Citrus Sinensis ID: 041030

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------25
Protein Sequence
MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHHHHELRDDGD
Secondary Structure (PSIPRED)
cccccccccEEEccccccccccEEEEEcccccEEccccccccccccccccccEEcccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccHHHHHccccccccccccccccHHHHHHcccEEEcccccccccccccccccccccccccccccccccccccEEcccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEccccccccccEEEEEEcccEEEEccccccccccccccccEEEEcccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccHHHHHccccEEEcHHHHHccccccccccccHccccccHHHcccccHHHHHccccccccccccHHHHHHHHccccccEcccccccccccccccccHccccccccccccc
Coil and Loop (DISEMBL)
mslaqnrprvivngtrrtrTFHYFWcqscqrttrfrstdpselfcphcsaqlyleldvsrprlvssspaavesfptpsgrfLDSLAQAldtpnndghnlhSWISlhfdeptpppppppppqpmieypmhdlqpdaaptpapvSAVEALKRVRISestqltrsnevqccpickeefrvrddvdddsdevmimelpckhlyhsdcivpwlrhysttcpvcryelkdsiigsggdnimndhhhhhelrddgd
Flexible Loop (DISEMBL)
mslaqnrprvivngtrrtrtfhyfwcqscqrtTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRIsestqltrsnevqccpickeefrvrddvdddSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHHHHELRDDGD
Low Complexity Region (SEG)
MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEptpppppppppqpMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFrvrddvdddsdEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHHHHELRDDGD
Disordered region (IsUnstruct)
*********VIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVS***************************************LHSWISL*********************************************************NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG*********************
Disordered Region (DISOPRED)
******R********RRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDS*******************************PPPPPQ**************************LKRVRISES******NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY*****************************
Disordered Region (DISEMBL)
MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHH*********
Disordered Region (DISPRO)
********RVI***TRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSR*********AVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL***************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHHHHELRDDGD
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	249	2.2.26 [Sep-21-2011]
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.389	0.286	0.347	5e-11
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.285	0.216	0.380	2e-10
Q6DIP3	311	RING finger protein 126 O	yes	no	0.309	0.247	0.373	4e-10
Q6IRP0	312	RING finger protein 126-B	N/A	no	0.301	0.240	0.382	5e-10
Q7T0Q3	312	RING finger protein 126-A	N/A	no	0.309	0.246	0.362	2e-09
Q9C1X4	513	Uncharacterized RING fing	yes	no	0.333	0.161	0.360	3e-09
Q9CY62	165	E3 ubiquitin-protein liga	yes	no	0.281	0.424	0.383	1e-08
Q9D0C1	305	E3 ubiquitin-protein liga	no	no	0.305	0.249	0.355	2e-08
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.305	0.25	0.366	2e-08
Q9SPL2	334	E3 ubiquitin-protein liga	no	no	0.285	0.212	0.376	6e-08

>sp|P0CH30|RING1_GOSHI E3 ubiquitin-protein ligase RING1 OS=Gossypium hirsutum GN=RING1 PE=2 SV=1

 Score = 68.2 bits (165), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 41/118 (34%), Positives = 64/118 (54%), Gaps = 21/118 (17%)

Query: 139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL 198
           PA  SA+EAL  V I++S   +  N+   C +C ++F          +     ++PCKHL
Sbjct: 198 PASKSAIEALPLVNITKSNLNSEFNQ---CAVCMDDFE---------EGTEAKQMPCKHL 245

Query: 199 YHSDCIVPWLRHYSTTCPVCRYEL-------KDSIIGSGGDNIMNDHHHHHELRDDGD 249
           YH DC++PWL  ++ +CPVCR+EL       +  + G+ G +  ND  +  + R DGD
Sbjct: 246 YHKDCLLPWLELHN-SCPVCRHELPTDDPDYERRVRGAQGTSGGNDGDNSGQ-RSDGD 301

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Gossypium hirsutum (taxid: 3635)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q8LPN7|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like OS=Arabidopsis thaliana GN=At3g19950 PE=2 SV=1

 Score = 66.2 bits (160), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 54/84 (64%), Gaps = 13/84 (15%)

Query: 139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL 198
           PA  SA++AL  V++++    +  N+   C +C +EF      +D SD   + ++PCKH+
Sbjct: 190 PASKSAIDALPTVKVTKDMLKSEMNQ---CAVCMDEF------EDGSD---VKQMPCKHV 237

Query: 199 YHSDCIVPWLRHYSTTCPVCRYEL 222
           +H DC++PWL  ++ +CPVCR+EL
Sbjct: 238 FHQDCLLPWLELHN-SCPVCRFEL 260

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6DIP3|RN126_XENTR RING finger protein 126 OS=Xenopus tropicalis GN=rnf126 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 34/91 (37%), Positives = 50/91 (54%), Gaps = 14/91 (15%)

Query: 134 DAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMEL 193
           +  P PA    ++AL  ++I+E   +    E   CP+CKE++ V + V          +L
Sbjct: 197 NTGPPPADTEKIQALPTIQITEE-HVGSGLE---CPVCKEDYTVGESV---------RQL 243

Query: 194 PCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224
           PC HL+H+DCI+PWL  +  TCPVCR  L  
Sbjct: 244 PCNHLFHNDCIIPWLEQHD-TCPVCRKSLSG 273

Xenopus tropicalis (taxid: 8364)

>sp|Q6IRP0|R126B_XENLA RING finger protein 126-B OS=Xenopus laevis GN=rnf126-b PE=2 SV=1

 Score = 64.7 bits (156), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 50/89 (56%), Gaps = 14/89 (15%)

Query: 134 DAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMEL 193
           +  P PA    ++AL  ++I+E   +    E   CP+CKE++ V + V          +L
Sbjct: 198 NTGPPPADTDKIQALPTIQITEE-HVGFGLE---CPVCKEDYTVGESV---------RQL 244

Query: 194 PCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           PC HL+H+DCI+PWL  +  TCPVCR  L
Sbjct: 245 PCNHLFHNDCIIPWLEQHD-TCPVCRKSL 272

Xenopus laevis (taxid: 8355)

>sp|Q7T0Q3|R126A_XENLA RING finger protein 126-A OS=Xenopus laevis GN=rnf126-a PE=2 SV=1

 Score = 63.2 bits (152), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 50/91 (54%), Gaps = 14/91 (15%)

Query: 134 DAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMEL 193
           +  P PA    ++AL  ++I+E   +    E   CP+CKE++ V +          + +L
Sbjct: 198 NTGPPPADNEKIQALPTIQITEE-HVGSGLE---CPVCKEDYTVGE---------CVRQL 244

Query: 194 PCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224
           PC HL+H+DCI+PWL  +  TCPVCR  L  
Sbjct: 245 PCNHLFHNDCIIPWLEQHD-TCPVCRKSLSG 274

Xenopus laevis (taxid: 8355)

>sp|Q9C1X4|YKW3_SCHPO Uncharacterized RING finger protein P32A8.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAP32A8.03c PE=4 SV=1

 Score = 62.4 bits (150), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 48/97 (49%), Gaps = 14/97 (14%)

Query: 123 MIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVD 182
           +I   M   Q   AP PAP   +  +K V+      +    E   C IC E F++ DDV 
Sbjct: 355 IISQLMEQAQGHNAPAPAPEDVIAKMK-VQKPPKELIDEEGE---CTICMEMFKINDDV- 409

Query: 183 DDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
                   ++LPCKH +H +CI PWLR  + TC +CR
Sbjct: 410 --------IQLPCKHYFHENCIKPWLR-VNGTCAICR 437

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9CY62|RN181_MOUSE E3 ubiquitin-protein ligase RNF181 OS=Mus musculus GN=Rnf181 PE=2 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 48/86 (55%), Gaps = 16/86 (18%)

Query: 137 PTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK 196
           P PA  + VE+L R  IS +    +      CP+C  EF           E  ++E+PC 
Sbjct: 63  PPPAAKAVVESLPRTVISSAKADLK------CPVCLLEFEA---------EETVIEMPCH 107

Query: 197 HLYHSDCIVPWLRHYSTTCPVCRYEL 222
           HL+HS+CI+PWL   + +CP+CR+EL
Sbjct: 108 HLFHSNCILPWLSK-TNSCPLCRHEL 132

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9D0C1|RN115_MOUSE E3 ubiquitin-protein ligase RNF115 OS=Mus musculus GN=Rnf115 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 46/90 (51%), Gaps = 14/90 (15%)

Query: 134 DAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMEL 193
           +  P PA    + +L  V +++     + N    CP+CKE++ V         E  + +L
Sbjct: 199 NTGPPPADKEKITSLPTVTVTQE----QVNTGLECPVCKEDYTV---------EEKVRQL 245

Query: 194 PCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
           PC H +HS CIVPWL  +  TCPVCR  L 
Sbjct: 246 PCNHFFHSSCIVPWLELHD-TCPVCRKSLN 274

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9Y4L5|RN115_HUMAN E3 ubiquitin-protein ligase RNF115 OS=Homo sapiens GN=RNF115 PE=1 SV=2

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 48/90 (53%), Gaps = 14/90 (15%)

Query: 134 DAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMEL 193
           +  P PA    + +L  V +++  Q+    E   CP+CKE++ V ++V          +L
Sbjct: 198 NTGPPPADKEKITSLPTVTVTQE-QVDMGLE---CPVCKEDYTVEEEV---------RQL 244

Query: 194 PCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
           PC H +HS CIVPWL  +  TCPVCR  L 
Sbjct: 245 PCNHFFHSSCIVPWLELHD-TCPVCRKSLN 273

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9SPL2|CIP8_ARATH E3 ubiquitin-protein ligase CIP8 OS=Arabidopsis thaliana GN=CIP8 PE=1 SV=1

 Score = 58.2 bits (139), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 44/85 (51%), Gaps = 14/85 (16%)

Query: 139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL 198
           PA  SA+EAL+   +S S        V  C +CK+   + +            +LPC H 
Sbjct: 232 PAAKSAIEALETFEVSSS----EGEMVMVCAVCKDGMVMGETGK---------KLPCGHC 278

Query: 199 YHSDCIVPWLRHYSTTCPVCRYELK 223
           YH DCIVPWL     +CPVCR++L+
Sbjct: 279 YHGDCIVPWL-GTRNSCPVCRFQLE 302

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. Probably forms a minimal ubiquitin ligase complex in cooperation with the E2 enzyme UBC8. Its interaction with COP1 suggests that it may participate in proteasome-mediated degradation of HY5 in vivo.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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	249
224120262	313	predicted protein [Populus trichocarpa]	0.827	0.658	0.421	8e-40
255581205	333	zinc finger protein, putative [Ricinus c	0.807	0.603	0.414	2e-39
356557503	315	PREDICTED: uncharacterized protein LOC10	0.911	0.720	0.392	9e-35
357445561	315	Thioredoxin-related protein [Medicago tr	0.911	0.720	0.407	6e-33
356528793	311	PREDICTED: uncharacterized protein LOC10	0.863	0.691	0.380	5e-30
30697639	248	RING/U-box domain-containing protein [Ar	0.783	0.786	0.373	2e-24
297838567	248	zinc finger family protein [Arabidopsis	0.742	0.745	0.370	3e-23
147821210	366	hypothetical protein VITISV_043084 [Viti	0.843	0.573	0.350	1e-22
298204569	278	unnamed protein product [Vitis vinifera]	0.811	0.726	0.347	2e-22
298204570	451	unnamed protein product [Vitis vinifera]	0.843	0.465	0.358	3e-22

>gi|224120262|ref|XP_002318286.1| predicted protein [Populus trichocarpa] gi|222858959|gb|EEE96506.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (429), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 110/261 (42%), Positives = 137/261 (52%), Gaps = 55/261 (21%)

Query: 1   MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSR 60
           MSL  NRPRV VNG RR RTFH+FWCQ+CQ  +RF S +  E+FCP+C + +  ELDVSR
Sbjct: 1   MSLI-NRPRVTVNGIRRMRTFHFFWCQNCQSISRFTSINRLEIFCPNCYSGMNHELDVSR 59

Query: 61  PRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNND-------------GHNLHSWISLHF 107
           PR  +     +ES  +P  RFL SLAQ LD P                G     WI+L F
Sbjct: 60  PRFFADI-TGLES--SPGARFLVSLAQMLDPPTRGQDADSGRRIRWVLGSANGPWITLQF 116

Query: 108 DEPTPPPPPP------------------------PPPQPMIEYPMHDLQPDAAPTPAPVS 143
            EP     P                              ++   M D      P PAPVS
Sbjct: 117 VEPPSLQRPTIAAPAPAVPPSNNAINRSNVDNIGNAENDLLTEDMIDHSDLPGPPPAPVS 176

Query: 144 AVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDC 203
           A+EAL  V+++E   +   N+++ CP+CKE F V  D          MELPCKHLYHSDC
Sbjct: 177 AIEALPIVKVTEQHLM---NDMR-CPVCKEIFEVGGDA---------MELPCKHLYHSDC 223

Query: 204 IVPWLRHYSTTCPVCRYELKD 224
           +VPWL  ++ TCPVCRYEL+D
Sbjct: 224 VVPWLNLHN-TCPVCRYELRD 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581205|ref|XP_002531415.1| zinc finger protein, putative [Ricinus communis] gi|223528965|gb|EEF30957.1| zinc finger protein, putative [Ricinus communis]

 Score =  168 bits (426), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 109/263 (41%), Positives = 139/263 (52%), Gaps = 62/263 (23%)

Query: 1   MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSR 60
           MSLA  RPR+ VNG RR RTFHYFWCQSCQRT+RF S +P E FCPHC + L  ELD+SR
Sbjct: 1   MSLAH-RPRITVNGNRRMRTFHYFWCQSCQRTSRFTSINPHENFCPHCFSVLNHELDISR 59

Query: 61  PRLVSSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHS--------------WISLH 106
           PRL ++     E  P+P+ R LDSLA  L+      +                  WI+L 
Sbjct: 60  PRLNAN---LTELEPSPAARLLDSLALMLNPSMRQQYTEFDGRLTRWDTERANAPWITLQ 116

Query: 107 FDEPTPPPPPPPPPQPM-----------------IEYPMHDLQPDA-------APTPAPV 142
           F +      PP P +PM                  E   ++  P+         P PAP 
Sbjct: 117 FLD------PPRPQRPMNALTDSTAAANDGNNDIFENAANEFVPNNMTDLDRPGPPPAPA 170

Query: 143 SAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSD 202
           S VEAL  V+I++   +  ++    CP+CK+EF +  +V          ELPCKHLYHSD
Sbjct: 171 SVVEALPVVKITQEHLMKDTH----CPVCKDEFEIDGEV---------RELPCKHLYHSD 217

Query: 203 CIVPWLRHYSTTCPVCRYELKDS 225
           CIVPWL  ++ TCPVCR+ L D 
Sbjct: 218 CIVPWLNLHN-TCPVCRFVLCDG 239

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557503|ref|XP_003547055.1| PREDICTED: uncharacterized protein LOC100803179 [Glycine max]

 Score =  152 bits (385), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 111/283 (39%), Positives = 149/283 (52%), Gaps = 56/283 (19%)

Query: 1   MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELDVSR 60
           MSL   RPR++VNG RRTRTFHYFWC  CQRT R   T+     CP+C  QL  ELD+SR
Sbjct: 1   MSLT-GRPRIVVNGVRRTRTFHYFWCLYCQRTVRLPFTNNDGSTCPYCFHQLRYELDISR 59

Query: 61  PRLVSSSPAAVESFPTPSGRFLDSLAQALD------------------TPNNDGHNLHSW 102
           PRL+ + P  +E  P+ + + + +LA  LD                  T N DG N  +W
Sbjct: 60  PRLLMNVPNNLE--PSQATQLMHNLALILDPPLRRQNNNHLNTTPHWETENEDGLNPQAW 117

Query: 103 ISLHFDEPTPPPPPPPPPQPMI------------EYPMHDLQPDA--------APTPAPV 142
           I+L F  PT PP P  PPQ ++            E  + D   D          P PA  
Sbjct: 118 ITLRFPRPTRPPRPISPPQNLVPQTNDTDHDTLFENTILDDFIDGVIQNNNRPGPPPATS 177

Query: 143 SAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSD 202
           SA+ AL  V+++++   +  N    CPICK+EF +         ++   ELPCKH YHSD
Sbjct: 178 SAIAALPMVKLTQTHLASDPN----CPICKDEFEL---------DMEARELPCKHFYHSD 224

Query: 203 CIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDHHHHHELR 245
           CI+PWLR ++ TCPVCRYEL+  +  SG  N     +  +++R
Sbjct: 225 CIIPWLRMHN-TCPVCRYELQ-GVSTSGNANYYRLQNDENDMR 265

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445561|ref|XP_003593058.1| Thioredoxin-related protein [Medicago truncatula] gi|355482106|gb|AES63309.1| Thioredoxin-related protein [Medicago truncatula]

 Score =  146 bits (369), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 117/287 (40%), Positives = 148/287 (51%), Gaps = 60/287 (20%)

Query: 1   MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSE---LFCPHCSAQLYLELD 57
           MSL   RPRVIVNG RR RTFHYFWC +CQRT R  ST+  +    FCP+C  QL  ELD
Sbjct: 1   MSLT-GRPRVIVNGVRRMRTFHYFWCLNCQRTVRIPSTNTIQNYGSFCPYCFHQLRYELD 59

Query: 58  VSRPRLVSSSPAAVESFPTPS-GRFLDSLAQALD-----------TP-------NNDGHN 98
           +SRPRL+ + P      P PS  + + SLA  LD           TP       ++   N
Sbjct: 60  ISRPRLLMNDPNNRNIDPPPSTNQLMGSLAFILDPSLRRQDQNNTTPQWGTEHEDDQNQN 119

Query: 99  LHSWISLHFDEPTPPPPPP--------PPPQPMIEYPMHDLQPDAA--------PTPAPV 142
             +WI+L F  PT P  P          P    IE P  D   D          P PA  
Sbjct: 120 PQAWITLRFVRPTRPTRPIAPPPPQNMAPQLNDIETPSLDEFFDGVIHNNIRPGPPPASP 179

Query: 143 SAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSD 202
           SA+EAL  V+++E+   +  N    CPICK+EF V         +V + ELPCKH YHSD
Sbjct: 180 SAIEALPMVKVTETHLASDPN----CPICKDEFEV---------DVQVRELPCKHFYHSD 226

Query: 203 CIVPWLRHYSTTCPVCRYELKDSIIGSGGDN-IMNDHHHHHELRDDG 248
           CI+PWL+ ++ TCPVCR+EL+      G DN   N +   +E+   G
Sbjct: 227 CILPWLQMHN-TCPVCRHELQ------GVDNHNANYYFFQNEIEQQG 266

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528793|ref|XP_003532982.1| PREDICTED: uncharacterized protein LOC100793656 [Glycine max]

 Score =  137 bits (344), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 104/273 (38%), Positives = 138/273 (50%), Gaps = 58/273 (21%)

Query: 1   MSLAQNRPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELF---CPHCSAQLYLELD 57
           MSL   RPRV+ NG RRTRTFHY WC  CQRT R   T+  + F   CP+C  QL  ELD
Sbjct: 1   MSLT-GRPRVVANGVRRTRTFHYLWCIYCQRTVRIPFTNNDDGFTSTCPYCFHQLRYELD 59

Query: 58  VSRPRLVSSSPAAVESFPTPSGRFLDSLAQALDTP----NN---------------DGHN 98
           +SRPRL+ + P  +E  P+P+ + L +LA  LD P    NN               DG N
Sbjct: 60  ISRPRLLMNVPNNLE--PSPATQLLHNLALILDPPLRRQNNHLINTIPHWETENYEDGSN 117

Query: 99  L----HSWISLHFDEPTPPPPPPPPP---------------QPMIEYPMHDLQPDAAPTP 139
                 +WI+L F  PT  P P                      I+  + +      P P
Sbjct: 118 SSNPHQAWITLRFPRPTRVPRPISNDTDDHDDTLFENNALLDDFIDGVIQNNNNRPGPPP 177

Query: 140 APVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLY 199
           A  SA+ AL  V+++++   +  N    CPICK+EF +         ++   ELPCKH Y
Sbjct: 178 AASSAIAALPMVKLTQTHLASDPN----CPICKDEFLL---------DMEARELPCKHFY 224

Query: 200 HSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGD 232
           HSDCI+PWLR ++ TCPVCRYEL+     +  +
Sbjct: 225 HSDCIIPWLRMHN-TCPVCRYELQGVTSANNAN 256

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30697639|ref|NP_176985.2| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|38454118|gb|AAR20753.1| At1g68180 [Arabidopsis thaliana] gi|60543341|gb|AAX22268.1| At1g68180 [Arabidopsis thaliana] gi|70905059|gb|AAZ14055.1| At1g68180 [Arabidopsis thaliana] gi|332196639|gb|AEE34760.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  118 bits (296), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 120/249 (48%), Gaps = 54/249 (21%)

Query: 7   RPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL--ELDVSRPRLV 64
           RPRVIVNGTRRTRTFHYF+C+ C RT R RS       CP CS ++ L  ELD+ RP   
Sbjct: 6   RPRVIVNGTRRTRTFHYFYCRHCSRTIRLRSFGLYGPICPFCSREINLHDELDIMRP--- 62

Query: 65  SSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHF-DEPTPPPPPPPPPQPM 123
            S P            + DS     DT          WI+LH  +EP             
Sbjct: 63  -SRP------------YWDS-----DT---------DWITLHLINEPRSNRFNHDDLVYN 95

Query: 124 IEYPMHDLQPDA--APTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDV 181
            +    D+ P     P PA  SA+EA++ V I++   +      + C ICKEEF V ++ 
Sbjct: 96  TDEEFADVMPSVQIGPPPASQSAIEAVRTVIITDEDLVKE----KVCAICKEEFEVGEEG 151

Query: 182 DDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK----DSIIGSGGD-NIMN 236
                     EL C HLYHS CIV WL  ++ TCP+CR+E+     +S +  GG  NI N
Sbjct: 152 K---------ELKCLHLYHSSCIVSWLNIHN-TCPICRFEVNLGVSESNVDEGGSYNIDN 201

Query: 237 DHHHHHELR 245
           D  +    R
Sbjct: 202 DRSNRFRTR 210

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297838567|ref|XP_002887165.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297333006|gb|EFH63424.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  114 bits (286), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 90/243 (37%), Positives = 117/243 (48%), Gaps = 58/243 (23%)

Query: 7   RPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL--ELDVSRPRLV 64
           RPRVIVNGTRRTRTFHYF+C+ C RT R RS       CP CS ++ L  ELD+ RP   
Sbjct: 6   RPRVIVNGTRRTRTFHYFYCRHCSRTIRLRSFGLYGPICPFCSREINLHDELDIMRP--- 62

Query: 65  SSSPAAVESFPTPSGRFLDSLAQALDTPNNDGHNLHSWISLHFDEPTPPPPPPPPPQPMI 124
            S P            + D+     DT          WI+LH      PP      +  +
Sbjct: 63  -SRP------------YWDT-----DT---------DWITLHL---INPPRSNRFNRDDL 92

Query: 125 EYPMHDLQPDAAPT------PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVR 178
            Y   +   D  P+      PA  SA+EA++ V I+E   L +    + C ICKEEF V 
Sbjct: 93  VYNTDEEFADVMPSVQIGPPPASQSAIEAVRTVTITEE-DLAKE---KVCAICKEEFEVG 148

Query: 179 DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDNIMNDH 238
           ++           EL C HLYHS CIV WL  ++ TCP+CR+E+    +G    N+    
Sbjct: 149 EEGK---------ELKCLHLYHSSCIVSWLNIHN-TCPICRFEVN---LGVPESNVDEGG 195

Query: 239 HHH 241
            HH
Sbjct: 196 SHH 198

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147821210|emb|CAN66450.1| hypothetical protein VITISV_043084 [Vitis vinifera]

 Score =  112 bits (281), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 93/265 (35%), Positives = 122/265 (46%), Gaps = 55/265 (20%)

Query: 1   MSLAQNRPRVIVN-GTRRTRTFHYFWCQSCQRTTRFRSTDPSE-LFCPHCSAQLYLELDV 58
           MSL + RPR+IV+ GTRR R++HY+WCQ CQRT R  S   SE L CP CS +L  E   
Sbjct: 1   MSLDR-RPRIIVHHGTRRMRSYHYYWCQHCQRTVRIASGILSEILLCPFCSCRLQYEFHA 59

Query: 59  SRPRLVSSSPA----AVESFPTPSGRFLDSLAQALDTPNNDGH--------NLHSWISLH 106
            R RLV +       A E         L    Q  D               N+ S +  H
Sbjct: 60  PRLRLVPTFTGLGVLAAELLEDVDVSLLPRRRQNTDLNGVLWGSEMRIPSINVPSGVGRH 119

Query: 107 FDEPTPPPPPPPPPQPMI-------EYPMHDLQPDAAP--TPAPVSA------------- 144
              P  P  P   P+ +         + M D+  +A    T   V+              
Sbjct: 120 LLTPPRPGRPVAAPENVAVPRLGGSNFTMRDVLNEAMEELTHNEVTGETTQNDRPGPPPA 179

Query: 145 ----VEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYH 200
               +EAL  VR++     T      CCP+CKEE++  ++V          E+PC HLYH
Sbjct: 180 APSAIEALPSVRLTP----THLRNDPCCPVCKEEYQAGEEVR---------EMPCNHLYH 226

Query: 201 SDCIVPWLRHYSTTCPVCRYELKDS 225
           SDCIVPWLR ++ +CPVCRYEL+ S
Sbjct: 227 SDCIVPWLRIHN-SCPVCRYELQAS 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204569|emb|CBI23844.3| unnamed protein product [Vitis vinifera]

 Score =  112 bits (280), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 95/273 (34%), Positives = 126/273 (46%), Gaps = 71/273 (26%)

Query: 1   MSLAQNRPRVIVN-GTRRTRTFHYFWCQSCQRTTRFRSTDPSE-LFCPHCSAQLYLELDV 58
           MSL + RPRVIV+ GTRR RT+HY+WCQ CQRT R  S + SE L CP CS +L  E   
Sbjct: 1   MSLDR-RPRVIVHHGTRRMRTYHYYWCQHCQRTVRIASGNLSEILLCPFCSCRLQYEFHA 59

Query: 59  SRPRLVSSSPAAVESFPTPSGRFLDSLAQALDT------PNNDGHNLHSW---------- 102
            R RLV +         T  G     L + +D       P   G N   W          
Sbjct: 60  PRQRLVPTF--------TGLGVLAAELLEDMDVILLPRRPQTTGLNGVLWGTEMRIPSIN 111

Query: 103 ----ISLHFDEPTPPPPPPPPPQPMI-------EYPMHDLQPDAAP--TPAPVSA----- 144
               +  H   P  P  P   P+ +         + M D+  +A    T   V+      
Sbjct: 112 VPSRVGRHLRRPPRPRRPVAAPENVAAPRVGGSNFTMRDVLNEAMEELTHNEVTGENTQN 171

Query: 145 ------------VEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIME 192
                       +EAL  VR++     T      CCP+CKEE++  ++V          E
Sbjct: 172 DRPGPPPAAPSAIEALPSVRLTP----THLRNDPCCPVCKEEYQAGEEVR---------E 218

Query: 193 LPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225
           +PCKH+YHSDCIVPWLR ++ +CPVCR+EL+ S
Sbjct: 219 MPCKHMYHSDCIVPWLRIHN-SCPVCRHELEAS 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204570|emb|CBI23845.3| unnamed protein product [Vitis vinifera]

 Score =  111 bits (277), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 95/265 (35%), Positives = 122/265 (46%), Gaps = 55/265 (20%)

Query: 1   MSLAQNRPRVIVN-GTRRTRTFHYFWCQSCQRTTRFRSTDPSE-LFCPHCSAQLYLELDV 58
           MSL + RPR+IV+ GTRR R++HY+WCQ CQRT R  S   SE L CP CS +L  E   
Sbjct: 1   MSLDR-RPRIIVHHGTRRMRSYHYYWCQHCQRTVRIASGILSEILLCPFCSCRLQYEFHA 59

Query: 59  SRPRLVSSSPA----AVESFPTPSGRFLDSLAQALDTPNNDGH--------NLHSWISLH 106
            R RLV +       A E         L    Q  D               N+ S +  H
Sbjct: 60  PRLRLVPTFTGLGVLAAELLEDVDVSLLPRRRQNTDLNGVLWGSEMRIPSINVPSGVGRH 119

Query: 107 FDEPTPPPPPPPPPQPM---------------IEYPMHDLQPDAAP-----------TPA 140
              P  P  P   P+ +               +   M +L  +               PA
Sbjct: 120 LLTPPRPGRPVAAPENVAVPRLDGSNFAIRDVLNEEMEELTHNEVTGENTQDDRPGPPPA 179

Query: 141 PVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYH 200
             SA+EAL  VR++     T      CCP+CKEE+R  ++V          E+PC HLYH
Sbjct: 180 APSAIEALPSVRLTP----THLRNDPCCPVCKEEYRAGEEVR---------EMPCNHLYH 226

Query: 201 SDCIVPWLRHYSTTCPVCRYELKDS 225
           SDCIVPWLR ++ +CPVCRYEL+ S
Sbjct: 227 SDCIVPWLRIHN-SCPVCRYELQAS 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

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	249
TAIR|locus:2199272	248	AT1G68180 [Arabidopsis thalian	0.220	0.221	0.614	6.1e-31
TAIR|locus:2195573	327	AT1G60360 [Arabidopsis thalian	0.345	0.262	0.386	2.8e-24
TAIR|locus:2102569	320	RZF1 "AT3G56580" [Arabidopsis	0.293	0.228	0.406	2.4e-20
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.337	0.256	0.402	3e-19
TAIR|locus:1006230278	199	AT3G10815 [Arabidopsis thalian	0.313	0.391	0.358	1.1e-15
DICTYBASE|DDB_G0280089	457	DDB_G0280089 "RING zinc finger	0.285	0.155	0.4	1.1e-15
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.281	0.177	0.416	2.3e-14
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.281	0.171	0.440	3.4e-14
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.285	0.216	0.345	1.7e-13
TAIR|locus:2063912	401	RHC2A "RING-H2 finger C2A" [Ar	0.321	0.199	0.393	3e-13

TAIR|locus:2199272 AT1G68180 [Arabidopsis thaliana (taxid:3702)]

 Score = 179 (68.1 bits), Expect = 6.1e-31, Sum P(2) = 6.1e-31
 Identities = 35/57 (61%), Positives = 40/57 (70%)

Query:     7 RPRVIVNGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL--ELDVSRP 61
             RPRVIVNGTRRTRTFHYF+C+ C RT R RS       CP CS ++ L  ELD+ RP
Sbjct:     6 RPRVIVNGTRRTRTFHYFYCRHCSRTIRLRSFGLYGPICPFCSREINLHDELDIMRP 62

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2195573 AT1G60360 [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 2.8e-24, Sum P(2) = 2.8e-24
 Identities = 39/101 (38%), Positives = 53/101 (52%)

Query:   124 IEYPMHDLQPDAAPTPAPVS--AVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXX 181
             +E  +  L  D  P P P S   + +L  V+I+    LT  N++  C +C EEF      
Sbjct:   181 LEQLIEQLTQDDRPGPPPASEPTINSLPSVKITPQ-HLT--NDMSQCTVCMEEFIVGGDA 237

Query:   182 XXXXXEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
                       ELPCKH+YH DCIVPWLR  + +CP+CR +L
Sbjct:   238 T---------ELPCKHIYHKDCIVPWLR-LNNSCPICRRDL 268

GO:0008270 "zinc ion binding" evidence=IEA;ISS

TAIR|locus:2102569 RZF1 "AT3G56580" [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 2.4e-20, Sum P(3) = 2.4e-20
 Identities = 35/86 (40%), Positives = 53/86 (61%)

Query:   137 PTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCK 196
             P PAP S+++AL  ++I++     +S++  C P+CK+EF                ++PC 
Sbjct:   158 PPPAPKSSIDALPTIKITQKH--LKSSDSHC-PVCKDEFELKSEAK---------QMPCH 205

Query:   197 HLYHSDCIVPWLRHYSTTCPVCRYEL 222
             H+YHSDCIVPWL  +++ CPVCR EL
Sbjct:   206 HIYHSDCIVPWLVQHNS-CPVCRKEL 230

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=ISS

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IEP

GO:1902006 "negative regulation of proline biosynthetic process" evidence=IMP

TAIR|locus:2058465 RHC1A "RING-H2 finger C1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 3.0e-19, Sum P(2) = 3.0e-19
 Identities = 39/97 (40%), Positives = 57/97 (58%)

Query:   137 PTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCK 196
             P PAP SA++AL  ++I++  +  RS++  C P+CK+EF                ++PC 
Sbjct:   162 PPPAPRSAIDALPTIKIAQ--RHLRSSDSNC-PVCKDEFELGSEAK---------QMPCN 209

Query:   197 HLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGDN 233
             H+YHSDCIVPWL  +++ CPVCR EL  +   S   N
Sbjct:   210 HIYHSDCIVPWLVQHNS-CPVCRQELPSASGPSSSQN 245

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0005618 "cell wall" evidence=IDA

TAIR|locus:1006230278 AT3G10815 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 1.1e-15, Sum P(2) = 1.1e-15
 Identities = 33/92 (35%), Positives = 52/92 (56%)

Query:   131 LQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMI 190
             LQ    P PA ++A+ +L++++I +   L        CP+C+++F               
Sbjct:    88 LQDRRGPPPASLAAINSLQKIKIRQK-HLGLD---PYCPVCQDQFEIGSDAR-------- 135

Query:   191 MELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
              ++PCKH+YHS+CI+PWL   +T CPVCR EL
Sbjct:   136 -KMPCKHIYHSECILPWLVQRNT-CPVCRKEL 165

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

DICTYBASE|DDB_G0280089 DDB_G0280089 "RING zinc finger-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 160 (61.4 bits), Expect = 1.1e-15, Sum P(2) = 1.1e-15
 Identities = 34/85 (40%), Positives = 49/85 (57%)

Query:   139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
             PA    +E LKR R+ ++       +V C  +CK+EF               +ELPC+HL
Sbjct:   331 PASKEEIEKLKRDRVDQTIV---DQKVDCA-VCKDEFKWGDDY---------IELPCQHL 377

Query:   199 YHSDCIVPWLRHYSTTCPVCRYELK 223
             YH +CI+PWL  +++ CPVCR+ELK
Sbjct:   378 YHPECILPWLEQHNS-CPVCRFELK 401

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

TAIR|locus:2075175 RDUF1 "RING and Domain of Unknown Function 1117 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 2.3e-14, Sum P(2) = 2.3e-14
 Identities = 35/84 (41%), Positives = 45/84 (53%)

Query:   139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
             PA  SA+E+L RV IS+      +N    C +C E F                E+PCKH+
Sbjct:   190 PASKSAIESLPRVEISDCHTKAEAN----CAVCTEVFEAGIEGR---------EMPCKHI 236

Query:   199 YHSDCIVPWLRHYSTTCPVCRYEL 222
             +H DCIVPWL     +CPVCR+EL
Sbjct:   237 FHGDCIVPWLS-IRNSCPVCRFEL 259

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2148318 RDUF2 "RING and Domain of Unknown Function 1117 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 3.4e-14, Sum P(2) = 3.4e-14
 Identities = 37/84 (44%), Positives = 47/84 (55%)

Query:   139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
             PA  SA+E+L RV IS+    + +N    C +C E F           E    E+PCKHL
Sbjct:   174 PASKSAIESLPRVEISDCHIGSEAN----CAVCTEIFET---------ETEAREMPCKHL 220

Query:   199 YHSDCIVPWLRHYSTTCPVCRYEL 222
             +H DCIVPWL     +CPVCR+EL
Sbjct:   221 FHDDCIVPWLS-IRNSCPVCRFEL 243

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 1.7e-13, Sum P(2) = 1.7e-13
 Identities = 29/84 (34%), Positives = 50/84 (59%)

Query:   139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
             PA  SA++AL  V++++    +  N+   C +C +EF              + ++PCKH+
Sbjct:   190 PASKSAIDALPTVKVTKDMLKSEMNQ---CAVCMDEFEDGSD---------VKQMPCKHV 237

Query:   199 YHSDCIVPWLRHYSTTCPVCRYEL 222
             +H DC++PWL  +++ CPVCR+EL
Sbjct:   238 FHQDCLLPWLELHNS-CPVCRFEL 260

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0010200 "response to chitin" evidence=RCA

TAIR|locus:2063912 RHC2A "RING-H2 finger C2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 3.0e-13, Sum P(2) = 3.0e-13
 Identities = 37/94 (39%), Positives = 50/94 (53%)

Query:   139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
             PA  SA+EAL  + I + T L   ++  C  +CKE F                E+PC H+
Sbjct:   174 PASKSAIEALPLIEI-DPTHLLSDSQSHCA-VCKENFVLKSSAR---------EMPCNHI 222

Query:   199 YHSDCIVPWLRHYSTTCPVCRYEL--KDSIIGSG 230
             YH DCI+PWL     +CPVCR+EL  +D   G+G
Sbjct:   223 YHPDCILPWLA-IRNSCPVCRHELPAEDLTDGTG 255

GO:0008270 "zinc ion binding" evidence=IEA;ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00121249 hypothetical protein (313 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	249
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-10
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-08
smart00184	40	smart00184, RING, Ring finger	4e-07
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	7e-07
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.001

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

 Score = 54.0 bits (130), Expect = 3e-10
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 11/56 (19%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
            CPIC EEFR         + V++  LPC H++   CI  WL+    TCP+CR  +
Sbjct: 1   ECPICLEEFR---------EPVVL--LPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 22/52 (42%), Positives = 31/52 (59%), Gaps = 10/52 (19%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
           CPIC +EF   ++V         + LPC H++H +C+  WLR  S TCP+CR
Sbjct: 3   CPICLDEFEPGEEV---------VVLPCGHVFHKECLDKWLRS-SNTCPLCR 44

Length = 46

>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 164 EVQCCPICKEEF-RVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
           E   C IC+  F     +     D+  ++   C H +H  CI  WL+    TCP+CR
Sbjct: 18  EDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKT-RNTCPLCR 73

There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. Length = 73

>gnl|CDD|214546 smart00184, RING, Ring finger

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 11/51 (21%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218
           CPIC EE+               + LPC H +   CI  WL   + TCP+C
Sbjct: 1   CPICLEEY-----------LKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s). Length = 40

>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 49.2 bits (117), Expect = 7e-07
 Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 9/55 (16%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           C IC   F   D +           LPC H +H  C+  WL  YS  CPVCR  +
Sbjct: 326 CAICMSNFIKNDRL---------RVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 23/51 (45%), Positives = 27/51 (52%), Gaps = 11/51 (21%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC 218
           CPIC EE           D V I  LPC HL+ S CI+ WL   + TCP+C
Sbjct: 1   CPICLEEP---------KDPVTI--LPCGHLFCSKCILSWLESGNVTCPLC 40

The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Length = 40

>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 12/54 (22%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220
            CPIC +  R             ++  PC H++  +CI+ +L+   + CP+CR 
Sbjct: 4   ECPICLDLLRD-----------PVVLTPCGHVFCRECILRYLKK-KSKCPICRT 45

Length = 45

>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 41.6 bits (97), Expect = 3e-04
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 18/62 (29%)

Query: 168  CPICKEEFRVRDDVDDDSDEVMIMELP------CKHLYHSDCIVPWLRHY-STTCPVCRY 220
            C IC   + V D VD          LP      CK+ +H+ C+  W      + CP+CR 
Sbjct: 1472 CAIC---YSVLDMVDR--------SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRS 1520

Query: 221  EL 222
            E+
Sbjct: 1521 EI 1522

Length = 1525

>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 23/63 (36%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 158 QLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIME-LPCKHLYHSDCIVPWLRHYSTTCP 216
           QLT S+    C IC +E    D         M  + LPC H+ H  C+  WL     TCP
Sbjct: 282 QLTNSDRT--CTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCP 338

Query: 217 VCR 219
           +CR
Sbjct: 339 ICR 341

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	249
PF14369	35	zf-RING_3: zinc-finger	99.64
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.56
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.54
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.33
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.31
PHA02929	238	N1R/p28-like protein; Provisional	99.26
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.05
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.05
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.01
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.99
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.97
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.95
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.94
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.88
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.85
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.84
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.8
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.78
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.75
PF14634	44	zf-RING_5: zinc-RING finger domain	98.7
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.68
PHA02926	242	zinc finger-like protein; Provisional	98.67
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.66
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.59
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.51
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.31
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.31
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.29
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.29
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.27
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.26
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.18
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.17
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.13
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.0
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.84
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.69
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.67
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.64
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.61
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.6
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.56
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.55
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.21
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.14
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.1
KOG4445	368	consensus Uncharacterized conserved protein, conta	96.97
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.96
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	96.93
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	96.88
KOG2660	331	consensus Locus-specific chromosome binding protei	96.84
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.83
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.31
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.27
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.08
COG5152	259	Uncharacterized conserved protein, contains RING a	96.04
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.02
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.98
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.91
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.74
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.63
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.55
PHA03096	284	p28-like protein; Provisional	95.45
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.29
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.1
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.08
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	94.85
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.5
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.48
KOG1002	791	consensus Nucleotide excision repair protein RAD16	94.23
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.98
PHA02862	156	5L protein; Provisional	93.92
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.82
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.63
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	93.55
KOG3039	303	consensus Uncharacterized conserved protein [Funct	93.38
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.25
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	93.15
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	93.01
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.63
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.34
KOG4739	233	consensus Uncharacterized protein involved in syna	92.25
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	91.59
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	91.35
PF04641	260	Rtf2: Rtf2 RING-finger	91.13
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	90.76
KOG1940	276	consensus Zn-finger protein [General function pred	90.46
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	90.14
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	89.49
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	88.97
KOG1001	674	consensus Helicase-like transcription factor HLTF/	88.92
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.85
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.72
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	88.67
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	88.51
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	88.06
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	86.68
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	86.6
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	86.35
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	85.64
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	85.46
COG5175	480	MOT2 Transcriptional repressor [Transcription]	85.37
KOG0298	1394	consensus DEAD box-containing helicase-like transc	84.97
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	84.92
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	84.9
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	84.85
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	84.7
KOG3002	299	consensus Zn finger protein [General function pred	83.85
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	82.68
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	82.02
PF13248	26	zf-ribbon_3: zinc-ribbon domain	81.98
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	81.9
PRK06266	178	transcription initiation factor E subunit alpha; V	81.32

>PF14369 zf-RING_3: zinc-finger

Probab=99.64  E-value=1.2e-16  Score=101.84  Aligned_cols=35  Identities=29%  Similarity=0.869  Sum_probs=30.8

Q ss_pred             CeeeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030           22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL   56 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl   56 (249)
                      ++||||+|+|+|++....+++++||+|+|||||||
T Consensus         1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            47999999999999866556677999999999997

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.56  E-value=1.4e-15  Score=140.90  Aligned_cols=81  Identities=26%  Similarity=0.610  Sum_probs=67.2

Q ss_pred             CCCCCCHHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCC
Q 041030          136 APTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTC  215 (249)
Q Consensus       136 ~~~pas~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sC  215 (249)
                      .-..+.+..++++|..+++......   ....|+||||+|+.|++         ++.|||+|.||..||++||...+..|
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~---~~~~CaIClEdY~~Gdk---------lRiLPC~H~FH~~CIDpWL~~~r~~C  270 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDED---ATDTCAICLEDYEKGDK---------LRILPCSHKFHVNCIDPWLTQTRTFC  270 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccC---CCceEEEeecccccCCe---------eeEecCCCchhhccchhhHhhcCccC
Confidence            4456788999999999988765433   12599999999999999         99999999999999999999933559


Q ss_pred             ccccccccCCCCC
Q 041030          216 PVCRYELKDSIIG  228 (249)
Q Consensus       216 PvCR~~l~~~~~~  228 (249)
                      |+||+++.+..-.
T Consensus       271 PvCK~di~~~~~~  283 (348)
T KOG4628|consen  271 PVCKRDIRTDSGS  283 (348)
T ss_pred             CCCCCcCCCCCCC
Confidence            9999998765443

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=99.54  E-value=2.8e-15  Score=99.66  Aligned_cols=43  Identities=49%  Similarity=1.292  Sum_probs=40.1

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      .|+||+++|..++.         ++.++|+|+||.+||.+|++. +++||+||
T Consensus         2 ~C~IC~~~~~~~~~---------~~~l~C~H~fh~~Ci~~~~~~-~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEK---------VVKLPCGHVFHRSCIKEWLKR-NNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSC---------EEEETTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred             CCcCCChhhcCCCe---------EEEccCCCeeCHHHHHHHHHh-CCcCCccC
Confidence            79999999998877         999999999999999999999 99999997

...

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.33  E-value=4e-13  Score=99.01  Aligned_cols=55  Identities=35%  Similarity=0.799  Sum_probs=40.2

Q ss_pred             CccccccccccccccCCCCCCCC-ccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSD-EVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~-~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      .+..|+||++.|.......+... +..++..+|+|.||..||.+||+. +++||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-NNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence            35569999999955443222222 233556679999999999999999 99999998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=99.31  E-value=8.7e-13  Score=119.51  Aligned_cols=52  Identities=38%  Similarity=0.888  Sum_probs=48.2

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ..+|+|||++|..++.         ++.|||+|.||..||.+|+..+++.||+||.++|+.
T Consensus       323 GveCaICms~fiK~d~---------~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         323 GVECAICMSNFIKNDR---------LRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             CceEEEEhhhhcccce---------EEEeccCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            5799999999998887         999999999999999999996699999999999873

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.26  E-value=4.1e-12  Score=113.01  Aligned_cols=78  Identities=21%  Similarity=0.429  Sum_probs=56.5

Q ss_pred             CCHHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          140 APVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       140 as~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      .++..++.+|.+......... ..++..|+||++.+......    ..+.++.++|+|.||..||.+|++. +.+||+||
T Consensus       150 ~~~~~i~~lp~vl~~~e~~~~-~~~~~eC~ICle~~~~~~~~----~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR  223 (238)
T PHA02929        150 NYKKFLKTIPSVLSEYEKLYN-RSKDKECAICMEKVYDKEIK----NMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCR  223 (238)
T ss_pred             hhHHHHHhcchhhhhhhhhhc-CCCCCCCccCCcccccCccc----cccceecCCCCCcccHHHHHHHHhc-CCCCCCCC
Confidence            378889999988654433322 23468999999998754310    0001344569999999999999999 99999999


Q ss_pred             cccc
Q 041030          220 YELK  223 (249)
Q Consensus       220 ~~l~  223 (249)
                      ..+.
T Consensus       224 ~~~~  227 (238)
T PHA02929        224 TPFI  227 (238)
T ss_pred             CEee
Confidence            9875

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=99.05  E-value=1.1e-10  Score=79.44  Aligned_cols=46  Identities=37%  Similarity=0.907  Sum_probs=40.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      +..|.||++....            +..+||+|. |+..|+..|++. ...||+||+++.
T Consensus         2 ~~~C~iC~~~~~~------------~~~~pCgH~~~C~~C~~~~~~~-~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD------------VVLLPCGHLCFCEECAERLLKR-KKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS------------EEEETTCEEEEEHHHHHHHHHT-TSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc------------eEEeCCCChHHHHHHhHHhccc-CCCCCcCChhhc
Confidence            5699999999776            889999999 999999999998 999999999874

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.05  E-value=1.2e-10  Score=100.39  Aligned_cols=51  Identities=27%  Similarity=0.654  Sum_probs=42.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---------------CCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---------------STTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---------------~~sCPvCR~~l~~~  225 (249)
                      .++.+|+||++.+..            .+.++|+|+||+.||..|+...               ...||+||..+...
T Consensus        16 ~~~~~CpICld~~~d------------PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         16 GGDFDCNICLDQVRD------------PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CCccCCccCCCcCCC------------cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            357899999999876            6678899999999999998631               35799999999653

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Probab=99.01  E-value=3e-10  Score=73.43  Aligned_cols=45  Identities=47%  Similarity=1.116  Sum_probs=36.8

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      +|+||++.+..  .         +..++|+|.||..|+..|++.++..||+||..+
T Consensus         1 ~C~iC~~~~~~--~---------~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE--P---------VVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC--c---------eEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            59999999832  2         445559999999999999997567799999864

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]

Probab=98.99  E-value=1.6e-10  Score=104.28  Aligned_cols=51  Identities=27%  Similarity=0.744  Sum_probs=45.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      .....|.|||+....            ..-+||||+||+.||..|... +..||+||..+.+..
T Consensus       237 ~a~~kC~LCLe~~~~------------pSaTpCGHiFCWsCI~~w~~e-k~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN------------PSATPCGHIFCWSCILEWCSE-KAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCCC------------CCcCcCcchHHHHHHHHHHcc-ccCCCcccccCCCcc
Confidence            446899999999888            455999999999999999999 999999999987654

>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

Probab=98.97  E-value=3.4e-10  Score=105.23  Aligned_cols=77  Identities=25%  Similarity=0.561  Sum_probs=53.3

Q ss_pred             CHHHHHhhhhheeccccccccccCcccccccccc-ccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          141 PVSAVEALKRVRISESTQLTRSNEVQCCPICKEE-FRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       141 s~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~-f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      .|..-+.++++.....     .+.+..|.||||+ |..+.+.-.-.-+-..++|||||++|.+|+.-|+.. .++||+||
T Consensus       268 ~kdl~~~~~t~t~eql-----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER-qQTCPICr  341 (491)
T COG5243         268 TKDLNAMYPTATEEQL-----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCPICR  341 (491)
T ss_pred             hhHHHhhcchhhhhhh-----cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh-ccCCCccc
Confidence            3444444555443332     2447899999999 554422111112233689999999999999999999 99999999


Q ss_pred             cccc
Q 041030          220 YELK  223 (249)
Q Consensus       220 ~~l~  223 (249)
                      .++.
T Consensus       342 ~p~i  345 (491)
T COG5243         342 RPVI  345 (491)
T ss_pred             Cccc
Confidence            9964

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=98.95  E-value=3.7e-10  Score=73.12  Aligned_cols=39  Identities=41%  Similarity=1.100  Sum_probs=33.8

Q ss_pred             cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC  218 (249)
                      |+||++.+...           ++.++|||+|+..||..|++. +.+||+|
T Consensus         1 C~iC~~~~~~~-----------~~~~~CGH~fC~~C~~~~~~~-~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDP-----------VVVTPCGHSFCKECIEKYLEK-NPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSE-----------EEECTTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred             CCCCCCcccCc-----------CEECCCCCchhHHHHHHHHHC-cCCCcCC
Confidence            89999998872           578899999999999999999 9999998

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.94  E-value=4.3e-10  Score=98.78  Aligned_cols=51  Identities=29%  Similarity=0.638  Sum_probs=43.0

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC--CCCCccccccccCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELKDSI  226 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~  226 (249)
                      ..++|.||||.-++            .+++.|||+||+.||-+||...  ++.|||||.++..+.
T Consensus        46 ~~FdCNICLd~akd------------PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   46 GFFDCNICLDLAKD------------PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CceeeeeeccccCC------------CEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            47999999999777            5566699999999999999985  446999999886544

>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger

Probab=98.88  E-value=1.6e-09  Score=81.95  Aligned_cols=60  Identities=28%  Similarity=0.588  Sum_probs=42.9

Q ss_pred             CccccccccccccccCCCCCCC-CccceEEeccCCccChhhHHHHHhhC--CCCCcccccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDS-DEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~-~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~  223 (249)
                      ++..|.||...|...-....-+ ++-.++.-.|+|.||..||.+||...  +..||+||++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            4789999999998543222222 12123333499999999999999973  568999999764

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A

Probab=98.85  E-value=1.8e-09  Score=71.45  Aligned_cols=39  Identities=36%  Similarity=0.928  Sum_probs=31.1

Q ss_pred             cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC---CCCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS---TTCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~---~sCPvC  218 (249)
                      |+||++.|..            .+.|+|||.|+..||..|++..+   ..||+|
T Consensus         1 CpiC~~~~~~------------Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD------------PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS------------EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC------------ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999998            88999999999999999998742   369988

>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

Probab=98.84  E-value=2.1e-09  Score=79.92  Aligned_cols=63  Identities=21%  Similarity=0.453  Sum_probs=50.7

Q ss_pred             ccCccccccccccccccCCCCCC---CCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          162 SNEVQCCPICKEEFRVRDDVDDD---SDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       162 ~~~~~~C~ICle~f~~~~~~~~~---~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ......|+||...+..-....+.   +.++.++... |+|.||..||.+||.. ++.||++|++..-.
T Consensus        17 di~id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~T-k~~CPld~q~w~~~   83 (88)
T COG5194          17 DIPIDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDT-KGVCPLDRQTWVLA   83 (88)
T ss_pred             ccccchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhh-CCCCCCCCceeEEe
Confidence            33457999999998776555554   4556777887 9999999999999999 99999999987543

>smart00184 RING Ring finger

Probab=98.80  E-value=3.7e-09  Score=65.92  Aligned_cols=39  Identities=46%  Similarity=1.166  Sum_probs=33.5

Q ss_pred             cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvC  218 (249)
                      |+||++....            ++.++|+|.||..|+..|++.++..||+|
T Consensus         1 C~iC~~~~~~------------~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD------------PVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC------------cEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998433            78899999999999999999437789997

E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

>smart00504 Ubox Modified RING finger domain

Probab=98.78  E-value=5.4e-09  Score=73.60  Aligned_cols=46  Identities=30%  Similarity=0.452  Sum_probs=41.4

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ..|+||++.+..            .+.++|||+|+..||..|++. +..||+|+..+..
T Consensus         2 ~~Cpi~~~~~~~------------Pv~~~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKD------------PVILPSGQTYERRAIEKWLLS-HGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCC------------CEECCCCCEEeHHHHHHHHHH-CCCCCCCcCCCCh
Confidence            579999999887            667899999999999999999 9999999988743

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.75  E-value=5.8e-09  Score=67.76  Aligned_cols=40  Identities=45%  Similarity=1.140  Sum_probs=34.3

Q ss_pred             cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHh-hCCCCCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR-HYSTTCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~-~~~~sCPvC  218 (249)
                      |+||++.+...           +..++|+|.||..||..|++ .+...||+|
T Consensus         1 C~iC~~~~~~~-----------~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP-----------VILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE-----------EEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC-----------CEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998873           34788999999999999999 337789998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.70  E-value=1e-08  Score=68.14  Aligned_cols=44  Identities=27%  Similarity=0.699  Sum_probs=37.2

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY  220 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~  220 (249)
                      .|+||++.+.....         ...++|+|+|+..||..+... ...||+||+
T Consensus         1 ~C~~C~~~~~~~~~---------~~l~~CgH~~C~~C~~~~~~~-~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERR---------PRLTSCGHIFCEKCLKKLKGK-SVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCC---------eEEcccCCHHHHHHHHhhcCC-CCCCcCCCC
Confidence            59999999944334         888999999999999999855 779999985

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.68  E-value=8e-09  Score=87.64  Aligned_cols=51  Identities=27%  Similarity=0.709  Sum_probs=43.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ++.+.|+|||+.+....          .+...|||+||+.||..-++. ...||+||..|..
T Consensus       129 ~~~~~CPiCl~~~sek~----------~vsTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKV----------PVSTKCGHVFCSQCIKDALKN-TNKCPTCRKKITH  179 (187)
T ss_pred             ccccCCCceecchhhcc----------ccccccchhHHHHHHHHHHHh-CCCCCCcccccch
Confidence            34689999999998753          345679999999999999999 9999999987644

>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.68  E-value=6.1e-09  Score=102.73  Aligned_cols=53  Identities=36%  Similarity=0.901  Sum_probs=45.6

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      .+..|+||+|.+..+..+.       +++|+|+|+||..|+..|++. .++||+||..+-.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~-------~~rL~C~Hifh~~CL~~W~er-~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNIT-------PKRLPCGHIFHDSCLRSWFER-QQTCPTCRTVLYD  342 (543)
T ss_pred             cCCeeeeechhhccccccc-------cceeecccchHHHHHHHHHHH-hCcCCcchhhhhc
Confidence            3789999999998864422       678999999999999999999 9999999995543

>PHA02926 zinc finger-like protein; Provisional

Probab=98.67  E-value=1e-08  Score=90.00  Aligned_cols=56  Identities=29%  Similarity=0.669  Sum_probs=40.0

Q ss_pred             CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-----CCCCcccccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-----STTCPVCRYELK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-----~~sCPvCR~~l~  223 (249)
                      .+.+|+||||.......    ..++....|+ |+|.||..||..|.+..     ..+||+||..+.
T Consensus       169 kE~eCgICmE~I~eK~~----~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        169 KEKECGICYEVVYSKRL----ENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             CCCCCccCccccccccc----cccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            46899999998754211    0111244564 99999999999999861     346999999764

>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]

Probab=98.66  E-value=5.2e-09  Score=81.37  Aligned_cols=75  Identities=20%  Similarity=0.392  Sum_probs=56.7

Q ss_pred             hhhheeccccccccccCccccccccccccccCCCCCCC----CccceEEec-cCCccChhhHHHHHhhCCCCCccccccc
Q 041030          148 LKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDS----DEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       148 lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~----~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      +...+.+.-.+.........|+||..-+.+-..+.+..    .++.++... |.|.||..||.+||+. ++.||+|.++-
T Consensus        29 F~lKKWnAvAlWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlkt-r~vCPLdn~eW  107 (114)
T KOG2930|consen   29 FELKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKT-RNVCPLDNKEW  107 (114)
T ss_pred             eEEeeeeeeeeeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhh-cCcCCCcCcce
Confidence            44445555556666666789999998876554444332    457788888 9999999999999999 99999998764


Q ss_pred             c
Q 041030          223 K  223 (249)
Q Consensus       223 ~  223 (249)
                      .
T Consensus       108 ~  108 (114)
T KOG2930|consen  108 V  108 (114)
T ss_pred             e
Confidence            3

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.59  E-value=2.6e-08  Score=94.67  Aligned_cols=51  Identities=35%  Similarity=0.688  Sum_probs=44.2

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      ....|+||++.|..            .+.++|+|.||..||..|+.. ...||+||..+....+
T Consensus        25 ~~l~C~IC~d~~~~------------PvitpCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~~~L   75 (397)
T TIGR00599        25 TSLRCHICKDFFDV------------PVLTSCSHTFCSLCIRRCLSN-QPKCPLCRAEDQESKL   75 (397)
T ss_pred             cccCCCcCchhhhC------------ccCCCCCCchhHHHHHHHHhC-CCCCCCCCCccccccC
Confidence            37899999999976            567899999999999999998 8899999998865433

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.51  E-value=2.4e-08  Score=73.74  Aligned_cols=63  Identities=24%  Similarity=0.523  Sum_probs=46.2

Q ss_pred             cccCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CCCCcccccccc
Q 041030          161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--STTCPVCRYELK  223 (249)
Q Consensus       161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~sCPvCR~~l~  223 (249)
                      ....+.+|-||.-.|....-....+-+....++. |.|.||..||.+|+...  ...||+||++..
T Consensus        16 W~~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   16 WDAPDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             EcCCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3345679999999997654433333333344566 99999999999999984  346999999763

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=2.5e-07  Score=82.95  Aligned_cols=51  Identities=29%  Similarity=0.690  Sum_probs=43.6

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHH-HHhhCCCC-CccccccccCCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVP-WLRHYSTT-CPVCRYELKDSII  227 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~-WL~~~~~s-CPvCR~~l~~~~~  227 (249)
                      .+..|.||++..+.            ...++|||+||..||.. |=+. +.. ||+||+.+.+..+
T Consensus       214 ~d~kC~lC~e~~~~------------ps~t~CgHlFC~~Cl~~~~t~~-k~~~CplCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEV------------PSCTPCGHLFCLSCLLISWTKK-KYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCC------------cccccccchhhHHHHHHHHHhh-ccccCchhhhhccchhh
Confidence            47899999999888            66789999999999999 9777 665 9999998866543

>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=2.5e-07  Score=88.93  Aligned_cols=61  Identities=31%  Similarity=0.768  Sum_probs=45.6

Q ss_pred             CccccccccccccccCCCCCCC-C----ccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDS-D----EVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~-~----~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...+|+|||..+..-....+-- .    .+-.+.+||.|+||..|+..|....+-.||+||..|++
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3679999999887654322111 1    12355679999999999999999636699999999975

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis

Probab=98.29  E-value=5.2e-07  Score=66.22  Aligned_cols=49  Identities=35%  Similarity=0.526  Sum_probs=40.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      .+.|+|+.+-+.+            .+.+++||.|...||..||..++..||+|+..|...
T Consensus         4 ~f~CpIt~~lM~d------------PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    4 EFLCPITGELMRD------------PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGB-TTTSSB-SS------------EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             ccCCcCcCcHhhC------------ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            6799999999998            888999999999999999998778999999888654

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.29  E-value=1.9e-07  Score=83.93  Aligned_cols=64  Identities=23%  Similarity=0.546  Sum_probs=47.1

Q ss_pred             cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccCCC
Q 041030          161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKDSI  226 (249)
Q Consensus       161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~  226 (249)
                      +..++..|+||-..+-...+  +++--+-.-+|.|+|+||..||..|--.| +.+||.|+..+....
T Consensus       220 khl~d~vCaVCg~~~~~s~~--eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  220 KHLSDSVCAVCGQQIDVSVD--EEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCCcchhHhhcchheeecc--hhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            34458899999998876552  01100125688999999999999998877 678999988775443

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A

Probab=98.27  E-value=5.1e-07  Score=60.06  Aligned_cols=40  Identities=40%  Similarity=0.973  Sum_probs=23.2

Q ss_pred             cccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---CCCCc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---STTCP  216 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~~sCP  216 (249)
                      |+||+| |...+-        ..+.|+|||+|+.+||.+|++.+   ...||
T Consensus         1 CpIc~e-~~~~~n--------~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEEN--------PPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS---------EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCC--------CCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 754332        17889999999999999999962   23566

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.27  E-value=4.1e-07  Score=87.91  Aligned_cols=49  Identities=29%  Similarity=0.695  Sum_probs=40.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----CCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~~l~~~  225 (249)
                      +..|+|||+....            +..+.|||+||..||..++..+    ..+||+||..|-..
T Consensus       186 ~~~CPICL~~~~~------------p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k  238 (513)
T KOG2164|consen  186 DMQCPICLEPPSV------------PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLK  238 (513)
T ss_pred             CCcCCcccCCCCc------------ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence            5799999999887            5556699999999999987773    45899999888653

>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins

Probab=98.26  E-value=6.9e-07  Score=60.97  Aligned_cols=43  Identities=28%  Similarity=0.862  Sum_probs=33.4

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCcccc
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCR  219 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR  219 (249)
                      .|.||++ ....+.         ...+||.     |.+|..|+.+|+... +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~---------~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGD---------PLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCC---------eeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 333334         6678985     899999999999773 45899995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]

Probab=98.18  E-value=3.6e-07  Score=84.53  Aligned_cols=50  Identities=34%  Similarity=0.709  Sum_probs=45.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      ...|-||.+-|..            .+.+||+|.||+-||...|.. +..||.|+.++....+
T Consensus        23 lLRC~IC~eyf~i------------p~itpCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   23 LLRCGICFEYFNI------------PMITPCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHhHHHHHhcC------------ceeccccchHHHHHHHHHhcc-CCCCCceecccchhhh
Confidence            6799999999998            788999999999999999999 9999999998865544

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=98.17  E-value=6.1e-07  Score=85.48  Aligned_cols=53  Identities=34%  Similarity=0.952  Sum_probs=42.6

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +..+|+||||.+-....        +++.+.|.|.||..|+..|...   +|||||+-..+...
T Consensus       174 ELPTCpVCLERMD~s~~--------gi~t~~c~Hsfh~~cl~~w~~~---scpvcR~~q~p~~v  226 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTT--------GILTILCNHSFHCSCLMKWWDS---SCPVCRYCQSPSVV  226 (493)
T ss_pred             cCCCcchhHhhcCcccc--------ceeeeecccccchHHHhhcccC---cChhhhhhcCcchh
Confidence            46799999999876553        2677779999999999999554   99999998774433

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.13  E-value=1.8e-06  Score=79.45  Aligned_cols=56  Identities=25%  Similarity=0.460  Sum_probs=41.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +..|+||+..-......      . +...+|||.||..||...+..+...||+|+..|.....
T Consensus         3 ~~~CP~Ck~~~y~np~~------k-l~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~f   58 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSL------K-LMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNF   58 (309)
T ss_pred             CCCCCcCCCCCccCccc------c-cccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhc
Confidence            56899999975443320      0 22237999999999999776657789999998876543

All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.08  E-value=9.9e-07  Score=76.57  Aligned_cols=43  Identities=42%  Similarity=0.891  Sum_probs=38.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      +...|+||++.|..            .+.++|+|.||..||..|+.. ...||.||
T Consensus        12 ~~~~C~iC~~~~~~------------p~~l~C~H~~c~~C~~~~~~~-~~~Cp~cr   54 (386)
T KOG2177|consen   12 EELTCPICLEYFRE------------PVLLPCGHNFCRACLTRSWEG-PLSCPVCR   54 (386)
T ss_pred             ccccChhhHHHhhc------------CccccccchHhHHHHHHhcCC-CcCCcccC
Confidence            47899999999998            567999999999999999884 77899999

>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=98.01  E-value=6.1e-07  Score=83.30  Aligned_cols=51  Identities=33%  Similarity=0.634  Sum_probs=44.2

Q ss_pred             ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +..|+|||+-++.            .+..+ |.|.||.+||..-+..++++||.||+.+.....
T Consensus        43 ~v~c~icl~llk~------------tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   43 QVICPICLSLLKK------------TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             hhccHHHHHHHHh------------hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            7899999999987            44454 999999999999999999999999998865443

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Probab=98.00  E-value=2.6e-06  Score=77.54  Aligned_cols=49  Identities=33%  Similarity=0.615  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      ...|-||.+.|..            ...++|||.||+-||...|.. +..||+||.+.....
T Consensus        25 ~lrC~IC~~~i~i------------p~~TtCgHtFCslCIR~hL~~-qp~CP~Cr~~~~esr   73 (391)
T COG5432          25 MLRCRICDCRISI------------PCETTCGHTFCSLCIRRHLGT-QPFCPVCREDPCESR   73 (391)
T ss_pred             HHHhhhhhheeec------------ceecccccchhHHHHHHHhcC-CCCCccccccHHhhh
Confidence            5799999999998            667899999999999999999 999999999875443

>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=97.84  E-value=4.6e-06  Score=85.44  Aligned_cols=55  Identities=25%  Similarity=0.711  Sum_probs=40.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-CCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-STTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-~~sCPvCR~~l~  223 (249)
                      .+-..|+||...+..-+.      .-.-.+-+ |+|.||..|+.+|++.+ ++.||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vdr------~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDR------SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhc------cCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            346899999998763111      00022334 99999999999999985 668999998875

>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A

Probab=97.69  E-value=1.1e-05  Score=58.86  Aligned_cols=54  Identities=19%  Similarity=0.419  Sum_probs=24.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe--ccCCccChhhHHHHHhhC----------CCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--PCKHLYHSDCIVPWLRHY----------STTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~WL~~~----------~~sCPvCR~~l~~  224 (249)
                      +..|.||++.+......      ..++--  .|+..||..|+..||..-          ...||.|+.+|.-
T Consensus         2 ~~~C~IC~~~~~~~~~~------p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEI------PDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----------B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCc------CceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            46899999987632210      002222  399999999999999852          1259999998853

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.67  E-value=1.6e-05  Score=72.64  Aligned_cols=56  Identities=25%  Similarity=0.419  Sum_probs=45.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCCCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGSGGD  232 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~~~~~  232 (249)
                      ...|+||+..-..            .+.|+|+|.||..||.--...+...|+|||++++...+.-...
T Consensus         7 ~~eC~IC~nt~n~------------Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~~~psl   62 (324)
T KOG0824|consen    7 KKECLICYNTGNC------------PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTIDFEPSL   62 (324)
T ss_pred             CCcceeeeccCCc------------CccccccchhhhhhhcchhhcCCCCCceecCCCCcchhcchhh
Confidence            4589999998776            6679999999999998866664778999999998877654433

>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.64  E-value=3.2e-05  Score=73.19  Aligned_cols=50  Identities=34%  Similarity=0.859  Sum_probs=40.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCcccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYE  221 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~  221 (249)
                      ..+|+||++.++.....       ..+.+.|+|.|-.+||.+||.+. ...||.|..+
T Consensus         4 g~tcpiclds~~~~g~h-------r~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNH-------RIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             cccCceeeeeeeecCce-------EEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            57999999999887652       26777799999999999999642 4579999654

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=97.61  E-value=1.1e-05  Score=57.98  Aligned_cols=44  Identities=27%  Similarity=0.680  Sum_probs=23.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      ...|++|.+-+...           |....|.|+|++.||..-+..   .||+|+.+.
T Consensus         7 lLrCs~C~~~l~~p-----------v~l~~CeH~fCs~Ci~~~~~~---~CPvC~~Pa   50 (65)
T PF14835_consen    7 LLRCSICFDILKEP-----------VCLGGCEHIFCSSCIRDCIGS---ECPVCHTPA   50 (65)
T ss_dssp             TTS-SSS-S--SS------------B---SSS--B-TTTGGGGTTT---B-SSS--B-
T ss_pred             hcCCcHHHHHhcCC-----------ceeccCccHHHHHHhHHhcCC---CCCCcCChH
Confidence            57899999998872           334459999999999885544   599998765

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=97.60  E-value=1.1e-05  Score=81.33  Aligned_cols=54  Identities=26%  Similarity=0.507  Sum_probs=47.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG  228 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~  228 (249)
                      ...|+||+..|.++..         ....+|+|+||..||..|-+. .++||+||.++....+.
T Consensus       123 ~~~CP~Ci~s~~DqL~---------~~~k~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~v~V~  176 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLE---------ESEKHTAHYFCEECVGSWSRC-AQTCPVDRGEFGEVKVL  176 (1134)
T ss_pred             hhhhhHHHHHHHHHhh---------ccccccccccHHHHhhhhhhh-cccCchhhhhhheeeee
Confidence            5789999999988876         667789999999999999999 99999999998654443

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.56  E-value=4.7e-05  Score=71.00  Aligned_cols=49  Identities=33%  Similarity=0.744  Sum_probs=41.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      +....|-|||.+-.+            ++.|||.|+ -|+.|.+..--+ ++.||+||+.+..
T Consensus       288 ~~gkeCVIClse~rd------------t~vLPCRHLCLCs~Ca~~Lr~q-~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD------------TVVLPCRHLCLCSGCAKSLRYQ-TNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc------------eEEecchhhehhHhHHHHHHHh-hcCCCccccchHh
Confidence            346899999999888            899999998 588998886656 8899999998854

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.55  E-value=3.1e-05  Score=72.89  Aligned_cols=53  Identities=23%  Similarity=0.764  Sum_probs=39.4

Q ss_pred             cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CCCCccccccccCCCC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--STTCPVCRYELKDSII  227 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~~  227 (249)
                      ..|.||.+-+-....         +.-+. |||+||..|+..|+...  +..||+||-.++...+
T Consensus         5 A~C~Ic~d~~p~~~~---------l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~   60 (465)
T KOG0827|consen    5 AECHICIDGRPNDHE---------LGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHV   60 (465)
T ss_pred             ceeeEeccCCccccc---------cccccchhhHHHHHHHHHHHccCCccCCCCceeecccceee
Confidence            589999555544444         66666 99999999999999984  3479999965654433

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.21  E-value=0.00014  Score=68.18  Aligned_cols=56  Identities=30%  Similarity=0.640  Sum_probs=40.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC------CCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY------STTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~------~~sCPvCR~~l~~  224 (249)
                      .+..|.||++.......     .+.....|| |.|.||..||..|-...      .++||.||....-
T Consensus       160 ~~k~CGICme~i~ek~~-----~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~  222 (344)
T KOG1039|consen  160 SEKECGICMETINEKAA-----SERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF  222 (344)
T ss_pred             ccccceehhhhccccch-----hhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence            37899999998766431     122245566 99999999999998442      3689999986543

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=97.14  E-value=0.00021  Score=68.25  Aligned_cols=47  Identities=30%  Similarity=0.668  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ++.|.||+.-|..            .+.+||||.||..||.+-+.. +..||.||.++..
T Consensus        84 ef~c~vc~~~l~~------------pv~tpcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   84 EFECCVCSRALYP------------PVVTPCGHSFCLECLDRSLDQ-ETECPLCRDELVE  130 (398)
T ss_pred             hhhhhhhHhhcCC------------CccccccccccHHHHHHHhcc-CCCCccccccccc
Confidence            8999999998887            667799999999999998888 9999999999985

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C

Probab=97.10  E-value=0.00022  Score=50.17  Aligned_cols=42  Identities=26%  Similarity=0.621  Sum_probs=28.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh-CCCCCcc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH-YSTTCPV  217 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~-~~~sCPv  217 (249)
                      ...|+|.+..|+..           |+...|+|+|-++.|..||+. +...||+
T Consensus        11 ~~~CPiT~~~~~~P-----------V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFEDP-----------VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SSE-----------EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhCC-----------cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            67999999999973           555679999999999999943 1557998

>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]

Probab=96.97  E-value=0.00022  Score=65.41  Aligned_cols=52  Identities=29%  Similarity=0.620  Sum_probs=43.5

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----------------------CCCCcccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----------------------STTCPVCRYE  221 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----------------------~~sCPvCR~~  221 (249)
                      +.-+|.|||--|..+..         ..+++|-|+||..|+.++|+.-                      ...|||||..
T Consensus       114 p~gqCvICLygfa~~~~---------ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~  184 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPA---------FTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRER  184 (368)
T ss_pred             CCCceEEEEEeecCCCc---------eeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhh
Confidence            35799999999999988         8999999999999998776540                      2369999998


Q ss_pred             ccC
Q 041030          222 LKD  224 (249)
Q Consensus       222 l~~  224 (249)
                      |..
T Consensus       185 i~~  187 (368)
T KOG4445|consen  185 IKI  187 (368)
T ss_pred             ccc
Confidence            864

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=96.96  E-value=0.00031  Score=67.06  Aligned_cols=51  Identities=33%  Similarity=0.750  Sum_probs=43.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +++..|+||...+.....           ...|+|.||..||..|+.. +..||.|+..+...
T Consensus        19 ~~~l~C~~C~~vl~~p~~-----------~~~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQ-----------TTTCGHRFCAGCLLESLSN-HQKCPVCRQELTQA   69 (391)
T ss_pred             cccccCccccccccCCCC-----------CCCCCCcccccccchhhcc-CcCCcccccccchh
Confidence            347899999999998422           2579999999999999999 99999998887543

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=96.93  E-value=0.00023  Score=71.89  Aligned_cols=49  Identities=16%  Similarity=0.599  Sum_probs=41.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      -..|++|...++.            ++..-|+|+||..||.+-+......||.|...+.+-
T Consensus       643 ~LkCs~Cn~R~Kd------------~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD------------AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             ceeCCCccCchhh------------HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            4799999999887            555669999999999999888678899998877543

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]

Probab=96.88  E-value=0.00033  Score=66.44  Aligned_cols=47  Identities=36%  Similarity=0.868  Sum_probs=40.4

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKD  224 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~  224 (249)
                      ..|-||-|.=++            |+.-||||+.|..|+..|-..- .++||.||.+|..
T Consensus       370 eLCKICaendKd------------vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  370 ELCKICAENDKD------------VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHhhccCCC------------cccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            689999988665            8888999999999999997542 6789999999964

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]

Probab=96.84  E-value=0.0003  Score=65.07  Aligned_cols=49  Identities=24%  Similarity=0.631  Sum_probs=41.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...+|.+|.--|.+            +.++. |-|.||+.||...|.. +++||.|...+-..
T Consensus        14 ~~itC~LC~GYliD------------ATTI~eCLHTFCkSCivk~l~~-~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   14 PHITCRLCGGYLID------------ATTITECLHTFCKSCIVKYLEE-SKYCPTCDIVIHKT   63 (331)
T ss_pred             cceehhhccceeec------------chhHHHHHHHHHHHHHHHHHHH-hccCCccceeccCc
Confidence            46799999999988            44455 9999999999999999 99999998877443

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.83  E-value=0.0002  Score=49.89  Aligned_cols=47  Identities=26%  Similarity=0.556  Sum_probs=35.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      +.+|.||+|.-.+.            +.--|||+ .|.+|-.+.++.++..||+||..+.
T Consensus         7 ~dECTICye~pvds------------VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDS------------VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchH------------HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            36899999986653            22349998 4788877755544999999999874

>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=96.31  E-value=0.0036  Score=55.55  Aligned_cols=56  Identities=27%  Similarity=0.593  Sum_probs=45.0

Q ss_pred             cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCccccccccCCC
Q 041030          161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPVCRYELKDSI  226 (249)
Q Consensus       161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPvCR~~l~~~~  226 (249)
                      +++....|..|.-.+..|+.          +.|-|-|+||++|+..|-..-       .-.||-|.++|-+..
T Consensus        46 DsDY~pNC~LC~t~La~gdt----------~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   46 DSDYNPNCRLCNTPLASGDT----------TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             hcCCCCCCceeCCccccCcc----------eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            34557899999999998875          456799999999999997762       337999999996543

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.27  E-value=0.0013  Score=62.25  Aligned_cols=48  Identities=29%  Similarity=0.842  Sum_probs=39.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRY  220 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~  220 (249)
                      +.-|..|=+.+....+.        .--|||.|+||..|+...|.+. -.+||-||.
T Consensus       365 ~L~Cg~CGe~~Glk~e~--------LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNER--------LQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCccc--------ccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            57899999998776542        6779999999999999998762 458999993

>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length

Probab=96.08  E-value=0.0022  Score=52.56  Aligned_cols=36  Identities=22%  Similarity=0.557  Sum_probs=30.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccC------CccChhhHHHHHh
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK------HLYHSDCIVPWLR  209 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~------H~FH~~CI~~WL~  209 (249)
                      ...|.||++.+.....         |+.++|+      |+||.+|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~G---------vV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDG---------VVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCC---------EEEEecCCeehHHHHHHHHHHHHHHh
Confidence            5799999999988333         7788886      9999999999943

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

Probab=96.04  E-value=0.002  Score=56.15  Aligned_cols=46  Identities=24%  Similarity=0.528  Sum_probs=40.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      .+.|.||.++|+.            .+...|||.||..|...-++. ...|-+|-.+.-
T Consensus       196 PF~C~iCKkdy~s------------pvvt~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t~  241 (259)
T COG5152         196 PFLCGICKKDYES------------PVVTECGHSFCSLCAIRKYQK-GDECGVCGKATY  241 (259)
T ss_pred             ceeehhchhhccc------------hhhhhcchhHHHHHHHHHhcc-CCcceecchhhc
Confidence            5799999999997            566779999999999998888 889999976543

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=96.02  E-value=0.0028  Score=48.61  Aligned_cols=33  Identities=27%  Similarity=0.686  Sum_probs=27.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHH
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIV  205 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~  205 (249)
                      .++..|+||-..+..+ .         ....||+|+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~~-~---------f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNS-V---------FVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCc-e---------EEEeCCCeEEeccccc
Confidence            3478899999999874 3         7888999999999974

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]

Probab=95.98  E-value=0.0042  Score=66.82  Aligned_cols=54  Identities=24%  Similarity=0.639  Sum_probs=41.6

Q ss_pred             cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---------CCCCcccccccc
Q 041030          161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---------STTCPVCRYELK  223 (249)
Q Consensus       161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---------~~sCPvCR~~l~  223 (249)
                      +.+.+..|-||+-+-....-         ..+|.|+|+||..|...-|...         --+||+|+.+|.
T Consensus      3482 kQD~DDmCmICFTE~L~AAP---------~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAP---------AIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hcccCceEEEEehhhhCCCc---------ceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            34557899999987665555         7889999999999998766652         128999998774

>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.91  E-value=0.0025  Score=53.94  Aligned_cols=29  Identities=38%  Similarity=0.835  Sum_probs=26.8

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccCh
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHS  201 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~  201 (249)
                      +.-+|.||||+++.+..         +..|||..+||+
T Consensus       176 dkGECvICLEdL~~Gdt---------IARLPCLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDT---------IARLPCLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCc---------eeccceEEEeec
Confidence            35699999999999999         999999999997

>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.0059  Score=57.26  Aligned_cols=44  Identities=30%  Similarity=0.790  Sum_probs=34.7

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ....|.||+++.+.            .+.+||||+-+  |+.-- +. ..+||+||+.+.
T Consensus       304 ~p~lcVVcl~e~~~------------~~fvpcGh~cc--ct~cs-~~-l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS------------AVFVPCGHVCC--CTLCS-KH-LPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCccc------------eeeecCCcEEE--chHHH-hh-CCCCchhHHHHH
Confidence            35799999999988            77899999966  66543 33 567999999774

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.63  E-value=0.013  Score=53.37  Aligned_cols=49  Identities=29%  Similarity=0.589  Sum_probs=37.7

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhC-CCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHY-STTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~  223 (249)
                      ..+.+|++|-+.-..            ..++ +|+|+||.-||..=+..- ..+||.|-.+..
T Consensus       237 t~~~~C~~Cg~~Pti------------P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTI------------PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCC------------CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            347899999988665            4444 499999999998855431 468999988776

>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B

Probab=95.55  E-value=0.0065  Score=41.34  Aligned_cols=45  Identities=31%  Similarity=0.616  Sum_probs=22.2

Q ss_pred             cccccccccccCCCCCCCCccceEEec--cCCccChhhHHHHHhhCCCCCccccccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELP--CKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~Lp--C~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      |++|.+++....          ...+|  |++..+..|-..-++.+...||-||.++
T Consensus         1 cp~C~e~~d~~d----------~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETD----------KDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCC----------TT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCC----------CccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999983322          23455  8999999998887764478999999875

>PHA03096 p28-like protein; Provisional

Probab=95.45  E-value=0.0067  Score=55.71  Aligned_cols=52  Identities=19%  Similarity=0.296  Sum_probs=36.6

Q ss_pred             cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC--CC---CCccccccc
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY--ST---TCPVCRYEL  222 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~--~~---sCPvCR~~l  222 (249)
                      ..|.||++.......     .++....|+ |.|.|+..||..|....  ..   .||+|+.-+
T Consensus       179 k~c~ic~e~~~~k~~-----~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYI-----IKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhcc-----ccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence            589999998775321     122367787 99999999999998873  22   355555443

>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A

Probab=95.29  E-value=0.014  Score=39.25  Aligned_cols=41  Identities=32%  Similarity=0.840  Sum_probs=27.2

Q ss_pred             cccccccccccCCCCCCCCccceEEecc--CC---ccChhhHHHHHhhC-CCCCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMELPC--KH---LYHSDCIVPWLRHY-STTCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~LpC--~H---~FH~~CI~~WL~~~-~~sCPvC  218 (249)
                      |-||++.-....          ....||  +-   ..|.+|+..|+... +.+|++|
T Consensus         1 CrIC~~~~~~~~----------~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE----------PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-----------EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC----------ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            678988866543          345675  44   78999999999962 5679887

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.10  E-value=0.0064  Score=55.75  Aligned_cols=49  Identities=22%  Similarity=0.458  Sum_probs=41.9

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +.|-||...|..            .++..|+|.||..|...=++. ...|.+|-+..-..+.
T Consensus       242 f~c~icr~~f~~------------pVvt~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~g~~~  290 (313)
T KOG1813|consen  242 FKCFICRKYFYR------------PVVTKCGHYFCEVCALKPYQK-GEKCYVCSQQTHGSFN  290 (313)
T ss_pred             cccccccccccc------------chhhcCCceeehhhhcccccc-CCcceecccccccccc
Confidence            579999999998            666789999999999998888 8899999887655443

>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.08  E-value=0.015  Score=54.75  Aligned_cols=53  Identities=28%  Similarity=0.542  Sum_probs=44.0

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG  228 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~  228 (249)
                      .++..|+||.-.-..            ++-.||+|.-|++||.+-|-. .+.|=.|+..+.+...+
T Consensus       420 sEd~lCpICyA~pi~------------Avf~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~~~ld  472 (489)
T KOG4692|consen  420 SEDNLCPICYAGPIN------------AVFAPCSHRSCYGCITQHLMN-CKRCFFCKTTVIDVILD  472 (489)
T ss_pred             cccccCcceecccch------------hhccCCCCchHHHHHHHHHhc-CCeeeEecceeeehhcc
Confidence            457899999876444            567899999999999999998 99999999988765444

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=94.85  E-value=0.012  Score=56.11  Aligned_cols=47  Identities=26%  Similarity=0.526  Sum_probs=38.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPVCRY  220 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPvCR~  220 (249)
                      ..+|.||+++.....-         ...+||+|+||+.|+..++..-       .-.||-+..
T Consensus       184 lf~C~ICf~e~~G~~c---------~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHC---------FKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcce---------eeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            6899999999877666         8899999999999999998772       225776643

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.50  E-value=0.026  Score=47.60  Aligned_cols=50  Identities=24%  Similarity=0.681  Sum_probs=36.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccC--C---ccChhhHHHHHhhC-CCCCccccccccCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK--H---LYHSDCIVPWLRHY-STTCPVCRYELKDSI  226 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~--H---~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~  226 (249)
                      .+..|-||.++-.  ..           .-||.  .   .-|.+|+..|+... ..+|++|++++....
T Consensus         7 ~~~~CRIC~~~~~--~~-----------~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~   62 (162)
T PHA02825          7 MDKCCWICKDEYD--VV-----------TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK   62 (162)
T ss_pred             CCCeeEecCCCCC--Cc-----------cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEE
Confidence            4679999988732  11           24754  4   56999999999985 557999999886543

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=94.48  E-value=0.022  Score=53.52  Aligned_cols=51  Identities=29%  Similarity=0.610  Sum_probs=41.7

Q ss_pred             ccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccC
Q 041030          162 SNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKD  224 (249)
Q Consensus       162 ~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~  224 (249)
                      .++...|-||-+.+.-            +..+||+|.-|--|..+.-..+ .+.||+||.+-..
T Consensus        58 DEen~~C~ICA~~~TY------------s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~  109 (493)
T COG5236          58 DEENMNCQICAGSTTY------------SARYPCGHQICHACAVRLRALYMQKGCPLCRTETEA  109 (493)
T ss_pred             ccccceeEEecCCceE------------EEeccCCchHHHHHHHHHHHHHhccCCCccccccce
Confidence            3557899999998876            7789999999999998755444 7799999998643

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=94.23  E-value=0.017  Score=56.91  Aligned_cols=51  Identities=25%  Similarity=0.634  Sum_probs=41.1

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----CCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~~l~~~  225 (249)
                      .+...|.+|-+.-++            ..+..|.|.||.-||..+....    +-+||+|-..|.-+
T Consensus       534 k~~~~C~lc~d~aed------------~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED------------YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhh------------hHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            346899999998776            6678899999999998887653    55899997766544

>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.98  E-value=0.0039  Score=59.06  Aligned_cols=52  Identities=33%  Similarity=0.652  Sum_probs=44.3

Q ss_pred             cccccccccccccc-CCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVR-DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~-~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      ...|+||.+.++.. +.         ...+-|+|.||.+||.+||.. ...||.||.+|+...
T Consensus       196 v~sl~I~~~slK~~y~k---------~~~~~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDK---------ISAIVCGHIYHHGKLSKWLAT-KRKLPSCRRELPKNG  248 (465)
T ss_pred             HhhhHhhHHHHHHHHHH---------HHHHhhcccchhhHHHHHHHH-HHHhHHHHhhhhhhh
Confidence            36899999998765 33         566779999999999999999 999999999997543

>PHA02862 5L protein; Provisional

Probab=93.92  E-value=0.031  Score=46.45  Aligned_cols=51  Identities=18%  Similarity=0.455  Sum_probs=37.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhC-CCCCccccccccCCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHY-STTCPVCRYELKDSIIG  228 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~~~~  228 (249)
                      +..|=||+++-..  .           .-||.     ..-|.+|+.+|++.. +.+|++|++++.....-
T Consensus         2 ~diCWIC~~~~~e--~-----------~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~y   58 (156)
T PHA02862          2 SDICWICNDVCDE--R-----------NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTY   58 (156)
T ss_pred             CCEEEEecCcCCC--C-----------cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEcc
Confidence            3589999997322  1           24653     688999999999873 55799999998655443

>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.82  E-value=0.014  Score=53.60  Aligned_cols=42  Identities=29%  Similarity=0.651  Sum_probs=32.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCcc-ChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLY-HSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~F-H~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ...|+|||+.-.+            -+-|+|||+. |.+|-..     -+.||+||+.+.
T Consensus       300 ~~LC~ICmDaP~D------------CvfLeCGHmVtCt~CGkr-----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRD------------CVFLECGHMVTCTKCGKR-----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcc------------eEEeecCcEEeehhhccc-----cccCchHHHHHH
Confidence            5789999998776            6789999974 6666433     458999998764

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=93.63  E-value=0.032  Score=51.52  Aligned_cols=46  Identities=33%  Similarity=0.728  Sum_probs=36.6

Q ss_pred             cccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccc-ccccc
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVC-RYELK  223 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvC-R~~l~  223 (249)
                      ..|+.|..-+..            .+.++ |+|.||.+||..-|...-..||.| |.++.
T Consensus       275 LkCplc~~Llrn------------p~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvl  322 (427)
T COG5222         275 LKCPLCHCLLRN------------PMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVL  322 (427)
T ss_pred             ccCcchhhhhhC------------cccCccccchHHHHHHhhhhhhccccCCCcccccch
Confidence            789999988877            45567 999999999997665537789999 55554

>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.55  E-value=0.044  Score=49.80  Aligned_cols=52  Identities=27%  Similarity=0.612  Sum_probs=42.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      -..|-||-++|..+..      ++..+.|.|||.|+..|+.+-+..+...||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~------~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDG------DHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCc------ccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            3589999999987632      233677889999999999998887666799999985

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.38  E-value=0.087  Score=47.50  Aligned_cols=55  Identities=22%  Similarity=0.416  Sum_probs=45.5

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      ..+.|+||.+.+....-        +++.-||||+|..+|+.+.+.. -..||||-.++....+
T Consensus       220 ~ryiCpvtrd~LtNt~~--------ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrdi  274 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTP--------CAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRDI  274 (303)
T ss_pred             cceecccchhhhcCccc--------eEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccce
Confidence            46899999999987654        2444569999999999999988 9999999888876554

>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]

Probab=93.25  E-value=0.05  Score=56.13  Aligned_cols=50  Identities=32%  Similarity=0.721  Sum_probs=38.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEec---cCCccChhhHHHHHhhC------CCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPWLRHY------STTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~WL~~~------~~sCPvCR~~l~  223 (249)
                      .....|.||.+.+....-           ++.   |-|+||..||..|-...      .-.||.|.....
T Consensus       189 ~~~yeCmIC~e~I~~t~~-----------~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAP-----------VWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             cCceEEEEeeeeccccCC-----------ceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence            457899999999987654           344   77999999999998763      125999985443

>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO)

Probab=93.15  E-value=0.03  Score=37.09  Aligned_cols=39  Identities=33%  Similarity=0.792  Sum_probs=23.4

Q ss_pred             cccccccccccCCCCCCCCccceEEe--ccCCccChhhHHHHHhhCCC--CCccc
Q 041030          168 CPICKEEFRVRDDVDDDSDEVMIMEL--PCKHLYHSDCIVPWLRHYST--TCPVC  218 (249)
Q Consensus       168 C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~FH~~CI~~WL~~~~~--sCPvC  218 (249)
                      |.+|.+-+..|.           +=-  .|+-.+|..|+..+++. ..  .||.|
T Consensus         1 C~~C~~iv~~G~-----------~C~~~~C~~r~H~~C~~~y~r~-~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQ-----------RCSNRDCNVRLHDDCFKKYFRH-RSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSE-----------E-SS--S--EE-HHHHHHHTTT--SS-B-TTT
T ss_pred             CcccchhHeeec-----------cCCCCccCchHHHHHHHHHHhc-CCCCCCcCC
Confidence            678888877763           222  38889999999999998 44  69987

; PDB: 3NW0_A 2CT0_A.

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=93.01  E-value=0.059  Score=43.18  Aligned_cols=32  Identities=19%  Similarity=0.616  Sum_probs=26.2

Q ss_pred             CeeeeccCCCeeEeccCCCCCccCCCCCccceeec
Q 041030           22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLEL   56 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEl   56 (249)
                      -..||..|+..+.+-..   +..||.|+|..++-+
T Consensus        69 ~~~~C~~C~~~~~~e~~---~~~CP~C~s~~~~i~  100 (115)
T COG0375          69 AECWCLDCGQEVELEEL---DYRCPKCGSINLRII  100 (115)
T ss_pred             cEEEeccCCCeecchhh---eeECCCCCCCceEEe
Confidence            35899999999887654   678999999998754

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.63  E-value=0.075  Score=54.91  Aligned_cols=43  Identities=30%  Similarity=0.790  Sum_probs=34.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      ...|..|--.+...           ++..-|+|.||..|+.   .. ...||-|+.++
T Consensus       840 ~skCs~C~~~LdlP-----------~VhF~CgHsyHqhC~e---~~-~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP-----------FVHFLCGHSYHQHCLE---DK-EDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc-----------eeeeecccHHHHHhhc---cC-cccCCccchhh
Confidence            46999999888874           5556699999999987   33 67899998855

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=92.34  E-value=0.15  Score=43.09  Aligned_cols=34  Identities=29%  Similarity=0.600  Sum_probs=23.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccC-------------CccChhhHHHHHhh
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-------------HLYHSDCIVPWLRH  210 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-------------H~FH~~CI~~WL~~  210 (249)
                      +..|+||||---.            ++.|-|.             -.=|+.|+++.-+.
T Consensus         2 d~~CpICme~PHN------------AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka   48 (162)
T PF07800_consen    2 DVTCPICMEHPHN------------AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKA   48 (162)
T ss_pred             CccCceeccCCCc------------eEEEEeccccCCccccccCCccchhHHHHHHHHH
Confidence            6799999998665            4455553             23478899887554

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=92.25  E-value=0.057  Score=48.22  Aligned_cols=51  Identities=20%  Similarity=0.540  Sum_probs=37.3

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCC-CCccccccccCCCCCCC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST-TCPVCRYELKDSIIGSG  230 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~-sCPvCR~~l~~~~~~~~  230 (249)
                      .+|..|.-.-. +..         ...+.|.|+||..|...-    +. .||+||..+....++..
T Consensus         4 VhCn~C~~~~~-~~~---------f~LTaC~HvfC~~C~k~~----~~~~C~lCkk~ir~i~l~~s   55 (233)
T KOG4739|consen    4 VHCNKCFRFPS-QDP---------FFLTACRHVFCEPCLKAS----SPDVCPLCKKSIRIIQLNRS   55 (233)
T ss_pred             EEeccccccCC-CCc---------eeeeechhhhhhhhcccC----Cccccccccceeeeeecccc
Confidence            46777766544 444         777889999999997542    33 89999999877666554

>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]

Probab=91.59  E-value=0.12  Score=48.24  Aligned_cols=45  Identities=22%  Similarity=0.558  Sum_probs=36.9

Q ss_pred             ccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      ...|+||+.......            .+. =|-+||..||...+.. ++.|||=-.++
T Consensus       300 ~~~CpvClk~r~Npt------------vl~vSGyVfCY~Ci~~Yv~~-~~~CPVT~~p~  345 (357)
T KOG0826|consen  300 REVCPVCLKKRQNPT------------VLEVSGYVFCYPCIFSYVVN-YGHCPVTGYPA  345 (357)
T ss_pred             cccChhHHhccCCCc------------eEEecceEEeHHHHHHHHHh-cCCCCccCCcc
Confidence            679999999887743            233 6999999999999999 99999965543

>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]

Probab=91.35  E-value=0.088  Score=48.89  Aligned_cols=43  Identities=23%  Similarity=0.669  Sum_probs=30.0

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccc
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL  222 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l  222 (249)
                      -.|--|--.+..  .         -+.+||+|+||.+|...  .. -+.||.|--.|
T Consensus        91 HfCd~Cd~PI~I--Y---------GRmIPCkHvFCl~CAr~--~~-dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIAI--Y---------GRMIPCKHVFCLECARS--DS-DKICPLCDDRV  133 (389)
T ss_pred             EeecccCCccee--e---------ecccccchhhhhhhhhc--Cc-cccCcCcccHH
Confidence            356666555554  2         56779999999999754  23 45899996555

>PF04641 Rtf2: Rtf2 RING-finger

Probab=91.13  E-value=0.23  Score=44.86  Aligned_cols=53  Identities=21%  Similarity=0.582  Sum_probs=41.0

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...+.|||...+|.....        -|...+|||+|...+|..- .. ...||+|-.++...
T Consensus       111 ~~~~~CPvt~~~~~~~~~--------fv~l~~cG~V~s~~alke~-k~-~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHK--------FVYLRPCGCVFSEKALKEL-KK-SKKCPVCGKPFTEE  163 (260)
T ss_pred             CceeECCCCCcccCCcee--------EEEEcCCCCEeeHHHHHhh-cc-cccccccCCccccC
Confidence            457899999999954433        1556689999999999986 33 56799998887644

>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=90.76  E-value=0.15  Score=43.91  Aligned_cols=62  Identities=21%  Similarity=0.496  Sum_probs=39.3

Q ss_pred             cccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---C-------CCCccccccccCCCC
Q 041030          161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---S-------TTCPVCRYELKDSII  227 (249)
Q Consensus       161 ~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~-------~sCPvCR~~l~~~~~  227 (249)
                      +.++.-.|-||..--..|..     .++.---.+|+.-||.-|+..||..-   +       ..||.|-.++.-..+
T Consensus       161 kdd~~~~cgicyayqldGTi-----pDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS  232 (234)
T KOG3268|consen  161 KDDELGACGICYAYQLDGTI-----PDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS  232 (234)
T ss_pred             cchhhhcccceeeeecCCcc-----ccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence            33445567777654444332     11223345699999999999999862   1       259999887755443

>KOG1940 consensus Zn-finger protein [General function prediction only]

Probab=90.46  E-value=0.13  Score=47.18  Aligned_cols=47  Identities=34%  Similarity=0.652  Sum_probs=40.2

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY  220 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~  220 (249)
                      ...|+||.+.+..+...        +..++|+|.-|..|....... +-.||+|..
T Consensus       158 ~~ncPic~e~l~~s~~~--------~~~~~CgH~~h~~cf~e~~~~-~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFED--------AGVLKCGHYMHSRCFEEMICE-GYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhcccccc--------CCccCcccchHHHHHHHHhcc-CCCCCcccc
Confidence            44699999988877652        788999999999999998888 689999977

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=90.14  E-value=0.17  Score=35.42  Aligned_cols=34  Identities=26%  Similarity=0.504  Sum_probs=26.8

Q ss_pred             eEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          190 IMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       190 v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      -+.+||+|+-+..|..-|  . -+.||+|-+.+....
T Consensus        20 ~~~~pCgH~I~~~~f~~~--r-YngCPfC~~~~~~~~   53 (55)
T PF14447_consen   20 GTVLPCGHLICDNCFPGE--R-YNGCPFCGTPFEFDD   53 (55)
T ss_pred             cccccccceeeccccChh--h-ccCCCCCCCcccCCC
Confidence            567899999999997665  3 558999988876544

>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=89.49  E-value=0.27  Score=46.93  Aligned_cols=49  Identities=31%  Similarity=0.515  Sum_probs=41.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC--CCCccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS--TTCPVCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~--~sCPvCR~~l  222 (249)
                      .+.|||=.+.-...+-         .+.|.|||+-.++-|.+-.+.|.  ..||.|=.+.
T Consensus       334 vF~CPVlKeqtsdeNP---------Pm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENP---------PMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             eeecccchhhccCCCC---------CeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            5899999998887777         89999999999999999888765  6799995443

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=88.97  E-value=0.21  Score=29.63  Aligned_cols=23  Identities=30%  Similarity=0.830  Sum_probs=18.7

Q ss_pred             eccCCCeeEeccCCCCCccCCCCCccce
Q 041030           26 CQSCQRTTRFRSTDPSELFCPHCSAQLY   53 (249)
Q Consensus        26 Cy~C~r~Vr~~~~~~s~~~CP~C~~gFl   53 (249)
                      |-+|...|.+..     .+||+||-.|.
T Consensus         3 CP~C~~~V~~~~-----~~Cp~CG~~F~   25 (26)
T PF10571_consen    3 CPECGAEVPESA-----KFCPHCGYDFE   25 (26)
T ss_pred             CCCCcCCchhhc-----CcCCCCCCCCc
Confidence            778999986654     59999998884

Several members are annotated as putative helicases.

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=88.92  E-value=0.17  Score=51.76  Aligned_cols=52  Identities=25%  Similarity=0.639  Sum_probs=40.3

Q ss_pred             cccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCC-CCccccccccCCCCCCC
Q 041030          166 QCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST-TCPVCRYELKDSIIGSG  230 (249)
Q Consensus       166 ~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~-sCPvCR~~l~~~~~~~~  230 (249)
                      ..|.||++ ..   .         ....+|+|.||.+|+..-+..-+. .||+||..+....+-+.
T Consensus       455 ~~c~ic~~-~~---~---------~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~  507 (674)
T KOG1001|consen  455 HWCHICCD-LD---S---------FFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSA  507 (674)
T ss_pred             cccccccc-cc---c---------ceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhc
Confidence            79999999 22   2         667789999999999987766333 59999998876665543

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=88.85  E-value=0.47  Score=31.42  Aligned_cols=32  Identities=19%  Similarity=0.615  Sum_probs=26.2

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCccceee
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLE   55 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEE   55 (249)
                      .|=|-+|...+.+.... ..+.||+|++.++..
T Consensus         3 ~y~C~~CG~~~~~~~~~-~~~~Cp~CG~~~~~~   34 (46)
T PRK00398          3 EYKCARCGREVELDEYG-TGVRCPYCGYRILFK   34 (46)
T ss_pred             EEECCCCCCEEEECCCC-CceECCCCCCeEEEc
Confidence            58899999999887542 268999999999854

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.72  E-value=0.44  Score=33.23  Aligned_cols=31  Identities=42%  Similarity=0.933  Sum_probs=27.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEec-cCCccChhhH
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCI  204 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI  204 (249)
                      ...|.+|-+.|..++.         +++-| |+-.||.+|-
T Consensus         5 ~~~C~~Cg~~~~~~dD---------iVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDD---------IVVCPECGAPYHRDCW   36 (54)
T ss_pred             CccChhhCCcccCCCC---------EEECCCCCCcccHHHH
Confidence            5689999999998887         88888 9999999994

>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.67  E-value=0.19  Score=52.24  Aligned_cols=35  Identities=23%  Similarity=0.747  Sum_probs=28.8

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHH
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPW  207 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~W  207 (249)
                      +....|.||...+....          ..+-||||.||++||.+-
T Consensus       815 ep~d~C~~C~~~ll~~p----------F~vf~CgH~FH~~Cl~~~  849 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIKP----------FYVFPCGHCFHRDCLIRH  849 (911)
T ss_pred             cCccchHHhcchhhcCc----------ceeeeccchHHHHHHHHH
Confidence            35789999999887643          677899999999999664

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=88.51  E-value=0.38  Score=38.29  Aligned_cols=29  Identities=17%  Similarity=0.430  Sum_probs=23.2

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      ..||..|...+.+...   ...||.|++..++
T Consensus        70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~   98 (115)
T TIGR00100        70 ECECEDCSEEVSPEID---LYRCPKCHGIMLQ   98 (115)
T ss_pred             EEEcccCCCEEecCCc---CccCcCCcCCCcE
Confidence            4899999988877543   5779999998764

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=88.06  E-value=0.15  Score=51.39  Aligned_cols=45  Identities=24%  Similarity=0.570  Sum_probs=35.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE  221 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~  221 (249)
                      -..|.||+..|......        .+.|.|||.-|..|+..-.   +.+|| |+++
T Consensus        11 ~l~c~ic~n~f~~~~~~--------Pvsl~cghtic~~c~~~ly---n~scp-~~~D   55 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLE--------PVSLQCGHTICGHCVQLLY---NASCP-TKRD   55 (861)
T ss_pred             HhhchHHHHHHHHHhcC--------cccccccchHHHHHHHhHh---hccCC-CCcc
Confidence            46899999999876532        7788899999999998754   55999 6554

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=86.68  E-value=0.27  Score=28.25  Aligned_cols=23  Identities=30%  Similarity=0.907  Sum_probs=17.2

Q ss_pred             eeccCCCeeEeccCCCCCccCCCCCccc
Q 041030           25 WCQSCQRTTRFRSTDPSELFCPHCSAQL   52 (249)
Q Consensus        25 WCy~C~r~Vr~~~~~~s~~~CP~C~~gF   52 (249)
                      +|.+|...|.-.     ..+||.|+..|
T Consensus         1 ~Cp~CG~~~~~~-----~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIEDD-----AKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCCc-----CcchhhhCCcC
Confidence            588898887532     56999998754

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=86.60  E-value=0.56  Score=37.31  Aligned_cols=30  Identities=23%  Similarity=0.738  Sum_probs=22.5

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      ..||..|+..+-+...  ....||.|++.-++
T Consensus        70 ~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~   99 (114)
T PRK03681         70 ECWCETCQQYVTLLTQ--RVRRCPQCHGDMLR   99 (114)
T ss_pred             EEEcccCCCeeecCCc--cCCcCcCcCCCCcE
Confidence            4899999988776533  12569999988765

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=86.35  E-value=0.58  Score=37.14  Aligned_cols=29  Identities=24%  Similarity=0.778  Sum_probs=22.2

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      .+||..|.....+...   ...||.|++.-++
T Consensus        70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~   98 (113)
T PRK12380         70 QAWCWDCSQVVEIHQH---DAQCPHCHGERLR   98 (113)
T ss_pred             EEEcccCCCEEecCCc---CccCcCCCCCCcE
Confidence            4899999977776533   4569999987654

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=85.64  E-value=0.47  Score=37.56  Aligned_cols=29  Identities=17%  Similarity=0.431  Sum_probs=21.8

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      ..||..|.....+...   ...||.|++..++
T Consensus        70 ~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~   98 (113)
T PF01155_consen   70 RARCRDCGHEFEPDEF---DFSCPRCGSPDVE   98 (113)
T ss_dssp             EEEETTTS-EEECHHC---CHH-SSSSSS-EE
T ss_pred             cEECCCCCCEEecCCC---CCCCcCCcCCCcE
Confidence            4899999999988765   4789999998764

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=85.46  E-value=0.7  Score=37.82  Aligned_cols=33  Identities=18%  Similarity=0.527  Sum_probs=23.0

Q ss_pred             CeeeeccCCCeeEecc--CC----------------CCCccCCCCCcccee
Q 041030           22 HYFWCQSCQRTTRFRS--TD----------------PSELFCPHCSAQLYL   54 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~--~~----------------~s~~~CP~C~~gFlE   54 (249)
                      ..|||.+|.....+..  ..                .....||.|++.-++
T Consensus        69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~  119 (135)
T PRK03824         69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFE  119 (135)
T ss_pred             eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcE
Confidence            4599999998877651  00                124669999987654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=85.37  E-value=0.54  Score=44.35  Aligned_cols=57  Identities=25%  Similarity=0.590  Sum_probs=36.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +++..|+.|+|++...++-        ..-.|||-..|..|-.---+.-+..||-||..+..+.+
T Consensus        12 deed~cplcie~mditdkn--------f~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv   68 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKN--------FFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENV   68 (480)
T ss_pred             cccccCcccccccccccCC--------cccCCcccHHHHHHHHHHHhhccCCChHhhhhccccce
Confidence            3355699999998776542        34456887666666322211115589999998877654

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=84.97  E-value=0.3  Score=52.67  Aligned_cols=44  Identities=30%  Similarity=0.656  Sum_probs=37.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY  220 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~  220 (249)
                      ...|.||++.+.....           ...|+|.|+..|+..|+.. +..||.|+.
T Consensus      1153 ~~~c~ic~dil~~~~~-----------I~~cgh~~c~~c~~~~l~~-~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGG-----------IAGCGHEPCCRCDELWLYA-SSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHHhcCC-----------eeeechhHhhhHHHHHHHH-hccCcchhh
Confidence            4699999999985332           3559999999999999999 999999973

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=84.92  E-value=0.71  Score=42.52  Aligned_cols=52  Identities=25%  Similarity=0.565  Sum_probs=38.6

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      .|++|+......-.-       ..+.-+|+|.-|..|++.-+..|...||.|-..|...
T Consensus         2 ~Cp~CKt~~Y~np~l-------k~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDL-------KLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccc-------eeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            599999876554330       0222369999999999999999788999997766543

>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans

Probab=84.90  E-value=0.51  Score=44.77  Aligned_cols=30  Identities=23%  Similarity=0.804  Sum_probs=23.8

Q ss_pred             cCCccChhhHHHHHhhC------------CCCCccccccccC
Q 041030          195 CKHLYHSDCIVPWLRHY------------STTCPVCRYELKD  224 (249)
Q Consensus       195 C~H~FH~~CI~~WL~~~------------~~sCPvCR~~l~~  224 (249)
                      |.=++|.+|+.+|+..+            +-.||+||..+.-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            56678899999999873            3479999998753

They are purported to be transmembrane protein-precursors but their function is unknown.

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=84.85  E-value=0.61  Score=37.23  Aligned_cols=31  Identities=13%  Similarity=0.359  Sum_probs=22.2

Q ss_pred             CeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      -.+||..|+....+...  ....||.|++..++
T Consensus        70 ~~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~  100 (117)
T PRK00564         70 VELECKDCSHVFKPNAL--DYGVCEKCHSKNVI  100 (117)
T ss_pred             CEEEhhhCCCccccCCc--cCCcCcCCCCCceE
Confidence            34899999977665432  12359999998775

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=84.70  E-value=0.51  Score=42.55  Aligned_cols=49  Identities=31%  Similarity=0.647  Sum_probs=39.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe--c-cCCccChhhHHHHHhhCCCCCc--cccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--P-CKHLYHSDCIVPWLRHYSTTCP--VCRYEL  222 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--p-C~H~FH~~CI~~WL~~~~~sCP--vCR~~l  222 (249)
                      +..|+||..+....-.         ++.|  | |-|..|..|+++-|..|...||  -|-.-|
T Consensus        10 d~~CPvCksDrYLnPd---------ik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220          10 DRRCPVCKSDRYLNPD---------IKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             cccCCccccccccCCC---------eEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            6799999998776544         4443  6 9999999999999999888999  775533

>KOG3002 consensus Zn finger protein [General function prediction only]

Probab=83.85  E-value=0.71  Score=42.81  Aligned_cols=42  Identities=31%  Similarity=0.725  Sum_probs=34.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEecc--CCccChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPC--KHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC--~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      -.+|+||.+.+...             .++|  ||+-|..|-.+   . .+.||.||.++.
T Consensus        48 lleCPvC~~~l~~P-------------i~QC~nGHlaCssC~~~---~-~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP-------------IFQCDNGHLACSSCRTK---V-SNKCPTCRLPIG   91 (299)
T ss_pred             hccCchhhccCccc-------------ceecCCCcEehhhhhhh---h-cccCCccccccc
Confidence            68999999999863             4567  79999999764   4 667999999886

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.68  E-value=0.4  Score=32.59  Aligned_cols=32  Identities=28%  Similarity=0.729  Sum_probs=22.7

Q ss_pred             ecc-CCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          193 LPC-KHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       193 LpC-~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +.| .|+.|..|+...|.. ...||+|..+||+.
T Consensus        16 i~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   16 IKCSDHYLCLNCLTLMLSR-SDRCPICGKPLPTK   48 (50)
T ss_dssp             EE-SS-EEEHHHHHHT-SS-SSEETTTTEE----
T ss_pred             eeecchhHHHHHHHHHhcc-ccCCCcccCcCccc
Confidence            346 599999999999999 99999999999864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=82.02  E-value=0.6  Score=33.47  Aligned_cols=26  Identities=35%  Similarity=0.755  Sum_probs=18.8

Q ss_pred             eccCCCeeEeccCCCCCccCCCCCcc-ceeec
Q 041030           26 CQSCQRTTRFRSTDPSELFCPHCSAQ-LYLEL   56 (249)
Q Consensus        26 Cy~C~r~Vr~~~~~~s~~~CP~C~~g-FlEEl   56 (249)
                      |..|.|.+.-     ..-+||.|++. |.||-
T Consensus         7 C~~Ck~l~~~-----d~e~CP~Cgs~~~te~W   33 (64)
T COG2093           7 CKNCKRLTPE-----DTEICPVCGSTDLTEEW   33 (64)
T ss_pred             HhhccccCCC-----CCccCCCCCCcccchhh
Confidence            8888876542     23589999998 77763

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=81.98  E-value=0.61  Score=27.36  Aligned_cols=24  Identities=33%  Similarity=0.944  Sum_probs=17.0

Q ss_pred             eeeccCCCeeEeccCCCCCccCCCCCccc
Q 041030           24 FWCQSCQRTTRFRSTDPSELFCPHCSAQL   52 (249)
Q Consensus        24 yWCy~C~r~Vr~~~~~~s~~~CP~C~~gF   52 (249)
                      ..|-+|...+..     .+.+||+|+..+
T Consensus         3 ~~Cp~Cg~~~~~-----~~~fC~~CG~~L   26 (26)
T PF13248_consen    3 MFCPNCGAEIDP-----DAKFCPNCGAKL   26 (26)
T ss_pred             CCCcccCCcCCc-----ccccChhhCCCC
Confidence            468899985432     257999998753

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=81.90  E-value=0.96  Score=36.48  Aligned_cols=31  Identities=16%  Similarity=0.327  Sum_probs=21.0

Q ss_pred             eeeeccCCCeeEeccCCC--C--CccCCCCCcccee
Q 041030           23 YFWCQSCQRTTRFRSTDP--S--ELFCPHCSAQLYL   54 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~--s--~~~CP~C~~gFlE   54 (249)
                      ..|| .|+....+.....  .  ...||.|++.-++
T Consensus        70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~  104 (124)
T PRK00762         70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAH  104 (124)
T ss_pred             eEEe-eCcCcccccccchhccccCCcCcCCCCCCCE
Confidence            4899 9998866542111  0  1469999988765

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=81.32  E-value=0.84  Score=39.11  Aligned_cols=34  Identities=24%  Similarity=0.598  Sum_probs=25.8

Q ss_pred             cCeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           21 FHYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        21 ~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      ...|.|-+|.+.+..-.--..+..||.|++.+++
T Consensus       115 ~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~  148 (178)
T PRK06266        115 NMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE  148 (178)
T ss_pred             CCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence            4789999999777664322346999999998876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	249
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		3e-07
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		6e-05

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 10/55 (18%)
Query: 168 CPICKEEFXXXXXXXXXXXEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           CP+CKE++              + +LPC HL+H  CIVPWL  +  +CPVCR  L
Sbjct: 18  CPVCKEDYALGES---------VRQLPCNHLFHDSCIVPWLEQHD-SCPVCRKSL 62

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 12/81 (14%)
Query: 139 PAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFXXXXXXXXXXXEVMIMELPCKHL 198
           PA   +++AL  + ++E        +  CCPIC  E+             +  ELPC H 
Sbjct: 16  PASKESIDALPEILVTEDHGAV--GQEMCCPICCSEYVKGD---------VATELPCHHY 64
Query: 199 YHSDCIVPWLRHYSTTCPVCR 219
           +H  C+  WL+  S TCPVCR
Sbjct: 65  FHKPCVSIWLQK-SGTCPVCR 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	249
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	8e-25
2ect_A	78	Ring finger protein 126; metal binding protein, st	6e-18
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-16
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-15
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-14
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	9e-14
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-11
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	3e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-10
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	7e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-10
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-09
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-08
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	5e-08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-07
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	6e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	8e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	9e-07
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-06
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-06
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	5e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	6e-06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	4e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	4e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	8e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-04
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	6e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	9e-04
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	9e-04

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score = 93.2 bits (232), Expect = 8e-25
 Identities = 30/99 (30%), Positives = 42/99 (42%), Gaps = 12/99 (12%)

Query: 124 IEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDD 183
           + +  H      A  PA   +++AL  + ++E           CCPIC  E+   D    
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEM--CCPICCSEYVKGDVA-- 56

Query: 184 DSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
                   ELPC H +H  C+  WL+  S TCPVCR   
Sbjct: 57  -------TELPCHHYFHKPCVSIWLQK-SGTCPVCRCMF 87

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score = 74.8 bits (184), Expect = 6e-18
 Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 10/56 (17%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
            CP+CKE++ + + V          +LPC HL+H  CIVPWL     +CPVCR  L
Sbjct: 17  ECPVCKEDYALGESV---------RQLPCNHLFHDSCIVPWLEQ-HDSCPVCRKSL 62

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 74

 Score = 70.6 bits (173), Expect = 2e-16
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 10/69 (14%)

Query: 154 SESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST 213
             S ++   N  + C +C E+F+ RD++            PCKH +H  C++ WL     
Sbjct: 4   GSSGKVKELNLHELCAVCLEDFKPRDEL---------GICPCKHAFHRKCLIKWLEV-RK 53

Query: 214 TCPVCRYEL 222
            CP+C   +
Sbjct: 54  VCPLCNMPV 62

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 75

 Score = 67.4 bits (165), Expect = 4e-15
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 13/83 (15%)

Query: 140 APVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLY 199
               +   L   R + +      +E   C +C  +F  R  +           LPC H +
Sbjct: 1   GSSGSSGQLPSYRFNPNN---HQSEQTLCVVCMCDFESRQLL---------RVLPCNHEF 48

Query: 200 HSDCIVPWLRHYSTTCPVCRYEL 222
           H+ C+  WL+    TCP+CR + 
Sbjct: 49  HAKCVDKWLKANR-TCPICRADS 70

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 65.5 bits (160), Expect = 2e-14
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 10/63 (15%)

Query: 160 TRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
           T  +  + C IC       +DV           LPC HL+H  C+  WL   +  CP+CR
Sbjct: 9   TEEDTEEKCTICLSILEEGEDV---------RRLPCMHLFHQVCVDQWLIT-NKKCPICR 58

Query: 220 YEL 222
            ++
Sbjct: 59  VDI 61

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 63.6 bits (155), Expect = 9e-14
 Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 14/66 (21%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227
           C IC +                   LPC H +   CI  W       CP+CR ++  +  
Sbjct: 18  CCICMDGRADL-------------ILPCAHSFCQKCIDKWSDR-HRNCPICRLQMTGANE 63

Query: 228 GSGGDN 233
            SG  +
Sbjct: 64  SSGPSS 69

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 61.9 bits (151), Expect = 2e-13
 Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 9/52 (17%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
           CPIC E+          S  V    LPC HL H  C    L+     CP+C 
Sbjct: 8   CPICLEDIH-------TSRVV-AHVLPCGHLLHRTCYEEMLKE-GYRCPLCS 50

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 69

 Score = 56.8 bits (137), Expect = 2e-11
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 154 SESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST 213
             S    R +    CPIC + +      +   +  +I+   C H++ S C+   L++ + 
Sbjct: 4   GSSGTGLRPSGTVSCPICMDGYS-----EIVQNGRLIVSTECGHVFCSQCLRDSLKN-AN 57

Query: 214 TCPVCRYELK 223
           TCP CR ++ 
Sbjct: 58  TCPTCRKKIN 67

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1 Length = 68

 Score = 56.6 bits (137), Expect = 3e-11
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 12/72 (16%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226
            CPIC E+          S+  M   LPC H +   CI  W+R  + TCP+C+  ++  +
Sbjct: 7   RCPICLEDP---------SNYSMA--LPCLHAFCYVCITRWIRQ-NPTCPLCKVPVESVV 54

Query: 227 IGSGGDNIMNDH 238
                D+   D 
Sbjct: 55  HTIESDSEFGDQ 66

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens} Length = 64

 Score = 53.6 bits (129), Expect = 3e-10
 Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
           CPIC + +      +   +  +I+   C H++ S C+   L++ + TCP CR ++ 
Sbjct: 6   CPICMDGY-----SEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKIN 55

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1 Length = 55

 Score = 52.6 bits (127), Expect = 7e-10
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 11/62 (17%)

Query: 162 SNEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRY 220
            ++   C +C  E    +             LP C H +H++C+  WL  +S TCP+CR 
Sbjct: 2   MDDGVECAVCLAELEDGE---------EARFLPRCGHGFHAECVDMWLGSHS-TCPLCRL 51

Query: 221 EL 222
            +
Sbjct: 52  TV 53

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 52.5 bits (126), Expect = 9e-10
 Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
           CPIC + +      +   +  +I+   C H++ S C+   L++ + TCP CR ++ 
Sbjct: 13  CPICMDGYS-----EIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKIN 62

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 53.0 bits (127), Expect = 1e-09
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 9/68 (13%)

Query: 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220
           R   +  C  C+ E           ++ +++   C H +H+ C+  W++  +  CP+C+ 
Sbjct: 22  RVQVMDACLRCQAEN--------KQEDCVVVWGECNHSFHNCCMSLWVKQNN-RCPLCQQ 72

Query: 221 ELKDSIIG 228
           +     IG
Sbjct: 73  DWVVQRIG 80

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 50.2 bits (119), Expect = 2e-08
 Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 10/77 (12%)

Query: 153 ISESTQLTRSNEVQCCPICKEEFRVRDDVDDD------SDEVMIMELPCKHLYHSDCIVP 206
           I + T+  +    + C IC E+  V     D          V+     C H +H  C++ 
Sbjct: 13  IRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLA 72

Query: 207 WLRH----YSTTCPVCR 219
              +     S  CP C+
Sbjct: 73  MYCNGNKDGSLQCPSCK 89

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 72

 Score = 48.2 bits (115), Expect = 5e-08
 Identities = 17/70 (24%), Positives = 22/70 (31%), Gaps = 12/70 (17%)

Query: 156 STQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTC 215
           S  L+       C ICK             D   I    C H +   CIV    + S  C
Sbjct: 6   SGNLSELTPYILCSICKGYLI---------DATTIT--ECLHTFCKSCIVRHFYY-SNRC 53

Query: 216 PVCRYELKDS 225
           P C   +  +
Sbjct: 54  PKCNIVVHQT 63

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 19/63 (30%), Positives = 22/63 (34%), Gaps = 11/63 (17%)

Query: 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
            EV  C IC E+ R         D  +     C  L    CI  WL      CP CR  L
Sbjct: 20  AEVFRCFICMEKLR---------DARLC--PHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

Query: 223 KDS 225
           +  
Sbjct: 69  QLR 71

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 10/95 (10%)

Query: 136 APTPAPVSAVEALKRVRISESTQLTRSN---EVQCCPICKEEFRVRDDV------DDDSD 186
             TP+  ++    KR  + +   +        V  C IC+                  S+
Sbjct: 5   VDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSE 64

Query: 187 EVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE 221
           E  +    C H +H  CI  WL+     CP+   E
Sbjct: 65  ECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNRE 98

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 12/72 (16%)

Query: 154 SESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST 213
           +   ++T  N    C +C   F          D   I+   C H +   CIV +L   S 
Sbjct: 4   TTRIKITELNPHLMCVLCGGYFI---------DATTII--ECLHSFCKTCIVRYLET-SK 51

Query: 214 TCPVCRYELKDS 225
            CP+C  ++  +
Sbjct: 52  YCPICDVQVHKT 63

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81

 Score = 44.8 bits (106), Expect = 8e-07
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 13/52 (25%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR 219
           C IC++ F+         + V+     C+H +   C +   R  +  C +C 
Sbjct: 18  CFICRQAFQ---------NPVV---TKCRHYFCESCALEHFRA-TPRCYICD 56

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 48.2 bits (114), Expect = 9e-07
 Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 12/62 (19%)

Query: 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
             Q C IC E  +         D  +    PC HL  + C+  W       CP CR E+K
Sbjct: 331 TFQLCKICAENDK---------DVKI---EPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 378

Query: 224 DS 225
            +
Sbjct: 379 GT 380

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B Length = 78

 Score = 42.8 bits (100), Expect = 4e-06
 Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 8/66 (12%)

Query: 162 SNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE 221
             +   CP+C E          + D++      C +     C        +  CP CR  
Sbjct: 8   KEDPVECPLCMEPL--------EIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 59

Query: 222 LKDSII 227
             +   
Sbjct: 60  YPEDPA 65

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster} Length = 381

 Score = 46.0 bits (108), Expect = 4e-06
 Identities = 22/150 (14%), Positives = 36/150 (24%), Gaps = 30/150 (20%)

Query: 103 ISLHFDEPTPPPPPPPP------PQPMIEYPMHDLQPDAAPTPAPVSAVEALKRV----- 151
           + L      P             P   +    H L    +   + ++  + L R+     
Sbjct: 230 VYLKLTIADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCY 289

Query: 152 -----RISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVP 206
                           NE   C IC            +   V      C    H+ C+  
Sbjct: 290 FPMPDWSDGPKLDEEDNEELRCNICFAYR----LDGGEVPLVSCDNAKCVLKCHAVCLEE 345

Query: 207 WLR----------HYSTTCPVCRYELKDSI 226
           W +               CP C+ +L  S 
Sbjct: 346 WFKTLMDGKTFLEVSFGQCPFCKAKLSTSF 375

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 17/74 (22%), Positives = 25/74 (33%), Gaps = 13/74 (17%)

Query: 154 SESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYST 213
             S     S  V  C IC +              V    LPCKH++   C+         
Sbjct: 4   GSSGNTAPSLTVPECAICLQTCV---------HPVS---LPCKHVFCYLCVKGASWL-GK 50

Query: 214 TCPVCRYELKDSII 227
            C +CR E+ +  +
Sbjct: 51  RCALCRQEIPEDFL 64

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 43.7 bits (102), Expect = 5e-06
 Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 7/64 (10%)

Query: 164 EVQCCPICKEEFRVR------DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPV 217
            V  C IC+            +     S+E  +    C H +H  CI  WL+     CP+
Sbjct: 47  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPL 105

Query: 218 CRYE 221
              E
Sbjct: 106 DNRE 109

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 42.1 bits (99), Expect = 6e-06
 Identities = 9/58 (15%), Positives = 13/58 (22%), Gaps = 12/58 (20%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224
            C  C                       C H +   C+   L   S  C  C+  +  
Sbjct: 17  KCEKCHLVLC---------SPKQT---ECGHRFCESCMAALLSSSSPKCTACQESIVK 62

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 14/72 (19%), Positives = 21/72 (29%), Gaps = 12/72 (16%)

Query: 160 TRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR-HYSTTCPVC 218
           T  + V+ C IC          +            C    H  C+  + + +    CP C
Sbjct: 10  TYPDAVKICNICHSLLIQGQSCET-----------CGIRMHLPCVAKYFQSNAEPRCPHC 58

Query: 219 RYELKDSIIGSG 230
                  I  SG
Sbjct: 59  NDYWPHEIPKSG 70

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 17/85 (20%), Positives = 30/85 (35%), Gaps = 12/85 (14%)

Query: 141 PVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYH 200
            +++++            L++  E   C  C+E              +      C+H   
Sbjct: 28  VLASLKDRPASGSPFQLFLSKVEETFQCICCQELVF---------RPIT---TVCQHNVC 75

Query: 201 SDCIVPWLRHYSTTCPVCRYELKDS 225
            DC+    R    +CP CRY+L  S
Sbjct: 76  KDCLDRSFRAQVFSCPACRYDLGRS 100

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 12/56 (21%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
            C  C+E              V      C H    DC+    +    +CP CR++L
Sbjct: 80  MCVCCQELVY---------QPVTT---ECFHNVCKDCLQRSFKAQVFSCPACRHDL 123

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 12/56 (21%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
            C IC+                  +E  CKHL+   CI+  L+   + CP CRY  
Sbjct: 25  SCQICEHILA------------DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase, protein binding complex; 4.80A {Homo sapiens} Length = 149

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 13/71 (18%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226
            C IC E F          + V +    C H + S CI  W++     CP+CR ++K   
Sbjct: 66  QCIICSEYF---------IEAVTL---NCAHSFCSYCINEWMKR-KIECPICRKDIKSKT 112

Query: 227 IGSGGDNIMND 237
                DN +N 
Sbjct: 113 YSLVLDNCINK 123

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens} Length = 99

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 12/68 (17%)

Query: 158 QLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPV 217
            +   +++  C IC E F            ++I +  C H Y S CI  +L +  T CP 
Sbjct: 15  VMKTIDDLLRCGICFEYFN---------IAMIIPQ--CSHNYCSLCIRKFLSY-KTQCPT 62

Query: 218 CRYELKDS 225
           C   + + 
Sbjct: 63  CCVTVTEP 70

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 12/57 (21%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
            CPIC    R         + V   + PC H +   CI+  +R     CPV    L 
Sbjct: 20  ECPICLMALR---------EAV---QTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus} Length = 133

 Score = 39.8 bits (92), Expect = 1e-04
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 6/63 (9%)

Query: 161 RSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRY 220
             +    CPIC + +      +   +  +I+   C H++ S C+   L++ + TCP CR 
Sbjct: 3   MGSGTVSCPICMDGYS-----EIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRK 56

Query: 221 ELK 223
           ++ 
Sbjct: 57  KIN 59

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 24/113 (21%), Positives = 37/113 (32%), Gaps = 21/113 (18%)

Query: 110 PTPPPPPPPPPQPMIEYPMHDLQPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCP 169
                    P     E  +++LQ            +    R   SE            CP
Sbjct: 9   QAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELM----------CP 58

Query: 170 ICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           IC +  +         + +   E  C H + +DCI+  LR  +  CP CR +L
Sbjct: 59  ICLDMLK---------NTMTTKE--CLHRFCADCIITALRSGNKECPTCRKKL 100

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 38.5 bits (89), Expect = 6e-04
 Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 12/57 (21%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
            CPIC    R              ++ PC H +   CI+  +R     CPV    L 
Sbjct: 20  ECPICLMALRE------------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens} Length = 238

 Score = 38.6 bits (89), Expect = 9e-04
 Identities = 11/65 (16%), Positives = 18/65 (27%), Gaps = 12/65 (18%)

Query: 163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR-HYSTTCPVCRYE 221
           + V+ C IC          +            C    H  C+  + + +    CP C   
Sbjct: 178 DAVKICNICHSLLIQGQSCET-----------CGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

Query: 222 LKDSI 226
               I
Sbjct: 227 WPHEI 231

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 37.2 bits (86), Expect = 9e-04
 Identities = 16/72 (22%), Positives = 21/72 (29%), Gaps = 12/72 (16%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI 226
            C IC E            + V    LPC H     C    +   S  CP CR  +    
Sbjct: 17  QCGICMEILV---------EPVT---LPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWT 64

Query: 227 IGSGGDNIMNDH 238
                 N + + 
Sbjct: 65  RYHTRRNSLVNV 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	249
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.72
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.64
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.55
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.55
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.54
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.53
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.5
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.49
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.44
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.44
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.43
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.42
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.42
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.41
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.38
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.37
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.37
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.36
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.33
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.33
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.32
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.31
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.31
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.31
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.3
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.28
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.27
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.25
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.24
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.23
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.22
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.2
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.2
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.2
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.19
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.19
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.16
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.16
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.15
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.14
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.14
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.12
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.12
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.1
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.09
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.06
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.06
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.05
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.05
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.02
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.02
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.0
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.93
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.9
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.88
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.88
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.87
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.85
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.81
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.7
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.68
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.65
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.65
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.57
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.54
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.52
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.49
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.36
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.34
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.24
3nw0_A	238	Non-structural maintenance of chromosomes element	97.43
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.07
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	93.94
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	91.83
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	91.34
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	90.37
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	84.4
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	84.29
1we9_A	64	PHD finger family protein; structural genomics, PH	82.87
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	82.72
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	80.16

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens}

Probab=99.72  E-value=3.6e-18  Score=128.87  Aligned_cols=82  Identities=35%  Similarity=0.768  Sum_probs=70.2

Q ss_pred             CCCCCCCCCCHHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC
Q 041030          132 QPDAAPTPAPVSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY  211 (249)
Q Consensus       132 ~~~~~~~pas~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~  211 (249)
                      .......+++++.+++||.+.+......  ..++..|+||++.|..+..         ++.|+|+|+||..||..||+. 
T Consensus         9 ~~~~~~~~~s~~~i~~lp~~~~~~~~~~--~~~~~~C~IC~~~~~~~~~---------~~~l~C~H~Fh~~Ci~~wl~~-   76 (91)
T 2l0b_A            9 SHMVANPPASKESIDALPEILVTEDHGA--VGQEMCCPICCSEYVKGDV---------ATELPCHHYFHKPCVSIWLQK-   76 (91)
T ss_dssp             CCSSCCCCCCHHHHHTSCEEECCTTCSS--SSSCSEETTTTEECCTTCE---------EEEETTTEEEEHHHHHHHHTT-
T ss_pred             CCCcCCCCCCHHHHHhCCCeeecccccc--cCCCCCCcccChhhcCCCc---------EEecCCCChHHHHHHHHHHHc-
Confidence            3456678999999999999988765432  2457899999999998877         889999999999999999999 


Q ss_pred             CCCCccccccccCC
Q 041030          212 STTCPVCRYELKDS  225 (249)
Q Consensus       212 ~~sCPvCR~~l~~~  225 (249)
                      +.+||+||+.+.+.
T Consensus        77 ~~~CP~Cr~~~~~~   90 (91)
T 2l0b_A           77 SGTCPVCRCMFPPP   90 (91)
T ss_dssp             TCBCTTTCCBSSCC
T ss_pred             CCcCcCcCccCCCC
Confidence            99999999998763

>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=4.1e-17  Score=118.24  Aligned_cols=71  Identities=30%  Similarity=0.715  Sum_probs=58.0

Q ss_pred             HHHHHhhhhheeccccccccccCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccc
Q 041030          142 VSAVEALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE  221 (249)
Q Consensus       142 ~~~i~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~  221 (249)
                      ++.++++|..++.....   ..+...|+||++.|..+..         ++.++|+|+||..||.+||+. +.+||+||++
T Consensus         3 ~~~i~~lp~~~~~~~~~---~~~~~~C~IC~~~~~~~~~---------~~~l~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~   69 (75)
T 1x4j_A            3 SGSSGQLPSYRFNPNNH---QSEQTLCVVCMCDFESRQL---------LRVLPCNHEFHAKCVDKWLKA-NRTCPICRAD   69 (75)
T ss_dssp             CCCCSSCCCEEBCSSSC---SSSCCEETTTTEECCBTCE---------EEEETTTEEEETTHHHHHHHH-CSSCTTTCCC
T ss_pred             HhhHhhCCcEEecCccc---cCCCCCCeECCcccCCCCe---------EEEECCCCHhHHHHHHHHHHc-CCcCcCcCCc
Confidence            34456677777654332   2347799999999998877         899999999999999999999 9999999998


Q ss_pred             ccCC
Q 041030          222 LKDS  225 (249)
Q Consensus       222 l~~~  225 (249)
                      +.+.
T Consensus        70 ~~~~   73 (75)
T 1x4j_A           70 SGPS   73 (75)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=4.6e-15  Score=105.43  Aligned_cols=55  Identities=31%  Similarity=0.864  Sum_probs=48.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .....|+||++.|..+..         ++.++|+|+||..||..|++. +.+||+||..+.....
T Consensus        12 ~~~~~C~IC~~~~~~~~~---------~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGED---------VRRLPCMHLFHQVCVDQWLIT-NKKCPICRVDIEAQLP   66 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSC---------EEECTTSCEEEHHHHHHHHHH-CSBCTTTCSBSCSCCC
T ss_pred             CCCCCCeeCCccccCCCc---------EEEeCCCCHHHHHHHHHHHHc-CCCCcCcCccccCcCC
Confidence            346799999999988777         899999999999999999999 9999999999876543

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=99.55  E-value=2.4e-15  Score=102.23  Aligned_cols=50  Identities=32%  Similarity=0.840  Sum_probs=46.0

Q ss_pred             CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ++..|+||++.|..++.         ++.++ |+|+||..||.+|++. +.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~---------~~~~~~C~H~f~~~Ci~~w~~~-~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEE---------ARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSC---------CEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCc---------eEECCCCCCcccHHHHHHHHHc-CCcCcCCCCEeE
Confidence            47799999999998887         88898 9999999999999999 999999999874

>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=7.5e-15  Score=105.71  Aligned_cols=54  Identities=33%  Similarity=0.903  Sum_probs=48.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      .+...|+||++.|..+..         ++.|+|+|+||..||.+|++. +.+||+||+++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~---------~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDE---------LGICPCKHAFHRKCLIKWLEV-RKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSC---------EEEETTTEEEEHHHHHHHHHH-CSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCc---------EEEcCCCCEecHHHHHHHHHc-CCcCCCcCccccccc
Confidence            346799999999998877         888999999999999999999 999999999986543

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.53  E-value=9.5e-15  Score=106.19  Aligned_cols=57  Identities=40%  Similarity=1.057  Sum_probs=50.5

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIGS  229 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~~  229 (249)
                      .+...|+||++.|.....         ++.++|+|+||..||..|++. +.+||+||..+....+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~---------~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           13 GSGLECPVCKEDYALGES---------VRQLPCNHLFHDSCIVPWLEQ-HDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSC---------EEECTTSCEEETTTTHHHHTT-TCSCTTTCCCCCCSCSCC
T ss_pred             CCCCCCeeCCccccCCCC---------EEEeCCCCeecHHHHHHHHHc-CCcCcCcCCccCCcccCC
Confidence            347899999999998777         889999999999999999999 899999999998766543

>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=7.2e-15  Score=108.58  Aligned_cols=64  Identities=22%  Similarity=0.543  Sum_probs=44.6

Q ss_pred             cCccccccccccccccCCCCCC--CCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDD--SDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~--~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .++..|+||++.|...-....+  ..+..++.++ |+|+||.+||.+||+. +++||+||+++....+
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~~~   79 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ-NNRCPLCQQDWVVQRI   79 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTT-CCBCTTTCCBCCEEEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHh-CCCCCCcCCCcchhhc
Confidence            3467899999998652000000  0001155555 9999999999999999 9999999999875543

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=99.49  E-value=2.3e-14  Score=97.13  Aligned_cols=51  Identities=33%  Similarity=0.713  Sum_probs=44.4

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      +...|+||++.|..+...        ++.++|+|+||..||.+|++. +.+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~--------~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVV--------AHVLPCGHLLHRTCYEEMLKE-GYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSC--------EEECTTSCEEETTHHHHHHHH-TCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcC--------eEecCCCCcccHHHHHHHHHc-CCcCCCCCCcCC
Confidence            367999999999765431        788899999999999999999 899999999875

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus}

Probab=99.44  E-value=5.6e-14  Score=99.92  Aligned_cols=55  Identities=27%  Similarity=0.696  Sum_probs=46.8

Q ss_pred             cCcccccccccccccc----CCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVR----DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~----~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .+...|+||++.|...    ..         ++.++|+|+||..||.+|++. +.+||+||..+....+
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~---------~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRL---------IVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY   66 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCC---------EEECTTSCEEEHHHHHHHHHH-CSBCTTTCCBCCCCSC
T ss_pred             CCCCCCcccChhhhccccccCC---------eEeCCCCChHhHHHHHHHHHc-CCCCCCCCCccChhhe
Confidence            3478999999999763    23         688899999999999999999 9999999999875543

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.44  E-value=6.4e-15  Score=116.88  Aligned_cols=79  Identities=20%  Similarity=0.365  Sum_probs=9.9

Q ss_pred             HhhhhheeccccccccccCccccccccccccccCCCCCC------CCccceEEeccCCccChhhHHHHHhhCCCCCcccc
Q 041030          146 EALKRVRISESTQLTRSNEVQCCPICKEEFRVRDDVDDD------SDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCR  219 (249)
Q Consensus       146 ~~lp~~~~~~~~~~~~~~~~~~C~ICle~f~~~~~~~~~------~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR  219 (249)
                      ..+...++..-.......++..|+||++.|.........      ..+..++.++|+|.||..||.+||+. +++||+||
T Consensus        29 ~r~~ikkw~ava~w~wd~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~-~~~CP~Cr  107 (117)
T 4a0k_B           29 KRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDN  107 (117)
T ss_dssp             CSEEEEEEEEEEEEEECCCC------------------------------------------------------------
T ss_pred             CceEEEEEEEEEEEeecCCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc-CCcCCCCC
Confidence            334444444444445556678999999999864321111      11223555689999999999999999 99999999


Q ss_pred             ccccCC
Q 041030          220 YELKDS  225 (249)
Q Consensus       220 ~~l~~~  225 (249)
                      +++.-.
T Consensus       108 ~~~~~~  113 (117)
T 4a0k_B          108 REWEFQ  113 (117)
T ss_dssp             ------
T ss_pred             Ceeeee
Confidence            987543

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=99.43  E-value=3.3e-14  Score=110.80  Aligned_cols=63  Identities=25%  Similarity=0.485  Sum_probs=47.4

Q ss_pred             ccccCccccccccccccccCCCCC------CCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          160 TRSNEVQCCPICKEEFRVRDDVDD------DSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       160 ~~~~~~~~C~ICle~f~~~~~~~~------~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ....++..|+||++.|........      ...+-.++.++|+|.||..||.+||.. +.+||+||+++.
T Consensus        32 ~~d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~Cr~~~~  100 (106)
T 3dpl_R           32 AWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWE  100 (106)
T ss_dssp             EESSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-CSBCSSSCSBCC
T ss_pred             ecCCCCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc-CCcCcCCCCcce
Confidence            344567899999999986522110      111223778899999999999999999 999999999864

>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.42  E-value=8.7e-14  Score=98.09  Aligned_cols=56  Identities=27%  Similarity=0.729  Sum_probs=45.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      .+...|+||++.|.....     ....++.++|+|+||..||..|++. +.+||+||..|..
T Consensus        13 ~~~~~C~IC~~~~~~~~~-----~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQ-----NGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTT-----TTCCEEECSSSCEEEHHHHHHHHHH-CSSCTTTCCCCCC
T ss_pred             CCCCCCcccCcccccccc-----ccCCeEeCCCCChhcHHHHHHHHHc-CCCCCCCCCccCc
Confidence            347899999999986421     0011588999999999999999999 9999999998854

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=99.42  E-value=1.7e-13  Score=106.32  Aligned_cols=61  Identities=25%  Similarity=0.461  Sum_probs=44.6

Q ss_pred             ccccccccccccccCCCCCC------CCccceEEeccCCccChhhHHHHHhh----CCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDD------SDEVMIMELPCKHLYHSDCIVPWLRH----YSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~------~~~~~v~~LpC~H~FH~~CI~~WL~~----~~~sCPvCR~~l~~~  225 (249)
                      +..|+||++.|..+......      .....++.++|+|+||..||..||..    .+.+||+||..+...
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            56999999999875421110      01123567889999999999999952    177999999988654

>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding; HET: SUC; 1.50A {Homo sapiens}

Probab=99.41  E-value=1.1e-13  Score=96.16  Aligned_cols=56  Identities=27%  Similarity=0.724  Sum_probs=45.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      +..|+||++.+.....     ....++.++|+|+||..||.+|++. +.+||+||..+....
T Consensus         3 ~~~C~IC~~~~~~~~~-----~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQ-----NGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCBCTTTCCBHHHHHH-----TTCCEEEETTSCEEEHHHHHHHHHH-CSBCTTTCCBCTTTC
T ss_pred             CCCCCccChhhhCccc-----cCCCEEeCCCCCchhHHHHHHHHHc-CCCCCCCCccCCccc
Confidence            6799999999986410     0011678899999999999999999 999999999987543

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=5.6e-13  Score=95.63  Aligned_cols=53  Identities=25%  Similarity=0.496  Sum_probs=45.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG  228 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~  228 (249)
                      .+...|+||++.|..            .+.+ +|+|.||..||..|++. +.+||+||..+....+.
T Consensus        13 ~~~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           13 TPYILCSICKGYLID------------ATTITECLHTFCKSCIVRHFYY-SNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CGGGSCTTTSSCCSS------------CEECSSSCCEECHHHHHHHHHH-CSSCTTTCCCCCSSCSC
T ss_pred             CCCCCCCCCChHHHC------------cCEECCCCCHHHHHHHHHHHHc-CCcCCCcCcccCccccc
Confidence            347899999999987            4455 89999999999999999 99999999999765543

>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid herpesvirus 1} SCOP: g.44.1.1

Probab=99.37  E-value=3.1e-13  Score=95.52  Aligned_cols=49  Identities=37%  Similarity=0.910  Sum_probs=43.4

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      .+..|+||++.+...           ++.++|+|.||..||..|++. +.+||+||..+..
T Consensus         4 ~~~~C~IC~~~~~~~-----------~~~~~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNY-----------SMALPCLHAFCYVCITRWIRQ-NPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC-----------EEETTTTEEESTTHHHHHHHH-SCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCC-----------cEecCCCCeeHHHHHHHHHhC-cCcCcCCChhhHh
Confidence            367999999998752           578999999999999999999 9999999998864

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.37  E-value=2e-13  Score=97.79  Aligned_cols=52  Identities=27%  Similarity=0.600  Sum_probs=45.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .+...|+||++.+..            .+.++|+|+||..||..|+.. +..||+||..+....+
T Consensus        13 ~~~~~C~IC~~~~~~------------~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~~   64 (71)
T 2d8t_A           13 LTVPECAICLQTCVH------------PVSLPCKHVFCYLCVKGASWL-GKRCALCRQEIPEDFL   64 (71)
T ss_dssp             SSCCBCSSSSSBCSS------------EEEETTTEEEEHHHHHHCTTC-SSBCSSSCCBCCHHHH
T ss_pred             CCCCCCccCCcccCC------------CEEccCCCHHHHHHHHHHHHC-CCcCcCcCchhCHhhc
Confidence            346899999999876            778899999999999999999 8999999999865433

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=4.5e-13  Score=95.77  Aligned_cols=53  Identities=25%  Similarity=0.589  Sum_probs=45.0

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh--CCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH--YSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~--~~~sCPvCR~~l~~~~~  227 (249)
                      .+...|+||++.|..            .+.++|+|.||..||..|++.  ++..||+||..+....+
T Consensus        18 ~~~~~C~IC~~~~~~------------~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           18 QEEVICPICLDILQK------------PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCBCTTTCSBCSS------------EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             ccCCEeccCCcccCC------------eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            347899999999986            777899999999999999973  26689999999876554

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.33  E-value=6.3e-13  Score=93.70  Aligned_cols=52  Identities=17%  Similarity=0.431  Sum_probs=43.7

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      .+...|+||++.+..            .+.++|+|+||..||..|++.++..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCS------------PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCEECTTTCCEESS------------CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CcCCCCCCCChHhcC------------eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            347899999999986            4458999999999999999643779999999987654

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens}

Probab=99.33  E-value=1.1e-12  Score=94.78  Aligned_cols=49  Identities=31%  Similarity=0.636  Sum_probs=42.6

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCC--CCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYS--TTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~--~sCPvCR~~l~~  224 (249)
                      .+...|+||++.|..            .+.++ |+|.||..||..|++. +  .+||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~-~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           13 PDELLCLICKDIMTD------------AVVIPCCGNSYCDECIRTALLE-SDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CGGGSCSSSCCCCTT------------CEECSSSCCEECTTHHHHHHHH-SSSSCCSSSCCSSCC
T ss_pred             CCCCCCcCCChHHhC------------CeEcCCCCCHHHHHHHHHHHHh-cCCCcCCCCCCcCCC
Confidence            347899999999986            67799 9999999999999997 5  689999997644

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.32  E-value=1.1e-12  Score=95.97  Aligned_cols=48  Identities=21%  Similarity=0.570  Sum_probs=43.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      .....|+||++.|..            .+.++|+|+||..||..|++. ..+||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN------------PVVTKCRHYFCESCALEHFRA-TPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS------------EEECTTSCEEEHHHHHHHHHH-CSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC------------eeEccCCCHhHHHHHHHHHHC-CCcCCCcCcccc
Confidence            346799999999976            667999999999999999999 999999999985

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=1.4e-12  Score=96.61  Aligned_cols=53  Identities=28%  Similarity=0.744  Sum_probs=44.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccC-----CccChhhHHHHHhhCC--CCCccccccccCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-----HLYHSDCIVPWLRHYS--TTCPVCRYELKDSI  226 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-----H~FH~~CI~~WL~~~~--~sCPvCR~~l~~~~  226 (249)
                      .++..|.||+++|..++.         + .+||+     |.||.+||.+||.. +  .+||+||+++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~---------l-~~pC~C~Gs~h~fH~~Cl~~Wl~~-~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESP---------L-ITPCHCTGSLHFVHQACLQQWIKS-SDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSC---------E-ECSSSCCSSSCCEETTHHHHHHHH-HCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCeEcCccccCCCe---------e-EeccccCCcCCeeCHHHHHHHHhh-CCCCCCCCCCCeeecCc
Confidence            346799999999987654         4 68996     99999999999998 5  48999999997543

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=99.31  E-value=1.4e-12  Score=94.52  Aligned_cols=50  Identities=26%  Similarity=0.424  Sum_probs=44.5

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|..            .+.++|||.||..||..|+..++.+||+||..+...
T Consensus         7 ~~~~C~IC~~~~~~------------Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMKD------------PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS------------EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCCCccccccC------------CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            37899999999987            777899999999999999987678999999998654

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.31  E-value=2.3e-12  Score=95.02  Aligned_cols=56  Identities=30%  Similarity=0.548  Sum_probs=46.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC---CCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS---TTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~---~sCPvCR~~l~~~~~  227 (249)
                      .+...|+||++.|......        ++.++|+|.||..||..|++. +   ..||+||..+....+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~--------~~~~~CgH~fC~~Ci~~~~~~-~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLR--------PKLLHCGHTICRQCLEKLLAS-SINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSC--------EEECSSSCEEEHHHHHHHHHH-CSSCBCCTTTCCCBCCSST
T ss_pred             cCCCCCccCCccccccCCC--------eEECCCCChhhHHHHHHHHHc-CCCCcCCCCCCCcccchhH
Confidence            3478999999999875531        678899999999999999998 5   789999999876544

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=99.30  E-value=6.4e-13  Score=107.08  Aligned_cols=48  Identities=35%  Similarity=0.849  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +..|+||++.|..            ++.++|||.||..||..|+.. +.+||+||.++...
T Consensus        53 ~~~C~iC~~~~~~------------~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIE------------AVTLNCAHSFCSYCINEWMKR-KIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSS------------EEEETTSCEEEHHHHHHHTTT-CSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCC------------ceECCCCCCccHHHHHHHHHc-CCcCCCCCCcCCCC
Confidence            5689999999976            778999999999999999999 99999999998643

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.28  E-value=8.5e-13  Score=100.87  Aligned_cols=48  Identities=35%  Similarity=0.668  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEE-eccCCccChhhHHHHHhhCC-CCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIME-LPCKHLYHSDCIVPWLRHYS-TTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~WL~~~~-~sCPvCR~~l~~~  225 (249)
                      ...|+||++.|..            .+. ++|||.||..||..|+.. + .+||+||..+...
T Consensus        22 ~~~C~IC~~~~~~------------p~~~~~CgH~FC~~Ci~~~~~~-~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           22 VFRCFICMEKLRD------------ARLCPHCSKLCCFSCIRRWLTE-QRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HTBCTTTCSBCSS------------EEECTTTCCEEEHHHHHHHHHH-TCSBCTTTCCBCCGG
T ss_pred             CCCCccCCccccC------------ccccCCCCChhhHHHHHHHHHH-CcCCCCCCCCcCCHH
Confidence            7899999999986            666 899999999999999999 6 7999999998644

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.27  E-value=2.9e-12  Score=90.00  Aligned_cols=55  Identities=27%  Similarity=0.518  Sum_probs=44.2

Q ss_pred             ccccccccc-cccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          165 VQCCPICKE-EFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle-~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +..|+||++ .|......        ++.++|||+||..||..|+..+..+||+||..+....+
T Consensus         3 ~~~C~IC~~~~~~~~~~~--------~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLK--------LMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCC--------EEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCcCCcCCCCccCCCccC--------eecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            679999999 77665431        45689999999999999987646789999999876544

>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=1.2e-12  Score=93.04  Aligned_cols=48  Identities=29%  Similarity=0.813  Sum_probs=42.5

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.+..             +.++|+|.||..||..|+.. +.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~-------------~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A           14 DEEECCICMDGRAD-------------LILPCAHSFCQKCIDKWSDR-HRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCSSSCCSCCS-------------EEETTTEEECHHHHHHSSCC-CSSCHHHHHCTTCC
T ss_pred             CCCCCeeCCcCccC-------------cccCCCCcccHHHHHHHHHC-cCcCCCcCCcccCC
Confidence            46899999999875             35899999999999999998 99999999998754

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=5.3e-12  Score=87.98  Aligned_cols=44  Identities=27%  Similarity=0.632  Sum_probs=38.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh--CCCCCccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH--YSTTCPVC  218 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~--~~~sCPvC  218 (249)
                      .+...|+||++.|..            .+.++|+|+||..||..|++.  ++..||+|
T Consensus        18 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK------------PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS------------CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC------------eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            447899999999986            677899999999999999984  26689998

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.23  E-value=9.2e-12  Score=90.73  Aligned_cols=50  Identities=30%  Similarity=0.620  Sum_probs=43.3

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-----CCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-----STTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-----~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|..            .+.++|+|.||..||..|+...     ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKE------------PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSS------------CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCc------------ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            47899999999976            5678999999999999999972     56899999998754

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.22  E-value=4.4e-12  Score=99.60  Aligned_cols=54  Identities=28%  Similarity=0.704  Sum_probs=46.6

Q ss_pred             Ccccccccccccccc----CCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          164 EVQCCPICKEEFRVR----DDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       164 ~~~~C~ICle~f~~~----~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      +...|+||++.|...    ..         ++.++|||+||..||..||+. +.+||+||+.+....+
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~---------~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRL---------IVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCC---------EEEETTCCEEEHHHHHHHHTT-CSBCTTTCCBCTTTCE
T ss_pred             CCCCCcccChhhhCccccccC---------eEecCCCChhhHHHHHHHHHh-CCCCCCCCCcCccccc
Confidence            367999999999764    23         588999999999999999999 9999999999976544

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=1.9e-11  Score=88.99  Aligned_cols=53  Identities=30%  Similarity=0.678  Sum_probs=44.3

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh-----CCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH-----YSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~-----~~~sCPvCR~~l~~~~~  227 (249)
                      .+...|+||++.|..            .+.++|+|.||..||..|+..     +...||+||..+....+
T Consensus        17 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~   74 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ------------PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENI   74 (85)
T ss_dssp             CCCCCCTTTCSCCSS------------CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSC
T ss_pred             cCCCCCCCCCcccCC------------ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhc
Confidence            347899999999976            456899999999999999986     26789999999876543

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=99.20  E-value=5.7e-12  Score=95.56  Aligned_cols=47  Identities=36%  Similarity=0.756  Sum_probs=42.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.|..            .+.+ +|||.||..||..|+.. +.+||+||..+..
T Consensus        22 ~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNI------------AMIIPQCSHNYCSLCIRKFLSY-KTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSS------------EEECTTTCCEEEHHHHHHHHTT-CCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCC------------cCEECCCCCHhhHHHHHHHHHC-CCCCCCCCCcCCh
Confidence            6799999999987            5566 89999999999999998 8999999998865

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A

Probab=99.20  E-value=8.8e-12  Score=96.07  Aligned_cols=48  Identities=27%  Similarity=0.692  Sum_probs=43.2

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...|+||++.|..            .+.+ +|||.||..||..|+.. +.+||+||..+...
T Consensus        15 ~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFID------------ATTIIECLHSFCKTCIVRYLET-SKYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSS------------EEEETTTCCEEEHHHHHHHHTS-CSBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhC------------cCEeCCCCChhhHHHHHHHHHh-CCcCcCCCcccccc
Confidence            7899999999986            5566 99999999999999999 89999999998653

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.19  E-value=8.1e-12  Score=98.53  Aligned_cols=48  Identities=29%  Similarity=0.589  Sum_probs=42.9

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.|..            .+.++|||.||..||..|+..+..+||+||..+..
T Consensus        52 ~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR------------PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS------------EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC------------cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            6799999999986            77889999999999999998635599999999865

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.19  E-value=2.4e-12  Score=93.16  Aligned_cols=51  Identities=29%  Similarity=0.585  Sum_probs=43.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC------CCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY------STTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~------~~sCPvCR~~l~~~  225 (249)
                      .+...|+||++.|..            .+.++|||.||..||..|+...      ...||+||..+...
T Consensus        10 ~~~~~C~IC~~~~~~------------p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           10 QEEVTCPICLELLTE------------PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCEETTTTEECSS------------CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             ccCCCCcCCCcccCC------------eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            347899999999976            4558999999999999999862      56899999998764

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.16  E-value=1e-11  Score=84.64  Aligned_cols=44  Identities=27%  Similarity=0.757  Sum_probs=37.0

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh--CCCCCccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH--YSTTCPVC  218 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~--~~~sCPvC  218 (249)
                      .+...|+||++.+..            .+.++|+|+||..||..|+..  .+.+||+|
T Consensus        13 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE------------PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS------------CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc------------cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            347899999999987            455899999999999999553  27899998

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.16  E-value=1.7e-11  Score=91.54  Aligned_cols=49  Identities=29%  Similarity=0.607  Sum_probs=42.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-CCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-STTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-~~sCPvCR~~l~  223 (249)
                      .+...|+||++.|..            .+.++ |||.||..||..|+... +..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTD------------AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSS------------CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcC------------ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            347899999999986            77899 99999999999999762 358999999873

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=99.15  E-value=1.7e-11  Score=100.55  Aligned_cols=50  Identities=24%  Similarity=0.513  Sum_probs=43.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|..            .+.++|+|.||..||..|+..+..+||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~------------pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ------------PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS------------EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC------------CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            36899999999987            777999999999999999998344899999998765

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=99.14  E-value=1.2e-11  Score=97.14  Aligned_cols=56  Identities=27%  Similarity=0.714  Sum_probs=45.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      ...|+||++.|.....     ....++.++|+|+||..||.+|++. +++||+||..+....
T Consensus        72 ~~~C~iC~~~~~~~~~-----~~~~~~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           72 TVSCPICMDGYSEIVQ-----NGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR  127 (133)
T ss_dssp             SCBCTTTCCBHHHHHH-----TTCCEEEETTSBEEEHHHHHHHHHH-CSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCccccccc-----cCcceEeCCCCChhhHHHHHHHHHc-CCCCCCCCCcCChhc
Confidence            6789999999986311     0011578899999999999999999 999999999987643

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=99.14  E-value=5.3e-12  Score=98.27  Aligned_cols=49  Identities=29%  Similarity=0.595  Sum_probs=43.2

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ++..|+||++.|..            .+.++|||.||..||..|+..++.+||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVE------------PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSS------------CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCc------------eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            36899999999986            67789999999999999998756789999999863

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=99.12  E-value=2.1e-11  Score=100.62  Aligned_cols=48  Identities=35%  Similarity=0.789  Sum_probs=42.2

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.|..            .+.+ +|||.||..||..|+..++..||+||..+..
T Consensus        54 ~~~C~IC~~~~~~------------p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           54 ELMCPICLDMLKN------------TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHBCTTTSSBCSS------------EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCcccChHhhC------------cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            6799999999987            5555 8999999999999999767789999999854

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.12  E-value=1.8e-11  Score=94.16  Aligned_cols=50  Identities=24%  Similarity=0.755  Sum_probs=42.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC---CCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS---TTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~---~sCPvCR~~l~~~~~  227 (249)
                      ...|+||++.|..            .+.++|||.||..||..|+.. +   .+||+||..+....+
T Consensus        21 ~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~-~~~~~~CP~Cr~~~~~~~~   73 (112)
T 1jm7_A           21 ILECPICLELIKE------------PVSTKCDHIFCKFCMLKLLNQ-KKGPSQCPLCKNDITKRSL   73 (112)
T ss_dssp             HTSCSSSCCCCSS------------CCBCTTSCCCCSHHHHHHHHS-SSSSCCCTTTSCCCCTTTC
T ss_pred             CCCCcccChhhcC------------eEECCCCCHHHHHHHHHHHHh-CCCCCCCcCCCCcCCHhhc
Confidence            6799999999976            455899999999999999997 4   389999999876544

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=99.10  E-value=3.5e-11  Score=94.27  Aligned_cols=51  Identities=29%  Similarity=0.634  Sum_probs=43.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      .+...|+||++.|..            .+.++|||.||..||..|+.....+||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           16 ESKYECPICLMALRE------------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CGGGBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCcCChhhcC------------eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            347899999999986            677899999999999999998334999999998654

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=99.09  E-value=3.6e-11  Score=93.64  Aligned_cols=51  Identities=31%  Similarity=0.680  Sum_probs=44.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      ...|+||++.|..            .+.++|||.||..||..|+.....+||+||..+....+
T Consensus        23 ~~~C~IC~~~~~~------------p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHILAD------------PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHhcC------------cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            6799999999986            67799999999999999999756689999999876543

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.06  E-value=2.5e-11  Score=83.35  Aligned_cols=50  Identities=24%  Similarity=0.483  Sum_probs=41.5

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG  228 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~  228 (249)
                      .+...|+||++.|..            .+.|+|+|.||..||..|    ...||+||+.+.....|
T Consensus         4 ~~~~~C~IC~~~~~~------------p~~l~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~~~   53 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC------------PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGADT   53 (56)
T ss_dssp             CCCSSCSSSCSSCBC------------CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCSSC
T ss_pred             ccCCCceEeCCccCC------------eEEcCCCCcccHHHHccC----CCCCCcCCcEeecCCcC
Confidence            347899999999987            567999999999999884    66899999998765443

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.06  E-value=8.7e-11  Score=87.43  Aligned_cols=49  Identities=22%  Similarity=0.232  Sum_probs=44.8

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|.+            .+.++|||.|+..||..|+.. +.+||+||..+...
T Consensus        13 ~~~~CpI~~~~m~d------------PV~~~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~   61 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD------------PVRLPSGTVMDRSIILRHLLN-SPTDPFNRQMLTES   61 (85)
T ss_dssp             TTTBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHH-CSBCTTTCCBCCGG
T ss_pred             hheECcccCchhcC------------CeECCCCCEECHHHHHHHHhc-CCCCCCCcCCCChH
Confidence            37899999999998            888999999999999999998 99999999988643

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=99.05  E-value=4.5e-11  Score=97.14  Aligned_cols=51  Identities=24%  Similarity=0.458  Sum_probs=43.7

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      .+...|+||++.|..            .++++|||.||..||..|++.+..+||+||.++...
T Consensus        29 ~~~~~C~IC~~~~~~------------pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           29 EAKYLCSACRNVLRR------------PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CGGGBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CcCcCCCCCChhhcC------------cEECCCCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            347899999999987            677899999999999999998345899999987443

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=1.4e-10  Score=84.81  Aligned_cols=50  Identities=20%  Similarity=0.486  Sum_probs=41.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCC--CCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYS--TTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~--~sCPvCR~~l~~~  225 (249)
                      ....|+||++.|..+.           +-..|+|.||..||.+||+. +  .+||+||.++...
T Consensus        14 ~i~~C~IC~~~i~~g~-----------~C~~C~h~fH~~Ci~kWl~~-~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQ-----------SCETCGIRMHLPCVAKYFQS-NAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSCBCSSSCCBCSSSE-----------ECSSSCCEECHHHHHHHSTT-CSSCCCTTTCSCCCSC
T ss_pred             CCCcCcchhhHcccCC-----------ccCCCCchhhHHHHHHHHHh-cCCCCCCCCcCcCCCC
Confidence            3579999999998643           23369999999999999998 6  8999999987644

>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B

Probab=99.05  E-value=8.8e-11  Score=86.39  Aligned_cols=57  Identities=19%  Similarity=0.397  Sum_probs=43.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .++..|+||++.+......        +..++|||.||..||..|+..+..+||+||+.+....+
T Consensus         9 ~~~~~CpICle~~~~~d~~--------~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDIN--------FFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTT--------CCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCcccccc--------ccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            3478999999988653220        22234999999999999886547899999999976554

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=99.02  E-value=1.5e-10  Score=81.62  Aligned_cols=46  Identities=24%  Similarity=0.513  Sum_probs=40.9

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe--ccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--PCKHL-YHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      +..|.||++.+..            ++.+  ||||+ |+..|+..|++. +..||+||+.+.
T Consensus         8 ~~~C~IC~~~~~~------------~~~~~~pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPKN------------GCIVHGKTGHLMACFTCAKKLKKR-NKPCPVCRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCSC------------EEEEETTEEEEEECHHHHHHHHHT-TCCCTTTCCCCC
T ss_pred             cCCCCcCCCCCCC------------EEEECCCCCChhhHHHHHHHHHHc-CCcCCCcCcchh
Confidence            6799999999876            5555  99999 899999999998 899999999884

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.02  E-value=1.5e-10  Score=88.84  Aligned_cols=49  Identities=22%  Similarity=0.252  Sum_probs=44.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|.+            .+.++|||.|+..||..||.. +.+||+||..+...
T Consensus        28 ~~~~CpI~~~~m~d------------PV~~~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~   76 (100)
T 2kre_A           28 DEFRDPLMDTLMTD------------PVRLPSGTIMDRSIILRHLLN-SPTDPFNRQTLTES   76 (100)
T ss_dssp             TTTBCTTTCSBCSS------------EEEETTTEEEEHHHHHHHTTS-CSBCSSSCCBCCTT
T ss_pred             HhhCCcCccCcccC------------CeECCCCCEEchHHHHHHHHc-CCCCCCCCCCCChh
Confidence            37899999999998            888999999999999999998 99999999988653

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.00  E-value=2.2e-10  Score=87.64  Aligned_cols=49  Identities=20%  Similarity=0.112  Sum_probs=44.9

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccC-CccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-HLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +.+.|+||++.|.+            .+.++|| |.|+..||..||.. +.+||+||..|...
T Consensus        21 ~~~~CpI~~~~m~d------------PV~~~cG~htf~r~cI~~~l~~-~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           21 DEFLDPIMSTLMCD------------PVVLPSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSS------------EEECTTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTT
T ss_pred             HhcCCcCccccccC------------CeECCCCCeEECHHHHHHHHHh-CCCCCCCCCCCChh
Confidence            37899999999998            8889999 99999999999998 89999999988653

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.93  E-value=5.6e-10  Score=78.48  Aligned_cols=46  Identities=22%  Similarity=0.538  Sum_probs=40.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe--ccCCc-cChhhHHHHHhhCCCCCcccccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL--PCKHL-YHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L--pC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ...|.||++.+..            ++.+  ||||+ |+..|+..|.+. +..||+||..+.
T Consensus         7 ~~~C~IC~~~~~~------------~~~~~~pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPRD------------GNIIHGRTGHLVTCFHCARRLKKA-GASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBSC------------EEEEETTEEEEEECHHHHHHHHHT-TCBCTTTCCBCC
T ss_pred             CCCCcccCCcCCC------------eEEEecCCCCHhHHHHHHHHHHHh-CCcCCCcCchhh
Confidence            6799999998776            4455  99999 999999999988 889999999884

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=98.90  E-value=7.7e-10  Score=103.59  Aligned_cols=49  Identities=35%  Similarity=0.830  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...|+||++.+..            ++.+||||+||..||..|+...+.+||+||..+...
T Consensus       332 ~~~C~ICle~~~~------------pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD------------VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC------------EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC------------eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            4699999999976            888999999999999999993388999999988653

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.88  E-value=3e-10  Score=88.77  Aligned_cols=45  Identities=29%  Similarity=0.642  Sum_probs=39.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.|..            .+.+ +|||.||..||..|+.   ..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~------------pv~~~~CgH~fC~~Ci~~~~~---~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCSRCTNILRE------------PVCLGGCEHIFCSNCVSDCIG---TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCSSSCSCCSS------------CBCCCSSSCCBCTTTGGGGTT---TBCSSSCCBCSC
T ss_pred             CCCCCCCChHhhC------------ccEeCCCCCHHHHHHHHHHhc---CCCcCCCCcCcc
Confidence            6799999999986            5567 8999999999999987   589999999854

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.88  E-value=9e-10  Score=96.45  Aligned_cols=49  Identities=24%  Similarity=0.243  Sum_probs=43.6

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      +...|+||++.|.+            .++++|||.||..||..|+..+..+||+||..+..
T Consensus       207 ~~~~c~i~~~~~~d------------Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMRE------------PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSS------------EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcC------------CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            47899999999998            88899999999999999999844559999998854

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=98.87  E-value=9.5e-10  Score=90.99  Aligned_cols=51  Identities=29%  Similarity=0.634  Sum_probs=44.1

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      .+...|+||++.|..            .+.++|||+||..||..|+..+..+||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~------------pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALRE------------AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcC------------cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            347899999999987            677899999999999999987345999999988653

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.85  E-value=4.1e-10  Score=81.43  Aligned_cols=43  Identities=28%  Similarity=0.634  Sum_probs=38.1

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      +..|+||++.+..            ++.+||+|. ||..|+..|     ..||+||..+..
T Consensus        24 ~~~C~iC~~~~~~------------~~~~pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIA------------IVFVPCGHLVTCKQCAEAV-----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCC------------EEEETTCCBCCCHHHHTTC-----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCC------------EEEcCCCChhHHHHhhhcC-----ccCCCcCcCccC
Confidence            6799999999877            788999999 999999988     479999998754

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.81  E-value=1.6e-09  Score=81.87  Aligned_cols=48  Identities=31%  Similarity=0.641  Sum_probs=41.0

Q ss_pred             CccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhC-----CCCCcc--cccc-cc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHY-----STTCPV--CRYE-LK  223 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~-----~~sCPv--CR~~-l~  223 (249)
                      +...|+||++.|.+            .+.++ |||+|+..||..||..+     ..+||+  |+.. +.
T Consensus         6 ~~~~CPI~~~~~~d------------PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~   62 (94)
T 2yu4_A            6 SGFTCPITKEEMKK------------PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIR   62 (94)
T ss_dssp             SCCBCTTTCSBCSS------------EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBC
T ss_pred             cEeECcCcCchhcC------------CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccC
Confidence            47899999999998            78886 99999999999999872     248999  9866 54

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.70  E-value=7.7e-09  Score=87.41  Aligned_cols=50  Identities=24%  Similarity=0.232  Sum_probs=43.5

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+||++.|.+            .+.++|||.|+..||..||..+..+||+||..+...
T Consensus       105 ~~f~CPI~~elm~D------------PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          105 DYLCGKISFELMRE------------PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             GGGBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             HhhcccCccccCCC------------CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            47899999999998            888999999999999999987334799999988643

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.68  E-value=1.4e-08  Score=72.50  Aligned_cols=45  Identities=24%  Similarity=0.665  Sum_probs=38.5

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      .+...|.||++.+..            ++.+||+|+ |+..|+..     ...||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~------------~v~~pCgH~~~C~~C~~~-----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN------------WVLLPCRHTCLCDGCVKY-----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCCC------------CEETTTTBCCSCTTHHHH-----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCCC------------EEEECCCChhhhHHHHhc-----CCCCCCCCcchhc
Confidence            346799999998876            888999999 99999973     5689999998864

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.65  E-value=5.2e-09  Score=75.57  Aligned_cols=43  Identities=28%  Similarity=0.646  Sum_probs=36.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.+..            ++.+||+|. ||..|+..     ...||+||..+..
T Consensus        25 ~~~C~IC~~~~~~------------~~~~pCgH~~~C~~C~~~-----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIA------------IVFVPCGHLVTCKQCAEA-----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCC------------BCCSSSCCCCBCHHHHHH-----CSBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCC------------EEEecCCCHHHHHHHhhC-----CCCCccCCceecC
Confidence            5699999999876            667999999 99999953     5689999998854

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.65  E-value=1.2e-08  Score=71.26  Aligned_cols=50  Identities=28%  Similarity=0.666  Sum_probs=38.4

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccC--C---ccChhhHHHHHhh-CCCCCccccccccC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK--H---LYHSDCIVPWLRH-YSTTCPVCRYELKD  224 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~--H---~FH~~CI~~WL~~-~~~sCPvCR~~l~~  224 (249)
                      ++...|.||+++.  ++.         . .+||.  +   .||..||.+|+.. ++.+||+||+++..
T Consensus         4 ~~~~~CrIC~~~~--~~~---------l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNE---------R-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEEC--SCC---------C-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCC--CCc---------e-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            3467999999973  222         3 58854  5   9999999999986 36789999998753

>3k1l_B Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A {Drosophila melanogaster}

Probab=98.57  E-value=1.6e-08  Score=93.14  Aligned_cols=59  Identities=27%  Similarity=0.492  Sum_probs=41.5

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC----------CCCCccccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY----------STTCPVCRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~----------~~sCPvCR~~l~~~  225 (249)
                      +....|+||++.+..+...   ++ ..-....|+|.||..||.+||+.-          ..+||+||.++...
T Consensus       306 e~~~ECaICys~~l~~g~l---Pd-k~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEV---PL-VSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCC---CC-BCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCC---cc-ccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            4578999999999873320   00 000123599999999999999861          14699999988643

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.54  E-value=1.6e-08  Score=74.16  Aligned_cols=43  Identities=30%  Similarity=0.644  Sum_probs=37.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|.||++.+..            ++.+||||. |+..|+..|     ..||+||..+..
T Consensus        18 ~~~C~IC~~~~~~------------~v~~pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEIN------------STFCPCGHTVCCESCAAQL-----QSCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCC------------EEEETTCBCCBCHHHHTTC-----SBCTTTCCBCCE
T ss_pred             CCEeEEeCcccCc------------EEEECCCCHHHHHHHHHhc-----CcCCCCCchhhC
Confidence            5699999999876            888999999 999999876     379999998865

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.52  E-value=2.7e-08  Score=74.66  Aligned_cols=52  Identities=19%  Similarity=0.591  Sum_probs=40.7

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCcc--cccc--ccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPV--CRYE--LKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPv--CR~~--l~~  224 (249)
                      +..+|+||++.+.....         +...+|+|.||.+|+..++...       .-+||.  |+..  +..
T Consensus         4 ~~~~C~IC~~~~~~~~~---------~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQM---------TTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGE---------EEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccc---------eEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            36799999999886543         4444799999999999998751       237999  9988  554

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.49  E-value=5.4e-08  Score=68.11  Aligned_cols=48  Identities=10%  Similarity=0.190  Sum_probs=42.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...|+||++.+.+            .+.+ +|||+|...||.+||+. +.+||+++..|...
T Consensus         3 ~~~CpIs~~~m~d------------PV~~~~sG~~yer~~I~~~l~~-~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRR------------PVLSPKSRTIFEKSLLEQYVKD-TGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSS------------EEEETTTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCC------------CEEeCCCCcEEcHHHHHHHHHh-CCCCcCCcCCCChh
Confidence            4689999999997            6777 79999999999999998 88999999988654

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.36  E-value=1.2e-07  Score=84.34  Aligned_cols=51  Identities=24%  Similarity=0.562  Sum_probs=42.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEE-eccCCccChhhHHHHHhhC-CCCCcc--ccccccCC
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIME-LPCKHLYHSDCIVPWLRHY-STTCPV--CRYELKDS  225 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~-LpC~H~FH~~CI~~WL~~~-~~sCPv--CR~~l~~~  225 (249)
                      ..+..|+||++.|..            .++ +.|||.|++.||..|+..+ ..+||+  ||..+...
T Consensus       179 ~~el~CPIcl~~f~D------------PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~  233 (267)
T 3htk_C          179 KIELTCPITCKPYEA------------PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR  233 (267)
T ss_dssp             BCCSBCTTTSSBCSS------------EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGG
T ss_pred             ceeeECcCccCcccC------------CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchh
Confidence            347899999999988            555 4899999999999999872 357999  99987543

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.34  E-value=1.1e-07  Score=87.79  Aligned_cols=44  Identities=30%  Similarity=0.774  Sum_probs=38.7

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCc-cChhhHHHHHhhCCCCCccccccccC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHL-YHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~-FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ++..|+||++.+..            ++.+||||. ||..|+..|     ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~------------~v~lpCgH~~fC~~C~~~~-----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS------------VVFIPCGHLVVCQECAPSL-----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC------------EEEETTCCEEECTTTGGGC-----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc------------eEEcCCCChhHhHHHHhcC-----CcCCCCCCCccC
Confidence            46799999999987            888999999 999999887     469999998853

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.24  E-value=6.5e-07  Score=68.60  Aligned_cols=47  Identities=26%  Similarity=0.607  Sum_probs=39.5

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      -|.+|--.+..-           .+.+||+|+||.+|+..|.+.+.++||.|+.++..
T Consensus         3 fC~~C~~Pi~iy-----------gRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVY-----------GRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEE-----------EEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEE-----------eeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            477887777763           78889999999999999987757899999998853

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=97.43  E-value=9.8e-05  Score=64.68  Aligned_cols=51  Identities=20%  Similarity=0.463  Sum_probs=40.2

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-CCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-~~sCPvCR~~l~~~  225 (249)
                      ....|.||.+-+..|.           +--.|+|.||..|+..|++.. +..||.|+...+..
T Consensus       179 ~i~~C~iC~~iv~~g~-----------~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQ-----------SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCE-----------ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCc-----------ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            3678999999988752           233399999999999999872 34899999876544

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.07  E-value=0.031  Score=41.51  Aligned_cols=34  Identities=15%  Similarity=0.379  Sum_probs=25.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHH
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPW  207 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~W  207 (249)
                      +..|+||++.+.....         ..-+.|+|.|+..|+..|
T Consensus         3 e~~C~~C~~~~~~~av---------~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAV---------KTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCC---------EEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCce---------EECCcCChHHhHHHCHHH
Confidence            6799999987533221         233889999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=91.83  E-value=0.088  Score=36.91  Aligned_cols=48  Identities=19%  Similarity=0.418  Sum_probs=33.9

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---CCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---STTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~~sCPvCR~~l~~  224 (249)
                      ...|.||.+.   +..         +.--.|...||..|+.+.|..-   .-.||.|+.+..+
T Consensus        12 ~~~C~vC~~~---~~l---------l~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~p   62 (66)
T 2lri_C           12 GARCGVCGDG---TDV---------LRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTP   62 (66)
T ss_dssp             TCCCTTTSCC---TTC---------EECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCCC
T ss_pred             CCCcCCCCCC---CeE---------EECCCCCCceecccCCCccCcCCCCCEECccccCCCcc
Confidence            5689999753   222         4333499999999999888762   2379999765433

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=91.34  E-value=0.1  Score=40.34  Aligned_cols=31  Identities=13%  Similarity=0.430  Sum_probs=24.6

Q ss_pred             CeeeeccCCCeeEeccCCCCCc-cCCCCCccceee
Q 041030           22 HYFWCQSCQRTTRFRSTDPSEL-FCPHCSAQLYLE   55 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~~~~s~~-~CP~C~~gFlEE   55 (249)
                      -.|||..|...+.+...   .. .||.|++..++-
T Consensus        72 ~~~~C~~CG~~~e~~~~---~~~~CP~Cgs~~~~i  103 (119)
T 2kdx_A           72 VELECKDCSHVFKPNAL---DYGVCEKCHSKNVII  103 (119)
T ss_dssp             CEEECSSSSCEECSCCS---TTCCCSSSSSCCCEE
T ss_pred             ceEEcCCCCCEEeCCCC---CCCcCccccCCCcEE
Confidence            35999999999887433   46 899999997763

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=90.37  E-value=0.17  Score=41.03  Aligned_cols=35  Identities=20%  Similarity=0.613  Sum_probs=27.2

Q ss_pred             CCceeccccCeeeeccCCCeeEeccCCCCCccCCCCCcc
Q 041030           13 NGTRRTRTFHYFWCQSCQRTTRFRSTDPSELFCPHCSAQ   51 (249)
Q Consensus        13 ~~~~~~rt~~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~g   51 (249)
                      .|.|+.|+|. |.|..|.+......   ...+||.|++.
T Consensus       123 ~~i~~~~~~~-y~C~~Cg~~~~~~~---~~~~Cp~CG~~  157 (165)
T 2lcq_A          123 RGIKKVIKWR-YVCIGCGRKFSTLP---PGGVCPDCGSK  157 (165)
T ss_dssp             CCCSSCCCCC-EEESSSCCEESSCC---GGGBCTTTCCB
T ss_pred             hhccccccEE-EECCCCCCcccCCC---CCCcCCCCCCc
Confidence            4677777776 99999998876432   24699999998

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=84.40  E-value=0.59  Score=33.96  Aligned_cols=32  Identities=22%  Similarity=0.771  Sum_probs=25.3

Q ss_pred             CeeeeccCCCeeEeccCCCCCccCCCCCcccee
Q 041030           22 HYFWCQSCQRTTRFRSTDPSELFCPHCSAQLYL   54 (249)
Q Consensus        22 ~~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlE   54 (249)
                      +.+||-.|...|..... ...+.||.|+..|==
T Consensus        24 ~~~wCP~C~~~~~~~~~-~~~v~C~~C~~~FC~   55 (86)
T 2ct7_A           24 KFLWCAQCSFGFIYERE-QLEATCPQCHQTFCV   55 (86)
T ss_dssp             CEECCSSSCCCEECCCS-CSCEECTTTCCEECS
T ss_pred             CEeECcCCCchheecCC-CCceEeCCCCCcccc
Confidence            56899999998876543 446899999998874

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=84.29  E-value=0.68  Score=47.75  Aligned_cols=49  Identities=20%  Similarity=0.146  Sum_probs=43.7

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccC-CccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-HLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +...|+|-++-+.+            .+++|-| +.|-..+|.+||.. +.+||+=|..|...
T Consensus       890 ~~F~cPIs~~lM~D------------PVilpsG~~TydR~~I~~wl~~-~~tdP~Tr~~L~~~  939 (968)
T 3m62_A          890 DEFLDPLMYTIMKD------------PVILPASKMNIDRSTIKAHLLS-DSTDPFNRMPLKLE  939 (968)
T ss_dssp             GGGBCTTTCSBCSS------------EEECTTTCCEEEHHHHHHHHTT-CCBCTTTCCBCCGG
T ss_pred             HHhCCcchhhHHhC------------CeEcCCCCEEECHHHHHHHHhc-CCCCCCCCCCCCcc
Confidence            36889999999998            8899987 68999999999999 99999999988643

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=82.87  E-value=0.36  Score=32.98  Aligned_cols=52  Identities=19%  Similarity=0.402  Sum_probs=33.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHh----hCCCCCccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLR----HYSTTCPVCRYEL  222 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~----~~~~sCPvCR~~l  222 (249)
                      ++...|+||...+..+..        |+.--.|..-||..|+.--..    .....||.|+..-
T Consensus         4 ~e~~~C~~C~~~~~~~~~--------mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            4 GSSGQCGACGESYAADEF--------WICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSC--------EEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCCCccCCCCC--------EEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            346789999987654332        233334999999999854322    1256799997643

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=82.72  E-value=0.83  Score=33.72  Aligned_cols=30  Identities=20%  Similarity=0.776  Sum_probs=22.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEec---cCCccChhhHHHH
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPW  207 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~W  207 (249)
                      +..|.||.. |..+.            .+|   |+-+||..|+.+-
T Consensus        15 D~~C~VC~~-~t~~~------------l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           15 DEMCDVCEV-WTAES------------LFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             SCCCTTTCC-CCSSC------------CSSCSSSSSCCCHHHHHHH
T ss_pred             CcccCcccc-ccccc------------eeccccccccccHhhcccc
Confidence            779999963 33322            245   8999999999885

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=80.16  E-value=2.3  Score=31.65  Aligned_cols=56  Identities=21%  Similarity=0.344  Sum_probs=42.8

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...|.||=+++......  +.+   |.-.-|+--.|+.|..-=.+.|+.+||.|+..+...
T Consensus        16 ~qiCqiCGD~VG~~~~G--e~F---VAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr~   71 (93)
T 1weo_A           16 GQFCEICGDQIGLTVEG--DLF---VACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             SCBCSSSCCBCCBCSSS--SBC---CSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             CCccccccCccccCCCC--CEE---EeeeccCChhhHHHHHHHHhccCccccccCCccccc
Confidence            57999999998765431  111   444458888999999888888899999999998743

---

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	249
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-10
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	5e-10
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	8e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	8e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	3e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	4e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-05
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	6e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	3e-04

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 53.3 bits (128), Expect = 1e-10
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 9/55 (16%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           C +C  E    ++              C H +H++C+  WL    +TCP+CR  +
Sbjct: 8   CAVCLAELEDGEEA--------RFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTV 53

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 2e-10
 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 12/64 (18%)

Query: 162 SNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYE 221
            +  Q C IC E  +             +   PC HL  + C+  W       CP CR E
Sbjct: 20  GSTFQLCKICAENDKD------------VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 67

Query: 222 LKDS 225
           +K +
Sbjct: 68  IKGT 71

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 5e-10
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 7/60 (11%)

Query: 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK 223
           + Q CP CK            +  + +M   C H     C+       +  CP C   L+
Sbjct: 2   DDQGCPRCKTTK-------YRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 51.5 bits (123), Expect = 8e-10
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 12/71 (16%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII 227
           CPIC E+           +  M   LPC H +   CI  W+R  + TCP+C+  ++  + 
Sbjct: 8   CPICLEDPS---------NYSMA--LPCLHAFCYVCITRWIRQ-NPTCPLCKVPVESVVH 55

Query: 228 GSGGDNIMNDH 238
               D+   D 
Sbjct: 56  TIESDSEFGDQ 66

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 1e-09
 Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 7/66 (10%)

Query: 164 EVQCCPICKEEFR------VRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPV 217
            V  C IC+            +     S+E  +    C H +H  CI  WL+     CP+
Sbjct: 20  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPL 78

Query: 218 CRYELK 223
              E +
Sbjct: 79  DNREWE 84

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 8e-08
 Identities = 11/57 (19%), Positives = 16/57 (28%), Gaps = 8/57 (14%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD 224
           CP+C E   + D               C +     C        +  CP CR    +
Sbjct: 3   CPLCMEPLEIDDIN--------FFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 44.5 bits (104), Expect = 3e-07
 Identities = 13/61 (21%), Positives = 18/61 (29%), Gaps = 8/61 (13%)

Query: 164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-STTCPVCRYEL 222
           +V  C IC EE         +               H  C+  WL    +T C +C    
Sbjct: 5   DVPVCWICNEEL-------GNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVY 57

Query: 223 K 223
            
Sbjct: 58  N 58

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.4 bits (106), Expect = 4e-07
 Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 10/77 (12%)

Query: 153 ISESTQLTRSNEVQCCPICKEEFRVRDDVDDDS------DEVMIMELPCKHLYHSDCIVP 206
           I + T+  +    + C IC E+  V     D +        V+     C H +H  C++ 
Sbjct: 13  IRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLA 72

Query: 207 WLRH----YSTTCPVCR 219
              +     S  CP C+
Sbjct: 73  MYCNGNKDGSLQCPSCK 89

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.2 bits (99), Expect = 3e-06
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 12/59 (20%)

Query: 167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS 225
            C IC+                  +E  CKHL+   CI+  L+   + CP CRY    +
Sbjct: 25  SCQICEHILA------------DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPT 71

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 15/79 (18%)

Query: 148 LKRVRISESTQLTRS-NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVP 206
           L  +R+ E   +  +  ++  CPIC E  +              +   C H++   C++ 
Sbjct: 3   LSALRVEEVQNVINAMQKILECPICLELIK------------EPVSTKCDHIFCKFCMLK 50

Query: 207 WLRHYST--TCPVCRYELK 223
            L        CP+C+ ++ 
Sbjct: 51  LLNQKKGPSQCPLCKNDIT 69

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 6e-05
 Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 16/55 (29%)

Query: 168 CPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYEL 222
           C  C+ E +                LPC H   S C+          CP+C+   
Sbjct: 9   CQQCQAEAK------------CPKLLPCLHTLCSGCLEAS----GMQCPICQAPW 47

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 3e-04
 Identities = 10/58 (17%), Positives = 19/58 (32%), Gaps = 11/58 (18%)

Query: 158 QLTRSNEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTC 215
            L R  ++  C  C    R             +    C+H++ S+C+   +      C
Sbjct: 15  ALDRLEKLLRCSRCTNILRE-----------PVCLGGCEHIFCSNCVSDCIGTGCPVC 61

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	249
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.66
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.49
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.48
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.46
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.45
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.41
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.3
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.29
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.22
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.22
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.13
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.1
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.06
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.03
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.77
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.42
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	89.92
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	86.76
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	85.56
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	80.8

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.66  E-value=1.7e-17  Score=113.28  Aligned_cols=51  Identities=31%  Similarity=0.838  Sum_probs=46.2

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      +++..|+||+++|..++.         +++++ |+|.||.+||.+||+. +++||+||++|.
T Consensus         3 ed~~~C~ICl~~~~~~~~---------~~~l~~C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEE---------ARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSC---------CEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCE---------EEEeCCCCCcccHHHHHHHHHh-CCcCCCCCCEeE
Confidence            346789999999999888         88886 9999999999999999 999999999874

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.49  E-value=5.8e-15  Score=104.28  Aligned_cols=48  Identities=38%  Similarity=0.935  Sum_probs=42.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.|..  .         ++.++|+|.||.+||.+||+. +++||+||+++..
T Consensus         5 ~d~C~IC~~~~~~--~---------~~~~~C~H~Fc~~Ci~~w~~~-~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSN--Y---------SMALPCLHAFCYVCITRWIRQ-NPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCS--C---------EEETTTTEEESTTHHHHHHHH-SCSTTTTCCCCCC
T ss_pred             CCCCccCCcCccC--C---------cEEeCCCCcCcHHHHHHHHHh-CCcCCCCCcchHh
Confidence            4589999999964  2         677899999999999999999 9999999998753

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4.8e-15  Score=99.62  Aligned_cols=50  Identities=22%  Similarity=0.469  Sum_probs=42.1

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      +|+||+++|..+...        ++.++|+|.||.+||.+|++.++++||+||+++..
T Consensus         2 eCpICl~~~~~~~~~--------~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDIN--------FFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTT--------CCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCce--------EEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            799999999876541        45568999999999999999746689999998864

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.8e-14  Score=100.95  Aligned_cols=55  Identities=25%  Similarity=0.489  Sum_probs=43.2

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ++..|+||++.+......       .++.++|+|+||.+||..||+.++.+||+||+.|...
T Consensus         2 dd~~CpIC~~~~~~~~~~-------~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSL-------KLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSC-------CEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCce-------EEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            367999999987654321       1566789999999999999977467899999988543

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=2.7e-14  Score=105.62  Aligned_cols=60  Identities=27%  Similarity=0.505  Sum_probs=45.9

Q ss_pred             cCccccccccccccccCCCC------CCCCccceEEeccCCccChhhHHHHHhhCCCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVD------DDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~------~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~  223 (249)
                      ..+..|+||++.+.......      .......++.++|+|+||.+||.+||+. +++||+||++..
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~   84 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWE   84 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-CSBCSSSCSBCC
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHH-CCcCCCCCCccc
Confidence            44668999999987654321      1112234788899999999999999999 999999999864

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=4.9e-14  Score=102.35  Aligned_cols=48  Identities=35%  Similarity=0.836  Sum_probs=42.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKD  224 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~  224 (249)
                      ...|+||++.+..            ++.++|||+||..||..||..++++||+||.+|..
T Consensus        23 ~~~C~IC~~~~~~------------~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~   70 (79)
T d1fbva4          23 FQLCKICAENDKD------------VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG   70 (79)
T ss_dssp             TTBCTTTSSSBCC------------EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCC
T ss_pred             CCCCccCCCcCCC------------eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccC
Confidence            4579999999876            78899999999999999998636789999999964

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=2.1e-13  Score=104.62  Aligned_cols=62  Identities=24%  Similarity=0.450  Sum_probs=45.4

Q ss_pred             ccccccccccccccCCCCCC------CCccceEEeccCCccChhhHHHHHhhC----CCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDD------SDEVMIMELPCKHLYHSDCIVPWLRHY----STTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~------~~~~~v~~LpC~H~FH~~CI~~WL~~~----~~sCPvCR~~l~~~~  226 (249)
                      +..|+||++.|.........      ..+..++.++|+|+||..||..||+..    +.+||+||..+....
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            56899999998764322111      122447778899999999999999862    348999999875543

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.30  E-value=4.4e-13  Score=99.00  Aligned_cols=52  Identities=31%  Similarity=0.662  Sum_probs=45.0

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSIIG  228 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~~  228 (249)
                      ...|+||++.|..            ++.++|||.||..||..|++.++..||+||.++....+-
T Consensus        23 ~l~C~IC~~~~~~------------pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          23 SISCQICEHILAD------------PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HTBCTTTCSBCSS------------EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CcCCccCCcchhc------------ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            5799999999987            888999999999999999987466899999988665443

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.29  E-value=4.8e-13  Score=90.88  Aligned_cols=48  Identities=15%  Similarity=0.277  Sum_probs=42.5

Q ss_pred             ccccccccccccCCCCCCCCccceEEec-cCCccChhhHHHHHhhCCCCCccccccccCCCC
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELP-CKHLYHSDCIVPWLRHYSTTCPVCRYELKDSII  227 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~Lp-C~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~~  227 (249)
                      .|+||++.|+.            .+.++ |||+||.+||.+||+. +.+||+||+++....+
T Consensus         2 ~C~Ic~~~~~~------------Pv~~~~cGh~fc~~cI~~~l~~-~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRR------------PVLSPKSRTIFEKSLLEQYVKD-TGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSS------------EEEETTTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHh------------cCccCCCCCcccHHHHHHHHhh-ccCCCccCCcCCHHhc
Confidence            69999999987            66675 9999999999999999 9999999998866543

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=8.1e-13  Score=90.00  Aligned_cols=46  Identities=26%  Similarity=0.570  Sum_probs=39.4

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDSI  226 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~~  226 (249)
                      ...|+||++.|..            ++.+||||+||..||..|    +.+||+||+++....
T Consensus         6 ~l~C~IC~~~~~~------------p~~lpCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAKC------------PKLLPCLHTLCSGCLEAS----GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC------------CSCSTTSCCSBTTTCSSS----SSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccCC------------CEEecCCCHHhHHHHHcC----CCcCcCCCCcccCCC
Confidence            5699999999986            567899999999999765    667999999997544

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=1.4e-12  Score=98.53  Aligned_cols=51  Identities=24%  Similarity=0.729  Sum_probs=42.7

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC--CCCCccccccccCCCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY--STTCPVCRYELKDSII  227 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~--~~sCPvCR~~l~~~~~  227 (249)
                      ...|+||++.|..            ++.++|||+||..||..|++..  ..+||+||.++....+
T Consensus        21 ~l~CpIC~~~~~~------------pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          21 ILECPICLELIKE------------PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             HTSCSSSCCCCSS------------CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CcCCCccCchhCC------------eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            5789999999986            5668999999999999999872  2479999999865543

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.13  E-value=1.4e-11  Score=89.00  Aligned_cols=50  Identities=24%  Similarity=0.240  Sum_probs=44.1

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ++..|+||++.|..            .+.++|||.|+..||..||..++.+||+||..+...
T Consensus         6 ~~l~CpIc~~l~~d------------Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           6 DYLCGKISFELMRE------------PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             STTBCTTTCSBCSS------------EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             ccccCcCcCchhhh------------hcccCCcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            37899999999998            778999999999999999987466899999987543

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.10  E-value=2.6e-11  Score=87.00  Aligned_cols=50  Identities=26%  Similarity=0.424  Sum_probs=44.1

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      +++.|+||++.|.+            .++++|||.|+..||..|+..+...||+|+..+...
T Consensus         7 ~~l~CpIc~~~m~d------------PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           7 EYFRCPISLELMKD------------PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS------------EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCcCcCchhhC------------ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            37899999999998            778999999999999999987456799999988654

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.06  E-value=2.8e-11  Score=82.77  Aligned_cols=54  Identities=24%  Similarity=0.431  Sum_probs=38.9

Q ss_pred             cCccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhh-CCCCCcccccccc
Q 041030          163 NEVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRH-YSTTCPVCRYELK  223 (249)
Q Consensus       163 ~~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~-~~~sCPvCR~~l~  223 (249)
                      ++...|.||++.+......       ...-..|+|+||..||..|+.. ++.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~-------~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFR-------ACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCC-------SCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeE-------ecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            4578999999987653220       0011224699999999999965 2668999999875

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=4.6e-11  Score=89.10  Aligned_cols=47  Identities=23%  Similarity=0.554  Sum_probs=38.6

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ...|+||++.|...           ++..+|||.||..||..|+..   .||+||..+...
T Consensus        22 ~l~C~IC~~~~~~p-----------v~~~~CgH~fC~~Ci~~~~~~---~CP~Cr~~~~~~   68 (97)
T d1jm7b_          22 LLRCSRCTNILREP-----------VCLGGCEHIFCSNCVSDCIGT---GCPVCYTPAWIQ   68 (97)
T ss_dssp             TTSCSSSCSCCSSC-----------BCCCSSSCCBCTTTGGGGTTT---BCSSSCCBCSCS
T ss_pred             cCCCccCCchhhcC-----------ceeCCCCCchhHHHHHHHHhc---cccccCCcCchh
Confidence            67999999999873           333479999999999999865   699999887543

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=2e-09  Score=80.48  Aligned_cols=48  Identities=21%  Similarity=0.096  Sum_probs=43.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEeccC-CccChhhHHHHHhhCCCCCccccccccCC
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELPCK-HLYHSDCIVPWLRHYSTTCPVCRYELKDS  225 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~-H~FH~~CI~~WL~~~~~sCPvCR~~l~~~  225 (249)
                      ++.|+||++.|.+            +++++|+ |.|++.||..||+. +..||+||..|...
T Consensus        22 ~f~CPI~~~lm~d------------PV~~~~~~~ty~r~~I~~~l~~-~~~~P~~~~~l~~~   70 (98)
T d1wgma_          22 EFLDPIMSTLMCD------------PVVLPSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTBCTTTCSBCSS------------EEECTTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTT
T ss_pred             HhCCcCchhHHHH------------HHhcccccchhhHHHHHHHHHh-cCCcccccccccch
Confidence            7899999999998            8899965 58999999999999 99999999988654

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.42  E-value=3.6e-08  Score=72.23  Aligned_cols=48  Identities=17%  Similarity=0.508  Sum_probs=37.7

Q ss_pred             CccccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC-------CCCCccccc
Q 041030          164 EVQCCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY-------STTCPVCRY  220 (249)
Q Consensus       164 ~~~~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~-------~~sCPvCR~  220 (249)
                      ....|+||++++...+.         +..++|+|.||.+|+..|++..       .-.||.|+-
T Consensus         4 ~~~~C~IC~~~~~~~~~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQM---------TTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGE---------EEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCce---------EEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            36799999999977554         6666799999999999999752       125998643

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.92  E-value=0.047  Score=34.30  Aligned_cols=45  Identities=24%  Similarity=0.614  Sum_probs=29.6

Q ss_pred             ccccccccccccCCCCCCCCccceEEeccCCccChhhHHHHHhhC---CCCCccccc
Q 041030          167 CCPICKEEFRVRDDVDDDSDEVMIMELPCKHLYHSDCIVPWLRHY---STTCPVCRY  220 (249)
Q Consensus       167 ~C~ICle~f~~~~~~~~~~~~~~v~~LpC~H~FH~~CI~~WL~~~---~~sCPvCR~  220 (249)
                      .|.||...-..+.         ++.--.|...||..|+.+-+..-   .-.||.||.
T Consensus         2 ~C~vC~~~~~~~~---------~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDK---------LILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSC---------CEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCC---------EEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            5888876533222         24333499999999998866541   225999875

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.76  E-value=0.092  Score=34.39  Aligned_cols=48  Identities=21%  Similarity=0.525  Sum_probs=32.3

Q ss_pred             ccccccccccccccCCCCCCCCccceEEe-ccCCccChhhHHHH---Hhh-CCCCCcccccc
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMEL-PCKHLYHSDCIVPW---LRH-YSTTCPVCRYE  221 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~L-pC~H~FH~~CI~~W---L~~-~~~sCPvCR~~  221 (249)
                      ...|.||.+....+..         .+.= .|+..||..|+..=   ... .+-.||.|+..
T Consensus         6 ~~~C~~C~~~~~~~~~---------~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           6 SGQCGACGESYAADEF---------WICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCCSSSCCCCCSSSC---------EEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCcCcCcCCCCCCCCC---------EEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            6799999887655433         3333 49999999998531   111 14579999764

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.56  E-value=0.27  Score=34.43  Aligned_cols=30  Identities=23%  Similarity=0.790  Sum_probs=24.5

Q ss_pred             ccccccccccccccCCCCCCCCccceEEec---cCCccChhhHHHH
Q 041030          165 VQCCPICKEEFRVRDDVDDDSDEVMIMELP---CKHLYHSDCIVPW  207 (249)
Q Consensus       165 ~~~C~ICle~f~~~~~~~~~~~~~~v~~Lp---C~H~FH~~CI~~W  207 (249)
                      +..|.|| +.|.....            +|   |+.+||..|+.+-
T Consensus        15 D~mC~vC-~v~t~~~l------------~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          15 DEMCDVC-EVWTAESL------------FPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             SCCCTTT-CCCCSSCC------------SSCSSSSSCCCHHHHHHH
T ss_pred             Ccccccc-Ccccccce------------ecceeecchhhHHHHHHh
Confidence            7899999 77776544            56   8999999999885

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.80  E-value=0.41  Score=31.94  Aligned_cols=31  Identities=26%  Similarity=0.661  Sum_probs=24.0

Q ss_pred             eeeeccCCCeeEeccCCCCCccCCCCCccceeecc
Q 041030           23 YFWCQSCQRTTRFRSTDPSELFCPHCSAQLYLELD   57 (249)
Q Consensus        23 ~yWCy~C~r~Vr~~~~~~s~~~CP~C~~gFlEEld   57 (249)
                      -+.||.|-.....    .+-.|||.||+.-|..+.
T Consensus         8 ~LrC~aCf~~t~~----~~k~FCpkCGn~TL~rvs   38 (66)
T d2cona1           8 ILRCHGCFKTTSD----MNRVFCGHCGNKTLKKVS   38 (66)
T ss_dssp             EEECSSSCCEESC----SSCCSCSSSCCSCCEEEE
T ss_pred             eeEeeecCcCcCC----cccccCcccCCCceeEEE
Confidence            4789999986553    235899999999997653