YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|225000856, gi...
Organism:	synthetic construct
Length:	1203 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|225000856, gi....

Description	E-value	Query Range	Subject Range
gi\|5734516 - gi\|5734516\|emb\|CAB52754.1\| hyperpolarization-activated channel type 4 [Homo sapiens]	0.0	[1..1203]	[1..1203]
HCN4_RAT - Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 OS=Rattus norvegicus ...	0.0	[1..1203]	[1..1198]
gi\|195934831 - gi\|195934831\|gb\|AAI68402.1\| Hyperpolarization-activated, cyclic nucleotide-gated K+ 4 [synthetic con... gi\|94387268, gi\|... - gi\|94387268\|ref\|XP_981893.1\| PREDICTED: similar to hyperpolarization-activated, cyclic nucleotide-ga...	0.0	[1..1203]	[1..1201]
HCN4_RABIT - Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 OS=Oryctolagus cunicu...	0.0	[1..1203]	[1..1175]
gi\|114581438 - gi\|114581438\|ref\|XP_525954.2\| PREDICTED: potassium voltage-gated channel, subfamily H, member 7 isof...	0.0	[6..963]	[163..1111]

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Predicted Domain #1

Region A:
Residues: [1-176]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDKLPPSMRK RLYSLPQQVG AKAWIMDEEE DAEEEGAGGR QDPSRRSIRL RPLPSPSPSA  60
   61 AAGGTESRSS ALGAADSEGP ARGAGKSSTN GDCRRFRGSL ASLGSRGGGS GGTGSGSSHG 120
  121 HLHDSAEERR LIAEGDASPG EDRTPPGLAA EPERPGASAQ PAASPPPPQQ PPQPAS

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [177-287]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ASCEQPSVDT AIKVEGGAAA GDQILPEAEV RLGQAGFMQR QFGAMLQPGV NKFSLRMFGS  60
   61 QKAVEREQER VKSAGFWIIH PYSDFRFYWD LTMLLLMVGN LIIIPVGITF F

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	55.366532
Match:	PF08412.1
Description:	No description for PF08412.1 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [288-525]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDENTTPWIV FNVVSDTFFL IDLVLNFRTG IVVEDNTEII LDPQRIKMKY LKSWFMVDFI  60
   61 SSIPVDYIFL IVETRIDSEV YKTARALRIV RFTKILSLLR LLRLSRLIRY IHQWEEIFHM 120
  121 TYDLASAVVR IVNLIGMMLL LCHWDGCLQF LVPMLQDFPD DCWVSINNMV NNSWGKQYSY 180
  181 ALFKAMSHML CIGYGRQAPV GMSDVWLTML SMIVGATCYA MFIGHATALI QSLDSSRR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.30103
Match:	2a79B
Description:	Mammalian Shaker Kv1.2 potassium channel- beta subunit complex
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [526-592]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QYQEKYKQVE QYMSFHKLPP DTRQRIHDYY EHRYQGKMFD EESILGELSE PLREEIINFN  60
   61 CRKLVAS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	63.69897
Match:	1q3eA
Description:	HCN2J 443-645 in the presence of cGMP
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
intracellular cyclic nucleotide activated cation channel activity	10.1422916734545	bayes_pls_golite062009
cyclic nucleotide-gated ion channel activity	10.1422916734545	bayes_pls_golite062009
intracellular ligand-gated ion channel activity	9.72053268940283	bayes_pls_golite062009
cation channel activity	9.48749374439976	bayes_pls_golite062009
ion channel activity	9.4846197809463	bayes_pls_golite062009
metal ion transmembrane transporter activity	9.3929063879608	bayes_pls_golite062009
passive transmembrane transporter activity	9.25176207085973	bayes_pls_golite062009
channel activity	9.25176207085973	bayes_pls_golite062009
substrate-specific channel activity	9.2472549851376	bayes_pls_golite062009
intracellular cGMP activated cation channel activity	9.19973076787954	bayes_pls_golite062009
gated channel activity	9.19042473454294	bayes_pls_golite062009
cGMP binding	7.7575871125398	bayes_pls_golite062009
ligand-gated channel activity	7.41584542512987	bayes_pls_golite062009
ligand-gated ion channel activity	7.41584542512987	bayes_pls_golite062009
cyclic nucleotide binding	7.37322432929433	bayes_pls_golite062009
voltage-gated ion channel activity	6.57272328088253	bayes_pls_golite062009
voltage-gated channel activity	6.54930851487319	bayes_pls_golite062009
ion transmembrane transporter activity	5.54400173845933	bayes_pls_golite062009
GMP binding	5.49455172024846	bayes_pls_golite062009
cation transmembrane transporter activity	5.34760703274696	bayes_pls_golite062009
potassium channel activity	5.29889968906368	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	5.1138025954757	bayes_pls_golite062009
voltage-gated cation channel activity	4.96516802098805	bayes_pls_golite062009
voltage-gated potassium channel activity	4.52895684111035	bayes_pls_golite062009
intracellular cAMP activated cation channel activity	3.95109938608832	bayes_pls_golite062009
transporter activity	3.30740141256752	bayes_pls_golite062009
substrate-specific transporter activity	3.24402760485462	bayes_pls_golite062009
transmembrane transporter activity	3.22443361822344	bayes_pls_golite062009
binding	1.10631659705555	bayes_pls_golite062009
protein binding	0.79369425144072	bayes_pls_golite062009
signal transducer activity	0.202809682876964	bayes_pls_golite062009
molecular transducer activity	0.202809682876964	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [593-740]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPLFANADPN FVTSMLTKLR FEVFQPGDYI IREGTIGKKM YFIQHGVVSV LTKGNKETKL  60
   61 ADGSYFGEIC LLTRGRRTAS VRADTYCRLY SLSVDNFNEV LEEYPMMRRA FETVALDRLD 120
  121 RIGKKNSILL HKVQHDLNSG VFNYQENE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.221849
Match:	1o7fA
Description:	Regulatory domain of epac2, domain 2; Regulatory domain of Epac2, domains 1 and 3
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
intracellular cyclic nucleotide activated cation channel activity	10.1422916734545	bayes_pls_golite062009
cyclic nucleotide-gated ion channel activity	10.1422916734545	bayes_pls_golite062009
intracellular ligand-gated ion channel activity	9.72053268940283	bayes_pls_golite062009
cation channel activity	9.48749374439976	bayes_pls_golite062009
ion channel activity	9.4846197809463	bayes_pls_golite062009
metal ion transmembrane transporter activity	9.3929063879608	bayes_pls_golite062009
passive transmembrane transporter activity	9.25176207085973	bayes_pls_golite062009
channel activity	9.25176207085973	bayes_pls_golite062009
substrate-specific channel activity	9.2472549851376	bayes_pls_golite062009
intracellular cGMP activated cation channel activity	9.19973076787954	bayes_pls_golite062009
gated channel activity	9.19042473454294	bayes_pls_golite062009
cGMP binding	7.7575871125398	bayes_pls_golite062009
ligand-gated channel activity	7.41584542512987	bayes_pls_golite062009
ligand-gated ion channel activity	7.41584542512987	bayes_pls_golite062009
cyclic nucleotide binding	7.37322432929433	bayes_pls_golite062009
voltage-gated ion channel activity	6.57272328088253	bayes_pls_golite062009
voltage-gated channel activity	6.54930851487319	bayes_pls_golite062009
ion transmembrane transporter activity	5.54400173845933	bayes_pls_golite062009
GMP binding	5.49455172024846	bayes_pls_golite062009
cation transmembrane transporter activity	5.34760703274696	bayes_pls_golite062009
potassium channel activity	5.29889968906368	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	5.1138025954757	bayes_pls_golite062009
voltage-gated cation channel activity	4.96516802098805	bayes_pls_golite062009
voltage-gated potassium channel activity	4.52895684111035	bayes_pls_golite062009
intracellular cAMP activated cation channel activity	3.95109938608832	bayes_pls_golite062009
transporter activity	3.30740141256752	bayes_pls_golite062009
substrate-specific transporter activity	3.24402760485462	bayes_pls_golite062009
transmembrane transporter activity	3.22443361822344	bayes_pls_golite062009
binding	1.10631659705555	bayes_pls_golite062009
protein binding	0.79369425144072	bayes_pls_golite062009
sequence-specific DNA binding	0.5243910425301	bayes_pls_golite062009
signal transducer activity	0.202809682876964	bayes_pls_golite062009
molecular transducer activity	0.202809682876964	bayes_pls_golite062009

Predicted Domain #6

Region A:
Residues: [741-1203]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IIQQIVQHDR EMAHCAHRVQ AAASATPTPT PVIWTPLIQA PLQAAAATTS VAIALTHHPR  60
   61 LPAAIFRPPP GSGLGNLGAG QTPRHLKRLQ SLIPSALGSA SPASSPSQVD TPSSSSFHIQ 120
  121 QLAGFSAPAG LSPLLPSSSS SPPPGACGSP SAPTPSAGVA ATTIAGFGHF HKALGGSLSS 180
  181 SDSPLLTPLQ PGARSPQAAQ PSPAPPGARG GLGLPEHFLP PPPSSRSPSS SPGQLGQPPG 240
  241 ELSLGLATGP LSTPETPPRQ PEPPSLVAGA SGGASPVGFT PRGGLSPPGH SPGPPRTFPS 300
  301 APPRASGSHG SLLLPPASSP PPPQVPQRRG TPPLTPGRLT QDLKLISASQ PALPQDGAQT 360
  361 LRRASPHSSG ESMAAFPLFP RAGGGSGGSG SSGGLGPPGR PYGAIPGQHV TLPRKTSSGS 420
  421 LPPPLSLFGA RATSSGGPPL TAGPQREPGA RPEPVRSKLP SNL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.0
Match:	1y0fA
Description:	No description for 1y0fA was found.

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: