Citrus Sinensis ID: 041503

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-------10
MSSSTNESRNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSKYGLS
cccccHHcccHHHHHHHcccEEEEEEccccccccccEEEEEEcccccHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
ccccccccccccEEEcccccEEEEEEccccccccccEEEEEEccccHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
mssstnesrnSLQVCNECggqielftshttknpnrkfwkcrvcknfqwaedrkfsnEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQlrskygls
mssstnesrnSLQVCNECGGQIELFtshttknpnrkfwKCRVCKNFqwaedrkfsnekiDLLVEEVRKLTLEIERLSDKFRLLHKelehtqlrskygls
MSSSTNESRNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSKYGLS
************QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHK**************
**************CNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQL***YG**
************QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ********
*********NSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSK****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSSSTNESRNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKFSNEKxxxxxxxxxxxxxxxxxxxxxxxxxxxxLEHTQLRSKYGLS
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

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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 ?
Query99
TAIR|locus:2159083 415 AT5G13920 [Arabidopsis thalian 0.555 0.132 0.349 0.00011
TAIR|locus:2143231169 AT5G15690 [Arabidopsis thalian 0.707 0.414 0.290 0.00051
TAIR|locus:2159083 AT5G13920 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 86 (35.3 bits), Expect = 0.00011, Sum P(2) = 0.00011
 Identities = 22/63 (34%), Positives = 37/63 (58%)

Query:     1 MSSSTNESRNSLQVCNECGGQI-ELFTSHTTKNPNRKFWKCRVCKN---FQWAEDRKFSN 56
             + S T++   ++Q C  CGG   E+  ++T +NP RKF+KC   +N   F+W +  K ++
Sbjct:    26 LKSYTDDPPPAIQ-C-PCGGGFCEIKVANTRENPGRKFYKCPTAQNCCFFKWCD--KVTD 81

Query:    57 EKI 59
             E I
Sbjct:    82 EDI 84
GO:0003676 "nucleic acid binding" evidence=IEA;ISS
GO:0005737 "cytoplasm" evidence=ISM
GO:0008150 "biological_process" evidence=ND
GO:0008270 "zinc ion binding" evidence=IEA
TAIR|locus:2143231 AT5G15690 [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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query99
pfam0683945 pfam06839, zf-GRF, GRF zinc finger 1e-04
>gnl|CDD|219199 pfam06839, zf-GRF, GRF zinc finger Back     alignment and domain information 
 Score = 36.2 bits (84), Expect = 1e-04
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 7/43 (16%)

Query: 15 CNECGGQIELFTSHTT-KNPNRKFWKCRVCKN-----FQWAED 51
          C  CG    + T   T  NP R+F+KC   +      FQW ++
Sbjct: 3  CP-CGQLAVILTVRKTGPNPGRQFYKCPYGREKQCGFFQWEDE 44

This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396. Length = 45

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 99
PF0683945 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc 99.68
KOG1956758 consensus DNA topoisomerase III alpha [Replication 98.0
PF05325122 DUF730: Protein of unknown function (DUF730); Inte 97.43
PF0139639 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc 97.3
PRK00464154 nrdR transcriptional regulator NrdR; Validated 97.03
TIGR0365553 anti_R_Lar restriction alleviation protein, Lar fa 95.98
PF0460647 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I 95.35
KOG4399 325 consensus C2HC-type Zn-finger protein [General fun 95.32
PF0109639 TFIIS_C: Transcription factor S-II (TFIIS); InterP 94.89
PRK0967872 DNA-binding transcriptional regulator; Provisional 94.85
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 94.17
smart0044040 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo 94.13
PF0388457 DUF329: Domain of unknown function (DUF329); Inter 93.95
PF1276046 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int 93.93
PF11672102 DUF3268: Protein of unknown function (DUF3268); In 93.8
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 93.56
PF01927147 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T 93.47
PRK0041862 DNA gyrase inhibitor; Reviewed 93.38
PF1340858 Zn_ribbon_recom: Recombinase zinc beta ribbon doma 93.3
TIGR01384104 TFS_arch transcription factor S, archaeal. There h 92.86
PF0728269 OrfB_Zn_ribbon: Putative transposase DNA-binding d 92.39
PHA0062659 hypothetical protein 92.33
PF1480334 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. 92.31
smart0066152 RPOL9 RNA polymerase subunit 9. 91.94
PRK06266178 transcription initiation factor E subunit alpha; V 91.4
COG1594113 RPB9 DNA-directed RNA polymerase, subunit M/Transc 91.09
PF04216290 FdhE: Protein involved in formate dehydrogenase fo 90.74
KOG2907116 consensus RNA polymerase I transcription factor TF 89.99
PRK0971064 lar restriction alleviation and modification prote 89.5
COG302465 Uncharacterized protein conserved in bacteria [Fun 88.99
PF14353128 CpXC: CpXC protein 88.93
PF0497780 DivIC: Septum formation initiator; InterPro: IPR00 88.92
TIGR0209838 MJ0042_CXXC MJ0042 family finger-like domain. This 88.55
PRK07220740 DNA topoisomerase I; Validated 88.27
smart00531147 TFIIE Transcription initiation factor IIE. 88.02
PF1345341 zf-TFIIB: Transcription factor zinc-finger 87.95
PF0537755 FlaC_arch: Flagella accessory protein C (FlaC); In 87.81
PF1435461 Lar_restr_allev: Restriction alleviation protein L 87.71
PRK00888105 ftsB cell division protein FtsB; Reviewed 87.29
PRK0134357 zinc-binding protein; Provisional 87.08
COG1571421 Predicted DNA-binding protein containing a Zn-ribb 86.61
PF05876 557 Terminase_GpA: Phage terminase large subunit (GpA) 86.52
COG199789 RPL43A Ribosomal protein L37AE/L43A [Translation, 86.29
PF0497780 DivIC: Septum formation initiator; InterPro: IPR00 86.18
PF0178090 Ribosomal_L37ae: Ribosomal L37ae protein family; I 86.08
COG1656165 Uncharacterized conserved protein [Function unknow 86.07
PF1057126 UPF0547: Uncharacterised protein family UPF0547; I 85.94
PHA02998195 RNA polymerase subunit; Provisional 85.91
PF04880 166 NUDE_C: NUDE protein, C-terminal conserved region; 85.65
PRK12380113 hydrogenase nickel incorporation protein HybF; Pro 85.53
PRK00420112 hypothetical protein; Validated 85.46
PF0381136 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0 84.94
PRK03564309 formate dehydrogenase accessory protein FdhE; Prov 84.77
PRK00888105 ftsB cell division protein FtsB; Reviewed 84.33
TIGR02159146 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu 84.05
PRK1489299 putative transcription elongation factor Elf1; Pro 83.53
PRK0043250 30S ribosomal protein S27ae; Validated 83.44
PF09788256 Tmemb_55A: Transmembrane protein 55A; InterPro: IP 82.95
PHA02942383 putative transposase; Provisional 82.73
COG0675364 Transposase and inactivated derivatives [DNA repli 82.61
TIGR01385299 TFSII transcription elongation factor S-II. This m 82.39
KOG2906105 consensus RNA polymerase III subunit C11 [Transcri 81.72
PF1420555 Cys_rich_KTR: Cysteine-rich KTR 81.59
TIGR03830127 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he 81.57
TIGR00100115 hypA hydrogenase nickel insertion protein HypA. In 81.32
COG3677129 Transposase and inactivated derivatives [DNA repli 81.28
PRK07220740 DNA topoisomerase I; Validated 80.68
PRK14810272 formamidopyrimidine-DNA glycosylase; Provisional 80.53
KOG3896 449 consensus Dynactin, subunit p62 [Cell motility] 80.17
TIGR00340163 zpr1_rel ZPR1-related zinc finger protein. A model 80.12
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 
Probab=99.68  E-value=2.5e-17  Score=97.72  Aligned_cols=38  Identities=42%  Similarity=0.907  Sum_probs=35.9

Q ss_pred             ccccCccccceeeeec-CCCCCCcceeeCC-----CCCeeEeccC
Q 041503           13 QVCNECGGQIELFTSH-TTKNPNRKFWKCR-----VCKNFQWAED   51 (99)
Q Consensus        13 ~~Cp~Cg~~~~~~tS~-t~~NPgR~Fy~C~-----~C~fF~W~De   51 (99)
                      |.| .||.+++++||+ +.+||||+||+||     .|+||+|+||
T Consensus         1 p~C-~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~De   44 (45)
T PF06839_consen    1 PKC-PCGEPAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWEDE   44 (45)
T ss_pred             CCC-CCCCEeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEeccC
Confidence            589 699999999999 9999999999999     5999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair] Back     alignment and domain information
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function 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
>PRK00464 nrdR transcriptional regulator NrdR; Validated Back     alignment and domain information
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family 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
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only] 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
>PRK09678 DNA-binding transcriptional regulator; Provisional 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
>smart00440 ZnF_C2C2 C2C2 Zinc finger Back     alignment and domain information
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc 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
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150 Back     alignment and domain information
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Back     alignment and domain information
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function Back     alignment and domain information
>PRK00418 DNA gyrase inhibitor; Reviewed Back     alignment and domain information
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain Back     alignment and domain information
>TIGR01384 TFS_arch transcription factor S, archaeal 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
>PHA00626 hypothetical protein Back     alignment and domain information
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C Back     alignment and domain information
>smart00661 RPOL9 RNA polymerase subunit 9 Back     alignment and domain information
>PRK06266 transcription initiation factor E subunit alpha; Validated Back     alignment and domain information
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription] 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
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12 Back     alignment and domain information
>PRK09710 lar restriction alleviation and modification protein; Reviewed Back     alignment and domain information
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PF14353 CpXC: CpXC protein Back     alignment and domain information
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation [] Back     alignment and domain information
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>smart00531 TFIIE Transcription initiation factor IIE Back     alignment and domain information
>PF13453 zf-TFIIB: Transcription factor zinc-finger Back     alignment and domain information
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct [] Back     alignment and domain information
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar Back     alignment and domain information
>PRK00888 ftsB cell division protein FtsB; Reviewed Back     alignment and domain information
>PRK01343 zinc-binding protein; Provisional Back     alignment and domain information
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only] Back     alignment and domain information
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA Back     alignment and domain information
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation [] 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
>COG1656 Uncharacterized conserved protein [Function unknown] 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
>PHA02998 RNA polymerase subunit; Provisional Back     alignment and domain information
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins Back     alignment and domain information
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional Back     alignment and domain information
>PRK00420 hypothetical protein; Validated 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
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Back     alignment and domain information
>PRK00888 ftsB cell division protein FtsB; Reviewed Back     alignment and domain information
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit Back     alignment and domain information
>PRK14892 putative transcription elongation factor Elf1; Provisional Back     alignment and domain information
>PRK00432 30S ribosomal protein S27ae; Validated Back     alignment and domain information
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate Back     alignment and domain information
>PHA02942 putative transposase; Provisional Back     alignment and domain information
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01385 TFSII transcription elongation factor S-II Back     alignment and domain information
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription] Back     alignment and domain information
>PF14205 Cys_rich_KTR: Cysteine-rich KTR Back     alignment and domain information
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family Back     alignment and domain information
>TIGR00100 hypA hydrogenase nickel insertion protein HypA Back     alignment and domain information
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>KOG3896 consensus Dynactin, subunit p62 [Cell motility] Back     alignment and domain information
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query99
1qyp_A57 RNA polymerase II; transcription, RPB9, Zn ribbon, 96.52
1tfi_A50 Transcriptional elongation factor SII; transcripti 94.67
3h0g_I113 DNA-directed RNA polymerases I, II, and III subuni 92.48
1twf_I122 B12.6, DNA-directed RNA polymerase II 14.2 kDa pol 92.34
3j20_Y50 30S ribosomal protein S27AE; archaea, archaeal, KI 92.28
3po3_S178 Transcription elongation factor S-II; RNA polymera 92.12
2yy0_A53 C-MYC-binding protein; conserved hypothetical prot 92.04
2gai_A633 DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A 90.63
1lv3_A68 Hypothetical protein YACG; zinc finger, rubredoxin 90.09
1pqv_S309 STP-alpha, transcription elongation factor S-II, D 89.48
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; 87.23
3cng_A 189 Nudix hydrolase; structural genomics, APC7497, PSI 86.31
3qt1_I133 DNA-directed RNA polymerases I, II, and III subun; 86.0
1k1f_A72 Breakpoint cluster region protein; oligomerization 85.83
2epr_A48 POZ-, at HOOK-, and zinc finger-containing protein 85.27
2yy0_A53 C-MYC-binding protein; conserved hypothetical prot 84.77
1vq8_Z83 50S ribosomal protein L37AE; ribosome 50S, protein 84.75
4a17_Y103 RPL37A, 60S ribosomal protein L32; eukaryotic ribo 83.58
1go4_E100 MAD1 (mitotic arrest deficient)-like 1; mitotic sp 82.65
3iz5_m92 60S ribosomal protein L43 (L37AE); eukaryotic ribo 80.25
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Back     alignment and structure
Probab=96.52  E-value=0.0021  Score=38.29  Aligned_cols=38  Identities=24%  Similarity=0.726  Sum_probs=28.1

Q ss_pred             cccccCcccc-ceeeeec--CCCCCCcceeeCCCCCeeEecc
Q 041503           12 LQVCNECGGQ-IELFTSH--TTKNPNRKFWKCRVCKNFQWAE   50 (99)
Q Consensus        12 ~~~Cp~Cg~~-~~~~tS~--t~~NPgR~Fy~C~~C~fF~W~D   50 (99)
                      .+.||.||.. +.-+...  +.++|--.||.|..|++ .|.+
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~-~w~~   55 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH-TWRS   55 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCC-EEEC
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCC-Eecc
Confidence            4789999974 4444444  45789999999999986 4654
>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Back     alignment and structure
>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
>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
>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus} 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
>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens} Back     alignment and structure
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima} PDB: 2gaj_A* Back     alignment and structure
>1lv3_A Hypothetical protein YACG; zinc finger, rubredoxin knuckle, C4 tetrahedral Zn+2, antiparallel beta strand and alpha helix, NESG project; NMR {Escherichia coli} SCOP: g.39.1.9 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
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A Back     alignment and structure
>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718} Back     alignment and structure
>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
>1k1f_A Breakpoint cluster region protein; oligomerization, coiled coil, BCR-ABL kinase, transferase; 2.20A {Homo sapiens} SCOP: a.147.1.1 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
>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens} 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
>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
>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query99
d1lv3a_65 Hypothetical zinc finger protein YacG {Escherichia 95.19
d1qypa_57 RBP9 subunit of RNA polymerase II {Archaeon Thermo 94.6
d1twfi272 RBP9 subunit of RNA polymerase II {Baker's yeast ( 93.06
d2ct7a173 Ring finger protein 31 {Human (Homo sapiens) [TaxI 91.27
d1tfia_50 Transcriptional factor SII, C-terminal domain {Hum 89.01
d1k1fa_67 Bcr-Abl oncoprotein oligomerization domain {Human 87.5
d1k3xa340 Endonuclease VIII {Escherichia coli [TaxId: 562]} 82.71
d1k82a344 DNA repair protein MutM (Fpg) {Escherichia coli [T 80.76
d1r2za346 DNA repair protein MutM (Fpg) {Bacillus stearother 80.58
d2fiya1290 FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId 80.38
>d1lv3a_ g.39.1.9 (A:) Hypothetical zinc finger protein YacG {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Hypothetical zinc finger protein YacG
domain: Hypothetical zinc finger protein YacG
species: Escherichia coli [TaxId: 562]

Probab=95.19  E-value=0.0016  Score=39.40  Aligned_cols=35  Identities=29%  Similarity=0.691  Sum_probs=28.2

Q ss_pred             cccccCccccceeeeecCCCCCCcceeeCC-CCC---eeEeccCC
Q 041503           12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR-VCK---NFQWAEDR   52 (99)
Q Consensus        12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-~C~---fF~W~De~   52 (99)
                      .+.||.||+++    .++..||-|+|  |. .|+   |-.|.++.
T Consensus         6 ~v~CP~C~k~~----~w~~~~~~rPF--CS~RCk~IDLg~W~~e~   44 (65)
T d1lv3a_           6 TVNCPTCGKTV----VWGEISPFRPF--CSKRCQLIDLGEWAAEE   44 (65)
T ss_dssp             EEECTTTCCEE----ECSSSSSCCSS--SSHHHHHHHHSCSSSSS
T ss_pred             eeeCCCCCCcc----ccCCCCCcCCc--hhHhhhhccHHHHhcCC
Confidence            37899999874    46789999999  55 564   89999887
>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Back     information, alignment and structure
>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
>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1k1fa_ a.147.1.1 (A:) Bcr-Abl oncoprotein oligomerization domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} 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