Psyllid ID: psy16237

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130---
Protein Sequence
MATDNSMDGSCPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEEEccccccccEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccHHccccccccEEEcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccEcccccEEEEEccccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccEEEEcc
Coil and Loop (DISEMBL)
matdnsmdgscpgYIISVKELTEDTEIRLnlgynnkrtklkisgavqketpqeIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSqsksfapsISMIKKCIESLIDKnyvertanstdeysyva
Flexible Loop (DISEMBL)
matdnsmdgscpGYIISVKELTEDTEIRlnlgynnkrtklkisgavqketpqeiertvssvdedrKLYLQAAIVRIMKSRKQIRHNALIQEVlsqsksfapsiSMIKKCIESlidknyvertanstdeysyva
Low Complexity Region (SEG)
MATDNSMDGSCPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Disordered region (IsUnstruct)
**********CPGYIISVKELTEDTEIRLNLGYNNKRTKL************************RKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVE*************
Disordered Region (DISOPRED)
****************SVKELTEDTEIRLNLGYNNKRTKLKI*********************DRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Disordered Region (DISEMBL)
********GSCPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN*********
Disordered Region (DISPRO)
**********CPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETP*EIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATDNSMDGSCPGYIISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	133	2.2.26 [Sep-21-2011]
Q9D4H8	745	Cullin-2 OS=Mus musculus	yes	N/A	0.894	0.159	0.612	1e-38
Q5RCF3	745	Cullin-2 OS=Pongo abelii	yes	N/A	0.894	0.159	0.612	1e-38
Q13617	745	Cullin-2 OS=Homo sapiens	yes	N/A	0.894	0.159	0.612	1e-38
Q9XZJ3	771	Cullin-2 OS=Dictyostelium	yes	N/A	0.812	0.140	0.550	7e-28
Q5R4G6	776	Cullin-1 OS=Pongo abelii	no	N/A	0.857	0.146	0.504	2e-24
Q13616	776	Cullin-1 OS=Homo sapiens	no	N/A	0.857	0.146	0.504	2e-24
Q9WTX6	776	Cullin-1 OS=Mus musculus	no	N/A	0.857	0.146	0.504	2e-24
O60999	770	Cullin-1 OS=Dictyostelium	no	N/A	0.864	0.149	0.465	2e-22
Q17390	850	Cullin-2 OS=Caenorhabditi	yes	N/A	0.857	0.134	0.444	4e-22
Q24311	774	Cullin homolog 1 OS=Droso	no	N/A	0.849	0.145	0.464	4e-21

>sp|Q9D4H8|CUL2_MOUSE Cullin-2 OS=Mus musculus GN=Cul2 PE=1 SV=2

 Score =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/129 (61%), Positives = 102/129 (79%), Gaps = 10/129 (7%)

Query: 15  IISVKELTEDTE---------IRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDR 65
           ++ VK +  D+E           LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDR
Sbjct: 617 LLDVKMINHDSEKEDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDR 676

Query: 66  KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124
           K+YLQAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  
Sbjct: 677 KMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQA 736

Query: 125 STDEYSYVA 133
           S DEYSYVA
Sbjct: 737 SADEYSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).
Mus musculus (taxid: 10090)

>sp|Q5RCF3|CUL2_PONAB Cullin-2 OS=Pongo abelii GN=CUL2 PE=2 SV=1

 Score =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/129 (61%), Positives = 102/129 (79%), Gaps = 10/129 (7%)

Query: 15  IISVKELTEDTE---------IRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDR 65
           ++ VK +  D+E           LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDR
Sbjct: 617 LLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDR 676

Query: 66  KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124
           K+YLQAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  
Sbjct: 677 KMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQA 736

Query: 125 STDEYSYVA 133
           S DEYSYVA
Sbjct: 737 SADEYSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).

Pongo abelii (taxid: 9601)

>sp|Q13617|CUL2_HUMAN Cullin-2 OS=Homo sapiens GN=CUL2 PE=1 SV=2

 Score =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/129 (61%), Positives = 102/129 (79%), Gaps = 10/129 (7%)

Query: 15  IISVKELTEDTE---------IRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDR 65
           ++ VK +  D+E           LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDR
Sbjct: 617 LLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDR 676

Query: 66  KLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTAN 124
           K+YLQAAIVRIMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  
Sbjct: 677 KMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQA 736

Query: 125 STDEYSYVA 133
           S DEYSYVA
Sbjct: 737 SADEYSYVA 745

Core component of multiple cullin-RING-based ECS (ElonginB/C-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of target proteins. May serve as a rigid scaffold in the complex and may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1 (By similarity). The functional specificity of the ECS complex depends on the substrate recognition component. ECS(VHL) mediates the ubiquitination of hypoxia-inducible factor (HIF).

Homo sapiens (taxid: 9606)

>sp|Q9XZJ3|CUL2_DICDI Cullin-2 OS=Dictyostelium discoideum GN=culB PE=2 SV=1

 Score =  122 bits (306), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 60/109 (55%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 26  EIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRH 85
           E  +N  Y+NKR+K+K+S ++QKETP + E T   +DEDRKLYLQA+IVRIMK+RK + H
Sbjct: 663 EYTVNSAYSNKRSKVKVSSSLQKETPLQNEETYKGIDEDRKLYLQASIVRIMKARKTMNH 722

Query: 86  NALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            +LIQEV+  S+  F P+I MIKKCIE LI+K Y+ R    +D Y Y A
Sbjct: 723 VSLIQEVIEHSRLRFQPNIPMIKKCIEQLIEKEYITRAEGESDRYLYAA 771

Probable core component of cullin-based SCF-like E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit (By similarity). Appears to ensure that the proper number of prestalk cells differentiate at the appropriate time in development. May govern prestalk cell differentiation.

Dictyostelium discoideum (taxid: 44689)

>sp|Q5R4G6|CUL1_PONAB Cullin-1 OS=Pongo abelii GN=CUL1 PE=2 SV=1

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)

Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 662 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 721

Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 722 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participates in Wnt signaling. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Pongo abelii (taxid: 9601)

>sp|Q13616|CUL1_HUMAN Cullin-1 OS=Homo sapiens GN=CUL1 PE=1 SV=2

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)

Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 662 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 721

Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 722 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Homo sapiens (taxid: 9606)

>sp|Q9WTX6|CUL1_MOUSE Cullin-1 OS=Mus musculus GN=Cul1 PE=1 SV=1

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)

Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 662 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 721

Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 722 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 776

Core component of multiple cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53 (By similarity). SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(Cyclin F) directs ubiquitination of CP110.

Mus musculus (taxid: 10090)

>sp|O60999|CUL1_DICDI Cullin-1 OS=Dictyostelium discoideum GN=culA PE=1 SV=1

 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 54/116 (46%), Positives = 80/116 (68%), Gaps = 1/116 (0%)

Query: 19  KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
           +E+ + T+  LN  + NK+TK+ I+  V  +  +EI+    +V+EDRKL +QAAIVRIMK
Sbjct: 655 EEIAKTTKFSLNKQFKNKKTKIFINVPVLTQVKEEIDSIHKTVEEDRKLQIQAAIVRIMK 714

Query: 79  SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            RKQ+ H+ L+ EV+SQ ++ F P +++IKKCI+ LI+K Y+ R     D YSYVA
Sbjct: 715 MRKQLAHSGLMTEVISQLQTRFNPKVNIIKKCIDILIEKEYLMRVEGKKDHYSYVA 770

Probable core component of cullin-based SCF-like E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit (By similarity). Required at several stages during development. CulA and fbxA regulate multicellular development by targeting regA for degradation via a pathway that requires erkB function, leading to an increase in cAMP and PKA activity.

Dictyostelium discoideum (taxid: 44689)

>sp|Q17390|CUL2_CAEEL Cullin-2 OS=Caenorhabditis elegans GN=cul-2 PE=1 SV=3

 Score =  103 bits (256), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 52/117 (44%), Positives = 79/117 (67%), Gaps = 3/117 (2%)

Query: 19  KELTEDTEIRLNLGYNNKRTKLKISGA-VQKETPQEIERTVSSVDEDRKLYLQAAIVRIM 77
           + LT D+ +RLN+   +KR K ++    V K   +E E   ++V +DRK Y++ AIVRIM
Sbjct: 735 QNLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIM 794

Query: 78  KSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           K+RK ++HNAL+ E++ Q+K  F+P +  IKK IE LI+K Y++RT +  DEY Y+A
Sbjct: 795 KTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRT-DQNDEYQYLA 850

Positive cell-cycle regulator that is required at two distinct points in the cell cycle; the G1-to-S-phase transition and mitosis. Also required for proper cytoskeletal movement and mitotic chromosome condensation. Core component of multiple cullin-RING-based CBC (Cul2-ElonginB-ElonginC) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. As a scaffold protein may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The functional specificity of the CBC complex depends on the variable substrate recognition component (By similarity). May function in ubiquitin-mediated degradation of CKIs to target cki-1 for degradation. CBC(zif-1) may ensure germline precursor cell asymmetry by targeting germline proteins for destruction if expressed in non-germline cells. CBC(fem-1) directs ubiquitination of tra-1.

Caenorhabditis elegans (taxid: 6239)

>sp|Q24311|CUL1_DROME Cullin homolog 1 OS=Drosophila melanogaster GN=lin19 PE=1 SV=2

 Score = 99.8 bits (247), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/114 (46%), Positives = 74/114 (64%), Gaps = 1/114 (0%)

Query: 21  LTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSR 80
           LT ++ + L L Y NK+ ++ I+  ++ E   E E     ++EDRKL +QAAIVRIMK R
Sbjct: 661 LTPESTVELFLDYKNKKRRININQPLKTELKVEQETVHKHIEEDRKLLIQAAIVRIMKMR 720

Query: 81  KQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           K++ H  LI EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 721 KRLNHTNLISEVLNQLSTRFKPKVPVIKKCIDILIEKEYLERMEGHKDTYSYLA 774

Core component of multiple SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme.

Drosophila melanogaster (taxid: 7227)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	133
158291834	766	AGAP003605-PA [Anopheles gambiae str. PE	0.894	0.155	0.691	2e-42
195030360	756	GH10784 [Drosophila grimshawi] gi|193904	0.879	0.154	0.728	3e-42
195384726	756	GJ14230 [Drosophila virilis] gi|19414752	0.879	0.154	0.728	4e-42
195116006	757	GI17442 [Drosophila mojavensis] gi|19391	0.894	0.157	0.716	5e-42
19921636	753	Cullin-2, isoform B [Drosophila melanoga	0.879	0.155	0.728	8e-42
194877946	753	GG21342 [Drosophila erecta] gi|190657164	0.879	0.155	0.728	8e-42
195354067	753	GM16141 [Drosophila sechellia] gi|194127	0.879	0.155	0.728	8e-42
195580685	753	GD24329 [Drosophila simulans] gi|1941921	0.879	0.155	0.728	9e-42
194760505	748	GF15487 [Drosophila ananassae] gi|190616	0.879	0.156	0.728	9e-42
195475880	753	GE12924 [Drosophila yakuba] gi|194176312	0.879	0.155	0.728	9e-42

>gi|158291834|ref|XP_313365.4| AGAP003605-PA [Anopheles gambiae str. PEST] gi|157017477|gb|EAA08832.5| AGAP003605-PA [Anopheles gambiae str. PEST]

 Score =  176 bits (447), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 83/120 (69%), Positives = 106/120 (88%), Gaps = 1/120 (0%)

Query: 15  IISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIV 74
           +++ +++ +DTE+ +N+ Y+NKRTK KI+  +QKETPQE+E T+++VDEDRK+YLQAAIV
Sbjct: 647 LLNEEKMNDDTEVSINVNYSNKRTKFKITTNLQKETPQEVEHTMNAVDEDRKMYLQAAIV 706

Query: 75  RIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RIMKSRK +RHN LIQE+LSQSK SFAP++SMIKKCIESLIDK Y+ERT NS DEYSYVA
Sbjct: 707 RIMKSRKVLRHNTLIQEILSQSKVSFAPNVSMIKKCIESLIDKQYIERTPNSGDEYSYVA 766

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195030360|ref|XP_001988036.1| GH10784 [Drosophila grimshawi] gi|193904036|gb|EDW02903.1| GH10784 [Drosophila grimshawi]

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 102/118 (86%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L+ DT I LN+ Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 639 SSENLSGDTRIELNMDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 698

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 699 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 756

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195384726|ref|XP_002051063.1| GJ14230 [Drosophila virilis] gi|194147520|gb|EDW63218.1| GJ14230 [Drosophila virilis]

 Score =  176 bits (445), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L+ DT I LN  Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 639 SSENLSGDTRIELNFDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 698

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 699 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 756

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195116006|ref|XP_002002547.1| GI17442 [Drosophila mojavensis] gi|193913122|gb|EDW11989.1| GI17442 [Drosophila mojavensis]

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 86/120 (71%), Positives = 102/120 (85%), Gaps = 1/120 (0%)

Query: 15  IISVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIV 74
           I + + L+ DT I LN  Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIV
Sbjct: 638 IANSENLSGDTRIELNFDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIV 697

Query: 75  RIMKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RIMK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 698 RIMKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 757

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|19921636|ref|NP_610117.1| Cullin-2, isoform B [Drosophila melanogaster] gi|24585698|ref|NP_724352.1| Cullin-2, isoform A [Drosophila melanogaster] gi|16769526|gb|AAL28982.1| LD36177p [Drosophila melanogaster] gi|22947032|gb|AAF57224.3| Cullin-2, isoform A [Drosophila melanogaster] gi|22947033|gb|AAG22124.2| Cullin-2, isoform B [Drosophila melanogaster] gi|220946800|gb|ACL85943.1| cul-2-PA [synthetic construct]

 Score =  174 bits (442), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194877946|ref|XP_001973977.1| GG21342 [Drosophila erecta] gi|190657164|gb|EDV54377.1| GG21342 [Drosophila erecta]

 Score =  174 bits (442), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195354067|ref|XP_002043522.1| GM16141 [Drosophila sechellia] gi|194127669|gb|EDW49712.1| GM16141 [Drosophila sechellia]

 Score =  174 bits (442), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195580685|ref|XP_002080165.1| GD24329 [Drosophila simulans] gi|194192174|gb|EDX05750.1| GD24329 [Drosophila simulans]

 Score =  174 bits (442), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194760505|ref|XP_001962480.1| GF15487 [Drosophila ananassae] gi|190616177|gb|EDV31701.1| GF15487 [Drosophila ananassae]

 Score =  174 bits (442), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 631 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 690

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 691 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 748

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195475880|ref|XP_002090211.1| GE12924 [Drosophila yakuba] gi|194176312|gb|EDW89923.1| GE12924 [Drosophila yakuba]

 Score =  174 bits (442), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 86/118 (72%), Positives = 101/118 (85%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
           S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct: 636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query: 77  MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct: 696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	133
FB|FBgn0032956	753	Cul-2 "Cullin-2" [Drosophila m	0.879	0.155	0.728	6.2e-40
UNIPROTKB|F1RUR7	510	CUL2 "Uncharacterized protein"	0.864	0.225	0.646	1.2e-35
UNIPROTKB|D4A0H4	725	Cul2 "Cullin 2 (Predicted), is	0.864	0.158	0.646	5.6e-35
UNIPROTKB|Q5T2B7	688	CUL2 "Cullin-2" [Homo sapiens	0.864	0.167	0.646	5.9e-35
MGI|MGI:1918995	745	Cul2 "cullin 2" [Mus musculus	0.864	0.154	0.646	6.1e-35
UNIPROTKB|E2QRU7	745	CUL2 "Uncharacterized protein"	0.864	0.154	0.646	7.9e-35
UNIPROTKB|Q13617	745	CUL2 "Cullin-2" [Homo sapiens	0.864	0.154	0.646	7.9e-35
UNIPROTKB|Q08DE9	745	CUL2 "Uncharacterized protein"	0.864	0.154	0.646	1e-34
UNIPROTKB|F1N829	747	CUL2 "Uncharacterized protein"	0.879	0.156	0.663	1e-34
ZFIN|ZDB-GENE-030131-8032	764	cul2 "cullin 2" [Danio rerio (	0.864	0.150	0.646	2.3e-34

FB|FBgn0032956 Cul-2 "Cullin-2" [Drosophila melanogaster (taxid:7227)]

 Score = 432 (157.1 bits), Expect = 6.2e-40, P = 6.2e-40
 Identities = 86/118 (72%), Positives = 101/118 (85%)

Query:    17 SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
             S + L  +T I LNL Y NKRTK KIS A+QKETPQE+E T++SVDEDRKL+LQAAIVRI
Sbjct:   636 SSENLAGETRIELNLDYTNKRTKFKISSALQKETPQEVEHTINSVDEDRKLFLQAAIVRI 695

Query:    77 MKSRKQIRHNALIQEVLSQSK-SFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             MK+RK ++HNALIQEVLS SK SF P+I+MIKKC+ESLIDK Y+ERTANS DEYSY+A
Sbjct:   696 MKARKVLKHNALIQEVLSLSKVSFTPNIAMIKKCVESLIDKQYIERTANSGDEYSYMA 753

GO:0000152 "nuclear ubiquitin ligase complex" evidence=ISS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

GO:0007295 "growth of a germarium-derived egg chamber" evidence=IMP

GO:0008582 "regulation of synaptic growth at neuromuscular junction" evidence=IMP

UNIPROTKB|F1RUR7 CUL2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 385 (140.6 bits), Expect = 1.2e-35, P = 1.2e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   395 EDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMK 454

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   455 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 510

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|D4A0H4 Cul2 "Cullin 2 (Predicted), isoform CRA_a" [Rattus norvegicus (taxid:10116)]

 Score = 386 (140.9 bits), Expect = 5.6e-35, P = 5.6e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   610 EDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYLQAAIVRIMK 669

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   670 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 725

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

UNIPROTKB|Q5T2B7 CUL2 "Cullin-2" [Homo sapiens (taxid:9606)]

 Score = 385 (140.6 bits), Expect = 5.9e-35, P = 5.9e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   573 EDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMK 632

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   633 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 688

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

MGI|MGI:1918995 Cul2 "cullin 2" [Mus musculus (taxid:10090)]

 Score = 386 (140.9 bits), Expect = 6.1e-35, P = 6.1e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   630 EDIDAESSFSLNMSFSSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYLQAAIVRIMK 689

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   690 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 745

GO:0005515 "protein binding" evidence=IPI

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IMP

GO:0030891 "VCB complex" evidence=ISO

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=ISO

GO:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0032403 "protein complex binding" evidence=ISO

UNIPROTKB|E2QRU7 CUL2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 385 (140.6 bits), Expect = 7.9e-35, P = 7.9e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   630 EDIDTESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMK 689

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   690 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 745

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|Q13617 CUL2 "Cullin-2" [Homo sapiens (taxid:9606)]

 Score = 385 (140.6 bits), Expect = 7.9e-35, P = 7.9e-35
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   630 EDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMK 689

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   690 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 745

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0031625 "ubiquitin protein ligase binding" evidence=IDA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IDA

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0008285 "negative regulation of cell proliferation" evidence=TAS

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=TAS

GO:0007050 "cell cycle arrest" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0033554 "cellular response to stress" evidence=TAS

GO:0061418 "regulation of transcription from RNA polymerase II promoter in response to hypoxia" evidence=TAS

GO:0071456 "cellular response to hypoxia" evidence=TAS

UNIPROTKB|Q08DE9 CUL2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 384 (140.2 bits), Expect = 1.0e-34, P = 1.0e-34
 Identities = 75/116 (64%), Positives = 99/116 (85%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +++  ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   630 EDIDVESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMK 689

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   690 ARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 745

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|F1N829 CUL2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 384 (140.2 bits), Expect = 1.0e-34, P = 1.0e-34
 Identities = 79/119 (66%), Positives = 100/119 (84%)

Query:    17 SVKELTE-DTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVR 75
             S KE  E ++   LN+ +++KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVR
Sbjct:   629 SDKEDVEAESTFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVR 688

Query:    76 IMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             IMK+RK +RHNALIQEV+SQS++ F PSISMIKKCIE LIDK Y+ER+  S DEYSYVA
Sbjct:   689 IMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVA 747

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0031462 "Cul2-RING ubiquitin ligase complex" evidence=IEA

ZFIN|ZDB-GENE-030131-8032 cul2 "cullin 2" [Danio rerio (taxid:7955)]

 Score = 381 (139.2 bits), Expect = 2.3e-34, P = 2.3e-34
 Identities = 75/116 (64%), Positives = 98/116 (84%)

Query:    19 KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
             +E+  ++   L + + +KRTK KI+ ++QK+TPQE+E+T S+VDEDRK+YLQAAIVRIMK
Sbjct:   649 EEIEPESTFSLIMSFTSKRTKFKITTSMQKDTPQELEQTRSAVDEDRKMYLQAAIVRIMK 708

Query:    79 SRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +RK +RHNALIQEV++QSK+ F PSISMIKKCIE LIDK Y+ER+ +S DEYSYVA
Sbjct:   709 ARKVLRHNALIQEVINQSKARFNPSISMIKKCIEVLIDKQYIERSQSSADEYSYVA 764

GO:0031461 "cullin-RING ubiquitin ligase complex" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0001944 "vasculature development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

---

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)
Q13617	CUL2_HUMAN	No assigned EC number	0.6124	0.8947	0.1597	yes	N/A
Q9XZJ3	CUL2_DICDI	No assigned EC number	0.5504	0.8120	0.1400	yes	N/A
Q9D4H8	CUL2_MOUSE	No assigned EC number	0.6124	0.8947	0.1597	yes	N/A
Q5RCF3	CUL2_PONAB	No assigned EC number	0.6124	0.8947	0.1597	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	133
pfam10557	68	pfam10557, Cullin_Nedd8, Cullin protein neddylatio	1e-28
smart00884	68	smart00884, Cullin_Nedd8, Cullin protein neddylati	5e-27
COG5647	773	COG5647, COG5647, Cullin, a subunit of E3 ubiquiti	1e-24

>gnl|CDD|204512 pfam10557, Cullin_Nedd8, Cullin protein neddylation domain

 Score = 99.2 bits (248), Expect = 1e-28
 Identities = 40/68 (58%), Positives = 51/68 (75%), Gaps = 1/68 (1%)

Query: 61  VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 119
           V+EDRKL +QAAIVRIMKSRK + HN L+ EV+ Q K  F PS++ IKK IESLI+K Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHNELVAEVIEQLKKRFPPSVADIKKRIESLIEKEYL 60

Query: 120 ERTANSTD 127
           ER  +  +
Sbjct: 61  ERDEDDRN 68

This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. Length = 68

>gnl|CDD|214883 smart00884, Cullin_Nedd8, Cullin protein neddylation domain

 Score = 94.9 bits (237), Expect = 5e-27
 Identities = 39/68 (57%), Positives = 51/68 (75%), Gaps = 1/68 (1%)

Query: 61  VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYV 119
           V+EDRKL +QAAIVRIMKSRK + H+ L+ EV+ Q K  F PS+S IKK IESLI++ Y+
Sbjct: 1   VEEDRKLEIQAAIVRIMKSRKTLSHSELVSEVIEQLKKRFKPSVSDIKKRIESLIEREYL 60

Query: 120 ERTANSTD 127
           ER  +  +
Sbjct: 61  ERDEDDPN 68

This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. Length = 68

>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 97.2 bits (242), Expect = 1e-24
 Identities = 50/135 (37%), Positives = 86/135 (63%), Gaps = 5/135 (3%)

Query: 3   TDNSMDGSCPGYIISV---KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVS 59
                  SC   ++ +   K ++ +T+  +N  +++K  ++KI+   + E  Q+   T  
Sbjct: 640 KRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHE 699

Query: 60  SVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNY 118
           +V+EDR+  LQA IVRIMK+RK+++H  L++EV++Q KS F P +SM+K+ IE+LI+K Y
Sbjct: 700 TVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEY 759

Query: 119 VERTANSTDEYSYVA 133
           +ER A+  + Y Y+A
Sbjct: 760 LERQADD-EIYVYLA 773

Length = 773

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	133
KOG2167|consensus	661		99.98
KOG2166|consensus	725		99.97
COG5647	773	Cullin, a subunit of E3 ubiquitin ligase [Posttran	99.97
PF10557	68	Cullin_Nedd8: Cullin protein neddylation domain; I	99.93
KOG2284|consensus	728		99.92
KOG2285|consensus	777		99.77
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	94.9
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	94.38
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	93.79
COG3682	123	Predicted transcriptional regulator [Transcription	93.29
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	90.17
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	89.29
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	88.05
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	86.59
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	86.18
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	82.43
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	82.32
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	82.09
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	80.33

>KOG2167|consensus

Probab=99.98  E-value=3.3e-33  Score=239.38  Aligned_cols=123  Identities=38%  Similarity=0.529  Sum_probs=117.4

Q ss_pred             CCCCCcceeecc-----ccCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccc
Q psy16237          7 MDGSCPGYIISV-----KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRK   81 (133)
Q Consensus         7 ~s~~~~~~~il~-----~~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k   81 (133)
                      +||+|++.+.|.     +++.+||.|.+|..|++|..||+|+++..+++.+|..++.++|-+||.++||||||||||+||
T Consensus       534 qsl~cgr~rvl~~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~ke~~ee~~~~~e~v~~drqy~idaaivrimk~rk  613 (661)
T KOG2167|consen  534 QSLACGRARVLQKVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMKETVEENKSTTERVFQDRQYQIDAAIVRIMKMRK  613 (661)
T ss_pred             HHHhcccceeeeeCCCCCCCCCCCEEEechhhcchhheehHhhhhHHHHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHH
Confidence            799999999885     568899999999999999999999999889999999999999999999999999999999999


Q ss_pred             cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         82 QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        82 ~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +|+|+.|++++.+||+ ||+.+ ++|++||+||+||||+|| ++ +.|.|+|
T Consensus       614 ~l~h~~l~~el~~qlk-fpv~~-d~kkriesli~rey~erd-~n-~~y~yva  661 (661)
T KOG2167|consen  614 TLSHNLLVTELFNQLK-FPVKP-DLKKRIESLIDREYLERD-DN-NIYNYVA  661 (661)
T ss_pred             hhchhHHHHHHHHhcC-CCCCh-hHHHHHHHHHhHHHhccc-cc-ccccccC
Confidence            9999999999999999 99999 999999999999999999 44 8999997

>KOG2166|consensus

Probab=99.97  E-value=2.5e-31  Score=235.06  Aligned_cols=120  Identities=41%  Similarity=0.631  Sum_probs=110.4

Q ss_pred             CCCCCcceeeccccC---CCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccc
Q psy16237          7 MDGSCPGYIISVKEL---TEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI   83 (133)
Q Consensus         7 ~s~~~~~~~il~~~~---~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l   83 (133)
                      +||+|.|+.++.++-   .|++.|.+|.+|+++.+||+++.+..+    |.+.+++.+++||++.|+||||||||+||+|
T Consensus       602 ~Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~~~~----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l  677 (725)
T KOG2166|consen  602 QSLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLPPMD----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVL  677 (725)
T ss_pred             HHHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCCCch----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccc
Confidence            688888877775511   589999999999999999999976544    6678999999999999999999999999999


Q ss_pred             cchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237         84 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSY  131 (133)
Q Consensus        84 ~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y  131 (133)
                      .|++|+.||++||++ |.|++.+||++||.|||||||+|| +|+++|.|
T Consensus       678 ~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~Y~Y  725 (725)
T KOG2166|consen  678 GHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNIYRY  725 (725)
T ss_pred             cHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCcccC
Confidence            999999999999999 999999999999999999999999 88999998

>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=4.7e-31  Score=229.94  Aligned_cols=126  Identities=40%  Similarity=0.649  Sum_probs=117.7

Q ss_pred             CCCCCcceeeccc---cCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccc
Q psy16237          7 MDGSCPGYIISVK---ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQI   83 (133)
Q Consensus         7 ~s~~~~~~~il~~---~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l   83 (133)
                      +|++|.++.++.+   .++|++.|.+|.+|++++.+|+++.+...+..++..++++++++||.+.+|||||||||++|+|
T Consensus       644 ~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l  723 (773)
T COG5647         644 QSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKL  723 (773)
T ss_pred             HHHHhhheeeeccccccCCCCceEEEccccccccceeeecccccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            7899999887764   4789999999999999999999999877766667788899999999999999999999999999


Q ss_pred             cchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         84 RHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        84 ~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      .|++|+.+|+.+.++ |.|++++||++||.|||||||+|.++| ..|+|+|
T Consensus       724 ~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd-~iY~YLa  773 (773)
T COG5647         724 KHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD-EIYVYLA  773 (773)
T ss_pred             cHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC-ceeeecC
Confidence            999999999999999 999999999999999999999999888 7899997

>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain

Probab=99.93  E-value=7.3e-27  Score=151.86  Aligned_cols=67  Identities=51%  Similarity=0.819  Sum_probs=61.7

Q ss_pred             HHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCC
Q psy16237         61 VDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTD  127 (133)
Q Consensus        61 v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~  127 (133)
                      |+++|.+.|+||||||||++|+|+|++|+.+|.+++++ |+|+..+||++||.||++|||+||++|+|
T Consensus         1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n   68 (68)
T PF10557_consen    1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN   68 (68)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred             CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence            47899999999999999999999999999999999998 99999999999999999999999999875

With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....

>KOG2284|consensus

Probab=99.92  E-value=2.3e-25  Score=186.86  Aligned_cols=113  Identities=45%  Similarity=0.793  Sum_probs=105.8

Q ss_pred             cCCCCCeEEEccCCCCCceeEEecCCC-cCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC
Q psy16237         20 ELTEDTEIRLNLGYNNKRTKLKISGAV-QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS   98 (133)
Q Consensus        20 ~~~~~d~f~~N~~F~~k~~kiki~~~~-~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~   98 (133)
                      .+..+..|++|.+|++|+.|++|..+. ++..++|.+.+...|.+||++-++||||||||.||.+.|+-|+.||+.|.+.
T Consensus       614 ~~~a~s~~~lnm~~tskr~kf~~~~p~~~k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~  693 (728)
T KOG2284|consen  614 NLTADSLVRLNMSMTSKRMKFRLQAPQVNKAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKG  693 (728)
T ss_pred             ccChhhhhhccccccccceeeEecchhhccccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcc
Confidence            356778899999999999999999865 6888889999999999999999999999999999999999999999999999


Q ss_pred             -CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         99 -FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        99 -F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                       |.|++++||++||.||++.||+|.+.+ +.|.|+|
T Consensus       694 rf~p~v~~ikk~ie~li~k~yi~rt~~~-dey~y~a  728 (728)
T KOG2284|consen  694 RFSPDVPFIKKSIEDLIEKMYIQRTDQN-DEYQYLA  728 (728)
T ss_pred             cCCCCchHHHHHHHHHHHHHHHhhcccc-ccchhcC
Confidence             999999999999999999999998776 8999997

>KOG2285|consensus

Probab=99.77  E-value=3.4e-19  Score=151.00  Aligned_cols=120  Identities=34%  Similarity=0.508  Sum_probs=104.8

Q ss_pred             eeeccccCCCCCeEEEccCCC-------CCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccch
Q psy16237         14 YIISVKELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHN   86 (133)
Q Consensus        14 ~~il~~~~~~~d~f~~N~~F~-------~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~   86 (133)
                      ....++++.+++.|.+|..|+       .++.|+++....+-..+...++.++.|-+-|....|-+|++|||.||+++..
T Consensus       650 ~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLIGRLQLstEr~~eeenesIVqLRiLRtQEaIikImK~RK~~~nA  729 (777)
T KOG2285|consen  650 TTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLIGRLQLSTERNAEEENESIVQLRILRTQEAIIKIMKTRKTYTNA  729 (777)
T ss_pred             ccCCcccccccceEEeechhhhhhccchhhcccceeeeeeeehhhhhhhhhcchhHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            344457788999999999996       3556777766555444444456678899999999999999999999999999


Q ss_pred             HHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         87 ALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        87 eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +|..|.++.|+. |.|+..+||++||+|||..|++||++|.|+|+|+|
T Consensus       730 qLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINtFiYia  777 (777)
T KOG2285|consen  730 QLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINTFIYIA  777 (777)
T ss_pred             HHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccceeeeC
Confidence            999999999999 99999999999999999999999999999999997

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=94.90  E-value=0.032  Score=38.92  Aligned_cols=59  Identities=14%  Similarity=0.254  Sum_probs=43.0

Q ss_pred             HhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         70 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +..|++++=....++-.|++..    +.. ..+..+.++.-+..|.+||||.|.... ..|+|-|
T Consensus         5 E~~IM~~lW~~~~~t~~eI~~~----l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g-r~~~Y~p   64 (115)
T PF03965_consen    5 ELEIMEILWESGEATVREIHEA----LPEERSWAYSTVQTLLNRLVEKGFLTREKIG-RAYVYSP   64 (115)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHH----HCTTSS--HHHHHHHHHHHHHTTSEEEEEET-TCEEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHH----HHhccccchhHHHHHHHHHHhCCceeEeecC-CceEEEe
Confidence            4456666666666766666554    555 678999999999999999999998654 6788864

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=94.38  E-value=0.044  Score=34.93  Aligned_cols=45  Identities=24%  Similarity=0.425  Sum_probs=35.9

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN  124 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~  124 (133)
                      |-.+|+.++.++..||-.+       |..++..+..-++.|+.+|||++.+.
T Consensus         5 i~~~l~~~~~~S~~eLa~~-------~~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELARE-------FGISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHH-------TT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHHcCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            4567888999998887755       88999999999999999999999644

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=93.79  E-value=0.16  Score=36.51  Aligned_cols=59  Identities=19%  Similarity=0.236  Sum_probs=43.2

Q ss_pred             HhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         70 QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +..|++++-....++-.|++..    +.. +.+....+...+..|.+||||.|..+. ..|.|-|
T Consensus         6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g-r~~~Y~p   65 (130)
T TIGR02698         6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEG-RKFIYTA   65 (130)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecCC-CcEEEEe
Confidence            3456666655666766555544    444 667888999999999999999998554 5788865

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=93.29  E-value=0.19  Score=36.22  Aligned_cols=62  Identities=19%  Similarity=0.295  Sum_probs=52.0

Q ss_pred             HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      ..++.+++||=+++..+-.|++.++...   +.++.+.|+.-|..|..||+|.|.-++ ..|.|-|
T Consensus         6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~---~ews~sTV~TLl~RL~KKg~l~~~kdg-r~~~y~p   67 (123)
T COG3682           6 AAEWEVMEILWSRGPATVREIIEELPAD---REWSYSTVKTLLNRLVKKGLLTRKKDG-RAFRYSP   67 (123)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHhhc---ccccHHHHHHHHHHHHhccchhhhhcC-Ceeeeec
Confidence            4578889999999999988888776544   779999999999999999999998654 6788864

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=90.17  E-value=1  Score=27.70  Aligned_cols=51  Identities=22%  Similarity=0.333  Sum_probs=32.5

Q ss_pred             Hhhhhhhhc-ccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC--CCCCC
Q psy16237         70 QAAIVRIMK-SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT--ANSTD  127 (133)
Q Consensus        70 ~AaIVRIMK-~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~--~~d~~  127 (133)
                      |..|.+.+. ....++-.+|...       +..+.+.+-+.|..|+++|||+|.  +.|..
T Consensus         5 q~~vL~~l~~~~~~~t~~~l~~~-------~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R   58 (68)
T PF13463_consen    5 QWQVLRALAHSDGPMTQSDLAER-------LGISKSTVSRIIKKLEEKGLVEKERDPHDKR   58 (68)
T ss_dssp             HHHHHHHHT--TS-BEHHHHHHH-------TT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred             HHHHHHHHHccCCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence            345555566 5666666665543       557788888999999999999774  44444

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=89.29  E-value=0.57  Score=28.79  Aligned_cols=47  Identities=21%  Similarity=0.399  Sum_probs=40.2

Q ss_pred             hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCC
Q psy16237         71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTAN  124 (133)
Q Consensus        71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~  124 (133)
                      ..|...++.+..++-.||.+.       |..+...|++-+..|-+.++|.|..+
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~-------~~VS~~TiRRDl~~L~~~g~i~r~~G   49 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEE-------FGVSEMTIRRDLNKLEKQGLIKRTHG   49 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            356778888999998888755       88999999999999999999999654

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=88.05  E-value=0.73  Score=28.82  Aligned_cols=52  Identities=19%  Similarity=0.234  Sum_probs=36.0

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY  131 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y  131 (133)
                      +-..+-.+..++-.||...    +   ..+.+.+-..+..|.++|+++|....+..|..
T Consensus        13 vy~~Ll~~~~~t~~eIa~~----l---~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a   64 (68)
T PF01978_consen   13 VYLALLKNGPATAEEIAEE----L---GISRSTVYRALKSLEEKGLVEREEGRPKVYRA   64 (68)
T ss_dssp             HHHHHHHHCHEEHHHHHHH----H---TSSHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred             HHHHHHHcCCCCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence            3333335556666665544    3   37788899999999999999999876544444

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=86.59  E-value=1.8  Score=29.53  Aligned_cols=57  Identities=11%  Similarity=0.223  Sum_probs=41.8

Q ss_pred             hhhhhcc-cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237         73 IVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY  131 (133)
Q Consensus        73 IVRIMK~-~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y  131 (133)
                      |..+|.. .+.++-.||+..+.++.  ..++.+.+=+.++.|.+.|+|.|-..+...+.|
T Consensus         6 Il~~l~~~~~~~sa~ei~~~l~~~~--~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y   63 (116)
T cd07153           6 ILEVLLESDGHLTAEEIYERLRKKG--PSISLATVYRTLELLEEAGLVREIELGDGKARY   63 (116)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEE
Confidence            4455544 56799999998886553  457889999999999999999996543233333

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=86.18  E-value=1.8  Score=25.34  Aligned_cols=45  Identities=13%  Similarity=0.225  Sum_probs=31.1

Q ss_pred             hhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCC
Q psy16237         74 VRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANST  126 (133)
Q Consensus        74 VRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~  126 (133)
                      ++.+. ...++..++...       +..+.+.+.+.++.|.+++++.+..+..
T Consensus         3 l~~l~-~~~~~~~~i~~~-------l~is~~~v~~~l~~L~~~g~i~~~~~~~   47 (66)
T smart00418        3 LKLLA-EGELCVCELAEI-------LGLSQSTVSHHLKKLREAGLVESRREGK   47 (66)
T ss_pred             HHHhh-cCCccHHHHHHH-------HCCCHHHHHHHHHHHHHCCCeeeeecCC
Confidence            33444 455665554433       3467788999999999999999876543

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=82.43  E-value=2.3  Score=28.62  Aligned_cols=47  Identities=13%  Similarity=0.220  Sum_probs=39.0

Q ss_pred             HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      +|-.|++.+.....+++.+|-..       +-.+.+.+.+++..|.++|+|+|-
T Consensus         4 ~D~~il~~L~~~~~~~~~~la~~-------l~~s~~tv~~~l~~L~~~g~i~~~   50 (108)
T smart00344        4 IDRKILEELQKDARISLAELAKK-------VGLSPSTVHNRVKRLEEEGVIKGY   50 (108)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCeece
Confidence            45678888888888998887655       458889999999999999999963

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=82.32  E-value=2.9  Score=26.53  Aligned_cols=56  Identities=14%  Similarity=0.238  Sum_probs=33.4

Q ss_pred             HhHHHHHhhhhhhhcccc-cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237         64 DRKLYLQAAIVRIMKSRK-QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS  125 (133)
Q Consensus        64 ~R~~~I~AaIVRIMK~~k-~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d  125 (133)
                      +|...|=.+|...+.... .-+..||..    .+. +. +...+...++.|.++|||+|+++-
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~----~~g-~~-S~~tv~~~L~~Le~kG~I~r~~~~   62 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAE----ALG-LK-STSTVQRHLKALERKGYIRRDPGK   62 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHH----HHT-SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHH----HhC-CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence            344444455555555443 233334332    232 22 578888999999999999998764

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=82.09  E-value=4.7  Score=25.53  Aligned_cols=53  Identities=11%  Similarity=0.150  Sum_probs=38.3

Q ss_pred             Hhhhhhhhccccc--ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237         70 QAAIVRIMKSRKQ--IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY  129 (133)
Q Consensus        70 ~AaIVRIMK~~k~--l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y  129 (133)
                      +..|...|+.+..  ++-.||-.+    |   -.+...+.+.+..|.++||+.++...+..|
T Consensus         8 ~~~IL~~L~~~g~~~~ta~eLa~~----l---gl~~~~v~r~L~~L~~~G~V~~~~~~~~~W   62 (68)
T smart00550        8 EEKILEFLENSGDETSTALQLAKN----L---GLPKKEVNRVLYSLEKKGKVCKQGGTPPLW   62 (68)
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHH----H---CCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence            4456778888766  775555433    3   367778999999999999999987653433

Helix-turn-helix-containing domain. Also known as Zab.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=80.33  E-value=1.4  Score=26.40  Aligned_cols=45  Identities=27%  Similarity=0.388  Sum_probs=30.8

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  123 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~  123 (133)
                      .+..+.-....++..+|-..       +..+.+.+-+.+..|.++|||+|..
T Consensus         7 ~iL~~l~~~~~~~~~~la~~-------~~~~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    7 RILRILYENGGITQSELAEK-------LGISRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHHSSEEHHHHHHH-------HTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHcCCCCHHHHHHH-------HCCChhHHHHHHHHHHHCCCEEecc
Confidence            33444445555565554433       5578999999999999999999954

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	133
3rtr_A	368	A Ring E3-Substrate Complex Poised For Ubiquitin-Li		1e-25
1ldk_B	366	Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiqu		1e-25
1ldj_A	760	Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiqu		2e-25
1u6g_A	776	Crystal Structure Of The Cand1-Cul1-Roc1 Complex Le		2e-25
3tdu_C	77	N-Terminal Acetylation Acts As An Avidity Enhancer		4e-18
1iuy_A	92	Solution Structure Of The Cullin-3 Homologue Length		3e-16
4a0k_A	742	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp		2e-15
2hye_C	759	Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Compl		2e-15
4a0c_C	741	Structure Of The Cand1-Cul4b-Rbx1 Complex Length =		5e-15
4a0l_E	726	Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp		5e-15
2do7_A	101	Solution Structure Of The Winged Helix-Turn-Helix M		2e-14
3o2p_E	88	A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn		9e-12
3o6b_B	76	A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn		2e-11
3dpl_C	382	Structural Insights Into Nedd8 Activation Of Cullin		2e-07
3dqv_C	382	Structural Insights Into Nedd8 Activation Of Cullin		2e-05

>pdb|3RTR|A Chain A, A Ring E3-Substrate Complex Poised For Ubiquitin-Like Protein Transfer: Structural Insights Into Cullin-Ring Ligases Length = 368

Iteration: 1
 Score =  111 bits (277), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)
Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 254 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 313
Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 314 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 368

>pdb|1LDK|B Chain B, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin Ligase Complex Length = 366

Iteration: 1
 Score =  111 bits (277), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)
Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 252 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 311
Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 312 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 366

>pdb|1LDJ|A Chain A, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin Ligase Complex Length = 760

Iteration: 1
 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)
Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 646 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 705
Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 706 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 760

>pdb|1U6G|A Chain A, Crystal Structure Of The Cand1-Cul1-Roc1 Complex Length = 776

Iteration: 1
 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/115 (50%), Positives = 79/115 (68%), Gaps = 1/115 (0%)
Query: 20  ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKS 79
           EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRIMK 
Sbjct: 662 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKM 721
Query: 80  RKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 722 RKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 776

>pdb|3TDU|C Chain C, N-Terminal Acetylation Acts As An Avidity Enhancer Within An Interconnected Multiprotein Complex: Structure Of A Human Cul1whb- Dcn1p-Acetylated Ubc12n Complex Length = 77

Iteration: 1
 Score = 86.7 bits (213), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 56/76 (73%), Gaps = 1/76 (1%)
Query: 59  SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQ-SKSFAPSISMIKKCIESLIDKN 117
           S+++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q S  F P + +IKKCI+ LI+K 
Sbjct: 2   SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKE 61
Query: 118 YVERTANSTDEYSYVA 133
           Y+ER     D YSY+A
Sbjct: 62  YLERVDGEKDTYSYLA 77

>pdb|1IUY|A Chain A, Solution Structure Of The Cullin-3 Homologue Length = 92

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)
Query: 44  GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 102
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61
Query: 103 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 742

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 46/115 (40%), Positives = 70/115 (60%), Gaps = 1/115 (0%)
Query: 19  KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
           KE+ +  +   N  + +K  ++KI+    KET +E   T   V +DR+  + AAIVRIMK
Sbjct: 629 KEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMK 688
Query: 79  SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            RK + HN L+ E+ +Q K F      +KK IESLID++Y+ER  ++ ++Y YVA
Sbjct: 689 MRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA 742

>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex Length = 759

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 46/115 (40%), Positives = 70/115 (60%), Gaps = 1/115 (0%)
Query: 19  KELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMK 78
           KE+ +  +   N  + +K  ++KI+    KET +E   T   V +DR+  + AAIVRIMK
Sbjct: 646 KEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMK 705
Query: 79  SRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            RK + HN L+ E+ +Q K F      +KK IESLID++Y+ER  ++ ++Y YVA
Sbjct: 706 MRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA 759

>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex Length = 741

Iteration: 1
 Score = 76.3 bits (186), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 44/104 (42%), Positives = 66/104 (63%), Gaps = 1/104 (0%)
Query: 30  NLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALI 89
           N  + +K  ++KI+    KET +E   T   V +DR+  + AAIVRIMK RK + HN L+
Sbjct: 639 NDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLV 698
Query: 90  QEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            EV +Q K F    + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 699 SEVYNQLK-FPVKPADLKKRIESLIDRDYMERDKENPNQYNYIA 741

>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex Length = 726

Iteration: 1
 Score = 76.3 bits (186), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 44/104 (42%), Positives = 66/104 (63%), Gaps = 1/104 (0%)
Query: 30  NLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALI 89
           N  + +K  ++KI+    KET +E   T   V +DR+  + AAIVRIMK RK + HN L+
Sbjct: 624 NDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLV 683
Query: 90  QEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            EV +Q K F    + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 684 SEVYNQLK-FPVKPADLKKRIESLIDRDYMERDKENPNQYNYIA 726

>pdb|2DO7|A Chain A, Solution Structure Of The Winged Helix-Turn-Helix Motif Of Human Cul-4b Length = 101

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)
Query: 43  SGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS 102
           SG   KET +E   T   V +DR+  + AAIVRIMK RK + HN L+ EV +Q K F   
Sbjct: 6   SGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVK 64
Query: 103 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 65  PADLKKRIESLIDRDYMERDKENPNQYNYIA 95

>pdb|3O2P|E Chain E, A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn1(P)-Cdc53(Whb) Length = 88

Iteration: 1
 Score = 65.5 bits (158), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 56/82 (68%), Gaps = 2/82 (2%)
Query: 53  EIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQS-KSFAPSISMIKKCIE 111
           E ER    ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS + F   +SM+K+ I+
Sbjct: 8   EDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAID 67
Query: 112 SLIDKNYVERTANSTDEYSYVA 133
           SLI K Y++R  +  + Y+Y+A
Sbjct: 68  SLIQKGYLQR-GDDGESYAYLA 88

>pdb|3O6B|B Chain B, A Dual E3 Mechanism For Rub1 Ligation To Cdc53: Dcn1(P)-Cdc53(Whb) Low Resolution Length = 76

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 54/76 (71%), Gaps = 2/76 (2%)
Query: 59  SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQS-KSFAPSISMIKKCIESLIDKN 117
           S ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS + F   +SM+K+ I+SLI K 
Sbjct: 2   SELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKG 61
Query: 118 YVERTANSTDEYSYVA 133
           Y++R  +  + Y+Y+A
Sbjct: 62  YLQR-GDDGESYAYLA 76

>pdb|3DPL|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 382

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/125 (32%), Positives = 64/125 (51%), Gaps = 8/125 (6%)
Query: 17  SVKELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 69
           S K+ TE T   +N  ++        KR K+ + G +Q  T +  E     + + R L  
Sbjct: 258 SPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRT 317
Query: 70  QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 128
           Q AI++IMK RK+I +  L  E++   K+ F P   MIK+ IE LI+  Y+ R  +  + 
Sbjct: 318 QEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINT 377
Query: 129 YSYVA 133
           + Y+A
Sbjct: 378 FIYMA 382

>pdb|3DQV|C Chain C, Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation Length = 382

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 61/125 (48%), Gaps = 8/125 (6%)
Query: 17  SVKELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 69
           S K+ TE T   +N  ++        KR K+ + G +Q  T +  E     + + R L  
Sbjct: 258 SPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERXREEENEGIVQLRILRT 317
Query: 70  QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 128
           Q AI++I K RK+I +  L  E++   K+ F P    IK+ IE LI+  Y+ R  +  + 
Sbjct: 318 QEAIIQIXKXRKKISNAQLQTELVEILKNXFLPQKKXIKEQIEWLIEHKYIRRDESDINT 377
Query: 129 YSYVA 133
           + Y A
Sbjct: 378 FIYXA 382

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	133
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	5e-39
2hye_C	759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	4e-33
1iuy_A	92	Cullin-3 homologue; winged helix, structural genom	1e-31
3dpl_C	382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	1e-30
2do7_A	101	Cullin-4B, CUL-4B; helix-turn-helix motif, structu	1e-29
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	1e-28
3o2p_E	88	Cell division control protein 53; ligase, cell cyc	2e-26
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A Length = 760

 Score =  137 bits (346), Expect = 5e-39
 Identities = 58/118 (49%), Positives = 79/118 (66%), Gaps = 1/118 (0%)

Query: 17  SVKELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRI 76
              EL  DT I+L LGY NK+ ++ I+  ++ E  QE E T  +++EDRKL +QAAIVRI
Sbjct: 643 DEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRI 702

Query: 77  MKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           MK RK ++H  L+ EVL+Q  S F P + +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 703 MKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA 760

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E* Length = 759

 Score =  121 bits (303), Expect = 4e-33
 Identities = 44/111 (39%), Positives = 67/111 (60%), Gaps = 1/111 (0%)

Query: 23  EDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQ 82
           +  +   N  + +K  ++KI+    KET +E   T   V +DR+  + AAIVRIMK RK 
Sbjct: 650 DGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKT 709

Query: 83  IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
           + HN L+ E+ +Q K F      +KK IESLID++Y+ER  ++ ++Y YVA
Sbjct: 710 LGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA 759

>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.34 Length = 92

 Score =  106 bits (267), Expect = 1e-31
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)

Query: 44  GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 102
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61

Query: 103 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C Length = 382

 Score =  111 bits (278), Expect = 1e-30
 Identities = 40/125 (32%), Positives = 64/125 (51%), Gaps = 8/125 (6%)

Query: 17  SVKELTEDTEIRLNLGYN-------NKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 69
           S K+ TE T   +N  ++        KR K+ + G +Q  T +  E     + + R L  
Sbjct: 258 SPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRT 317

Query: 70  QAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDE 128
           Q AI++IMK RK+I +  L  E++   K+ F P   MIK+ IE LI+  Y+ R  +  + 
Sbjct: 318 QEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINT 377

Query: 129 YSYVA 133
           + Y+A
Sbjct: 378 FIYMA 382

>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score =  101 bits (254), Expect = 1e-29
 Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)

Query: 43  SGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPS 102
           SG   KET +E   T   V +DR+  + AAIVRIMK RK + HN L+ EV +Q K F   
Sbjct: 6   SGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVK 64

Query: 103 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
            + +KK IESLID++Y+ER   + ++Y+Y+A
Sbjct: 65  PADLKKRIESLIDRDYMERDKENPNQYNYIA 95

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C Length = 77

 Score = 98.7 bits (246), Expect = 1e-28
 Identities = 42/76 (55%), Positives = 56/76 (73%), Gaps = 1/76 (1%)

Query: 59  SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKN 117
           S+++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q  S F P + +IKKCI+ LI+K 
Sbjct: 2   SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKE 61

Query: 118 YVERTANSTDEYSYVA 133
           Y+ER     D YSY+A
Sbjct: 62  YLERVDGEKDTYSYLA 77

>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A {Saccharomyces cerevisiae} PDB: 3o6b_B Length = 88

 Score = 93.8 bits (233), Expect = 2e-26
 Identities = 31/87 (35%), Positives = 56/87 (64%), Gaps = 2/87 (2%)

Query: 48  KETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMI 106
            +   E ER    ++ +R+++L+A IVRIMK+++ + H  L+ E ++QS   F   +SM+
Sbjct: 3   NKRLTEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMV 62

Query: 107 KKCIESLIDKNYVERTANSTDEYSYVA 133
           K+ I+SLI K Y++R  +  + Y+Y+A
Sbjct: 63  KRAIDSLIQKGYLQRGDDG-ESYAYLA 88

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 7e-05
 Identities = 19/118 (16%), Positives = 36/118 (30%), Gaps = 26/118 (22%)

Query: 12  PGYIISVKELTEDTEIRLN--LGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYL 69
           P  +  + E   D     +     N  +    I  ++    P           E RK++ 
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP----------AEYRKMFD 376

Query: 70  QAAIVRIMKSRKQIRHNALI-QEVLS----QSKSFAPSISMIKKCIESLIDKNYVERT 122
           + ++            +A I   +LS            + + K    SL++K   E T
Sbjct: 377 RLSV---------FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST 425

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	133
3dpl_C	382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	100.0
2do7_A	101	Cullin-4B, CUL-4B; helix-turn-helix motif, structu	100.0
3o2p_E	88	Cell division control protein 53; ligase, cell cyc	100.0
1iuy_A	92	Cullin-3 homologue; winged helix, structural genom	100.0
2hye_C	759	Cullin-4A, CUL-4A; beta propeller, ring finger, zi	100.0
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	100.0
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	100.0
1p6r_A	82	Penicillinase repressor; transcription regulation,	93.7
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	93.38
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	93.05
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	91.98
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	91.85
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	91.26
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	91.09
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	90.54
1okr_A	123	MECI, methicillin resistance regulatory protein ME	87.9
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	87.0
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	86.4
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	86.32
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.95
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	84.56
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	83.55
3r0a_A	123	Putative transcriptional regulator; structural gen	82.84
2vn2_A	128	DNAD, chromosome replication initiation protein; D	82.66
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	80.68

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C

Probab=100.00  E-value=9.7e-37  Score=252.09  Aligned_cols=127  Identities=29%  Similarity=0.356  Sum_probs=109.3

Q ss_pred             CCCCCc---ceeecc--------ccCCCCCeEEEccCCCCC-----ceeEEecCC--CcCCChHHHhhhhhhHHHHhHHH
Q psy16237          7 MDGSCP---GYIISV--------KELTEDTEIRLNLGYNNK-----RTKLKISGA--VQKETPQEIERTVSSVDEDRKLY   68 (133)
Q Consensus         7 ~s~~~~---~~~il~--------~~~~~~d~f~~N~~F~~k-----~~kiki~~~--~~~~~~~e~~~~~~~v~~~R~~~   68 (133)
                      +||++.   |+++|.        +++.++|+|+||.+|++.     .+|++|+.+  .+.++..+.+++++.|+++|.+.
T Consensus       237 ~sL~~~~k~k~~iL~~~~~~~~~~~~~~~d~f~~N~~F~~~k~~k~~~r~ki~~~~~~q~~~~~e~~~~~~~v~edR~~~  316 (382)
T 3dpl_C          237 WSLVAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILR  316 (382)
T ss_dssp             HHHHCCTTCSSCSEEESSCCSSGGGCCTTCEEEECTTCCEESSSSEESEEEEECCTTTTSCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcccchhcceeeecCCccccCcCCCCCEEEEcCCCcCCcccccceeEEEecccccccccchhhhhhHHHHHHHhhhe
Confidence            355553   466774        346789999999999972     256677654  24455667778899999999999


Q ss_pred             HHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      ||||||||||+||+|+|++|+.+|+++|++ |+|++.+||++||.|||||||+|+++|+++|+|+|
T Consensus       317 i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~Ie~LIereYleR~~~d~~~y~YlA  382 (382)
T 3dpl_C          317 TQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYIRRDESDINTFIYMA  382 (382)
T ss_dssp             HHHHHHHHHTTSSEECHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEECC
T ss_pred             eeEEEehhhhccCcccHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhhhhhccCCCCCCeEEEcC
Confidence            999999999999999999999999999999 99999999999999999999999999999999998

>2do7_A Cullin-4B, CUL-4B; helix-turn-helix motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=100.00  E-value=4.9e-36  Score=207.81  Aligned_cols=93  Identities=45%  Similarity=0.620  Sum_probs=87.2

Q ss_pred             EEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhcc
Q psy16237         40 LKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYV  119 (133)
Q Consensus        40 iki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl  119 (133)
                      ++|+.+..+++..|..++++.|++||.+.||||||||||++|+|+|++|+++|+++|+ |+|++.+||++||.|||+|||
T Consensus         3 ~ki~~i~~ke~~~e~~~t~~~v~~dR~~~iqAaIVRIMK~rK~l~h~~Lv~eV~~ql~-F~p~~~~IKk~IE~LIereYl   81 (101)
T 2do7_A            3 SGSSGIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVSEVYNQLK-FPVKPADLKKRIESLIDRDYM   81 (101)
T ss_dssp             CSSCSCCCCCCCCCCSSCCSHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHCS-SCCCHHHHHHHHHHHHHTTSE
T ss_pred             eeecccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhhhhHH
Confidence            5666666667777888899999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             ccCCCCCCceEecC
Q psy16237        120 ERTANSTDEYSYVA  133 (133)
Q Consensus       120 ~R~~~d~~~y~Yva  133 (133)
                      +|+++|+++|+|+|
T Consensus        82 eR~~~d~~~y~YlA   95 (101)
T 2do7_A           82 ERDKENPNQYNYIA   95 (101)
T ss_dssp             EECSSCTTEEEECC
T ss_pred             hcCCCCCCeEEEec
Confidence            99999999999997

>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A {Saccharomyces cerevisiae} PDB: 3o6b_B

Probab=100.00  E-value=7.9e-35  Score=197.27  Aligned_cols=81  Identities=38%  Similarity=0.760  Sum_probs=78.4

Q ss_pred             HHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceE
Q psy16237         52 QEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYS  130 (133)
Q Consensus        52 ~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~  130 (133)
                      .|..++++.|+++|.+.||||||||||++|+|+|++|+++|+++|++ |+|++++||++||+|||+|||+|+++| ++|+
T Consensus         7 ~e~~~t~~~v~~dR~~~iqAaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIekeYleR~~~~-~~y~   85 (88)
T 3o2p_E            7 TEDERIEKELNTERQIFLEACIVRIMKAKRNLPHTTLVNECIAQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDG-ESYA   85 (88)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEECTTS-SEEE
T ss_pred             chHHHHHHHHHHHhhhhhheeeehhhcccccccHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhHHhcCCCC-CeEE
Confidence            46778999999999999999999999999999999999999999999 999999999999999999999999998 9999


Q ss_pred             ecC
Q psy16237        131 YVA  133 (133)
Q Consensus       131 Yva  133 (133)
                      |+|
T Consensus        86 YlA   88 (88)
T 3o2p_E           86 YLA   88 (88)
T ss_dssp             ECC
T ss_pred             eeC
Confidence            997

>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.34

Probab=100.00  E-value=9.6e-36  Score=203.33  Aligned_cols=87  Identities=51%  Similarity=0.721  Sum_probs=82.0

Q ss_pred             cCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237         47 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  125 (133)
Q Consensus        47 ~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d  125 (133)
                      ++++..|..++++.|++||.+.||||||||||++|+|+|++|+++|+++|++ |+|++.+||++||+|||+|||+|+++|
T Consensus         5 ~~e~~~e~~~t~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIereYleR~~~d   84 (92)
T 1iuy_A            5 QGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPED   84 (92)
T ss_dssp             CCCCCCCCCCCCSCSCCCTTTHHHHHHHHHHHHHCEEEHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSC
T ss_pred             ccccHHHHHHHHHHHHHHHHHHeeeeeeehhhccccccHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhhhhhhhcCCCC
Confidence            4566667778899999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCceEecC
Q psy16237        126 TDEYSYVA  133 (133)
Q Consensus       126 ~~~y~Yva  133 (133)
                      +++|+|+|
T Consensus        85 ~~~y~Y~A   92 (92)
T 1iuy_A           85 RKVYTYVA   92 (92)
T ss_dssp             SSEEEEC-
T ss_pred             CCeeEecC
Confidence            99999997

>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger, propeller cluster, helical repeats, cullin repeats, protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*

Probab=100.00  E-value=4.6e-34  Score=252.58  Aligned_cols=126  Identities=37%  Similarity=0.528  Sum_probs=117.7

Q ss_pred             CCCCCcceeeccc-----cCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccc
Q psy16237          7 MDGSCPGYIISVK-----ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRK   81 (133)
Q Consensus         7 ~s~~~~~~~il~~-----~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k   81 (133)
                      +|++++|+++|.+     ++.++|.|+||.+|++++.||+|+.+..+++..|...+++.|+++|.+.||||||||||++|
T Consensus       629 ~sL~~~k~~vL~~~p~~~~v~~~d~f~lN~~f~~~~~riki~~i~~~e~~~e~~~t~~~v~~dR~~~i~AaIVRIMK~rK  708 (759)
T 2hye_C          629 QSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRK  708 (759)
T ss_dssp             HTTTTTTTCSEEETTCSSSCCSSCEEEECCCCCCSCSSEECGGGGGCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHccCCceeecCCCCCCCCCCCEEEeeccccCCceEEEeccccccccchhhhhhHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            5788888888863     46799999999999999999999976667777888889999999999999999999999999


Q ss_pred             cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         82 QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        82 ~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +|+|++|+++|+++++ |+|++.+||++||.|||||||+|+++|+++|+|+|
T Consensus       709 ~l~h~~Lv~ev~~ql~-F~p~~~~IKk~Ie~LIereYleR~~~~~~~y~YlA  759 (759)
T 2hye_C          709 TLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA  759 (759)
T ss_dssp             EEETHHHHHHHHHHSS-SCCCHHHHHHHHHHHHHTTSCBCCSSCTTEEECCC
T ss_pred             CCCHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhcccceecCCCCCCeeEecC
Confidence            9999999999999999 99999999999999999999999999999999998

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C

Probab=100.00  E-value=8.9e-35  Score=192.67  Aligned_cols=75  Identities=56%  Similarity=0.919  Sum_probs=72.8

Q ss_pred             hhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         59 SSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        59 ~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +.|++||.+.||||||||||++|+|+|++|+++|+++|++ |+|++++||++||+|||+|||+|+++|+++|+|+|
T Consensus         2 k~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk~IE~LIereYl~R~~~~~~~y~Y~A   77 (77)
T 3tdu_C            2 SNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA   77 (77)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEECC
T ss_pred             cchhhhhhheEeeEEeeeecccceeeHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhHhhcCCCCCceEEEeC
Confidence            4689999999999999999999999999999999999999 99999999999999999999999999999999998

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A

Probab=100.00  E-value=9.6e-34  Score=250.61  Aligned_cols=114  Identities=51%  Similarity=0.804  Sum_probs=108.2

Q ss_pred             cCCCCCeEEEccCCCCCceeEEecCCCcCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-
Q psy16237         20 ELTEDTEIRLNLGYNNKRTKLKISGAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-   98 (133)
Q Consensus        20 ~~~~~d~f~~N~~F~~k~~kiki~~~~~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-   98 (133)
                      ++.++|.|+||.+|++|+.||+|+.+.++++..|...+++.|+++|.+.||||||||||++|+|+|++|+++|+++|++ 
T Consensus       646 ~~~~~~~f~lN~~F~~k~~ri~i~~~~~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~r  725 (760)
T 1ldj_A          646 ELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSR  725 (760)
T ss_dssp             CCCTTCEEEECSSCCCSSSSBCCCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHHTTT
T ss_pred             CCCCCCEEEeeccccCCceEEEecCccccccchhhhhHHHHHHHHHHhHheeeehhhhhccCCCcHHHHHHHHHHHHhcc
Confidence            4678999999999999999999997767777777788999999999999999999999999999999999999999999 


Q ss_pred             CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         99 FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        99 F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      |+|++.+||++||.|||||||+|+++|+++|+|+|
T Consensus       726 F~p~~~~IKk~Ie~LIereYl~R~~~~~~~y~YlA  760 (760)
T 1ldj_A          726 FKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA  760 (760)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEECSSSTTEEEECC
T ss_pred             CCCCHHHHHHHHHHHhhccceeeCCCCCcceeeCC
Confidence            99999999999999999999999999999999998

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=93.70  E-value=0.084  Score=33.11  Aligned_cols=58  Identities=17%  Similarity=0.276  Sum_probs=42.9

Q ss_pred             hhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237         71 AAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  132 (133)
Q Consensus        71 AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv  132 (133)
                      ..|.+++-....++-.||...+-..   ...+.+.+...++.|.++|||.|..++ ..|.|.
T Consensus        12 ~~vL~~L~~~~~~t~~ei~~~l~~~---~~~s~~Tv~~~l~rL~~kGlv~r~~~g-r~~~y~   69 (82)
T 1p6r_A           12 LEVMKVIWKHSSINTNEVIKELSKT---STWSPKTIQTMLLRLIKKGALNHHKEG-RVFVYT   69 (82)
T ss_dssp             HHHHHHHHTSSSEEHHHHHHHHHHH---SCCCHHHHHHHHHHHHHTTSEEEEEET-TEEEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHhhc---CCccHHHHHHHHHHHHHCCCeEEEecC-CEEEEE
Confidence            3445555456678888888876542   236788899999999999999998654 567775

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=93.38  E-value=0.076  Score=35.45  Aligned_cols=60  Identities=13%  Similarity=0.308  Sum_probs=41.9

Q ss_pred             HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      |..|.+++-....++-.||...+...   ..++.+.+...|+.|.++|||+|..+ ...|.|-|
T Consensus        37 e~~VL~~L~~~~~~t~~eL~~~l~~~---~~~s~sTVt~~L~rLe~KGlV~R~~~-gR~~~Y~p   96 (99)
T 2k4b_A           37 ELIVMRVIWSLGEARVDEIYAQIPQE---LEWSLATVKTLLGRLVKKEMLSTEKE-GRKFVYRP   96 (99)
T ss_dssp             CSHHHHHHHHHSCEEHHHHHHTCCGG---GCCCHHHHHHHHHHHHHTTSCEEEEE-TTEEEEEC
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHhcc---cCCCHhhHHHHHHHHHHCCCEEEEeC-CCEEEEEE
Confidence            34445555545566666666543221   34678999999999999999999765 46899865

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=93.05  E-value=0.11  Score=33.29  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=37.0

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      .|...++.+..++-.||..+       |.++...|++-++.|.++|+|+|.
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~-------l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQT-------LNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHH-------TTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEe
Confidence            35666777788887776644       889999999999999999999997

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=91.98  E-value=0.22  Score=31.83  Aligned_cols=55  Identities=11%  Similarity=0.220  Sum_probs=46.7

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      ..|...|.+|.+.-.+|-.+       |..+.+++-.+|+.|.+.+-|.---+|+..|+|+.
T Consensus        11 ~Fi~yIk~~Kvv~LedLA~~-------F~l~t~~~i~RI~~Le~~g~ltGViDDRGKfIyIs   65 (72)
T 1wi9_A           11 EFINYIKKSKVVLLEDLAFQ-------MGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             HHHHHHHHCSEECHHHHHHH-------HCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHHcCeeeHHHHHHH-------hCCChHHHHHHHHHHHHCCCeEEEEeCCCCEEEec
Confidence            34777888888887776544       88999999999999999999998878888999984

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=91.85  E-value=0.14  Score=33.63  Aligned_cols=44  Identities=11%  Similarity=0.206  Sum_probs=36.2

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  123 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~  123 (133)
                      |...++.+..++-.||...       |..+...|++-++.|.++|+|.|..
T Consensus         7 Il~~L~~~g~vsv~eLA~~-------l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            7 VRDMLALQGRMEAKQLSAR-------LQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHSCSEEHHHHHHH-------TTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHcCCCcHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            5566677777777766544       8899999999999999999999973

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=91.26  E-value=0.44  Score=29.67  Aligned_cols=59  Identities=8%  Similarity=0.224  Sum_probs=43.0

Q ss_pred             hhhhhhhccc--ccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237         71 AAIVRIMKSR--KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY  131 (133)
Q Consensus        71 AaIVRIMK~~--k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y  131 (133)
                      .+|..++...  ..++-.||...+.+..  ...+.+.|-+.++.|.+.|+|.|...+.....|
T Consensus        20 ~~IL~~l~~~~~~~~s~~el~~~l~~~~--~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y   80 (83)
T 2fu4_A           20 LKILEVLQEPDNHHVSAEDLYKRLIDMG--EEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF   80 (83)
T ss_dssp             HHHHHHHTSGGGSSBCHHHHHHHHHHTT--CCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEE
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHhC--CCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEe
Confidence            3455666554  5799999988875542  356889999999999999999997653334444

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=91.09  E-value=0.3  Score=31.34  Aligned_cols=56  Identities=16%  Similarity=0.279  Sum_probs=38.4

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEe
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSY  131 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Y  131 (133)
                      |...+.....++-.+|...+.+.   +..+.+.+-+.|..|.++||+.|..+.+..+.+
T Consensus        13 iL~~l~~~~~~~~~el~~~la~~---l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~   68 (99)
T 1tbx_A           13 VLAYLYDNEGIATYDLYKKVNAE---FPMSTATFYDAKKFLIQEGFVKERQERGEKRLY   68 (99)
T ss_dssp             HHHHHTTCTTCBHHHHHHHHHTT---SCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEE
T ss_pred             HHHHHHHcCCcCHHHHHHHHHHH---cCCCHHHHHHHHHHHHHCCCEEEEecCCceEEE
Confidence            33444445567766665544333   558899999999999999999997654444443

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=90.54  E-value=0.25  Score=32.91  Aligned_cols=59  Identities=20%  Similarity=0.308  Sum_probs=41.6

Q ss_pred             HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237         70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  132 (133)
Q Consensus        70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv  132 (133)
                      |..|.+++-....++-.||...+-..   ..++.+.+...|+.|.++|||.|..++ ..+.|.
T Consensus        12 q~~vL~~L~~~~~~t~~el~~~l~~~---~~~~~~Tvt~~l~rLe~kGlv~R~~~~-r~~~~~   70 (126)
T 1sd4_A           12 EWDVMNIIWDKKSVSANEIVVEIQKY---KEVSDKTIRTLITRLYKKEIIKRYKSE-NIYFYS   70 (126)
T ss_dssp             HHHHHHHHHHSSSEEHHHHHHHHHTT---SCCCHHHHHHHHHHHHHTTSEEEEEET-TEEEEE
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHhhc---CCCChhhHHHHHHHHHHCCceEEEeCC-CeEEEE
Confidence            34445555555667777777665321   346789999999999999999998764 467774

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=87.90  E-value=0.55  Score=30.97  Aligned_cols=56  Identities=23%  Similarity=0.373  Sum_probs=40.6

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  132 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv  132 (133)
                      |..++.....++-.+|...+-..   ...+.+.+-+.++.|.++|||+|..+| ..+.|+
T Consensus        15 vL~~l~~~~~~t~~ela~~l~~~---~~~s~~tv~~~l~~L~~~Glv~r~~~~-rr~~~~   70 (123)
T 1okr_A           15 VMNIIWMKKYASANNIIEEIQMQ---KDWSPKTIRTLITRLYKKGFIDRKKDN-KIFQYY   70 (123)
T ss_dssp             HHHHHHHHSSEEHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHTSEEEEEET-TEEEEE
T ss_pred             HHHHHHhCCCcCHHHHHHHHhcc---CCCcHhhHHHHHHHHHHCCCeEEEecC-CeEEEE
Confidence            34444445678888888776433   346788899999999999999998765 455554

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=87.00  E-value=0.58  Score=32.72  Aligned_cols=27  Identities=15%  Similarity=0.204  Sum_probs=23.4

Q ss_pred             hcCC-CCCCHHHHHHHHHHhhhhhcccc
Q psy16237         95 QSKS-FAPSISMIKKCIESLIDKNYVER  121 (133)
Q Consensus        95 ~l~~-F~p~~~~iK~~IE~LIekeYl~R  121 (133)
                      .|+. +..++..|-+.|..|+++|||.|
T Consensus        56 ~LA~~~~~s~~~v~~~L~~L~~KGlI~i   83 (135)
T 2v79_A           56 QLQEGMSISVEECTNRLRMFIQKGFLFI   83 (135)
T ss_dssp             HHHTTSSSCHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3445 67888999999999999999999

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=86.40  E-value=2.6  Score=28.17  Aligned_cols=59  Identities=10%  Similarity=0.121  Sum_probs=50.4

Q ss_pred             HHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccC
Q psy16237         63 EDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        63 ~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      +-++..++.+|..++.. +.+.-.+|...+.+.... |.++...+-..+..|-+.|||++.
T Consensus         7 ~~~~g~l~~~IL~~L~~-~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~   66 (116)
T 3f8b_A            7 EMLRAQTNVILLNVLKQ-GDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSY   66 (116)
T ss_dssp             HHHHHHHHHHHHHHHHH-CCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhchHHHHHHHHHHh-CCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEE
Confidence            34566788888888874 677778999998887776 899999999999999999999985

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=86.32  E-value=0.75  Score=31.46  Aligned_cols=59  Identities=12%  Similarity=0.161  Sum_probs=40.2

Q ss_pred             Hhhhhhhhcc-cccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEec
Q psy16237         70 QAAIVRIMKS-RKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYV  132 (133)
Q Consensus        70 ~AaIVRIMK~-~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yv  132 (133)
                      |..|.+++-. ...++-.||...+-..   -..+.+.+...|+.|.++|||.|..++ ..+.|.
T Consensus        11 e~~vL~~L~~~~~~~t~~el~~~l~~~---~~~~~~Tvt~~l~rLe~kGlv~r~~~~-r~~~~~   70 (138)
T 2g9w_A           11 ERAVMDHLWSRTEPQTVRQVHEALSAR---RDLAYTTVMAVLQRLAKKNLVLQIRDD-RAHRYA   70 (138)
T ss_dssp             HHHHHHHHHTCSSCEEHHHHHHHHTTT---CCCCHHHHHHHHHHHHHTTSEEEEC----CCEEE
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHhcc---CCCCHHHHHHHHHHHHHCCCEEEEecC-CeEEEE
Confidence            4445555554 4667777777665322   346888999999999999999998754 466663

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=85.95  E-value=0.74  Score=29.31  Aligned_cols=54  Identities=11%  Similarity=0.127  Sum_probs=36.2

Q ss_pred             hHHHHHhhhhhhhccc--ccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237         65 RKLYLQAAIVRIMKSR--KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANS  125 (133)
Q Consensus        65 R~~~I~AaIVRIMK~~--k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d  125 (133)
                      |...|=..|-+-++.+  ...+..||...       |-.+...+..-+..|-++|||+|+.+.
T Consensus         5 r~~~IL~~I~~~i~~~~g~~psv~EIa~~-------lgvS~~TVrr~L~~Le~kG~I~R~~gg   60 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGAPVKTRDIADA-------AGLSIYQVRLYLEQLHDVGVLEKVNAG   60 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCEEHHHHHHH-------HTCCHHHHHHHHHHHHHTTSEEEESCS
T ss_pred             HHHHHHHHHHHHHhhccCCCcCHHHHHHH-------HCCCHHHHHHHHHHHHHCCcEEecCCC
Confidence            3334444444444443  56666666644       345788899999999999999998653

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=84.56  E-value=1.4  Score=27.65  Aligned_cols=54  Identities=9%  Similarity=0.118  Sum_probs=39.0

Q ss_pred             HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237         69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY  129 (133)
Q Consensus        69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y  129 (133)
                      .+..|...+.....++..||...       +..+.+.+-+.+..|.+.|||.|..+.+..|
T Consensus        25 ~~~~il~~l~~~~~~s~~ela~~-------l~is~~tvs~~l~~L~~~glv~~~~~~r~~~   78 (99)
T 3cuo_A           25 KRLLILCMLSGSPGTSAGELTRI-------TGLSASATSQHLARMRDEGLIDSQRDAQRIL   78 (99)
T ss_dssp             HHHHHHHHHTTCCSEEHHHHHHH-------HCCCHHHHHHHHHHHHHTTSEEEEECSSCEE
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEEecCCEEE
Confidence            44556666666657777776654       3468888999999999999999976554333

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=83.55  E-value=2.1  Score=26.50  Aligned_cols=43  Identities=12%  Similarity=0.155  Sum_probs=32.0

Q ss_pred             hhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         73 IVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        73 IVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      |...+.....++-.||...       |..+.+.+.+.+..|.+.|+|.|.
T Consensus         5 Il~~L~~~~~~s~~eLa~~-------lgvs~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            5 ILEFLNRHNGGKTAEIAEA-------LAVTDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHSCCCCHHHHHHH-------HTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHcCCCCHHHHHHH-------HCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4555555556666666544       457888999999999999999964

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=82.84  E-value=1.4  Score=29.74  Aligned_cols=58  Identities=16%  Similarity=0.300  Sum_probs=41.1

Q ss_pred             HHHhhhhhhhccccc--ccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC--CCC--CceEec
Q psy16237         68 YLQAAIVRIMKSRKQ--IRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA--NST--DEYSYV  132 (133)
Q Consensus        68 ~I~AaIVRIMK~~k~--l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~--~d~--~~y~Yv  132 (133)
                      ..+..|..++.....  ++-.||...+       ..+.+.+-+.++.|.++|||.|..  .|.  ..|.|.
T Consensus        26 ~~e~~il~~L~~~~~~~~t~~eLa~~l-------~~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~~~~~y~   89 (123)
T 3r0a_A           26 KADLNVMKSFLNEPDRWIDTDALSKSL-------KLDVSTVQRSVKKLHEKEILQRSQQNLDGGGYVYIYK   89 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHH-------TSCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEE
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHH-------CcCHHHHHHHHHHHHHCCCEEeeCCccCCCcceEEEe
Confidence            345666777766555  8888876553       368899999999999999999953  222  245664

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=82.66  E-value=0.67  Score=31.73  Aligned_cols=25  Identities=12%  Similarity=0.185  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHHHhhhhhccccCC
Q psy16237         99 FAPSISMIKKCIESLIDKNYVERTA  123 (133)
Q Consensus        99 F~p~~~~iK~~IE~LIekeYl~R~~  123 (133)
                      ...+...+.+.|..|+++|||.|..
T Consensus        61 l~~s~~~V~~~l~~Le~kGlI~~~~   85 (128)
T 2vn2_A           61 MTVSAAECMEMVRRLLQKGMIAIEE   85 (128)
T ss_dssp             SSSCHHHHHHHHHHHHHTTSSEECC
T ss_pred             HCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            5678899999999999999999953

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=80.68  E-value=2.4  Score=26.54  Aligned_cols=49  Identities=14%  Similarity=0.216  Sum_probs=38.2

Q ss_pred             hhhhhhhcccc---cccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCC
Q psy16237         71 AAIVRIMKSRK---QIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANST  126 (133)
Q Consensus        71 AaIVRIMK~~k---~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~  126 (133)
                      -.|..+|+...   .++..||-..    |   -.+...|.+.|..|.+.|+|.|..+.+
T Consensus        17 ~~IL~~L~~~~~~~~~t~~eLA~~----L---gvs~~tV~~~L~~L~~~G~I~~~g~~~   68 (77)
T 1qgp_A           17 QRILKFLEELGEGKATTAHDLSGK----L---GTPKKEINRVLYSLAKKGKLQKEAGTP   68 (77)
T ss_dssp             HHHHHHHHHHCSSSCEEHHHHHHH----H---CCCHHHHHHHHHHHHHHTSEEEECSSS
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHH----H---CcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            34667788887   8888777654    3   377789999999999999999975544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	133
d1iuya_	92	a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus muscu	3e-31
d1ldja1	90	a.4.5.34 (A:687-776) Anaphase promoting complex (A	4e-31
d2hyec1	84	a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapien	1e-30

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  104 bits (262), Expect = 3e-31
 Identities = 45/91 (49%), Positives = 60/91 (65%), Gaps = 1/91 (1%)

Query: 44  GAVQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPS 102
            A Q E+  E + T   VD+DRK  ++AAIVRIMKSRK+++HN L+ EV  Q K+ F PS
Sbjct: 2   AAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPS 61

Query: 103 ISMIKKCIESLIDKNYVERTANSTDEYSYVA 133
             +IKK IE LI++ Y+ RT      Y+YVA
Sbjct: 62  PVVIKKRIEGLIEREYLARTPEDRKVYTYVA 92

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  104 bits (261), Expect = 4e-31
 Identities = 46/89 (51%), Positives = 62/89 (69%), Gaps = 1/89 (1%)

Query: 46  VQKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSIS 104
           ++ E  QE E T  +++EDRKL +QAAIVRIMK RK ++H  L+ EVL+Q  S F P + 
Sbjct: 2   MKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVP 61

Query: 105 MIKKCIESLIDKNYVERTANSTDEYSYVA 133
           +IKKCI+ LI+K Y+ER     D YSY+A
Sbjct: 62  VIKKCIDILIEKEYLERVDGEKDTYSYLA 90

>d2hyec1 a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (257), Expect = 1e-30
 Identities = 39/85 (45%), Positives = 55/85 (64%), Gaps = 1/85 (1%)

Query: 49  ETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKK 108
           ET +E   T   V +DR+  + AAIVRIMK RK + HN L+ E+ +Q K F      +KK
Sbjct: 1   ETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKK 59

Query: 109 CIESLIDKNYVERTANSTDEYSYVA 133
            IESLID++Y+ER  ++ ++Y YVA
Sbjct: 60  RIESLIDRDYMERDKDNPNQYHYVA 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	133
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	100.0
d2hyec1	84	Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1iuya_	92	Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 1	99.97
d2hyec3	273	Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}	96.97
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	95.37
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	95.08
d1okra_	120	Methicillin resistance regulatory protein MecI {St	94.53
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	93.45
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	91.81
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	86.08
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	85.62
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.43
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	84.06
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	82.83
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	81.97
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	81.87

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.9e-34  Score=194.57  Aligned_cols=87  Identities=53%  Similarity=0.833  Sum_probs=82.6

Q ss_pred             cCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237         47 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  125 (133)
Q Consensus        47 ~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d  125 (133)
                      +.++.+|...+++.|+++|.+.|+||||||||++|+|+|++|+++|+++|++ |+|++++||++||.||++|||+|+++|
T Consensus         3 ~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~k~l~h~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIereYi~R~~~~   82 (90)
T d1ldja1           3 KTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGE   82 (90)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSS
T ss_pred             CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhHHHhcCCCC
Confidence            3445567888999999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCceEecC
Q psy16237        126 TDEYSYVA  133 (133)
Q Consensus       126 ~~~y~Yva  133 (133)
                      +++|+|+|
T Consensus        83 ~~~y~YvA   90 (90)
T d1ldja1          83 KDTYSYLA   90 (90)
T ss_dssp             TTEEEECC
T ss_pred             CceeeeeC
Confidence            99999998

>d2hyec1 a.4.5.34 (C:676-759) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.1e-34  Score=190.72  Aligned_cols=84  Identities=46%  Similarity=0.654  Sum_probs=80.3

Q ss_pred             CChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCc
Q psy16237         49 ETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDE  128 (133)
Q Consensus        49 ~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~  128 (133)
                      ++.+|...+.+.|+++|.+.|+||||||||++|+|+|++|+++|.++|+ |+|++++||++||.||++|||+|+++|+++
T Consensus         1 e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~~k~l~h~eL~~~v~~~l~-f~~~~~~iK~~Ie~LIereYi~R~~~~~~~   79 (84)
T d2hyec1           1 ETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLK-FPVKPGDLKKRIESLIDRDYMERDKDNPNQ   79 (84)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEETHHHHHHHHHHSS-SCCCHHHHHHHHHHHHHTTSCBCCSSCTTE
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCcHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHhhhHhhcCCCCCce
Confidence            3566788899999999999999999999999999999999999999997 999999999999999999999999999999


Q ss_pred             eEecC
Q psy16237        129 YSYVA  133 (133)
Q Consensus       129 y~Yva  133 (133)
                      |+|+|
T Consensus        80 y~Y~A   84 (84)
T d2hyec1          80 YHYVA   84 (84)
T ss_dssp             EECCC
T ss_pred             eeeeC
Confidence            99998

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.97  E-value=1.2e-33  Score=191.30  Aligned_cols=87  Identities=51%  Similarity=0.721  Sum_probs=81.0

Q ss_pred             cCCChHHHhhhhhhHHHHhHHHHHhhhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCC
Q psy16237         47 QKETPQEIERTVSSVDEDRKLYLQAAIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANS  125 (133)
Q Consensus        47 ~~~~~~e~~~~~~~v~~~R~~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d  125 (133)
                      +.++..|...+.+.++++|.+.|+||||||||++|+|+|++|+++|+++|++ |+|+.++||++||.||++|||+|+++|
T Consensus         5 ~~e~~~e~~~~~~~i~~dR~~~i~AaIVRIMK~~k~l~~~~L~~~v~~~l~~~F~p~~~~iK~~Ie~LIekeYi~R~~~d   84 (92)
T d1iuya_           5 QGESDPERKETRQKVDDDRKHEIEAAIVRIMKSRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPED   84 (92)
T ss_dssp             CCCCCCCCCCCCSCSCCCTTTHHHHHHHHHHHHHCEEEHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSC
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhhhhcCCCC
Confidence            3455556677889999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCceEecC
Q psy16237        126 TDEYSYVA  133 (133)
Q Consensus       126 ~~~y~Yva  133 (133)
                      +++|+|+|
T Consensus        85 ~~~y~Y~A   92 (92)
T d1iuya_          85 RKVYTYVA   92 (92)
T ss_dssp             SSEEEEC-
T ss_pred             CCeeeeeC
Confidence            99999997

>d2hyec3 e.40.1.1 (C:403-675) Cullin-4A {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin-4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.97  E-value=0.00022  Score=53.54  Aligned_cols=40  Identities=18%  Similarity=0.272  Sum_probs=32.7

Q ss_pred             CCCCCcceeecc-----ccCCCCCeEEEccCCCCCceeEEecCCC
Q psy16237          7 MDGSCPGYIISV-----KELTEDTEIRLNLGYNNKRTKLKISGAV   46 (133)
Q Consensus         7 ~s~~~~~~~il~-----~~~~~~d~f~~N~~F~~k~~kiki~~~~   46 (133)
                      .+|...|++|+.     .++.++|.|.||.+|++|++||+|+++.
T Consensus       227 ~~L~~~k~~iL~~~~~~~~~~~~~~~~~N~~F~~k~~kiki~~~~  271 (273)
T d2hyec3         227 QSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQ  271 (273)
T ss_dssp             HTTTTTTTCSEEETTCSSSCCSSCEEEECCCCCCSCSSEECGGGG
T ss_pred             HHHHhcccceeeecCCCCcCCCCCEEEEeccCCCCCeEEeecccc
Confidence            356677777775     3467899999999999999999999764

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=95.37  E-value=0.0058  Score=38.17  Aligned_cols=60  Identities=17%  Similarity=0.269  Sum_probs=45.7

Q ss_pred             HhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         70 QAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        70 ~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      +..|++++=.+..++-.|++..+.+.   +.-..+.++.-+..|.+||||.|... ...|+|-|
T Consensus        11 E~~IM~~lW~~~~~t~~ei~~~l~~~---~~~~~tTv~T~L~rL~~KG~l~~~k~-gr~~~Y~p   70 (82)
T d1p6ra_          11 ELEVMKVIWKHSSINTNEVIKELSKT---STWSPKTIQTMLLRLIKKGALNHHKE-GRVFVYTP   70 (82)
T ss_dssp             HHHHHHHHHTSSSEEHHHHHHHHHHH---SCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhccc---cCCcHhHHHHHHHHHHHCCCeEEEec-CCeEEEEe
Confidence            45567777777778877777665443   55577899999999999999999755 46788854

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.08  E-value=0.01  Score=39.34  Aligned_cols=60  Identities=15%  Similarity=0.183  Sum_probs=41.7

Q ss_pred             HHhhhhhhhcccc-cccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         69 LQAAIVRIMKSRK-QIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        69 I~AaIVRIMK~~k-~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      .+..|+++.=... .++-.|++..    +.. .++..+.++.-+..|.+||||+|... ...|.|-|
T Consensus         8 ~E~~IM~~lW~~g~~~t~~eI~~~----l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~-gr~~~Y~~   69 (122)
T d2g9wa1           8 LERAVMDHLWSRTEPQTVRQVHEA----LSARRDLAYTTVMAVLQRLAKKNLVLQIRD-DRAHRYAP   69 (122)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHH----HTTTCCCCHHHHHHHHHHHHHTTSEEEEC----CCEEEE
T ss_pred             HHHHHHHHHHcCCCCccHHHHHHH----HhccCCCcHHHHHHHHHHHHHCCCEEEeec-CCeEEEEe
Confidence            4455566664443 4566666655    554 67889999999999999999999765 46788864

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.53  E-value=0.0094  Score=39.05  Aligned_cols=58  Identities=22%  Similarity=0.365  Sum_probs=43.0

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      .|.++.=....++-.||+..+...   .....+.+..-+..|.+||||.|..+ ...|+|.|
T Consensus        11 ~VM~~lW~~~~~t~~ei~~~l~~~---~~~~~sTv~t~L~rL~~Kg~l~r~~~-gr~~~Y~~   68 (120)
T d1okra_          11 EVMNIIWMKKYASANNIIEEIQMQ---KDWSPKTIRTLITRLYKKGFIDRKKD-NKIFQYYS   68 (120)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHcCCCCCHHHHHHHHhcc---cCccHHhHHHHHHHHHHCCCeEEEec-CCceEEee
Confidence            344444455666767776665432   67889999999999999999999765 47889865

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.45  E-value=0.025  Score=37.34  Aligned_cols=57  Identities=21%  Similarity=0.363  Sum_probs=41.8

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCC-CCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKS-FAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~-F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      -|+++.=....++-.|++..+    .. ++...+.+..-+..|.+||||.|... ...|+|-|
T Consensus        10 ~VM~~lW~~~~~t~~ei~~~l----~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~-gr~~~Y~~   67 (122)
T d1sd4a_          10 DVMNIIWDKKSVSANEIVVEI----QKYKEVSDKTIRTLITRLYKKEIIKRYKS-ENIYFYSS   67 (122)
T ss_dssp             HHHHHHHHSSSEEHHHHHHHH----HTTSCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHcCCCCCHHHHHHHh----hccCCCcHhHHHHHHHHHHhhhceeeecc-CCeEEEee
Confidence            344444455667766666554    34 66789999999999999999999755 47899964

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.81  E-value=0.11  Score=31.63  Aligned_cols=55  Identities=11%  Similarity=0.220  Sum_probs=46.2

Q ss_pred             hhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCceEecC
Q psy16237         72 AIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEYSYVA  133 (133)
Q Consensus        72 aIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y~Yva  133 (133)
                      ..|...|.+|.+...||-.+       |....++...+|+.|.+.+-|.---+|+..|+|+.
T Consensus        11 ~FI~~Ik~~Kvv~LedLAa~-------F~lktqd~i~RIq~Le~~g~ltGViDDRGKfIyIS   65 (72)
T d1wi9a_          11 EFINYIKKSKVVLLEDLAFQ-------MGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             HHHHHHHHCSEECHHHHHHH-------HCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHHCCEeeHHHHHHH-------cCCcHHHHHHHHHHHHHCCCeeeEEcCCCCEEEEc
Confidence            44677788888887776544       99999999999999999999998878888999983

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=86.08  E-value=0.71  Score=27.25  Aligned_cols=59  Identities=14%  Similarity=0.139  Sum_probs=38.3

Q ss_pred             hHHHHHhhhhhhhccc-ccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCCCCCCce
Q psy16237         65 RKLYLQAAIVRIMKSR-KQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTANSTDEY  129 (133)
Q Consensus        65 R~~~I~AaIVRIMK~~-k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~~d~~~y  129 (133)
                      |...|=.+|+...+.+ ..-++.||..    .+. |. +++.+..-+..|.++|||+|.++.+-.+
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~----~~g-~~-S~stv~~~l~~Le~kG~I~r~~~~~R~i   65 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQ----RLG-FR-SPNAAEEHLKALARKGVIEIVSGASRGI   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHH----HTT-CS-SHHHHHHHHHHHHHTTSEEECSSSSSCE
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHH----HcC-CC-CHHHHHHHHHHHHHCcCeecCCCCCcee
Confidence            3334444555555554 3456666543    332 44 7888999999999999999987644333

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=85.62  E-value=0.47  Score=27.27  Aligned_cols=48  Identities=13%  Similarity=0.167  Sum_probs=40.5

Q ss_pred             HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      .+|..|++.+...-++++.+|-..+       ..+.+.+..+|+.|.+.|.|.+.
T Consensus         5 ~~D~~IL~~L~~~~r~s~~eiA~~l-------~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           5 NLDRGILEALMGNARTAYAELAKQF-------GVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHHHCTTSCHHHHHHHH-------TSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH-------CcCHHHHHHHHHHHHHCCCeEeE
Confidence            3567799999999999998885443       47899999999999999999874

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=85.43  E-value=0.47  Score=27.08  Aligned_cols=48  Identities=15%  Similarity=0.277  Sum_probs=40.1

Q ss_pred             HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237         69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  123 (133)
Q Consensus        69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~  123 (133)
                      ++--|++++...-++++.+|-..+       -.+.+.+..+|..|.+.|+|.|..
T Consensus         4 ~D~kIl~~L~~n~r~s~~~lA~~~-------gls~~~v~~Ri~~L~~~giI~~~~   51 (60)
T d1i1ga1           4 RDKIILEILEKDARTPFTEIAKKL-------GISETAVRKRVKALEEKGIIEGYT   51 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHH-------TSCHHHHHHHHHHHHHHTSSCCCC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHH-------CcCHHHHHHHHHHHHHCCCeEeEE
Confidence            456788889999999998886553       378899999999999999999854

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=84.06  E-value=0.64  Score=26.34  Aligned_cols=49  Identities=12%  Similarity=0.214  Sum_probs=41.4

Q ss_pred             HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccCC
Q psy16237         68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERTA  123 (133)
Q Consensus        68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~~  123 (133)
                      .+|..|++.+...-++++.+|-..+       ..+...+..+|..|.+.|.|.|..
T Consensus         3 ~~D~~Il~~L~~n~r~s~~eiA~~l-------~ls~~~v~~Ri~~L~~~giI~~~~   51 (60)
T d2cyya1           3 EIDKKIIKILQNDGKAPLREISKIT-------GLAESTIHERIRKLRESGVIKKFT   51 (60)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHH-------CSCHHHHHHHHHHHHHHTSSCCCC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH-------CcCHHHHHHHHHHHHHCCCeEeEE
Confidence            3567889999999999998887553       378999999999999999999864

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=82.83  E-value=1.1  Score=25.67  Aligned_cols=48  Identities=13%  Similarity=0.190  Sum_probs=40.1

Q ss_pred             HHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         68 YLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        68 ~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      .+|..|...+...-++++.+|-..+    .   .+.+.+..+|..|.+.|+|.|.
T Consensus         5 ~~D~~IL~~L~~n~r~s~~~iA~~l----g---is~~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           5 QIDLNIIEELKKDSRLSMRELGRKI----K---LSPPSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHH----T---CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH----C---cCHHHHHHHHHHHHHCCCeeeE
Confidence            4567788899999999988877654    3   6788999999999999999884

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=81.97  E-value=1  Score=27.47  Aligned_cols=47  Identities=11%  Similarity=0.164  Sum_probs=36.9

Q ss_pred             HHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC
Q psy16237         69 LQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT  122 (133)
Q Consensus        69 I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~  122 (133)
                      .+-.|..++..+..++..||...       +..+.+.+-..+..|.+.||++|.
T Consensus        17 ~r~~IL~~L~~~~~~~~~eLa~~-------l~is~~~vs~~l~~L~~~glV~~~   63 (100)
T d1ub9a_          17 VRLGIMIFLLPRRKAPFSQIQKV-------LDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHH-------TTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhccCCCeeHHHHHHH-------HhhccccccHHHHHHhhhceeEEE
Confidence            34556667766777887777543       668999999999999999999875

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.87  E-value=0.54  Score=29.58  Aligned_cols=60  Identities=18%  Similarity=0.322  Sum_probs=42.2

Q ss_pred             HHHHhhhhhhhcccccccchHHHHHHHHhcCCCCCCHHHHHHHHHHhhhhhccccC--CCCCCceEecC
Q psy16237         67 LYLQAAIVRIMKSRKQIRHNALIQEVLSQSKSFAPSISMIKKCIESLIDKNYVERT--ANSTDEYSYVA  133 (133)
Q Consensus        67 ~~I~AaIVRIMK~~k~l~h~eL~~ev~~~l~~F~p~~~~iK~~IE~LIekeYl~R~--~~d~~~y~Yva  133 (133)
                      ..-|+.|-..+-.+..++-.||...       .-.+.+.+-..++.|.++||+.|.  +.|...|.|.|
T Consensus        19 t~~e~~v~~~L~~~g~~t~~eia~~-------~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a   80 (109)
T d1sfxa_          19 KPSDVRIYSLLLERGGMRVSEIARE-------LDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSA   80 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHH-------HTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEE
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHH-------hCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccC
Confidence            3456666666666677776655543       337788889999999999999984  34555666653