79
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 85.73
1s24_A87 Rubredoxin 2; electron transport; NMR {Pseudomonas 85.66
2epq_A45 POZ-, at HOOK-, and zinc finger-containing protein 85.54
4gzn_C60 ZFP-57, zinc finger protein 57; transcription-DNA 85.31
3j21_i83 50S ribosomal protein L37AE; archaea, archaeal, KI 84.97
2zet_C153 Melanophilin; complex, GTP-binding protein, GTPase 84.87
2akl_A138 PHNA-like protein PA0128; two domains, Zn binding 84.77
1vd4_A62 Transcription initiation factor IIE, alpha subunit 84.62
2k2d_A79 Ring finger and CHY zinc finger domain- containing 84.57
4a17_Y103 RPL37A, 60S ribosomal protein L32; eukaryotic ribo 84.18
4rxn_A54 Rubredoxin; electron transfer(iron-sulfur protein) 83.84
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 83.6
2ayj_A56 50S ribosomal protein L40E; Zn-binding, beta-stran 83.57
2lce_A74 B-cell lymphoma 6 protein; structural genomics, no 83.36
3izc_m92 60S ribosomal protein RPL43 (L37AE); eukaryotic ri 83.0
1bbo_A57 Human enhancer-binding protein MBP-1; DNA-binding 82.99
1zbd_B134 Rabphilin-3A; G protein, effector, RABCDR, synapti 82.33
2adr_A60 ADR1; transcription regulation, zinc finger,; NMR 82.16
2epr_A48 POZ-, at HOOK-, and zinc finger-containing protein 81.91
1x6e_A72 Zinc finger protein 24; ZNF24, KOX17, ZNF191, zsca 81.78
1dxg_A36 Desulforedoxin; non-heme iron protein, rubredoxin 81.29
>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
Probab=99.87  E-value=1e-23  Score=129.78  Aligned_cols=50  Identities=38%  Similarity=0.701  Sum_probs=43.1

Q ss_pred             cccCCcceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244           9 GKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFK   58 (73)
Q Consensus         9 ~~~~~~~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~   58 (73)
                      +...+++|.|+|++||.+++++.+++|||++||||||||+|+++++||.+
T Consensus        13 ~~~~~~~v~Y~C~~Cg~~~~l~~~~~iRC~~CG~RILyK~Rt~r~~~~~A   62 (63)
T 3h0g_L           13 NPPRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEA   62 (63)
T ss_dssp             ------CCCCBCSSSCCBCCCCSSSCCCCSSSCCCCCBCCCCCCCEEECC
T ss_pred             CCCCCCCeEEECCCCCCeeecCCCCceECCCCCcEEEEEecCCceEEEEC
Confidence            56678899999999999999999999999999999999999999999986
>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
>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii} 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
>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
>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
>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
>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
>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
>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1 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
>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
>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
>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
>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A 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
>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} 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
>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
>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
>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
>3uk3_C Zinc finger protein 217; transcription factor, DNA binding, DNA-metal BI protein complex; 2.10A {Homo sapiens} Back     alignment and structure
>1ltl_A DNA replication initiator (CDC21/CDC54); HET: DNA; 3.00A {Methanothermobacterthermautotrophicus} SCOP: b.40.4.11 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
>1x5w_A Zinc finger protein 64, isoforms 1; ZNF338, nuclear protein, DNA binding, transcription, C2H2 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 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
>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1 Back     alignment and structure
>2epq_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 Back     alignment and structure
>4gzn_C ZFP-57, zinc finger protein 57; transcription-DNA complex; HET: DNA 5CM; 0.99A {Mus musculus} 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
>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB, RAB27B, effector, SLP homology domain, acetylation, lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus} 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
>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>2k2d_A Ring finger and CHY zinc finger domain- containing protein 1; zinc-binding protein, cytoplasm, metal-binding, nucleus, metal binding protein; NMR {Homo sapiens} Back     alignment and structure
>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y 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
>2ayj_A 50S ribosomal protein L40E; Zn-binding, beta-strand protein, structural genomics, PSI, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: g.41.8.7 Back     alignment and structure
>2lce_A B-cell lymphoma 6 protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>1bbo_A Human enhancer-binding protein MBP-1; DNA-binding protein; HET: ABA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 PDB: 3znf_A 4znf_A Back     alignment and structure
>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1 Back     alignment and structure
>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 g.37.1.1 Back     alignment and structure
>2epr_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 Back     alignment and structure
>1x6e_A Zinc finger protein 24; ZNF24, KOX17, ZNF191, zscan3, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 Back     alignment and structure
>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_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 73
d1twfl_46 g.41.9.2 (L:) RBP12 subunit of RNA polymerase II { 2e-14
>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 46 Back     information, alignment and structure

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.6 bits (142), Expect = 2e-14
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          EC  +  +   D +RC++CG+RI+ K RTKR + +
Sbjct: 9  ECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQF 43

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query73
d1twfl_46 RBP12 subunit of RNA polymerase II {Baker's yeast 99.91
d1yuza236 Nigerythrin, C-terminal domain {Desulfovibrio vulg 94.13
d2akla238 Hypothetical protein PA0128, N-terminal domain {Ps 94.12
d2gmga1105 Hypothetical protein PF0610 {Pyrococcus furiosus [ 93.8
d1nnqa237 Rubrerythrin, C-terminal domain {Archaeon Pyrococc 93.4
d1lkoa244 Rubrerythrin, C-terminal domain {Desulfovibrio vul 93.26
d1ltla_239 DNA replication initiator (cdc21/cdc54) N-terminal 88.6
d2csha153 Zinc finger protein 297b {Human (Homo sapiens) [Ta 86.49
d2dsxa152 Rubredoxin {Desulfovibrio gigas [TaxId: 879]} 86.34
d1x68a234 Four and a half LIM domains protein 5, FHL-5 {Huma 85.92
d1s24a_56 Two-iron rubredoxin {Pseudomonas oleovorans [TaxId 85.88
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 84.82
d6rxna_45 Rubredoxin {Desulfovibrio desulfuricans, strain 27 83.75
d1zbdb_124 Effector domain of rabphilin-3a {Rat (Rattus norve 82.52
d1brfa_53 Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2 82.27
d1iroa_53 Rubredoxin {Clostridium pasteurianum [TaxId: 1501] 81.82
d1hxra_115 RabGEF Mss4 {Rat (Rattus norvegicus) [TaxId: 10116 81.61
d2ayja156 Ribosomal protein L40e {Sulfolobus solfataricus [T 81.6
d1dx8a_70 Rubredoxin {Guillardia theta [TaxId: 55529]} 80.56
d2ct7a173 Ring finger protein 31 {Human (Homo sapiens) [TaxI 80.24
d1x6ea226 Zinc finger protein 24 {Human (Homo sapiens) [TaxI 80.18
d1zina235 Microbial and mitochondrial ADK, insert "zinc fing 80.04
>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=7.9e-26  Score=131.47  Aligned_cols=44  Identities=32%  Similarity=0.662  Sum_probs=42.6

Q ss_pred             ceEEEcCcCCcceecCCCCCeecCCCCCeEEEeeeCCeeEEEee
Q psy2244          15 DIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFK   58 (73)
Q Consensus        15 ~v~YiC~~Cg~e~~ik~~d~IRC~~CG~RILyKkRt~r~vqf~~   58 (73)
                      .|.|+|++||.+++|+++|+|||.+||||||||+||++|+||++
T Consensus         2 ~v~YiCgeCg~~~~l~~~d~irCreCG~RIlYK~RTkr~vqfeA   45 (46)
T d1twfl_           2 TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEA   45 (46)
T ss_dssp             CCCEECSSSCCEECCCTTSTTCCSSSCCCCCBCCCCSSCEEECC
T ss_pred             ceEEEcccCCCceEeCCCCcEEeccCCcEEEEeecccceeeEec
Confidence            47899999999999999999999999999999999999999986
>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} 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
>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {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
>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1ltla_ b.40.4.11 (A:) DNA replication initiator (cdc21/cdc54) N-terminal domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d2csha1 g.37.1.1 (A:8-60) Zinc finger protein 297b {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure
>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]} 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
>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]} Back     information, alignment and structure
>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]} Back     information, alignment and structure
>d1hxra_ b.88.1.1 (A:) RabGEF Mss4 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]} 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
>d1x6ea2 g.37.1.1 (A:41-66) Zinc finger protein 24 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure