Citrus Sinensis ID: 045986

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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-------15
Protein Sequence
DETLFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHcccEEEEcccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHccccccccHHHHHHccccEEEEcccccccccccEEEEEHHHcccccEEEEcccccccccHHHHHHHHHcccccccccccccccc
Coil and Loop (DISEMBL)
DETLFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYqrmhdpevgsfdvlrlwdrplrhqrvieklppaekydghlhnkkfTSECVICLeefvsgdlfrilpfckhvyhshciirwfsdeftcpicrssiylda
Flexible Loop (DISEMBL)
DETLFVIRRLmdlrsnrqAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIeklppaekydghlhNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA
Low Complexity Region (SEG)
DETLFVIRRLMDLRSNRQAEIVltytltialsllllIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA
Disordered region (IsUnstruct)
***LFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL**
Disordered Region (DISOPRED)
****F*I**************VLTYTLTIALSLLLLIWVYEICIWAR******************************EKLPPAE*************ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY***
Disordered Region (DISEMBL)
DETLFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA
Disordered Region (DISPRO)
DETLFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
DETLFVIRRLMDLRSNRQAEIVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA
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	148	2.2.26 [Sep-21-2011]
Q9LZV8	159	RING-H2 finger protein AT	yes	no	0.520	0.484	0.392	2e-10
P0C034	251	RING-H2 finger protein AT	no	no	0.412	0.243	0.426	3e-10
Q9LS99	220	RING-H2 finger protein AT	no	no	0.425	0.286	0.412	4e-10
Q8LC69	185	RING-H2 finger protein AT	no	no	0.817	0.654	0.289	4e-10
Q9LM69	197	RING-H2 finger protein AT	no	no	0.756	0.568	0.295	5e-10
Q9XF63	324	RING-H2 finger protein AT	no	no	0.317	0.145	0.531	6e-10
Q8H7N9	353	E3 ubiquitin-protein liga	no	no	0.479	0.201	0.383	7e-10
Q07G42	639	E3 ubiquitin-protein liga	yes	no	0.304	0.070	0.5	9e-10
Q9WTV7	600	E3 ubiquitin-protein liga	yes	no	0.304	0.075	0.5	9e-10
Q9NVW2	624	E3 ubiquitin-protein liga	yes	no	0.304	0.072	0.5	9e-10

>sp|Q9LZV8|ATL74_ARATH RING-H2 finger protein ATL74 OS=Arabidopsis thaliana GN=ATL74 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 66  LWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSH 125
           + DR    +R ++K P AE   G +  K   +EC ICL EF  G+  R+LP C H +H  
Sbjct: 74  VADRAGLKKRELKKFPVAEYGSGEV--KIAATECAICLGEFADGERVRVLPPCNHSFHMS 131

Query: 126 CIIRWFSDEFTCPICRSSI 144
           CI  W     +CP CR S+
Sbjct: 132 CIDTWLVSHSSCPNCRHSL 150

Arabidopsis thaliana (taxid: 3702)

>sp|P0C034|ATL10_ARATH RING-H2 finger protein ATL10 OS=Arabidopsis thaliana GN=ATL10 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 34/61 (55%)

Query: 82  PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           P   Y   ++      ECVICL +FVSG+  R+LP C H +H  CI +W     TCP CR
Sbjct: 118 PVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCR 177

Query: 142 S 142
           +
Sbjct: 178 N 178

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS99|ATL77_ARATH RING-H2 finger protein ATL77 OS=Arabidopsis thaliana GN=ATL77 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 36/63 (57%)

Query: 79  KLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCP 138
           K+ P   Y   ++      ECVICL +FV+G+  R+LP C H +H  CI +W +   TCP
Sbjct: 110 KMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCP 169

Query: 139 ICR 141
            CR
Sbjct: 170 KCR 172

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LC69|ATL8_ARATH RING-H2 finger protein ATL8 OS=Arabidopsis thaliana GN=ATL8 PE=2 SV=2

 Score = 63.5 bits (153), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 46/159 (28%), Positives = 66/159 (41%), Gaps = 38/159 (23%)

Query: 5   FVIRRLMDLRSNRQAE---------IVLTYTLTIALSLLLLIWVYEICIWARDLYQR--- 52
            + R L +  S   AE         +++   L  AL+ ++ +     C W R +  R   
Sbjct: 4   LLFRLLQEANSTSPAEASPPFNSDLVLILAVLLCALTCIIGLIAVSRCAWLRRIASRNRS 63

Query: 53  --MHDPEVGSFDVLRLWDRPLRHQ--RVIEKL------PPAEKYDGHLHNKKFTSECVIC 102
              H P V + +      + L+ +  R + KL      PPAEK            EC IC
Sbjct: 64  DQTHPPPVAAAN------KGLKKKVLRSLPKLTYSPDSPPAEKL----------VECAIC 107

Query: 103 LEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           L EF +GD  R+LP C H +H  CI  W     +CP CR
Sbjct: 108 LTEFAAGDELRVLPQCGHGFHVSCIDTWLGSHSSCPSCR 146

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LM69|ATL80_ARATH RING-H2 finger protein ATL80 OS=Arabidopsis thaliana GN=ATL80 PE=1 SV=1

 Score = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 57/132 (43%), Gaps = 20/132 (15%)

Query: 21  IVLTYTLTIALSLLLLIWVYEICIWARDLY-----------QRMHDPEVGSFDVLRLWDR 69
           +V+   L  AL  +L +     C+W R L            Q    P   +   L+    
Sbjct: 31  VVILAALLCALICVLGLIAVSRCVWLRRLAAGNRTVSGSQTQSPQPPVAAANKGLK---- 86

Query: 70  PLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIR 129
               ++V++ LP          ++KF +EC ICL EF +GD  R+LP C H +H  CI  
Sbjct: 87  ----KKVLQSLPKLTFSPESPESEKF-AECAICLAEFSAGDELRVLPQCGHGFHVACIDT 141

Query: 130 WFSDEFTCPICR 141
           W     +CP CR
Sbjct: 142 WLGSHSSCPSCR 153

May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XF63|ATL3_ARATH RING-H2 finger protein ATL3 OS=Arabidopsis thaliana GN=ATL3 PE=2 SV=1

 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 30/47 (63%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           EC ICL E V GD  R+LP C H +H  CI  WF    TCPICR+++
Sbjct: 126 ECSICLSELVKGDKARLLPKCNHSFHVECIDMWFQSHSTCPICRNTV 172

Arabidopsis thaliana (taxid: 3702)

>sp|Q8H7N9|ATL31_ORYSJ E3 ubiquitin-protein ligase Os03g0188200 OS=Oryza sativa subsp. japonica GN=Os03g0188200 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 74  QRVIEKLPPAEKYD--GHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF 131
           + V+E  P A   D    +  K    EC +CL EF   D  R+LP C HV+H  CI  W 
Sbjct: 106 KEVVEAFPTAVYGDVKARMAAKSGPLECAVCLAEFADSDELRVLPACCHVFHPDCIDPWL 165

Query: 132 SDEFTCPICRSSI 144
           +   TCP+CR+++
Sbjct: 166 AAAVTCPLCRANL 178

Possesses E3 ubiquitin-protein ligase in vitro.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q07G42|RNF12_XENTR E3 ubiquitin-protein ligase RNF12 OS=Xenopus tropicalis GN=rnf12 PE=2 SV=1

 Score = 62.4 bits (150), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C +C+ E+  G+  R LP C H YH HCI RW S+  TCPICR ++
Sbjct: 585 CSVCITEYTEGNKLRKLP-CSHEYHVHCIDRWLSENSTCPICRRAV 629

Acts as a E3 ubiquitin-protein ligase specific for ldb1, mediating ubiquitination and proteasome-dependent degradation of excess ldb1 in a RING-dependent manner. Does not degrade ldb1 bound to lhx1/lim1, nor lim1 itself and thus contributes to the establishment of proper ldb1-lhx1/lim1 stoichiometry and the formation of a ldb1-lhx1/lim1 complex. Interferes with Spemann organizer function and suppresses secondary axis formation induced by ldb1 and lhx1/lim1.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9WTV7|RNF12_MOUSE E3 ubiquitin-protein ligase RLIM OS=Mus musculus GN=Rlim PE=1 SV=2

 Score = 62.4 bits (150), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C +C+ E+  G+  R LP C H YH HCI RW S+  TCPICR ++
Sbjct: 546 CSVCITEYTEGNKLRKLP-CSHEYHVHCIDRWLSENSTCPICRRAV 590

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. Acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9NVW2|RNF12_HUMAN E3 ubiquitin-protein ligase RLIM OS=Homo sapiens GN=RLIM PE=1 SV=3

 Score = 62.4 bits (150), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C +C+ E+  G+  R LP C H YH HCI RW S+  TCPICR ++
Sbjct: 570 CSVCITEYTEGNKLRKLP-CSHEYHVHCIDRWLSENSTCPICRRAV 614

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. Acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Homo sapiens (taxid: 9606)

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	148
449466635	162	PREDICTED: putative RING-H2 finger prote	0.810	0.740	0.311	3e-12
226491490	192	RING-H2 finger protein ATL2A [Zea mays]	0.932	0.718	0.246	3e-10
302756931	1406	hypothetical protein SELMODRAFT_403293 [	0.763	0.080	0.377	4e-10
432094725	795	E3 ubiquitin-protein ligase RLIM [Myotis	0.304	0.056	0.565	6e-10
356538405	226	PREDICTED: RING-H2 finger protein ATL8-l	0.770	0.504	0.314	8e-10
255636983	239	unknown [Glycine max]	0.405	0.251	0.5	9e-10
356508999	239	PREDICTED: RING-H2 finger protein ATL78-	0.405	0.251	0.5	9e-10
255540713	189	conserved hypothetical protein [Ricinus	0.790	0.619	0.328	1e-09
357484247	215	Ring finger protein [Medicago truncatula	0.770	0.530	0.305	1e-09
449447215	159	PREDICTED: RING-H2 finger protein ATL10-	0.439	0.408	0.454	2e-09

>gi|449466635|ref|XP_004151031.1| PREDICTED: putative RING-H2 finger protein ATL53-like [Cucumis sativus] gi|449521203|ref|XP_004167619.1| PREDICTED: putative RING-H2 finger protein ATL53-like [Cucumis sativus]

 Score = 76.6 bits (187), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 66/135 (48%), Gaps = 15/135 (11%)

Query: 23  LTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPP 82
           L +    AL+L+ L +V+  C   R  + R  D E G    + + + P        +  P
Sbjct: 24  LNFAGLSALALMFLYFVFTCC--ERKYWNRNGDIEGGRLPTVTMDESPASETEDSPRRRP 81

Query: 83  AEKY-----------DGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF 131
           + +             G +  K   ++C ICL+EF  G++ R+LP CKHV+H  CI RW 
Sbjct: 82  SSRAVISTRLFQYGVGGGVIGKN--ADCSICLDEFTEGEICRMLPKCKHVFHRFCIDRWL 139

Query: 132 SDEFTCPICRSSIYL 146
            +E  CP+CRS +Y+
Sbjct: 140 PNERNCPVCRSPVYV 154

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226491490|ref|NP_001150741.1| RING-H2 finger protein ATL2A [Zea mays] gi|195641404|gb|ACG40170.1| RING-H2 finger protein ATL2A [Zea mays]

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 62/154 (40%), Gaps = 16/154 (10%)

Query: 11  MDLRSNRQAEIVLTYTLTI----ALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRL 66
           +D     Q E  +  T T+     +S + L  ++          QR   P+       R 
Sbjct: 21  LDAPQRAQLERAIGATTTVLFVATVSYVALSAIFSCLCTGGGSSQRRQQPDGSDTGPQRP 80

Query: 67  WDRPLRHQRVIEKLP-----------PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRIL 115
                  +R +E++P           PA    G     +   EC +CL E+  G+  R+L
Sbjct: 81  SAAAEETKRALEEIPVVVVAAQVTRDPAGSGGGAEDGSEEPGECAVCLAEYAGGEEVRVL 140

Query: 116 PFCKHVYHSHCIIRW-FSDEFTCPICRSSIYLDA 148
           P C+H +H  C+ RW  +   TCP+CR+ +   A
Sbjct: 141 PACRHGFHRACVDRWLLTRAPTCPVCRAPVAAHA 174

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302756931|ref|XP_002961889.1| hypothetical protein SELMODRAFT_403293 [Selaginella moellendorffii] gi|300170548|gb|EFJ37149.1| hypothetical protein SELMODRAFT_403293 [Selaginella moellendorffii]

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 46/122 (37%), Positives = 64/122 (52%), Gaps = 9/122 (7%)

Query: 23   LTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPP 82
            + + +T+ L L +L+  Y   I    L QR   P  G+   + L ++ L  Q VI+ L P
Sbjct: 1150 VAFFITLDLCLRVLLRRYTGII---PLGQRQ--PGTGTH--VNLLNKGL-DQGVIDSLLP 1201

Query: 83   AEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS 142
            A  Y G       T+EC +CL EF  G+  R+LP C H +H+ CI  WF    TCPICRS
Sbjct: 1202 AFVY-GKEGYVGATTECAVCLSEFEDGERGRLLPKCNHAFHAGCIDMWFQSHATCPICRS 1260

Query: 143  SI 144
             +
Sbjct: 1261 PV 1262

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|432094725|gb|ELK26205.1| E3 ubiquitin-protein ligase RLIM [Myotis davidii]

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/46 (56%), Positives = 31/46 (67%), Gaps = 1/46 (2%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C+IC+ E+  G+  RILP C H YH HCI RW SD  TCPICR  +
Sbjct: 747 CIICITEYTEGNKLRILP-CSHEYHVHCIDRWLSDNSTCPICRREV 791

Source: Myotis davidii

Species: Myotis davidii

Genus: Myotis

Family: Vespertilionidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|356538405|ref|XP_003537694.1| PREDICTED: RING-H2 finger protein ATL8-like [Glycine max]

 Score = 68.6 bits (166), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 38/121 (31%), Positives = 56/121 (46%), Gaps = 7/121 (5%)

Query: 21  IVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKL 80
           +V+   L  AL  ++ +     C W R      + P         L ++ L+ ++V++ L
Sbjct: 34  VVILAALLCALICVVGLVAVARCAWLRRGSGAGNSPRQA------LANKGLK-KKVLQSL 86

Query: 81  PPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC 140
           P     D +      TSEC ICL EF +GD  R+LP C H +H  CI  W     +CP C
Sbjct: 87  PKFAYVDSNPSKWLATSECAICLAEFAAGDEIRVLPQCGHGFHVPCIDTWLGSHSSCPSC 146

Query: 141 R 141
           R
Sbjct: 147 R 147

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255636983|gb|ACU18824.1| unknown [Glycine max]

 Score = 68.6 bits (166), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 34/60 (56%)

Query: 82  PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           P   Y   L+     SECVICL EF SGD  RILP C H +H  CI +W S   +CP CR
Sbjct: 123 PTVSYSAELNLPSLDSECVICLSEFTSGDKVRILPKCNHRFHVRCIDKWLSSHSSCPKCR 182

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508999|ref|XP_003523240.1| PREDICTED: RING-H2 finger protein ATL78-like [Glycine max]

 Score = 68.6 bits (166), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 34/60 (56%)

Query: 82  PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           P   Y   L+     SECVICL EF SGD  RILP C H +H  CI +W S   +CP CR
Sbjct: 123 PTVSYSAELNLPSLDSECVICLSEFTSGDKVRILPKCNHRFHVRCIDKWLSSHSSCPKCR 182

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540713|ref|XP_002511421.1| conserved hypothetical protein [Ricinus communis] gi|223550536|gb|EEF52023.1| conserved hypothetical protein [Ricinus communis]

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 41/125 (32%), Positives = 60/125 (48%), Gaps = 8/125 (6%)

Query: 21  IVLTYTLTIALSLLLLIWVYEICIWARDL---YQRMHDPEVGSFDVLRLWDRPLRHQRVI 77
           IV    L + +++L+ I V   CI  R     Y+   +   GSF   R   + + ++ + 
Sbjct: 6   IVSVVLLFVGIAVLVAIHV---CIVGRAFRRGYETGQEIGPGSFSSSRYGIKKISNEEL- 61

Query: 78  EKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTC 137
            K  P   Y         +S+CV+CLE F  GD  ++LP CKH +HS CI  W      C
Sbjct: 62  -KNLPCFDYKAAEKEGSSSSDCVVCLENFNVGDKCKLLPNCKHSFHSQCIDSWLVKTPIC 120

Query: 138 PICRS 142
           PICR+
Sbjct: 121 PICRT 125

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357484247|ref|XP_003612411.1| Ring finger protein [Medicago truncatula] gi|355513746|gb|AES95369.1| Ring finger protein [Medicago truncatula] gi|388496508|gb|AFK36320.1| unknown [Medicago truncatula]

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 37/121 (30%), Positives = 57/121 (47%), Gaps = 7/121 (5%)

Query: 21  IVLTYTLTIALSLLLLIWVYEICIWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKL 80
           +V+   L  AL  ++ +     C W R       D   G+     L ++ L+ ++V++ L
Sbjct: 34  VVILAALLCALICVVGLIAVARCAWLR------RDSGAGNSPQQALANKGLK-KKVLQSL 86

Query: 81  PPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC 140
           P     D +      T+EC ICL +F +GD  R+LP C H +H  CI  W     +CP C
Sbjct: 87  PKFSYVDSNPGKWLATTECAICLSDFAAGDEIRVLPQCGHGFHVACIDTWLGSHSSCPSC 146

Query: 141 R 141
           R
Sbjct: 147 R 147

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447215|ref|XP_004141364.1| PREDICTED: RING-H2 finger protein ATL10-like [Cucumis sativus]

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 42/66 (63%), Gaps = 1/66 (1%)

Query: 80  LPPAEKYDGH-LHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCP 138
           LPP  ++    +  ++   EC ICLEEF+ G+  + LP C H +HS CI  WFS +FTCP
Sbjct: 92  LPPTVRFGSEKMVRRRSEEECAICLEEFLIGENCQALPECNHFFHSECIDVWFSKKFTCP 151

Query: 139 ICRSSI 144
           ICR+ +
Sbjct: 152 ICRNCV 157

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	148
UNIPROTKB|G3MWN3	136	G3MWN3 "Uncharacterized protei	0.452	0.492	0.485	5.6e-13
TAIR|locus:505006414	126	AT4G00305 [Arabidopsis thalian	0.608	0.714	0.391	6.4e-12
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.425	0.250	0.412	1.4e-11
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.425	0.286	0.412	1.7e-11
TAIR|locus:505006488	166	AT4G17245 [Arabidopsis thalian	0.439	0.391	0.424	2.2e-11
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.405	0.266	0.433	3.5e-11
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.506	0.471	0.402	3.5e-11
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.405	0.265	0.433	4.5e-11
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.358	0.259	0.471	4.5e-11
TAIR|locus:504955576	248	BB "BIG BROTHER" [Arabidopsis	0.472	0.282	0.432	5.4e-11

UNIPROTKB|G3MWN3 G3MWN3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 34/70 (48%), Positives = 44/70 (62%)

Query:    72 RHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF 131
             R  R+I+  PP + Y G    +  T+EC +CL + V GDL R LP CKHVYH  CI +W 
Sbjct:    57 RRIRLIQS-PPRDVY-GRDGCETKTTECAVCLMDLVPGDLIRPLP-CKHVYHLDCINQWL 113

Query:   132 SDEFTCPICR 141
             +  FTCP+CR
Sbjct:   114 TRSFTCPLCR 123

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:505006414 AT4G00305 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 38/97 (39%), Positives = 49/97 (50%)

Query:    58 VGSF-DVLRLWDRPLRHQRVIEKLP-----PAEKYDGHLHNKKFTSECVICLEEFVSGDL 111
             V SF D+ RL+        +I+K+P     PA K++           C IC +EF  GD 
Sbjct:    24 VRSFLDIRRLFGSASSGSTIIDKIPMDDMLPATKFEDISSRVNPPESCRICQDEFDGGDE 83

Query:   112 FRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYLD 147
              R L  C HVYH  CI RW  D+  TCP+CR+ I  D
Sbjct:    84 VRCLRNCVHVYHKTCIDRWIQDDKMTCPLCRTPIVPD 120

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2028506 AT1G49220 [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 26/63 (41%), Positives = 35/63 (55%)

Query:    82 PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
             P   Y   ++      ECVICL +FVSG+  R+LP C H +H  CI +W     TCP CR
Sbjct:   118 PVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCR 177

Query:   142 SSI 144
             + +
Sbjct:   178 NCL 180

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

TAIR|locus:2830088 AT3G18773 [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 26/63 (41%), Positives = 36/63 (57%)

Query:    79 KLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCP 138
             K+ P   Y   ++      ECVICL +FV+G+  R+LP C H +H  CI +W +   TCP
Sbjct:   110 KMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCP 169

Query:   139 ICR 141
              CR
Sbjct:   170 KCR 172

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

TAIR|locus:505006488 AT4G17245 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 28/66 (42%), Positives = 39/66 (59%)

Query:    81 PPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFT-CPI 139
             PP   Y   L+     +EC+ICL EF  GD  R+L  CKH +H +CI +W S   + CP 
Sbjct:    84 PPTLVYSPGLNLAGNEAECIICLSEFQDGDTLRVLERCKHGFHVYCIQKWLSSSHSSCPT 143

Query:   140 CRSSIY 145
             CR++I+
Sbjct:   144 CRTNIF 149

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

TAIR|locus:2028406 AT1G49210 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 26/60 (43%), Positives = 33/60 (55%)

Query:    82 PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
             P   Y   ++      ECVICL +FVSG+  R+LP C H +H  CI +W     TCP CR
Sbjct:   118 PVVSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCR 177

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2181032 DAFL2 "DAF-Like gene 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 31/77 (40%), Positives = 41/77 (53%)

Query:    68 DRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCI 127
             DR    +R ++K P AE   G +  K   +EC ICL EF  G+  R+LP C H +H  CI
Sbjct:    76 DRAGLKKRELKKFPVAEYGSGEV--KIAATECAICLGEFADGERVRVLPPCNHSFHMSCI 133

Query:   128 IRWFSDEFTCPICRSSI 144
               W     +CP CR S+
Sbjct:   134 DTWLVSHSSCPNCRHSL 150

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

TAIR|locus:2028411 AT1G49200 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 26/60 (43%), Positives = 33/60 (55%)

Query:    82 PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
             P   Y   ++      ECVICL +FVSG+  R+LP C H +H  CI +W     TCP CR
Sbjct:   119 PVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCR 178

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

TAIR|locus:2090980 AT3G14320 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 25/53 (47%), Positives = 30/53 (56%)

Query:    94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL 146
             K+  ECV+CL E   GD  R+LP C H +H  CI  W     TCPICR  + L
Sbjct:    83 KYVLECVVCLSELADGDKARVLPSCDHWFHVECIDSWLQSNSTCPICRKRVCL 135

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

TAIR|locus:504955576 BB "BIG BROTHER" [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 5.4e-11, P = 5.4e-11
 Identities = 32/74 (43%), Positives = 44/74 (59%)

Query:    74 QRVIEKLPPAEKYD-GHLHNKKFTSE-CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF 131
             Q +IE LP  +KY  G + ++K   E CVIC  ++  G+    LP CKHVYHS CI +W 
Sbjct:   171 QELIETLP-TKKYKFGSIFSRKRAGERCVICQLKYKIGERQMNLP-CKHVYHSECISKWL 228

Query:   132 SDEFTCPICRSSIY 145
             S    CP+C S ++
Sbjct:   229 SINKVCPVCNSEVF 242

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0031624 "ubiquitin conjugating enzyme binding" evidence=IPI

GO:0046621 "negative regulation of organ growth" evidence=IMP

GO:0048437 "floral organ development" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	148
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	6e-13
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	5e-10
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-07
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-07
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-07
smart00184	40	smart00184, RING, Ring finger	7e-07
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	6e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	7e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	3e-04

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

 Score = 58.9 bits (143), Expect = 6e-13
 Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS 143
           EC ICL+EF  G+   +LP C HV+H  C+ +W     TCP+CR+ 
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 57.3 bits (138), Expect = 2e-10
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSI 144
           EC IC+  F+  D  R+LP C H +H  C+ +W       CP+CR++I
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

>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 = 51.3 bits (123), Expect = 5e-10
 Identities = 22/48 (45%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPICRSSI 144
           EC ICLEEF       +L  C HV+   CI +W  S + TCP+CR+ I
Sbjct: 1   ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 4/57 (7%)

Query: 89  HLHNKKFTSECVICLEEF----VSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
            L+N+    EC IC+E+     +    F IL  C HV+   CI  W  ++ TCP+CR
Sbjct: 167 KLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS 142
           EC ICL+     D   + P C HV+   CI+R+   +  CPICR+
Sbjct: 4   ECPICLDLLR--DPVVLTP-CGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 9/52 (17%)

Query: 99  CVICLEEFV---------SGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           C IC   F            D   +   C H +H HCI RW     TCP+CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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 = 43.3 bits (102), Expect = 7e-07
 Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPIC 140
           C ICLEE++      ILP C H +   CI +W  S   TCPIC
Sbjct: 1   CPICLEEYL--KDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 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|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 25/68 (36%), Positives = 33/68 (48%), Gaps = 16/68 (23%)

Query: 84   EKYDGHLHNKKFTSECVICLEEFVSGDLFRILP-----FCKHVYHSHCIIRWF--SDEFT 136
            EK+ GH        EC IC    V   + R LP      CK+ +H+ C+ +WF  S    
Sbjct: 1464 EKFSGH-------EECAICY--SVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSN 1514

Query: 137  CPICRSSI 144
            CP+CRS I
Sbjct: 1515 CPLCRSEI 1522

Length = 1525

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

 Score = 40.5 bits (95), Expect = 7e-06
 Identities = 20/43 (46%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPIC 140
           C ICLEE    D   ILP C H++ S CI+ W      TCP+C
Sbjct: 1   CPICLEEPK--DPVTILP-CGHLFCSKCILSWLESGNVTCPLC 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|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 11/59 (18%)

Query: 99  CVICLEEFVSGDLFRI----------LPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD 147
           C IC++E    D   +          LP C H+ H HC+  W   + TCPICR  +  D
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIFD 347

Length = 491

>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 118 CKHVYHSHCIIRWFSDEFTCPICR 141
           C H +H HCI RW   +  CP+ R
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 3/32 (9%)

Query: 118 CKHVYHSHCIIRWFSDEFT---CPICRSSIYL 146
           CKH +H HCI++W + E +   CP+CR +   
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCRQTFVF 83

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.92
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.83
PHA02929	238	N1R/p28-like protein; Provisional	99.75
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.72
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.69
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.63
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.62
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.48
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.47
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.47
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.46
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.46
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.38
PF14634	44	zf-RING_5: zinc-RING finger domain	99.36
PHA02926	242	zinc finger-like protein; Provisional	99.35
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.34
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.3
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.29
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.27
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.26
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.25
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.21
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.19
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	99.18
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	99.09
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.08
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.03
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.01
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.01
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.88
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.83
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.83
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.77
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.74
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.74
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.72
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.7
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.66
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.66
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.63
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.58
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.47
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.44
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.42
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.39
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.39
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.36
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.35
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.35
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.28
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.1
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	98.08
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.98
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.9
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.82
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.77
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.7
PHA02862	156	5L protein; Provisional	97.65
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.61
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.58
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.52
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.45
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.44
KOG2660	331	consensus Locus-specific chromosome binding protei	97.42
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.39
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.35
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.32
COG5152	259	Uncharacterized conserved protein, contains RING a	97.32
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.27
PHA03096	284	p28-like protein; Provisional	97.22
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.19
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.17
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.13
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	97.08
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.06
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.0
KOG1940	276	consensus Zn-finger protein [General function pred	96.97
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.86
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.81
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.78
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.55
KOG4739	233	consensus Uncharacterized protein involved in syna	96.54
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.33
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.32
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.22
PF04641	260	Rtf2: Rtf2 RING-finger	96.11
KOG1001	674	consensus Helicase-like transcription factor HLTF/	95.89
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	95.87
KOG3002	299	consensus Zn finger protein [General function pred	95.81
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.73
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.66
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	95.6
KOG3053	293	consensus Uncharacterized conserved protein [Funct	95.6
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.59
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.46
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.43
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.39
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.2
KOG1609	323	consensus Protein involved in mRNA turnover and st	95.07
KOG3899	381	consensus Uncharacterized conserved protein [Funct	94.46
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	94.25
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.17
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.66
KOG0269	839	consensus WD40 repeat-containing protein [Function	93.0
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	92.56
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	92.33
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	92.2
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	91.75
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	91.7
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.31
KOG1829	580	consensus Uncharacterized conserved protein, conta	91.12
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	90.93
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	90.81
KOG2807	378	consensus RNA polymerase II transcription initiati	89.61
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.56
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	88.53
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	88.33
KOG0825	1134	consensus PHD Zn-finger protein [General function	87.95
KOG3005	276	consensus GIY-YIG type nuclease [General function	87.3
KOG3113	293	consensus Uncharacterized conserved protein [Funct	86.82
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	86.66
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	86.07
KOG4367	699	consensus Predicted Zn-finger protein [Function un	85.55
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	84.6
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	84.19
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	83.23
PF04423	54	Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IP	82.77
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	82.74
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	82.45
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	82.16
KOG2068	327	consensus MOT2 transcription factor [Transcription	80.09

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

Probab=99.92  E-value=2.2e-25  Score=163.64  Aligned_cols=75  Identities=37%  Similarity=0.836  Sum_probs=66.8

Q ss_pred             CCCCHHHHhcCCCccccCCccCCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCC-CcccCCCCCCC
Q 045986           70 PLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFT-CPICRSSIYLD  147 (148)
Q Consensus        70 ~~~~~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~~~~~  147 (148)
                      ..+.++.++++|...|...+.....  +.|+||||+|++||.+|+|| |+|.||..|||+||..+.+ ||+||+++.++
T Consensus       205 ~r~~k~~l~~~p~~~f~~~~~~~~~--~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  205 NRLIKRLLKKLPVRTFTKGDDEDAT--DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhHHHHHhhCCcEEeccccccCCC--ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            3678899999999999998766553  68999999999999999999 9999999999999998755 99999988764

>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=99.83  E-value=2.2e-21  Score=103.80  Aligned_cols=44  Identities=50%  Similarity=1.202  Sum_probs=40.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR  141 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  141 (148)
                      ++|+||+++|..++.+..++ |||.||.+||.+|++++.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            37999999999999999999 999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.75  E-value=1.1e-18  Score=123.33  Aligned_cols=77  Identities=29%  Similarity=0.659  Sum_probs=60.3

Q ss_pred             CCCCCHHHHhcCCCccccCCccCCCCCccccccccccccCCC----eeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           69 RPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGD----LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        69 ~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ..+..+..++.+|.+............+.+|+||++++.+++    .+.+++.|+|.||.+||.+|+..+.+||+||..+
T Consensus       147 k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             hcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            345678889999998766555444445689999999987654    1335545999999999999999999999999876


Q ss_pred             C
Q 045986          145 Y  145 (148)
Q Consensus       145 ~  145 (148)
                      .
T Consensus       227 ~  227 (238)
T PHA02929        227 I  227 (238)
T ss_pred             e
Confidence            4

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

Probab=99.72  E-value=2.8e-18  Score=122.66  Aligned_cols=51  Identities=37%  Similarity=0.996  Sum_probs=47.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHh-CCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~  147 (148)
                      +.+|+|||++|.++|.+++|| |+|.||..|+++|+. .+..||+||++++|.
T Consensus       323 GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             CceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            478999999999999999999 999999999999998 577899999999874

>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=99.69  E-value=2.5e-17  Score=97.07  Aligned_cols=44  Identities=39%  Similarity=0.968  Sum_probs=35.9

Q ss_pred             cccccccccccCC----------CeeeecCCCCccchHHhHHHHHhCCCCCcccC
Q 045986           97 SECVICLEEFVSG----------DLFRILPFCKHVYHSHCIIRWFSDEFTCPICR  141 (148)
Q Consensus        97 ~~C~ICl~~~~~~----------~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  141 (148)
                      +.|+||+++|.+.          -.+...+ |||.||..||.+||+.+.+||+||
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            4699999999432          2455566 999999999999999999999998

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 ....

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

Probab=99.63  E-value=7.2e-16  Score=109.88  Aligned_cols=49  Identities=33%  Similarity=0.844  Sum_probs=43.3

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +...|.+||+...+   ..-+| |||+||+.||..|...+..||+||..+.|.
T Consensus       238 a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  238 ATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            34789999999654   47899 999999999999999999999999998775

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

Probab=99.62  E-value=1e-15  Score=112.44  Aligned_cols=68  Identities=31%  Similarity=0.748  Sum_probs=50.3

Q ss_pred             HHHHhcCCCccccCCccCCCCCccccccccccccCCC----------eeeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986           74 QRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGD----------LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus        74 ~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----------~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      ++.-+.+|++..++.    .+++..|+||++++-..+          ....|| |||+||-+|++.|++++++||.||.+
T Consensus       269 kdl~~~~~t~t~eql----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p  343 (491)
T COG5243         269 KDLNAMYPTATEEQL----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRP  343 (491)
T ss_pred             hHHHhhcchhhhhhh----cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCc
Confidence            334444565543333    233468999999953322          567899 99999999999999999999999999


Q ss_pred             CCC
Q 045986          144 IYL  146 (148)
Q Consensus       144 ~~~  146 (148)
                      +.-
T Consensus       344 ~if  346 (491)
T COG5243         344 VIF  346 (491)
T ss_pred             ccc
Confidence            643

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.48  E-value=4.6e-14  Score=96.34  Aligned_cols=49  Identities=27%  Similarity=0.672  Sum_probs=40.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC----------------CCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD----------------EFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~----------------~~~CP~CR~~~~~~  147 (148)
                      ++.+|+||++.+++.   .+++ |||.||+.||..|+..                +.+||+||+.+..+
T Consensus        17 ~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~   81 (193)
T PLN03208         17 GDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA   81 (193)
T ss_pred             CccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence            347899999998654   6678 9999999999999852                34699999988653

>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=99.47  E-value=4.8e-14  Score=73.16  Aligned_cols=39  Identities=33%  Similarity=0.974  Sum_probs=33.3

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  140 (148)
                      |+||++.+.+  .+.+++ |||.|+.+|+..|++.+.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999766  456788 99999999999999999999998

>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=99.47  E-value=5e-14  Score=75.05  Aligned_cols=44  Identities=50%  Similarity=1.195  Sum_probs=37.8

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSI  144 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~  144 (148)
                      +|+||++.+  .+.+..++ |||.||.+|++.|+.. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  45566677 9999999999999997 77899999864

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

Probab=99.46  E-value=5.1e-14  Score=83.71  Aligned_cols=50  Identities=36%  Similarity=0.829  Sum_probs=38.6

Q ss_pred             ccccccccccccC--------CC-eeeecCCCCccchHHhHHHHHhC---CCCCcccCCCCC
Q 045986           96 TSECVICLEEFVS--------GD-LFRILPFCKHVYHSHCIIRWFSD---EFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~--------~~-~vr~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~~  145 (148)
                      ++.|.||...|+.        |+ ...++..|+|.||..||.+||..   +.+||+||++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            4689999988872        22 23344459999999999999986   467999999764

>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=99.46  E-value=5.5e-14  Score=76.96  Aligned_cols=46  Identities=37%  Similarity=0.824  Sum_probs=39.0

Q ss_pred             ccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +..|.||++...   .+..+| |||. |+.+|+..|++.+.+||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            368999999854   468889 9999 999999999999999999999874

...

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

Probab=99.38  E-value=3.8e-13  Score=93.49  Aligned_cols=50  Identities=22%  Similarity=0.657  Sum_probs=40.0

Q ss_pred             CCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC---CCCcccCCCCCC
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE---FTCPICRSSIYL  146 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~  146 (148)
                      +.+..+|.|||+.-++   ..++. |||+||+.||-+||..+   ..||+||+.|..
T Consensus        44 ~~~~FdCNICLd~akd---PVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD---PVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI   96 (230)
T ss_pred             CCCceeeeeeccccCC---CEEee-cccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence            3455899999998444   35666 99999999999999874   349999998754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.36  E-value=6.6e-13  Score=70.64  Aligned_cols=44  Identities=30%  Similarity=0.844  Sum_probs=39.1

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      .|+||+++|.+....++|+ |||+|+.+|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4999999996667788899 9999999999999866778999985

>PHA02926 zinc finger-like protein; Provisional

Probab=99.35  E-value=2.6e-13  Score=93.84  Aligned_cols=53  Identities=34%  Similarity=0.747  Sum_probs=39.4

Q ss_pred             CCCCccccccccccccCC-----CeeeecCCCCccchHHhHHHHHhCC------CCCcccCCCC
Q 045986           92 NKKFTSECVICLEEFVSG-----DLFRILPFCKHVYHSHCIIRWFSDE------FTCPICRSSI  144 (148)
Q Consensus        92 ~~~~~~~C~ICl~~~~~~-----~~vr~lp~C~H~FH~~Ci~~Wl~~~------~~CP~CR~~~  144 (148)
                      ..+.+.+|+|||+..-+.     ...-+|+.|+|.||..||+.|-..+      .+||+||..+
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f  229 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRF  229 (242)
T ss_pred             hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCccee
Confidence            334457999999986332     1234676699999999999998753      3499999865

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

Probab=99.34  E-value=3.4e-13  Score=106.80  Aligned_cols=48  Identities=44%  Similarity=1.084  Sum_probs=43.8

Q ss_pred             ccccccccccccCCCe--eeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDL--FRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~--vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      +..|+||++++..+..  .+.|| |+|+||..|+..|++++.+||+||..+
T Consensus       291 ~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  291 DELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             CCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence            5789999999988765  78899 999999999999999999999999844

>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=99.30  E-value=1.7e-12  Score=68.06  Aligned_cols=39  Identities=38%  Similarity=1.133  Sum_probs=33.7

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHh--CCCCCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS--DEFTCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~--~~~~CP~C  140 (148)
                      |+||++.+.+.  ++.++ |||.|+.+|+..|++  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998665  35788 999999999999999  46679998

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 ....

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

Probab=99.29  E-value=1.7e-12  Score=75.33  Aligned_cols=49  Identities=33%  Similarity=0.837  Sum_probs=36.8

Q ss_pred             ccccccccccc-----------CCC-eeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFV-----------SGD-LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~-----------~~~-~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +.|+||...|.           .++ ...+...|+|.||..||..||..+..||++|+...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            46777776653           333 33333349999999999999999999999998754

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

Probab=99.27  E-value=3.9e-12  Score=85.05  Aligned_cols=54  Identities=31%  Similarity=0.585  Sum_probs=42.7

Q ss_pred             cCCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           90 LHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        90 ~~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ....++...|+|||+.+.+...  +-.+|||+||+.||+.-++....||+||..|.
T Consensus       125 ~~~~~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt  178 (187)
T KOG0320|consen  125 PLRKEGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT  178 (187)
T ss_pred             ccccccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence            3344445789999999876533  42339999999999999999999999997654

>smart00184 RING Ring finger

Probab=99.26  E-value=5.2e-12  Score=64.94  Aligned_cols=38  Identities=47%  Similarity=1.089  Sum_probs=33.2

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHh-CCCCCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS-DEFTCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~C  140 (148)
                      |+||++.   ......++ |||.||..|++.|+. .+.+||+|
T Consensus         1 C~iC~~~---~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998   45677888 999999999999998 57779998

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)

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

Probab=99.25  E-value=4.9e-12  Score=66.42  Aligned_cols=38  Identities=39%  Similarity=1.032  Sum_probs=29.5

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHhCC----CCCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE----FTCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~----~~CP~C  140 (148)
                      |+||++-|.+.   ..|+ |||.|+..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999776   6788 99999999999999763    359988

>smart00504 Ubox Modified RING finger domain

Probab=99.21  E-value=1.6e-11  Score=70.28  Aligned_cols=47  Identities=26%  Similarity=0.428  Sum_probs=41.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ..|+||++.+.+.   .++| |||+|..+||.+|++.+.+||+|+.++..+
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~   48 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHE   48 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence            3699999998775   5678 999999999999999989999999987543

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

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

Probab=99.19  E-value=2.8e-12  Score=73.75  Aligned_cols=49  Identities=33%  Similarity=0.876  Sum_probs=37.0

Q ss_pred             cccccccccccC---------CCeeeecCCCCccchHHhHHHHHhCC---CCCcccCCCCC
Q 045986           97 SECVICLEEFVS---------GDLFRILPFCKHVYHSHCIIRWFSDE---FTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~---------~~~vr~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~  145 (148)
                      +.|-||..+|..         ++..-++..|.|.||..||.+|+..+   ..||+||+...
T Consensus        21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            478888888863         23333454599999999999999874   44999998653

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

Probab=99.18  E-value=3e-11  Score=91.95  Aligned_cols=49  Identities=31%  Similarity=1.035  Sum_probs=40.0

Q ss_pred             cccccccccccC---C-----------CeeeecCCCCccchHHhHHHHHh-CCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVS---G-----------DLFRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~---~-----------~~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  146 (148)
                      ..|+|||.+..-   +           ....++| |+|+||..|+..|+. .+..||+||+++++
T Consensus       572 ~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  572 NDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            689999988742   1           1234678 999999999999999 56689999999976

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

Probab=99.09  E-value=9.2e-11  Score=63.55  Aligned_cols=42  Identities=31%  Similarity=0.771  Sum_probs=33.7

Q ss_pred             ccccccccccCCCeeeecCCCC-----ccchHHhHHHHHhCC--CCCcccC
Q 045986           98 ECVICLEEFVSGDLFRILPFCK-----HVYHSHCIIRWFSDE--FTCPICR  141 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR  141 (148)
                      .|.||++ ..+++...++| |.     |.+|.+|++.|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3899999 44455666899 84     999999999999664  4799995

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.08  E-value=8.5e-11  Score=89.04  Aligned_cols=47  Identities=32%  Similarity=0.687  Sum_probs=41.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ...|+||++.|.+.   .++| |||.||..||..|+..+..||+||..+..
T Consensus        26 ~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        26 SLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             ccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            46899999998665   4678 99999999999999998899999997754

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

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

Probab=99.03  E-value=7e-11  Score=83.83  Aligned_cols=50  Identities=30%  Similarity=0.708  Sum_probs=41.4

Q ss_pred             CccccccccccccCCC-------eeeecCCCCccchHHhHHHHH--hCCCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGD-------LFRILPFCKHVYHSHCIIRWF--SDEFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~-------~vr~lp~C~H~FH~~Ci~~Wl--~~~~~CP~CR~~~~  145 (148)
                      ++..|+||-..+...+       ..-.|. |+|.||..||+-|-  .++++||.|+..+.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            4578999998886554       667788 99999999999995  46889999987654

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

Probab=99.01  E-value=2e-10  Score=60.35  Aligned_cols=38  Identities=37%  Similarity=0.927  Sum_probs=22.9

Q ss_pred             cccccccccCCC-eeeecCCCCccchHHhHHHHHhCC----CCCc
Q 045986           99 CVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFSDE----FTCP  138 (148)
Q Consensus        99 C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~~----~~CP  138 (148)
                      |+||.+ |.+.+ ...+|| |||.|..+||+.++.++    -+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 568899 99999999999999854    2477

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

Probab=99.01  E-value=1.6e-10  Score=81.94  Aligned_cols=49  Identities=31%  Similarity=0.948  Sum_probs=41.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHH-HHhCCCC-CcccCCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIR-WFSDEFT-CPICRSSIYLDA  148 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~-Wl~~~~~-CP~CR~~~~~~~  148 (148)
                      +..|+||++..   +....+| |||+|+..||-. |=.++.. ||+||+.+.|++
T Consensus       215 d~kC~lC~e~~---~~ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         215 DYKCFLCLEEP---EVPSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccceeeeeccc---CCccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            47899999984   4457788 999999999999 9777666 999999888753

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

Probab=98.88  E-value=1.1e-09  Score=80.68  Aligned_cols=48  Identities=40%  Similarity=0.737  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ++..+|.|||.+-   -...+|| |+|. .|.+|-+..--.+..||+||+++.
T Consensus       288 ~~gkeCVIClse~---rdt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSES---RDTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCC---cceEEec-chhhehhHhHHHHHHHhhcCCCccccchH
Confidence            3457999999994   4458999 9999 999999998777888999999874

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

Probab=98.83  E-value=1.8e-09  Score=81.59  Aligned_cols=47  Identities=30%  Similarity=0.836  Sum_probs=39.3

Q ss_pred             ccccccccccccCCC-eeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      -..|||||+.+.+.- .++... |+|.||..|+..|  ...+||+||.-..
T Consensus       175 LPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  175 LPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             CCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            478999999997653 567777 9999999999999  5678999997554

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

Probab=98.83  E-value=2.4e-09  Score=65.30  Aligned_cols=47  Identities=30%  Similarity=0.777  Sum_probs=36.7

Q ss_pred             ccccccccccc-------------CCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986           97 SECVICLEEFV-------------SGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~-------------~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      +.|+||...+.             .++....-..|+|.||-.||..||+.+..||+|.+.
T Consensus        47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            57999876552             234444445599999999999999999999999764

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

Probab=98.77  E-value=2.2e-09  Score=87.52  Aligned_cols=49  Identities=41%  Similarity=0.963  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCeeeecCC-----CCccchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPF-----CKHVYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~-----C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      +.++||||..-...-|  |.||.     |.|-||..|+-+|++.  +.+||+||..++
T Consensus      1468 G~eECaICYsvL~~vd--r~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1468 GHEECAICYSVLDMVD--RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CcchhhHHHHHHHHHh--ccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3589999987664111  23332     8999999999999987  566999998875

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

Probab=98.74  E-value=7.4e-09  Score=60.96  Aligned_cols=48  Identities=29%  Similarity=0.403  Sum_probs=37.4

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      ...|+|+.+-|.+.   .++| +||.|-..+|..|++. +.+||+|+.++..+
T Consensus         4 ~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    4 EFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             ccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            46899999998775   6788 9999999999999999 88899999988653

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 ....

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

Probab=98.74  E-value=4.9e-09  Score=80.54  Aligned_cols=48  Identities=35%  Similarity=0.814  Sum_probs=37.5

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-----CCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-----FTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~~~~~  147 (148)
                      +..|||||++....   ..+- |||+||..||-..+...     ..||+||..|.+.
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k  238 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLK  238 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence            46899999985443   3344 99999999998888653     4599999988763

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

Probab=98.72  E-value=5.1e-09  Score=76.78  Aligned_cols=45  Identities=36%  Similarity=0.772  Sum_probs=40.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ..|-||.+-|...   .++| |+|.||.-||+..|..++.||.|+..+.
T Consensus        24 LRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~   68 (442)
T KOG0287|consen   24 LRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVT   68 (442)
T ss_pred             HHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccc
Confidence            4699999999876   6788 9999999999999999999999998764

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.70  E-value=1.4e-08  Score=74.48  Aligned_cols=49  Identities=18%  Similarity=0.470  Sum_probs=36.8

Q ss_pred             ccccccccc-ccCCC-eeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           97 SECVICLEE-FVSGD-LFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~-~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ..||+|..+ |.+.+ .+.+.+ |||.||..||+..+.. ...||.|+.++..
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            579999986 44444 233446 9999999999996644 5679999987754

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).

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

Probab=98.66  E-value=3.1e-09  Score=61.95  Aligned_cols=49  Identities=31%  Similarity=0.695  Sum_probs=23.6

Q ss_pred             cccccccccccCCC-ee-ee--cCCCCccchHHhHHHHHhC---C--------CCCcccCCCCC
Q 045986           97 SECVICLEEFVSGD-LF-RI--LPFCKHVYHSHCIIRWFSD---E--------FTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~-~v-r~--lp~C~H~FH~~Ci~~Wl~~---~--------~~CP~CR~~~~  145 (148)
                      .+|.||.+...+++ .. .+  -+.|++.||..|+.+||+.   .        .+||.|+++|.
T Consensus         3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            57999999876333 21 22  2248999999999999964   1        24999998764

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

Probab=98.66  E-value=1.4e-08  Score=73.09  Aligned_cols=44  Identities=30%  Similarity=0.601  Sum_probs=38.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ..|-||-+-+...   ..++ |||.||.-||...|..++.||+||.+.
T Consensus        26 lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~   69 (391)
T COG5432          26 LRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDP   69 (391)
T ss_pred             HHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccH
Confidence            5799998887665   5667 999999999999999999999999863

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

Probab=98.63  E-value=1.5e-08  Score=75.47  Aligned_cols=45  Identities=31%  Similarity=0.937  Sum_probs=36.3

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC---CCCCcccC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD---EFTCPICR  141 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR  141 (148)
                      ..|.||-+-+....++.....|||+||..|+..|+..   +.+||.||
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            5799995555555566666669999999999999987   34699998

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

Probab=98.58  E-value=2.2e-08  Score=73.59  Aligned_cols=44  Identities=36%  Similarity=0.891  Sum_probs=38.8

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      +...|+||++.|...   +++| |+|.|+..|+..++.....||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            346899999999888   8899 9999999999999885567999993

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

Probab=98.47  E-value=4e-08  Score=70.99  Aligned_cols=49  Identities=39%  Similarity=0.948  Sum_probs=41.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHh------------------C-----CCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS------------------D-----EFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~------------------~-----~~~CP~CR~~~~~  146 (148)
                      ..|+|||-.|.+++...+++ |-|+||..|+..+|.                  .     +..||+||..|.-
T Consensus       116 gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            57999999999999999999 999999999988771                  1     2349999987754

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

Probab=98.44  E-value=1.5e-07  Score=70.65  Aligned_cols=47  Identities=30%  Similarity=0.926  Sum_probs=37.0

Q ss_pred             ccccccccccccC-CCeeeecCCCCccchHHhHHHHHhC--CCCCcccCC
Q 045986           96 TSECVICLEEFVS-GDLFRILPFCKHVYHSHCIIRWFSD--EFTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~-~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~  142 (148)
                      ...|+|||+.++- ++...+.+.|||.|-.+||+.||.+  ...||.|..
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~   53 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG   53 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence            3689999999974 4555555559999999999999964  334999964

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

Probab=98.42  E-value=4.4e-08  Score=78.72  Aligned_cols=47  Identities=21%  Similarity=0.410  Sum_probs=41.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ..|++||..+.++.....-+ |+|+||..||+.|-+.-.+||+||..+
T Consensus       124 ~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF  170 (1134)
T KOG0825|consen  124 NQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEF  170 (1134)
T ss_pred             hhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhh
Confidence            67889998888877777777 999999999999999999999999754

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

Probab=98.39  E-value=6.3e-08  Score=54.45  Aligned_cols=46  Identities=26%  Similarity=0.727  Sum_probs=22.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      -.|++|.+-+.+.   ..|..|.|+|+..||..-+.  ..||+|+.+.+-.
T Consensus         8 LrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~q   53 (65)
T PF14835_consen    8 LRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQ   53 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-S
T ss_pred             cCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChHHHH
Confidence            4699999987664   33445999999999988544  4599999886543

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

Probab=98.39  E-value=1e-07  Score=76.49  Aligned_cols=48  Identities=19%  Similarity=0.651  Sum_probs=40.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLDA  148 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~~  148 (148)
                      -.|++|-..+.+    ++++.|||+||..||.+-+.. +..||.|.+++.++|
T Consensus       644 LkCs~Cn~R~Kd----~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  644 LKCSVCNTRWKD----AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             eeCCCccCchhh----HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            579999987766    355669999999999999975 677999999998876

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

Probab=98.36  E-value=1.9e-07  Score=67.67  Aligned_cols=47  Identities=30%  Similarity=0.534  Sum_probs=38.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      .+|+||+....-   ...|+ |+|.|+..||+-=..+ ..+||+||.++..+
T Consensus         8 ~eC~IC~nt~n~---Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    8 KECLICYNTGNC---PVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CcceeeeccCCc---Ccccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            589999998443   46677 9999999999876555 66799999998753

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

Probab=98.35  E-value=4.9e-08  Score=72.02  Aligned_cols=48  Identities=25%  Similarity=0.530  Sum_probs=40.8

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      +..|+|||+-++..   +.++.|.|.|+.+||..-++. +.+||.||+.+..
T Consensus        43 ~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   43 QVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            46899999998776   666779999999999999876 7789999997653

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

Probab=98.35  E-value=9.1e-08  Score=51.72  Aligned_cols=44  Identities=39%  Similarity=0.737  Sum_probs=33.5

Q ss_pred             cccccccccccCCCeeeecCCCCcc-chHHhHHHHHh-CCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFS-DEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~-~~~~CP~CR~~~  144 (148)
                      ++|.||++.-.+.    +|--|||. .+-+|-.+-++ .+..||+||+++
T Consensus         8 dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi   53 (62)
T KOG4172|consen    8 DECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPI   53 (62)
T ss_pred             cceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence            6899999885443    33239999 88999655444 789999999986

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

Probab=98.33  E-value=5.2e-07  Score=62.93  Aligned_cols=49  Identities=29%  Similarity=0.815  Sum_probs=42.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--------CCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--------EFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~~~~~  147 (148)
                      ..|..|-..+.++|.+|..  |-|.||++|+++|-..        ...||-|-.+|+|+
T Consensus        51 pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   51 PNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            4699999999999999976  9999999999999754        23499999999986

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

Probab=98.28  E-value=4.2e-07  Score=67.95  Aligned_cols=50  Identities=36%  Similarity=0.834  Sum_probs=38.0

Q ss_pred             CccccccccccccCCC----eeeecCCCCccchHHhHHHHHh--C-----CCCCcccCCCC
Q 045986           95 FTSECVICLEEFVSGD----LFRILPFCKHVYHSHCIIRWFS--D-----EFTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~----~vr~lp~C~H~FH~~Ci~~Wl~--~-----~~~CP~CR~~~  144 (148)
                      .+.+|.||++...+..    -...||.|.|.|+..||+.|-.  +     ...||.||...
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            3578999999865432    1235677999999999999973  3     36699999854

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

Probab=98.10  E-value=9.4e-07  Score=66.45  Aligned_cols=45  Identities=36%  Similarity=0.855  Sum_probs=38.1

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      +.|-||-+.   +-.|++-| |||..|..|+..|=..  ..+||.||..|.
T Consensus       370 eLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  370 ELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             HHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            679999876   56789999 9999999999999644  467999998764

>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=98.08  E-value=1.5e-06  Score=56.14  Aligned_cols=34  Identities=24%  Similarity=0.556  Sum_probs=30.1

Q ss_pred             cccccccccccCCCeeeecCCCC------ccchHHhHHHHH
Q 045986           97 SECVICLEEFVSGDLFRILPFCK------HVYHSHCIIRWF  131 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~------H~FH~~Ci~~Wl  131 (148)
                      .+|+||++...+++.+..++ ||      |+||.+|+..|=
T Consensus        27 ~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   27 VECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             eeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            68999999999877788888 75      999999999994

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.

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

Probab=98.05  E-value=3.3e-06  Score=64.47  Aligned_cols=48  Identities=27%  Similarity=0.741  Sum_probs=40.8

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ..+.+|.||+.-+...   .++| |||.|+..||+.-+..+..||.||..+.
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~  129 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELV  129 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCcccccccc
Confidence            3358899998887665   6778 9999999999998787888999999876

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

Probab=97.98  E-value=2.6e-06  Score=63.98  Aligned_cols=44  Identities=30%  Similarity=0.782  Sum_probs=37.5

Q ss_pred             cccccccccccC-CCeeeecCCCCccchHHhHHHHHhCCC--CCcccC
Q 045986           97 SECVICLEEFVS-GDLFRILPFCKHVYHSHCIIRWFSDEF--TCPICR  141 (148)
Q Consensus        97 ~~C~ICl~~~~~-~~~vr~lp~C~H~FH~~Ci~~Wl~~~~--~CP~CR  141 (148)
                      -.|-.|-+.+.. ++.+.-|| |.|+||..|+.+.|.++.  +||.||
T Consensus       366 L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  366 LYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             hhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            569999888753 45788899 999999999999998754  599998

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

Probab=97.90  E-value=9.7e-06  Score=45.19  Aligned_cols=40  Identities=23%  Similarity=0.619  Sum_probs=27.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CCCCcc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EFTCPI  139 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~  139 (148)
                      ..|||.+..|++  .|+-.. |||.|-++.|..|+++  ...||+
T Consensus        12 ~~CPiT~~~~~~--PV~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   12 LKCPITLQPFED--PVKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB-TTTSSB-SS--EEEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cCCCCcCChhhC--CcCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            679999999865  456566 9999999999999944  445998

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

Probab=97.82  E-value=9.5e-06  Score=62.29  Aligned_cols=48  Identities=23%  Similarity=0.640  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      +..|++|...+.+.-  ..+. |||.|+..|+..|+..+..||.|++.+..
T Consensus        21 ~l~C~~C~~vl~~p~--~~~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~   68 (391)
T KOG0297|consen   21 NLLCPICMSVLRDPV--QTTT-CGHRFCAGCLLESLSNHQKCPVCRQELTQ   68 (391)
T ss_pred             cccCccccccccCCC--CCCC-CCCcccccccchhhccCcCCcccccccch
Confidence            468999999987752  2235 99999999999999999999999887643

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

Probab=97.77  E-value=1.8e-05  Score=42.35  Aligned_cols=40  Identities=38%  Similarity=0.908  Sum_probs=27.6

Q ss_pred             cccccccccCCCeeeecCCCC-----ccchHHhHHHHHhC--CCCCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCK-----HVYHSHCIIRWFSD--EFTCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~-----H~FH~~Ci~~Wl~~--~~~CP~C  140 (148)
                      |-||+++-.+++ .-+.| |+     -..|.+|+..|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999876665 44567 63     58999999999974  5669988

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

Probab=97.70  E-value=1.6e-05  Score=57.85  Aligned_cols=48  Identities=31%  Similarity=0.722  Sum_probs=36.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCccc-CCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPIC-RSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~C-R~~~~~~  147 (148)
                      ..|+.|-.-..+.   ..+|+|+|.|+.+||..-|.. ...||.| |.+++.|
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld  324 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLD  324 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCcccccchhh
Confidence            5799998776554   445889999999999987765 5569999 5566655

>PHA02862 5L protein; Provisional

Probab=97.65  E-value=5e-05  Score=49.58  Aligned_cols=44  Identities=23%  Similarity=0.535  Sum_probs=32.7

Q ss_pred             cccccccccccCCCeeeecCC-C---CccchHHhHHHHHhC--CCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPF-C---KHVYHSHCIIRWFSD--EFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~-C---~H~FH~~Ci~~Wl~~--~~~CP~CR~~~  144 (148)
                      +.|-||.++-++  .  .-|+ |   ...-|.+|+..|++.  +.+||+|+.+.
T Consensus         3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY   52 (156)
T PHA02862          3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY   52 (156)
T ss_pred             CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence            579999998433  2  3560 2   367999999999976  44599999864

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

Probab=97.61  E-value=0.00021  Score=52.68  Aligned_cols=46  Identities=17%  Similarity=0.428  Sum_probs=35.8

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      .....|+||+..-.++-.+.+   -|-+||..||-+.+.++..||+=-.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT~~  343 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVTGY  343 (357)
T ss_pred             CccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCccCC
Confidence            344789999999666532222   6999999999999999999998433

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

Probab=97.58  E-value=2.4e-05  Score=52.01  Aligned_cols=28  Identities=50%  Similarity=1.079  Sum_probs=26.1

Q ss_pred             ccccccccccccCCCeeeecCCCCccchH
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHS  124 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~  124 (148)
                      ..+|.|||++++.++.|..|| |--+||+
T Consensus       177 kGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  177 KGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             CCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            368999999999999999999 9999986

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

Probab=97.52  E-value=8.1e-05  Score=64.27  Aligned_cols=51  Identities=31%  Similarity=0.760  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC----------CCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE----------FTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~----------~~CP~CR~~~~  145 (148)
                      +.++.|.||+.+--.......|- |+|+||-.|.+.-|++.          .+||+|+.++.
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            34588999998877777777888 99999999998776552          25999998764

>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=97.45  E-value=5.9e-05  Score=47.37  Aligned_cols=31  Identities=32%  Similarity=0.873  Sum_probs=26.7

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHH
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCII  128 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~  128 (148)
                      +..|++|-..+.. ....+.| |||+||..|++
T Consensus        78 ~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            3679999999977 5777889 99999999975

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 [].

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.44  E-value=0.00019  Score=47.83  Aligned_cols=44  Identities=27%  Similarity=0.746  Sum_probs=32.8

Q ss_pred             ccccccccccccCCCeeeecCCC--Cc---cchHHhHHHHHhC--CCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFC--KH---VYHSHCIIRWFSD--EFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C--~H---~FH~~Ci~~Wl~~--~~~CP~CR~~~  144 (148)
                      +..|-||.++..  +.  .-| |  ..   .-|.+|++.|+..  ..+||+|+++.
T Consensus         8 ~~~CRIC~~~~~--~~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y   58 (162)
T PHA02825          8 DKCCWICKDEYD--VV--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPY   58 (162)
T ss_pred             CCeeEecCCCCC--Cc--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence            468999998843  22  346 5  44   6799999999976  44599999864

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

Probab=97.42  E-value=3.2e-05  Score=56.99  Aligned_cols=46  Identities=22%  Similarity=0.657  Sum_probs=38.3

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ...|.+|-.-|.+...|.   .|-|.||+.||-..|..+.+||+|...+
T Consensus        15 ~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~i   60 (331)
T KOG2660|consen   15 HITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVI   60 (331)
T ss_pred             ceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceec
Confidence            368999988887764333   3999999999999999999999998755

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

Probab=97.39  E-value=7.7e-05  Score=58.33  Aligned_cols=49  Identities=24%  Similarity=0.656  Sum_probs=38.1

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-----CCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-----EFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~~~~~  147 (148)
                      ++.+|-+|-++-   +...+.. |.|.||.-||.++...     +.+||+|.-.+.-|
T Consensus       535 ~~~~C~lc~d~a---ed~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  535 GEVECGLCHDPA---EDYIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             CceeecccCChh---hhhHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            347899999884   3445666 9999999999988854     66799998776543

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

Probab=97.37  E-value=6.4e-06  Score=61.79  Aligned_cols=51  Identities=24%  Similarity=0.603  Sum_probs=45.2

Q ss_pred             ccccccccccccCC-CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSG-DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~-~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ...|+||...|++. +.+..+. |||.+|.+|+.+||.....||.||+.++.+
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            36899999999887 6777777 999999999999999988999999988654

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

Probab=97.37  E-value=0.00011  Score=55.75  Aligned_cols=45  Identities=33%  Similarity=0.853  Sum_probs=37.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--------CCCCcccCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--------EFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~  142 (148)
                      ..|.||+++.........|| |+|+|++.|...+...        ..+||-+..
T Consensus       185 f~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             ccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            68999999988878999999 9999999999999854        234877654

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

Probab=97.35  E-value=0.00017  Score=53.79  Aligned_cols=48  Identities=21%  Similarity=0.436  Sum_probs=40.7

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      .++..|+||...   ...-...| |+|.=+.+||...|.+.+.|=.|++.+-
T Consensus       420 sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             cccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            556899999876   44446788 9999999999999999999999998654

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

Probab=97.32  E-value=0.00015  Score=54.13  Aligned_cols=43  Identities=37%  Similarity=0.783  Sum_probs=31.4

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      .+.|.||+++..+   ...+| |||+-+  |..-- +...+||+||+.+-
T Consensus       305 p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            3689999999666   56788 999955  55443 23455999998763

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

Probab=97.32  E-value=9.1e-05  Score=50.96  Aligned_cols=43  Identities=28%  Similarity=0.648  Sum_probs=37.2

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      ..|.||-.+|+..   .++. |||.|+..|...=++.-.+|-+|-..
T Consensus       197 F~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         197 FLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             eeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchh
Confidence            5899999999886   5566 99999999999888888999999653

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

Probab=97.27  E-value=0.00026  Score=37.79  Aligned_cols=45  Identities=27%  Similarity=0.513  Sum_probs=22.2

Q ss_pred             cccccccccCCC-eeeecCCCCccchHHhHHHHHh-CCCCCcccCCCC
Q 045986           99 CVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSI  144 (148)
Q Consensus        99 C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~  144 (148)
                      |++|.+++...+ ...-=+ ||+..+..|...-++ .+..||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999984433 333344 799999999888876 377899999863

>PHA03096 p28-like protein; Provisional

Probab=97.22  E-value=0.00019  Score=52.74  Aligned_cols=37  Identities=32%  Similarity=0.688  Sum_probs=29.7

Q ss_pred             cccccccccccCCC----eeeecCCCCccchHHhHHHHHhC
Q 045986           97 SECVICLEEFVSGD----LFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        97 ~~C~ICl~~~~~~~----~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      ..|.||++...+..    .--.|+.|.|.|+..|+..|-..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            47999999876432    34468889999999999999854

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.19  E-value=0.00019  Score=39.20  Aligned_cols=45  Identities=29%  Similarity=0.619  Sum_probs=34.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ..|..|...   +..-.++| |||+....|.+-+  +.+-||+|-+++.++
T Consensus         8 ~~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFD   52 (55)
T ss_pred             eeEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccCC
Confidence            356666554   33446889 9999999998875  667799999988765

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

Probab=97.17  E-value=0.00022  Score=58.53  Aligned_cols=47  Identities=34%  Similarity=0.764  Sum_probs=37.4

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-C------CCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-F------TCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-~------~CP~CR~  142 (148)
                      ..+|.||.+.+...+.+---..|-|+||-.||..|-+.. .      .||.|+.
T Consensus       191 ~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  191 KYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             ceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            478999999998877665544488999999999998651 1      3999984

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.13  E-value=0.00053  Score=48.79  Aligned_cols=51  Identities=12%  Similarity=0.258  Sum_probs=45.3

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ..|+||.+.+.+.-.+.+|..|||+|..+|+++.+..-..||+|-.++...
T Consensus       222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr  272 (303)
T KOG3039|consen  222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR  272 (303)
T ss_pred             eecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence            679999999999888888877999999999999999999999998777543

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

Probab=97.08  E-value=0.00048  Score=51.02  Aligned_cols=47  Identities=34%  Similarity=0.862  Sum_probs=39.4

Q ss_pred             cccccccccccCCC---eeeecCCCCccchHHhHHHHHhC-CCCCcccCCCC
Q 045986           97 SECVICLEEFVSGD---LFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~---~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~  144 (148)
                      .+|-||-++|..++   ..|+|. |||.|+..|+.+-+.. ...||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998774   567788 9999999999998876 44599999874

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

Probab=97.06  E-value=0.00084  Score=48.51  Aligned_cols=49  Identities=31%  Similarity=0.549  Sum_probs=36.2

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      ..+.+|++|-+.=..  .-...+ |+|+||.-||..=+..  ..+||.|-.++.
T Consensus       237 t~~~~C~~Cg~~Pti--P~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTI--PHVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCC--Ceeecc-ccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            345899999776222  233445 9999999999987654  467999988775

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

Probab=97.00  E-value=0.00023  Score=51.86  Aligned_cols=44  Identities=20%  Similarity=0.587  Sum_probs=38.2

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ..|-||-..|..+   .++. |+|.|+..|--.=+++...|++|-++.
T Consensus       242 f~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             ccccccccccccc---hhhc-CCceeehhhhccccccCCcceeccccc
Confidence            5699999999886   5566 999999999988888889999997764

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

Probab=96.97  E-value=0.00044  Score=50.40  Aligned_cols=45  Identities=33%  Similarity=0.707  Sum_probs=38.5

Q ss_pred             cccccccccccCCC-eeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           97 SECVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      ..|+||.+.+-... .+.+++ |||.-|..|...-...+.+||+|..
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            44999998876554 567888 9999999999999888899999977

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

Probab=96.86  E-value=0.0019  Score=48.26  Aligned_cols=47  Identities=26%  Similarity=0.603  Sum_probs=35.9

Q ss_pred             CCCccccccccccccCCCeeeecCCCCccchHHhHHHH--HhCCCCCcccCCC
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRW--FSDEFTCPICRSS  143 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~W--l~~~~~CP~CR~~  143 (148)
                      +++...|.||-+..   --..++| |+|..+.-|--..  |-.+..||+||..
T Consensus        58 DEen~~C~ICA~~~---TYs~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE  106 (493)
T COG5236          58 DEENMNCQICAGST---TYSARYP-CGHQICHACAVRLRALYMQKGCPLCRTE  106 (493)
T ss_pred             ccccceeEEecCCc---eEEEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence            34457899998874   3457899 9999999996443  5568889999974

>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=96.81  E-value=0.00089  Score=35.05  Aligned_cols=41  Identities=27%  Similarity=0.676  Sum_probs=22.7

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHhCCC--CCccc
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF--TCPIC  140 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~--~CP~C  140 (148)
                      |.+|-+-...|....... |+=.+|..|++.+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            566666655554333323 888899999999998755  69988

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.78  E-value=0.00021  Score=52.03  Aligned_cols=41  Identities=34%  Similarity=0.716  Sum_probs=32.2

Q ss_pred             ccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ...|+||++.   ......|+ |||. =+.+|-..    -..||+||+-+
T Consensus       300 ~~LC~ICmDa---P~DCvfLe-CGHmVtCt~CGkr----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFLE-CGHMVTCTKCGKR----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcC---CcceEEee-cCcEEeehhhccc----cccCchHHHHH
Confidence            4689999997   66678899 9998 67788554    33799999854

>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=96.55  E-value=0.0013  Score=34.75  Aligned_cols=29  Identities=28%  Similarity=0.656  Sum_probs=22.0

Q ss_pred             C-CccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986          118 C-KHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus       118 C-~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      | .|+.+-.|+...|.+...||+|..+++.
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            7 5999999999999999999999999875

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.

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

Probab=96.54  E-value=0.00082  Score=47.74  Aligned_cols=44  Identities=32%  Similarity=0.726  Sum_probs=31.7

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      .|..|..- ..++....+- |+|+||..|...=  ....||+||.++-
T Consensus         5 hCn~C~~~-~~~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir   48 (233)
T KOG4739|consen    5 HCNKCFRF-PSQDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIR   48 (233)
T ss_pred             Eecccccc-CCCCceeeee-chhhhhhhhcccC--Cccccccccceee
Confidence            46666543 3367777777 9999999997652  2338999998753

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

Probab=96.33  E-value=0.0018  Score=53.61  Aligned_cols=34  Identities=29%  Similarity=0.790  Sum_probs=27.8

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHH
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF  131 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl  131 (148)
                      +++|.+|...+... .-.+-| |||.||++|+..-.
T Consensus       817 ~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  817 QDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             ccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            47899999888664 455678 99999999997765

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

Probab=96.32  E-value=0.0017  Score=53.50  Aligned_cols=41  Identities=32%  Similarity=0.704  Sum_probs=31.1

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      ..|..|-..++-+   .|--.|||.||.+|+.   .+...||-|+..
T Consensus       841 skCs~C~~~LdlP---~VhF~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  841 SKCSACEGTLDLP---FVHFLCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eeecccCCccccc---eeeeecccHHHHHhhc---cCcccCCccchh
Confidence            5899998876543   2322299999999999   456779999873

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

Probab=96.22  E-value=0.011  Score=44.87  Aligned_cols=28  Identities=29%  Similarity=1.043  Sum_probs=21.2

Q ss_pred             CCccchHHhHHHHHhC-------------CCCCcccCCCCC
Q 045986          118 CKHVYHSHCIIRWFSD-------------EFTCPICRSSIY  145 (148)
Q Consensus       118 C~H~FH~~Ci~~Wl~~-------------~~~CP~CR~~~~  145 (148)
                      |+-+.|-+|+.+|+..             +.+||+||+.+-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            4566789999999843             335999999764

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

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.11  E-value=0.01  Score=43.28  Aligned_cols=52  Identities=19%  Similarity=0.434  Sum_probs=39.9

Q ss_pred             CCccccccccccccCCCeee-ecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFR-ILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr-~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .....|||...+|....... .-| |||+|-..+++.- .....||+|-.++..+
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~-cG~V~s~~alke~-k~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRP-CGCVFSEKALKEL-KKSKKCPVCGKPFTEE  163 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcC-CCCEeeHHHHHhh-cccccccccCCccccC
Confidence            34578999999996655444 446 9999999999997 2356799998877544

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

Probab=95.89  E-value=0.0031  Score=51.71  Aligned_cols=44  Identities=30%  Similarity=0.707  Sum_probs=34.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      ..|.||++    .+....++ |+|.|+.+|+..-+..  ...||+||..+.
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~  500 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLK  500 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence            58999999    35556677 9999999999888765  335999998653

>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]

Probab=95.87  E-value=0.005  Score=50.43  Aligned_cols=22  Identities=41%  Similarity=1.105  Sum_probs=21.1

Q ss_pred             CCccchHHhHHHHHhCCCCCcc
Q 045986          118 CKHVYHSHCIIRWFSDEFTCPI  139 (148)
Q Consensus       118 C~H~FH~~Ci~~Wl~~~~~CP~  139 (148)
                      |+|+.|.+|...|+.....||.
T Consensus      1048 C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1048 CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccHHHHHHHHhcCCcCCC
Confidence            9999999999999999999985

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

Probab=95.81  E-value=0.0059  Score=45.33  Aligned_cols=41  Identities=29%  Similarity=0.716  Sum_probs=33.2

Q ss_pred             cccccccccccCCCeeeecCCC--CccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFC--KHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C--~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      .+||||.+.+...    ... |  ||+-+..|=.+   .+..||.||-++.
T Consensus        49 leCPvC~~~l~~P----i~Q-C~nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   49 LDCPVCFNPLSPP----IFQ-CDNGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             ccCchhhccCccc----cee-cCCCcEehhhhhhh---hcccCCccccccc
Confidence            6899999998775    344 6  79999999653   4777999999886

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=95.73  E-value=0.0048  Score=43.47  Aligned_cols=38  Identities=37%  Similarity=0.748  Sum_probs=29.6

Q ss_pred             cccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCC
Q 045986           99 CVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      |-.|-+.   +..|..+| |+|+ ++..|=..    -.+||+|+...
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChh
Confidence            7777665   77899999 9987 88999554    34599998764

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.66  E-value=0.013  Score=32.05  Aligned_cols=39  Identities=28%  Similarity=0.618  Sum_probs=32.6

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI  139 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~  139 (148)
                      ..|++|-+.|.+++.+.+=|.||--+|.+|-+.    ...|-.
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            579999999998999999999999999999654    445544

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

Probab=95.60  E-value=0.0042  Score=50.00  Aligned_cols=43  Identities=30%  Similarity=0.572  Sum_probs=32.6

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      ..|+||+..|......-+-+.|||..+..|+..-  .+.+|| |+.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            5799999998776543343449999999999885  567888 654

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.60  E-value=0.0068  Score=43.51  Aligned_cols=49  Identities=27%  Similarity=0.776  Sum_probs=34.6

Q ss_pred             CCccccccccccccCCCee-eecCCC-----CccchHHhHHHHHhCC--------CCCcccCCC
Q 045986           94 KFTSECVICLEEFVSGDLF-RILPFC-----KHVYHSHCIIRWFSDE--------FTCPICRSS  143 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~v-r~lp~C-----~H~FH~~Ci~~Wl~~~--------~~CP~CR~~  143 (148)
                      +.+..|-||+..=+++..- -+-| |     +|..|..|+..|+-.+        -+||-|++.
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE   80 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE   80 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence            3457899999875444322 3556 5     4999999999999432        249999874

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.59  E-value=0.0097  Score=44.51  Aligned_cols=49  Identities=24%  Similarity=0.429  Sum_probs=34.1

Q ss_pred             CccccccccccccCCCe-eeecCCCCccchHHhHHHHHh-CCCCCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDL-FRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~-vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~  144 (148)
                      +++-|+.|++++...|. ..--| ||-..|.=|-..--+ -+..||-||+-.
T Consensus        13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y   63 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKY   63 (480)
T ss_pred             ccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhc
Confidence            34569999999987763 34455 898766666444322 377899999854

>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=95.46  E-value=0.018  Score=38.44  Aligned_cols=33  Identities=27%  Similarity=0.550  Sum_probs=21.2

Q ss_pred             ccccccccccccCCCeeeecC------C-----CC-ccchHHhHHHHH
Q 045986           96 TSECVICLEEFVSGDLFRILP------F-----CK-HVYHSHCIIRWF  131 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp------~-----C~-H~FH~~Ci~~Wl  131 (148)
                      +..|+|||+-=-+.   ..|-      +     |+ -.=|..|+|..-
T Consensus         2 d~~CpICme~PHNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCCCce---EEEEeccccCCccccccCCccchhHHHHHHH
Confidence            35799999874443   2222      0     33 346899999886

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.

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

Probab=95.43  E-value=0.0089  Score=40.68  Aligned_cols=29  Identities=31%  Similarity=0.911  Sum_probs=24.1

Q ss_pred             CCccchHHhHHHHHhC----C-------CCCcccCCCCCC
Q 045986          118 CKHVYHSHCIIRWFSD----E-------FTCPICRSSIYL  146 (148)
Q Consensus       118 C~H~FH~~Ci~~Wl~~----~-------~~CP~CR~~~~~  146 (148)
                      ||.-||.-|+..||+.    .       ..||.|-.++..
T Consensus       190 CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  190 CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            9999999999999964    1       249999888754

>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0

Probab=95.39  E-value=0.016  Score=37.53  Aligned_cols=50  Identities=22%  Similarity=0.458  Sum_probs=37.5

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC---CCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD---EFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~~~  146 (148)
                      .+|.||-+.-.+..-+..--+||-..+-.|-...++.   ++.||+|++++..
T Consensus        81 YeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs  133 (140)
T PF05290_consen   81 YECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS  133 (140)
T ss_pred             eeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence            6899999886665444444448988999887665554   7789999998764

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

Probab=95.20  E-value=0.0066  Score=52.34  Aligned_cols=44  Identities=30%  Similarity=0.623  Sum_probs=36.5

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  142 (148)
                      ...|.||++...+.-.+  .. |||.++..|...|+..+..||.|+.
T Consensus      1153 ~~~c~ic~dil~~~~~I--~~-cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGI--AG-CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHHhcCCe--ee-echhHhhhHHHHHHHHhccCcchhh
Confidence            35899999998743222  22 9999999999999999999999975

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=95.07  E-value=0.022  Score=42.44  Aligned_cols=48  Identities=38%  Similarity=0.766  Sum_probs=35.7

Q ss_pred             ccccccccccccCCCe-eeecCCCC-----ccchHHhHHHHHhC--CCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDL-FRILPFCK-----HVYHSHCIIRWFSD--EFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~-vr~lp~C~-----H~FH~~Ci~~Wl~~--~~~CP~CR~~~  144 (148)
                      +..|=||..+...... .-..| |.     +..|..|++.|+..  +..|..|....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~  133 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF  133 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence            4689999998654432 45666 63     77899999999984  55699998754

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.46  E-value=0.025  Score=41.51  Aligned_cols=28  Identities=25%  Similarity=0.851  Sum_probs=22.3

Q ss_pred             CCccchHHhHHHHH-------------hCCCCCcccCCCCC
Q 045986          118 CKHVYHSHCIIRWF-------------SDEFTCPICRSSIY  145 (148)
Q Consensus       118 C~H~FH~~Ci~~Wl-------------~~~~~CP~CR~~~~  145 (148)
                      |+-..+.+|+..|+             +.+.+||+||+++.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            67788999999887             33567999998753

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

Probab=94.25  E-value=0.019  Score=46.29  Aligned_cols=44  Identities=34%  Similarity=0.910  Sum_probs=37.7

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .+.|++|+.+.    ..|..+ |.   |..|..+|+..+..||+|+..+..+
T Consensus       479 ~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~  522 (543)
T KOG0802|consen  479 NDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKED  522 (543)
T ss_pred             cCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcc
Confidence            47899999998    457778 88   9999999999999999998876554

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

Probab=94.17  E-value=0.022  Score=42.11  Aligned_cols=43  Identities=28%  Similarity=0.644  Sum_probs=28.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      -.|--|--.  ...-=|..| |.|+||-+|-..  ..-+.||.|-..|
T Consensus        91 HfCd~Cd~P--I~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFP--IAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCc--ceeeecccc-cchhhhhhhhhc--CccccCcCcccHH
Confidence            457666333  233447889 999999999755  2345799996543

>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=93.66  E-value=0.026  Score=43.51  Aligned_cols=36  Identities=31%  Similarity=0.709  Sum_probs=27.9

Q ss_pred             cccccccccccCC-CeeeecCCCCccchHHhHHHHHhC
Q 045986           97 SECVICLEEFVSG-DLFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        97 ~~C~ICl~~~~~~-~~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      .+|.||..++..+ +...+.. |+|.|+.+|+...+..
T Consensus       147 ~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  147 EECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhh
Confidence            6899999555444 4555555 9999999999988764

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=93.00  E-value=0.096  Score=43.20  Aligned_cols=41  Identities=20%  Similarity=0.386  Sum_probs=29.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI  139 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~  139 (148)
                      ..|.+|-..... .. ..-+.|||.-|.+|+.+|+..+.-||.
T Consensus       780 ~~CtVC~~vi~G-~~-~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG-VD-VWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee-eE-eecccccccccHHHHHHHHhcCCCCcc
Confidence            368888544322 22 223449999999999999999888877

>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=92.56  E-value=0.14  Score=37.68  Aligned_cols=46  Identities=28%  Similarity=0.613  Sum_probs=33.7

Q ss_pred             cccccccc-ccCCC-eeeecCCCCccchHHhHHHHHhC-CCCCcccCCCC
Q 045986           98 ECVICLEE-FVSGD-LFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSI  144 (148)
Q Consensus        98 ~C~ICl~~-~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~  144 (148)
                      .|++|-.+ |.+.+ .+.+-| |+|..+.+|++.-+.. ...||.|-..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~-C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINE-CGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeecc-ccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            48888744 44444 333446 9999999999999866 56799996654

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

Probab=92.33  E-value=0.13  Score=39.37  Aligned_cols=45  Identities=22%  Similarity=0.384  Sum_probs=37.6

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC---CCcccCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF---TCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~---~CP~CR~  142 (148)
                      ..|||=-+.=.+......|. |||+..++=+...-+...   .||.|=.
T Consensus       335 F~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  335 FICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             eecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            78999888777777888899 999999999999877643   5999944

>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=92.20  E-value=0.076  Score=37.98  Aligned_cols=44  Identities=32%  Similarity=0.723  Sum_probs=34.2

Q ss_pred             ccccccccc-ccCCC-eeeecCCCCccchHHhHHHHHhC-CCCCc--cc
Q 045986           97 SECVICLEE-FVSGD-LFRILPFCKHVYHSHCIIRWFSD-EFTCP--IC  140 (148)
Q Consensus        97 ~~C~ICl~~-~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP--~C  140 (148)
                      .-||||-.+ |-+++ .+-+-|.|-|..|.+|++.-+.. ...||  -|
T Consensus        11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC   59 (314)
T COG5220          11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGC   59 (314)
T ss_pred             ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccH
Confidence            579999865 33444 55566779999999999999876 66799  66

>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=91.75  E-value=0.21  Score=41.78  Aligned_cols=47  Identities=30%  Similarity=0.717  Sum_probs=35.4

Q ss_pred             ccccccccccccCCCeeeecCCCC-----ccchHHhHHHHHhCCC--CCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCK-----HVYHSHCIIRWFSDEF--TCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~-----H~FH~~Ci~~Wl~~~~--~CP~CR~~~  144 (148)
                      ...|-||..+=..++.+- -| |.     -+.|.+|+-+|+.-..  .|-+|+.++
T Consensus        12 ~~~CRICr~e~~~d~pLf-hP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~   65 (1175)
T COG5183          12 KRSCRICRTEDIRDDPLF-HP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY   65 (1175)
T ss_pred             chhceeecCCCCCCCcCc-cc-ccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence            378999998866655543 45 52     5699999999998644  499998765

>TIGR00622 ssl1 transcription factor ssl1

Probab=91.70  E-value=0.32  Score=30.81  Aligned_cols=72  Identities=17%  Similarity=0.227  Sum_probs=42.7

Q ss_pred             CCCHHHHhcCCCccccCCccCCCCCccccccccccccCCC----------eeeecCCCCccchHHhHHHHHhCCCCCccc
Q 045986           71 LRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGD----------LFRILPFCKHVYHSHCIIRWFSDEFTCPIC  140 (148)
Q Consensus        71 ~~~~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----------~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  140 (148)
                      .+++.--...|...+.+...........|--|+..|.+..          ..-.=+.|++.|+.+|=.-+-+.=.+||-|
T Consensus        30 HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC  109 (112)
T TIGR00622        30 HLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGC  109 (112)
T ss_pred             hHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCC
Confidence            3444443444554444432222222356999999886531          112244499999999966666666779999


Q ss_pred             CC
Q 045986          141 RS  142 (148)
Q Consensus       141 R~  142 (148)
                      -.
T Consensus       110 ~~  111 (112)
T TIGR00622       110 IH  111 (112)
T ss_pred             CC
Confidence            63

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

>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]

Probab=91.31  E-value=0.055  Score=44.25  Aligned_cols=45  Identities=33%  Similarity=0.843  Sum_probs=35.3

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCC---CCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE---FTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~  145 (148)
                      .+|+||+..+.+.   ..+. |.|.|...|+..-+...   ..||+|+..+.
T Consensus        22 lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   22 LECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             ccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            4899999999886   3344 99999999987766553   45999997654

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=91.12  E-value=0.079  Score=42.74  Aligned_cols=40  Identities=30%  Similarity=0.722  Sum_probs=26.2

Q ss_pred             cccccccc-----cccCCCeeeecCCCCccchHHhHHHHHhCCCCCccc
Q 045986           97 SECVICLE-----EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC  140 (148)
Q Consensus        97 ~~C~ICl~-----~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  140 (148)
                      ..|.+|-.     .|+.....+-.. |+++||++|...   .+..||-|
T Consensus       512 fiCe~Cq~~~iiyPF~~~~~~rC~~-C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  512 FICELCQHNDIIYPFETRNTRRCST-CLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             eeeeeccCCCcccccccccceeHHH-HHHHHHHHHHhc---cCCCCCch
Confidence            57888821     222222344455 999999999665   45559999

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=90.93  E-value=0.18  Score=35.49  Aligned_cols=40  Identities=33%  Similarity=0.695  Sum_probs=27.5

Q ss_pred             cccccccccc-----ccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccC
Q 045986           96 TSECVICLEE-----FVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR  141 (148)
Q Consensus        96 ~~~C~ICl~~-----~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  141 (148)
                      +..|.+|-++     |+.+ .+..=+.|+-+||++|..     +..||-|-
T Consensus       152 GfiCe~C~~~~~IfPF~~~-~~~~C~~C~~v~H~~C~~-----~~~CpkC~  196 (202)
T PF13901_consen  152 GFICEICNSDDIIFPFQID-TTVRCPKCKSVFHKSCFR-----KKSCPKCA  196 (202)
T ss_pred             CCCCccCCCCCCCCCCCCC-CeeeCCcCccccchhhcC-----CCCCCCcH
Confidence            3678888753     3332 344444599999999976     26799994

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=90.81  E-value=0.36  Score=36.07  Aligned_cols=50  Identities=26%  Similarity=0.559  Sum_probs=35.0

Q ss_pred             ccccccccccc--c-------CC-------CeeeecCCCCccchHHhHHHHHhC---------CCCCcccCCCCCC
Q 045986           96 TSECVICLEEF--V-------SG-------DLFRILPFCKHVYHSHCIIRWFSD---------EFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~--~-------~~-------~~vr~lp~C~H~FH~~Ci~~Wl~~---------~~~CP~CR~~~~~  146 (148)
                      +.+|++|+..=  .       .+       -.-...| |||+--.+-+.-|-+.         +..||.|-+.+..
T Consensus       341 ~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~g  415 (429)
T KOG3842|consen  341 ERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAG  415 (429)
T ss_pred             cCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhhcc
Confidence            47899998641  1       00       0123467 9999999999999865         3459999887754

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]

Probab=89.61  E-value=0.45  Score=35.66  Aligned_cols=74  Identities=19%  Similarity=0.328  Sum_probs=49.8

Q ss_pred             CCCCCHHHHhcCCCccccCCccCCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986           69 RPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus        69 ~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      ++.+++..-.-.|...+.+.......+...|-.|.++.......+--. |.|.|+.+|=.---+.-..||-|...
T Consensus       303 s~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~-Ck~~FCldCDv~iHesLh~CpgCeh~  376 (378)
T KOG2807|consen  303 SPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCES-CKNVFCLDCDVFIHESLHNCPGCEHK  376 (378)
T ss_pred             chHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchh-ccceeeccchHHHHhhhhcCCCcCCC
Confidence            344555555666777776665555444567999988777766666555 99999999943332344569999754

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.56  E-value=0.18  Score=41.94  Aligned_cols=42  Identities=29%  Similarity=0.670  Sum_probs=31.3

Q ss_pred             cccccccccccC-C---CeeeecCCCCccchHHhHHHHHhCCCCCccc
Q 045986           97 SECVICLEEFVS-G---DLFRILPFCKHVYHSHCIIRWFSDEFTCPIC  140 (148)
Q Consensus        97 ~~C~ICl~~~~~-~---~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  140 (148)
                      ..|.-|.+.... +   +.+.++. |||.||+.|+..-..++. |-.|
T Consensus       785 ~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  785 ERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             hhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChh
Confidence            579999887642 2   5778888 999999999987766654 4444

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=88.53  E-value=0.51  Score=25.52  Aligned_cols=42  Identities=26%  Similarity=0.584  Sum_probs=21.1

Q ss_pred             cccccccccCCC------eeeecCCCCccchHHhHHHHH-hCCCCCcccC
Q 045986           99 CVICLEEFVSGD------LFRILPFCKHVYHSHCIIRWF-SDEFTCPICR  141 (148)
Q Consensus        99 C~ICl~~~~~~~------~vr~lp~C~H~FH~~Ci~~Wl-~~~~~CP~CR  141 (148)
                      |.-|+..|..+.      ..-.=|.|++.|+.+| |..+ +.-.+||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC-DVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHH-HHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCc-ChhhhccccCCcCCC
Confidence            555677776642      3445566999999999 3333 2345699884

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>smart00249 PHD PHD zinc finger

Probab=88.33  E-value=0.35  Score=24.75  Aligned_cols=30  Identities=27%  Similarity=0.635  Sum_probs=21.3

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHH
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIR  129 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~  129 (148)
                      |.+|......+..+.=-. |+..||..|+..
T Consensus         2 C~~C~~~~~~~~~i~C~~-C~~~~H~~C~~~   31 (47)
T smart00249        2 CSVCGKPDDGGELLQCDG-CDRWYHQTCLGP   31 (47)
T ss_pred             cccCCCcCCCCCEEECCC-CCchhhhhhCCC
Confidence            778877764444444344 899999999865

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

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

Probab=87.95  E-value=0.38  Score=40.21  Aligned_cols=49  Identities=8%  Similarity=0.159  Sum_probs=34.5

Q ss_pred             ccccccccccccCC---CeeeecCCCCccchHHhHHHHHhC------CCCCcccCCCC
Q 045986           96 TSECVICLEEFVSG---DLFRILPFCKHVYHSHCIIRWFSD------EFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~---~~vr~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~~  144 (148)
                      ...|.+|.-++...   -.+-.+..|+|.|+..||..|...      +-.|++|.+-|
T Consensus        96 s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   96 SDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             ccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            36788887777662   223333349999999999999844      44589997654

>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]

Probab=87.30  E-value=0.42  Score=34.85  Aligned_cols=48  Identities=29%  Similarity=0.628  Sum_probs=35.7

Q ss_pred             cccccccccccCCCeeee---cCCCCccchHHhHHHHHhC---------CCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRI---LPFCKHVYHSHCIIRWFSD---------EFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~---lp~C~H~FH~~Ci~~Wl~~---------~~~CP~CR~~~  144 (148)
                      .+|.+|.+++.+.+..+.   -|.|+-.+|..|+..-+..         ...||.|+..+
T Consensus       183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~  242 (276)
T KOG3005|consen  183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL  242 (276)
T ss_pred             hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence            589999999976665554   3448889999999984422         34599998754

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.82  E-value=0.79  Score=33.19  Aligned_cols=50  Identities=18%  Similarity=0.297  Sum_probs=37.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ...|+|=--+|........+-+|||+|-..=+.+-  ...+|++|.+.+..+
T Consensus       111 ~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~  160 (293)
T KOG3113|consen  111 RFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQED  160 (293)
T ss_pred             eeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCccccc
Confidence            36799988787766655556669999998877774  477899998876543

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.66  E-value=0.29  Score=26.05  Aligned_cols=42  Identities=29%  Similarity=0.706  Sum_probs=28.9

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHh------CCCCCcccC
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS------DEFTCPICR  141 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~------~~~~CP~CR  141 (148)
                      |.||...-..++.|.=-. |+-.||..|+..=..      ..-.||.|+
T Consensus         2 C~vC~~~~~~~~~i~C~~-C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    2 CPVCGQSDDDGDMIQCDS-CNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             BTTTTSSCTTSSEEEBST-TSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             CcCCCCcCCCCCeEEcCC-CChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            889988555555565555 899999999865432      123488875

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 entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.07  E-value=0.86  Score=24.47  Aligned_cols=42  Identities=21%  Similarity=0.577  Sum_probs=18.5

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-----CCCcccCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-----FTCPICRSS  143 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~  143 (148)
                      .|+|-...+..  .+|-.. |.|.-+-+ ++.||..+     -.||+|.++
T Consensus         4 ~CPls~~~i~~--P~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIRI--PVRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-SS--EEEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEEe--CccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            57777766543  466666 88772211 45566442     249999864

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 entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=85.55  E-value=0.64  Score=36.32  Aligned_cols=34  Identities=24%  Similarity=0.513  Sum_probs=28.2

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      +..|+||-.=|++.   .+|| |+|..+..|-..-+..
T Consensus         4 elkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    4 ELKCPVCGSFYREP---IILP-CSHNLCQACARNILVQ   37 (699)
T ss_pred             cccCceehhhccCc---eEee-cccHHHHHHHHhhccc
Confidence            46799999988776   7899 9999999998866543

>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=84.60  E-value=0.7  Score=36.43  Aligned_cols=36  Identities=22%  Similarity=0.495  Sum_probs=29.4

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      ...+|-||.+.+..  .+..+. |||.|+..|....+.+
T Consensus        69 ~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   69 GDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             ccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            34689999999866  445566 9999999999999865

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.19  E-value=1.2  Score=24.18  Aligned_cols=38  Identities=16%  Similarity=0.509  Sum_probs=22.9

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      |+-|-..+..++.+.. . -|..||.+|+        +|-.|+.+|..
T Consensus         1 C~~C~~~I~~~~~~~~-~-~~~~~H~~Cf--------~C~~C~~~l~~   38 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIK-A-MGKFWHPECF--------KCSKCGKPLND   38 (58)
T ss_dssp             BTTTSSBESSSSEEEE-E-TTEEEETTTS--------BETTTTCBTTT
T ss_pred             CCCCCCCccCcEEEEE-e-CCcEEEcccc--------ccCCCCCccCC
Confidence            5666666665544322 2 5677887663        47777766654

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 entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=83.23  E-value=1.5  Score=21.32  Aligned_cols=37  Identities=24%  Similarity=0.659  Sum_probs=24.4

Q ss_pred             cccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        99 C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      |+.|-+.+..++.. +.. =+..||.+|.        +|..|+.+|.
T Consensus         2 C~~C~~~i~~~~~~-~~~-~~~~~H~~Cf--------~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELV-LRA-LGKVWHPECF--------KCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEE-EEe-CCccccccCC--------CCcccCCcCc
Confidence            77888877665333 222 4788998874        5778877663

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association

Probab=82.77  E-value=0.21  Score=27.21  Aligned_cols=11  Identities=27%  Similarity=0.887  Sum_probs=5.6

Q ss_pred             CCcccCCCCCC
Q 045986          136 TCPICRSSIYL  146 (148)
Q Consensus       136 ~CP~CR~~~~~  146 (148)
                      .||+|.+++..
T Consensus        22 ~CPlC~r~l~~   32 (54)
T PF04423_consen   22 CCPLCGRPLDE   32 (54)
T ss_dssp             E-TTT--EE-H
T ss_pred             cCCCCCCCCCH
Confidence            79999888754

The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.

>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]

Probab=82.74  E-value=0.78  Score=32.32  Aligned_cols=41  Identities=29%  Similarity=0.743  Sum_probs=33.1

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCccc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC  140 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  140 (148)
                      ..|.+|..-.-.+  +|--. ||-.+|..|+...+.+.+.||.|
T Consensus       182 k~Cn~Ch~LvIqg--~rCg~-c~i~~h~~c~qty~q~~~~cphc  222 (235)
T KOG4718|consen  182 KNCNLCHCLVIQG--IRCGS-CNIQYHRGCIQTYLQRRDICPHC  222 (235)
T ss_pred             HHHhHhHHHhhee--eccCc-ccchhhhHHHHHHhcccCcCCch
Confidence            6799998765443  44444 77889999999999999999999

>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=82.45  E-value=0.73  Score=21.20  Aligned_cols=9  Identities=33%  Similarity=0.829  Sum_probs=4.4

Q ss_pred             CCCCCcccC
Q 045986          133 DEFTCPICR  141 (148)
Q Consensus       133 ~~~~CP~CR  141 (148)
                      ....||.|-
T Consensus        13 ~~~~Cp~CG   21 (26)
T PF10571_consen   13 SAKFCPHCG   21 (26)
T ss_pred             hcCcCCCCC
Confidence            344455553

Several members are annotated as putative helicases.

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length

Probab=82.16  E-value=2.1  Score=23.51  Aligned_cols=44  Identities=18%  Similarity=0.502  Sum_probs=30.7

Q ss_pred             ccccccccccCCC-eeeecCCCC--ccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           98 ECVICLEEFVSGD-LFRILPFCK--HVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        98 ~C~ICl~~~~~~~-~vr~lp~C~--H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      .|--|-.++..+. +-++   |.  -.|+.+|.+.-|  +..||.|-..+..
T Consensus         7 nCE~C~~dLp~~s~~A~I---CSfECTFC~~C~e~~l--~~~CPNCgGelv~   53 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI---CSFECTFCADCAETML--NGVCPNCGGELVR   53 (57)
T ss_pred             CccccCCCCCCCCCcceE---EeEeCcccHHHHHHHh--cCcCcCCCCcccc
Confidence            4667777766554 2222   65  459999999976  7789999877653

This family contains a number of conserved cysteine residues and its function is unknown.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=80.09  E-value=1.7  Score=32.68  Aligned_cols=48  Identities=27%  Similarity=0.494  Sum_probs=35.8

Q ss_pred             cccccccccccCCC-eeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      .+|+||-++...++ ...--| |+|..|..|...-...+.+||.||.+..
T Consensus       250 ~s~p~~~~~~~~~d~~~lP~~-~~~~~~l~~~~t~~~~~~~~~~~rk~~~  298 (327)
T KOG2068|consen  250 PSCPICYEDLDLTDSNFLPCP-CGFRLCLFCHKTISDGDGRCPGCRKPYE  298 (327)
T ss_pred             CCCCCCCCccccccccccccc-ccccchhhhhhcccccCCCCCccCCccc
Confidence            78999999874433 333334 7888888888887788999999997654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	148
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		4e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		5e-05

>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5 Length = 55

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL 146
           EC +CL E   G+  R LP C H +H+ C+  W     TCP+CR ++ +
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein 38 Length = 75

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 82  PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           P+ +++ + H  + T  CV+C+ +F S  L R+LP C H +H+ C+ +W     TCPICR
Sbjct: 10  PSYRFNPNNHQSEQT-LCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67
Query: 142 S 142
           +
Sbjct: 68  A 68

>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 = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           EC +C E++  G+  R LP C H++H  CI+ W     +CP+CR S+
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 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 = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
           C IC  E+V GD+   LP C H +H  C+  W     TCP+CR
Sbjct: 43  CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C +CLE+F   D   I P CKH +H  C+I+W      CP+C   +
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	148
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-19
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-19
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-18
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	5e-18
2ect_A	78	Ring finger protein 126; metal binding protein, st	7e-18
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	3e-17
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-14
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-13
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	1e-12
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	5e-12
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-10
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	6e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	6e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-08
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-08
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-07
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	5e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	9e-07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	8e-05
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	9e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	3e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	4e-04
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	6e-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 = 76.2 bits (188), Expect = 2e-19
 Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 74  QRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD 133
           +  I+ LP                 C IC  E+V GD+   LP C H +H  C+  W   
Sbjct: 19  KESIDALP-EILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQK 76

Query: 134 EFTCPICRSSI 144
             TCP+CR   
Sbjct: 77  SGTCPVCRCMF 87

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

 Score = 75.1 bits (185), Expect = 4e-19
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 74  QRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD 133
                +LP + +++ + H  + T  CV+C+ +F S  L R+LP C H +H+ C+ +W   
Sbjct: 3   SGSSGQLP-SYRFNPNNHQSEQT-LCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59

Query: 134 EFTCPICRSSI 144
             TCPICR+  
Sbjct: 60  NRTCPICRADS 70

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

 Score = 72.6 bits (179), Expect = 3e-18
 Identities = 19/48 (39%), Positives = 27/48 (56%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
            EC +CL E   G+  R LP C H +H+ C+  W     TCP+CR ++
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 72.5 bits (178), Expect = 5e-18
 Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
             C +CLE+F   D   I P CKH +H  C+I+W      CP+C   +
Sbjct: 16  ELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 = 72.1 bits (177), Expect = 7e-18
 Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
            EC +C E++  G+  R LP C H++H  CI+ W     +CP+CR S+
Sbjct: 16  LECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>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 = 70.1 bits (172), Expect = 3e-17
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
            +C ICL     G+  R LP C H++H  C+ +W      CPICR  I
Sbjct: 15  EKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

>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 = 67.3 bits (165), Expect = 3e-16
 Identities = 13/48 (27%), Positives = 21/48 (43%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           S C ICLE+  +  +   +  C H+ H  C      + + CP+C    
Sbjct: 6   SGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 62.8 bits (153), Expect = 2e-14
 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 5/47 (10%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           EC IC++         ILP C H +   CI +W      CPICR  +
Sbjct: 17  ECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQM 58

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

 Score = 59.5 bits (144), Expect = 5e-13
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 95  FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
               C+ C  E    D   +   C H +H+ C+  W      CP+C+
Sbjct: 25  VMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 58.4 bits (141), Expect = 1e-12
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 5/53 (9%)

Query: 96  TSECVICLEEFV----SGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           T  C IC++ +     +G L      C HV+ S C+     +  TCP CR  I
Sbjct: 15  TVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 5e-12
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 97  SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
             C ICLE+    +    LP C H +   CI RW     TCP+C+  +
Sbjct: 6   ERCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50

>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 = 53.0 bits (127), Expect = 2e-10
 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 5/49 (10%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF--SDEFTCPICRSSI 144
            C IC    + G   +    C    H  C+ ++F  + E  CP C    
Sbjct: 17  ICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

>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 = 52.1 bits (125), Expect = 3e-10
 Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 3/52 (5%)

Query: 96  TSECVICLEEFVSGDLFRILPF---CKHVYHSHCIIRWFSDEFTCPICRSSI 144
           T  C IC++ +        L     C HV+ S C+     +  TCP CR  I
Sbjct: 10  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 50.9 bits (122), Expect = 8e-10
 Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 98  ECVICLEEFVSGDLFRILPF---CKHVYHSHCIIRWFSDEFTCPICRSSI 144
            C IC++ +        L     C HV+ S C+     +  TCP CR  I
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 49.1 bits (117), Expect = 6e-09
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 4/44 (9%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
            C IC + F +     ++  C+H +   C +  F     C IC 
Sbjct: 17  RCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICD 56

>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 = 49.5 bits (118), Expect = 6e-09
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYLD 147
            C IC+E+       R+ P C  +    CI RW +++   CP CR+ + L 
Sbjct: 24  RCFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 71

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 3/48 (6%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY 145
            C IC    +  D   I   C H +   CI+R F     CP C   ++
Sbjct: 17  LCSICKGYLI--DATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVH 61

>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 = 47.9 bits (113), Expect = 3e-08
 Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 19/64 (29%)

Query: 98  ECVICLEEFVSG--------------DLFRILPFCKHVYHSHCIIRWFSD-----EFTCP 138
           +C+IC+E+                   +   L  C H +H  C++  + +        CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 139 ICRS 142
            C++
Sbjct: 87  SCKT 90

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

 Score = 46.4 bits (110), Expect = 5e-08
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           EC ICL+  V       LP CKHV+   C+         C +CR  I
Sbjct: 17  ECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEI 59

>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 = 49.4 bits (117), Expect = 5e-08
 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 82  PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPIC 140
             E+Y+ +         C IC E        +I P C H+  + C+  W  S+   CP C
Sbjct: 318 TQEQYELYCEMGSTFQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFC 373

Query: 141 RSSI 144
           R  I
Sbjct: 374 RCEI 377

>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 = 46.0 bits (108), Expect = 1e-07
 Identities = 11/41 (26%), Positives = 14/41 (34%)

Query: 101 ICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
                  S +       C H +H HCI RW      CP+  
Sbjct: 56  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 44.8 bits (105), Expect = 5e-07
 Identities = 11/41 (26%), Positives = 14/41 (34%)

Query: 101 ICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
                  S +       C H +H HCI RW      CP+  
Sbjct: 67  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 46.8 bits (110), Expect = 5e-07
 Identities = 13/80 (16%), Positives = 22/80 (27%), Gaps = 15/80 (18%)

Query: 80  LPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRIL----PFCKHVYHSHCIIRWFSDE- 134
           +P                 C IC    + G    ++      C    H+ C+  WF    
Sbjct: 292 MPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLM 351

Query: 135 ----------FTCPICRSSI 144
                       CP C++ +
Sbjct: 352 DGKTFLEVSFGQCPFCKAKL 371

>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 = 44.0 bits (104), Expect = 9e-07
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
            CV+C   F+  D   I+  C H +   CI+R+      CPIC   +
Sbjct: 17  MCVLCGGYFI--DATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQV 60

>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein of testis, proliferation potential-related protein, protein P2P-R; NMR {Homo sapiens} Length = 74

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 11/51 (21%)

Query: 99  CVICLEEFVSGDLFR---ILPFCKHVYHSHCIIRWF--SDEFTCPICRSSI 144
           C+IC       D+     ++P C + Y   CI      SDE TCP C  + 
Sbjct: 18  CLICK------DIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND 62

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

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           +C+IC E F+      +   C H + S+CI  W   +  CPICR  I
Sbjct: 66  QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 9/49 (18%)

Query: 99  CVICLEEFVSGDLFR---ILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           C IC       + F    I+P C H Y S CI ++ S +  CP C  ++
Sbjct: 25  CGICF------EYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 98  ECVICLEEFVSGDLFRILPF---CKHVYHSHCIIRWFSDEFTCPICRSSI 144
            C IC++ +        L     C HV+ S C+     +  TCP CR  I
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58

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

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 17/71 (23%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 77  IEKLPPAEKYDGHLHNKKFTSECVICLEEF---VSGDLFRILPFCKHVYHSHCIIRWFSD 133
             +     K    ++    T  C IC++ +   V      +   C HV+ S C+     +
Sbjct: 53  TCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN 112

Query: 134 EFTCPICRSSI 144
             TCP CR  I
Sbjct: 113 ANTCPTCRKKI 123

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 5/47 (10%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF--SDEFTCPICRS 142
            C IC    + G        C    H  C+ ++F  + E  CP C  
Sbjct: 182 ICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens} Length = 92

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 11/50 (22%)

Query: 99  CVICLEEFVSGDLFR---ILPFCKHVYHSHCIIRWF--SDEFTCPICRSS 143
           C+IC       D+     ++P C + Y   CI      SDE TCP C  +
Sbjct: 16  CLICK------DIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 88

 Score = 38.1 bits (89), Expect = 8e-05
 Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 5/54 (9%)

Query: 98  ECVICLEEFVSGDLF-RILPFCKHVYHSHCIIRWF---SDEFTCPICRSSIYLD 147
           EC IC+E F    L  ++L  C H     C+ +      +   CP C     + 
Sbjct: 17  ECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT 69

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

 Score = 37.5 bits (87), Expect = 9e-05
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 5/51 (9%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD 147
           +C  C     S         C H +   C+    S     C  C+ SI  D
Sbjct: 17  KCEKCHLVLCS----PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD 63

>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 = 38.5 bits (89), Expect = 2e-04
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 11/51 (21%)

Query: 98  ECVICLEEF---VSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPICRSSI 144
            CV C E     V+ +       C H     C+ R F +  F+CP CR  +
Sbjct: 80  MCVCCQELVYQPVTTE-------CFHNVCKDCLQRSFKAQVFSCPACRHDL 123

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

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 92  NKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSI 144
            K+   EC +C+E     D+      C +     C  R  +DE   CP CR   
Sbjct: 7   AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 60

>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 = 36.9 bits (85), Expect = 4e-04
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPICRSSI 144
           +C+ C E             C+H     C+ R F +  F+CP CR  +
Sbjct: 54  QCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDL 97

>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 Length = 94

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 9/53 (16%)

Query: 96  TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS--------DEFTCPIC 140
           +S C +CL E+    +  I   C+ ++ + C+ ++             +CP  
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDA 56

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	148
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.89
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.87
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.82
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.82
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.81
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.8
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.78
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.76
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.74
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.74
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.73
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.73
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.73
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.72
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.69
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.68
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.68
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.68
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.67
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.67
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.65
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.64
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.63
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.63
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.61
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.6
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.6
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.59
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.58
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.58
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.58
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.57
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.57
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.56
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.56
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.55
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.53
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.53
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.51
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.5
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.49
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.47
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.47
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.45
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.44
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.44
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.43
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.43
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.41
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.4
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.39
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.38
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.36
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.34
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.32
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.31
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.31
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.28
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.24
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.21
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.17
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.15
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.14
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.13
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.06
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.94
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.89
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.86
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.69
3nw0_A	238	Non-structural maintenance of chromosomes element	98.38
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	97.44
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.69
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.69
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.14
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	95.86
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	95.38
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	95.23
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	95.15
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	95.12
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	95.07
1we9_A	64	PHD finger family protein; structural genomics, PH	94.99
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	94.95
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	94.67
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	94.64
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.6
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	94.11
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	94.09
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	94.06
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	93.65
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	93.42
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	93.28
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	92.9
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	92.77
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	92.5
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	92.4
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	92.39
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	92.2
1wem_A	76	Death associated transcription factor 1; structura	92.02
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	91.84
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	91.74
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	91.4
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	90.98
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	90.79
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	90.04
1weu_A	91	Inhibitor of growth family, member 4; structural g	89.84
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	89.83
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	89.65
1wew_A	78	DNA-binding family protein; structural genomics, P	89.54
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	89.4
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	88.9
2yt5_A	66	Metal-response element-binding transcription facto	88.11
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	87.21
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	87.14
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	87.11
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	86.76
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	86.74
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	84.82
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	84.55
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	83.76
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	83.65
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	83.03
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	82.91
1wee_A	72	PHD finger family protein; structural genomics, PH	82.74
1z60_A	59	TFIIH basal transcription factor complex P44 subun	82.36
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	81.33
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	81.07

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

Probab=99.89  E-value=1.3e-23  Score=128.67  Aligned_cols=78  Identities=31%  Similarity=0.636  Sum_probs=67.9

Q ss_pred             CCCCCCHHHHhcCCCccccCCccCCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           68 DRPLRHQRVIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        68 ~~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ...+++++.++.+|...+...... ..++..|+||+++|..++.++.+| |||.||..||+.|+..+.+||+||+.+.++
T Consensus        13 ~~~~~s~~~i~~lp~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   90 (91)
T 2l0b_A           13 ANPPASKESIDALPEILVTEDHGA-VGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPPP   90 (91)
T ss_dssp             CCCCCCHHHHHTSCEEECCTTCSS-SSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSSCC
T ss_pred             CCCCCCHHHHHhCCCeeecccccc-cCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCCCC
Confidence            456899999999999888765432 234578999999999999999999 999999999999999999999999998764

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

Probab=99.87  E-value=5e-23  Score=121.71  Aligned_cols=69  Identities=32%  Similarity=0.752  Sum_probs=58.7

Q ss_pred             HHhcCCCccccCCccCCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           76 VIEKLPPAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        76 ~i~~lp~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .++++|..++.....  ..++..|+||+++|..++.++.+| |+|.||.+||+.|++.+.+||+||+++.+.
T Consensus         5 ~i~~lp~~~~~~~~~--~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            5 SSGQLPSYRFNPNNH--QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCSSCCCEEBCSSSC--SSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hHhhCCcEEecCccc--cCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            456788887765432  233578999999999999999999 999999999999999999999999999875

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

Probab=99.82  E-value=4.7e-21  Score=106.57  Aligned_cols=50  Identities=38%  Similarity=0.971  Sum_probs=46.5

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +.+|+||+++|.+++.+..+|.|||.||.+||++|++.+.+||+||+++.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            46899999999999988888779999999999999999999999999875

>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=99.82  E-value=1.8e-20  Score=108.85  Aligned_cols=52  Identities=37%  Similarity=0.885  Sum_probs=47.5

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ..+..|+||++.|..++.++.+| |||.||..||..|+..+.+||+||+.+..
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            34478999999999988999999 99999999999999999999999998764

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

Probab=99.81  E-value=3.3e-20  Score=109.20  Aligned_cols=51  Identities=35%  Similarity=0.989  Sum_probs=47.2

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      .+..|+||+++|..++.++++| |+|.||.+||..|++.+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             CCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            3478999999999999999999 99999999999999999999999998864

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

Probab=99.80  E-value=5.1e-20  Score=109.45  Aligned_cols=52  Identities=37%  Similarity=0.979  Sum_probs=47.7

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +..+|+||++.|..++.++++| |+|.||..||..|++.+.+||+||+.+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            3478999999999999999999 999999999999999999999999988653

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

Probab=99.78  E-value=5.6e-20  Score=110.04  Aligned_cols=50  Identities=24%  Similarity=0.734  Sum_probs=41.5

Q ss_pred             cccccccccccC-----------CCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVS-----------GDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~-----------~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      +.|+||+++|.+           ++.++++|.|||.||.+||++||+.+.+||+||+++..
T Consensus        16 ~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           16 DTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             SCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            568888877754           45566666699999999999999999999999998754

>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=99.76  E-value=3.3e-19  Score=98.97  Aligned_cols=49  Identities=31%  Similarity=0.827  Sum_probs=43.5

Q ss_pred             ccccccccccccCC-CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSG-DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~-~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +..|+||+++|.++ +.++.+| |||.||.+||+.|+..+.+||+||+.+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            5 SSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            46899999999654 4677888 9999999999999999999999999874

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

Probab=99.74  E-value=7.3e-19  Score=102.52  Aligned_cols=52  Identities=31%  Similarity=0.644  Sum_probs=45.3

Q ss_pred             CccccccccccccCC----CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSG----DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~----~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ++..|+||++.|.+.    +.+..++ |||.||.+||+.|++.+.+||+||+++..+
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            347899999999763    5667888 999999999999999999999999998764

>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=99.74  E-value=1.3e-18  Score=108.85  Aligned_cols=48  Identities=27%  Similarity=0.665  Sum_probs=42.0

Q ss_pred             ccccccccccccCCC---------------eeeecCCCCccchHHhHHHHHhCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGD---------------LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~---------------~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  144 (148)
                      ++.|+||+++|.+.-               .++.++ |+|.||..||++||..+.+||+||+.+
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~   99 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREW   99 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcc
Confidence            468999999998641               367788 999999999999999999999999985

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

Probab=99.73  E-value=1.3e-18  Score=99.38  Aligned_cols=51  Identities=29%  Similarity=0.670  Sum_probs=44.8

Q ss_pred             ccccccccccccCC----CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSG----DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~----~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +.+|+||++.+.+.    +.+..++ |||.||.+||..|++.+.+||+||+++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            46899999999763    4567888 999999999999999999999999998764

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

Probab=99.73  E-value=2e-18  Score=102.64  Aligned_cols=52  Identities=25%  Similarity=0.652  Sum_probs=44.0

Q ss_pred             CCccccccccccccCCCeeeecCCCC-----ccchHHhHHHHHhCC--CCCcccCCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCK-----HVYHSHCIIRWFSDE--FTCPICRSSIYLD  147 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~~  147 (148)
                      .++..|+||+++|.+++.+ ++| |+     |.||.+||++||..+  .+||+||+.+..+
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            3457899999999887776 689 96     999999999999875  4899999988653

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

Probab=99.73  E-value=3.2e-18  Score=99.18  Aligned_cols=51  Identities=31%  Similarity=0.653  Sum_probs=44.3

Q ss_pred             CccccccccccccCC----CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSG----DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~----~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      +...|+||++.|.+.    ..+..++ |||.||.+||+.|+..+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            347899999999764    4557788 99999999999999999999999998864

>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=99.72  E-value=4.1e-18  Score=108.16  Aligned_cols=49  Identities=24%  Similarity=0.813  Sum_probs=41.0

Q ss_pred             ccccccccccccCCC---------------eeeecCCCCccchHHhHHHHH-----hCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGD---------------LFRILPFCKHVYHSHCIIRWF-----SDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~---------------~vr~lp~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~~~  145 (148)
                      +..|+|||++|..+.               .++.++ |+|.||.+||+.|+     ..+.+||+||+.+.
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~   93 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYG   93 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccC
Confidence            358999999997653               455788 99999999999999     45778999999774

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

Probab=99.69  E-value=6e-18  Score=98.40  Aligned_cols=47  Identities=36%  Similarity=0.878  Sum_probs=42.2

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ...|+||++.+.+    ..+| |||.||..||..|+..+.+||+||+.+...
T Consensus        15 ~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A           15 EEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCC
T ss_pred             CCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCC
Confidence            4689999999876    6789 999999999999999999999999988653

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

Probab=99.68  E-value=3.8e-17  Score=95.53  Aligned_cols=50  Identities=26%  Similarity=0.548  Sum_probs=42.4

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +...|+||++.|.+.  +..++ |||.||..||..|+..+.+||+||+.+..+
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           14 PYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             GGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             CCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            347899999998763  33347 999999999999999999999999988754

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

Probab=99.68  E-value=2.2e-17  Score=96.25  Aligned_cols=48  Identities=35%  Similarity=0.625  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ++..|+||++.+.+.   ..+| |||.||..||..|+..+.+||+||..+..
T Consensus        14 ~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           14 TVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            347899999998654   6678 99999999999999999999999998753

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

Probab=99.68  E-value=5.4e-17  Score=98.28  Aligned_cols=52  Identities=27%  Similarity=0.693  Sum_probs=44.7

Q ss_pred             CccccccccccccCCCe-eeecCCCCccchHHhHHHHHhCC---CCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDL-FRILPFCKHVYHSHCIIRWFSDE---FTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~-vr~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~~  147 (148)
                      +..+|+||++.|.+++. .+.+| |||.||.+||..|+..+   .+||+||..+..+
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             CCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            34789999999988664 77888 99999999999999875   7899999987653

>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=99.67  E-value=3.7e-18  Score=108.17  Aligned_cols=49  Identities=27%  Similarity=0.673  Sum_probs=0.4

Q ss_pred             ccccccccccccCC-------------C--eeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSG-------------D--LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~-------------~--~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ++.|+||+++|++.             +  .+..++ |+|.||.+||++||+.+.+||+||+++.
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             C----------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            46899999999752             2  233356 9999999999999999999999999853

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

Probab=99.67  E-value=2.6e-17  Score=95.08  Aligned_cols=47  Identities=36%  Similarity=0.890  Sum_probs=41.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +..|+||++.+.+  .+..+| |||.||.+|+..|+..+.+||+||+++.
T Consensus         5 ~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            5 AERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            4689999999864  357889 9999999999999999999999999875

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

Probab=99.65  E-value=1.7e-16  Score=91.17  Aligned_cols=49  Identities=24%  Similarity=0.518  Sum_probs=41.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHh-CCCCCcccCCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSIYLDA  148 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~~  148 (148)
                      ...|+||++.+.+.   ..++ |||.||..||..|+. .+.+||+||+.+..++
T Consensus        15 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           15 KYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            47899999999765   3478 999999999999994 5678999999987653

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

Probab=99.64  E-value=3e-16  Score=91.79  Aligned_cols=50  Identities=28%  Similarity=0.606  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHh---CCCCCcccCCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---DEFTCPICRSSIYLDA  148 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~~~~~~  148 (148)
                      +...|+||++.|.+   ...+| |||.||.+||..|++   .+.+||+||+.+..++
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            34789999999875   35678 999999999999997   4568999999987653

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

Probab=99.63  E-value=2.9e-16  Score=92.21  Aligned_cols=49  Identities=24%  Similarity=0.597  Sum_probs=41.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC--CCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE--FTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~  146 (148)
                      +...|+||++.|.+.   ..+|.|||.||..||..|+..+  .+||+||+.+..
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           14 DELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             GGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            357899999999764   4577699999999999999865  689999998654

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

Probab=99.63  E-value=2.7e-16  Score=93.90  Aligned_cols=47  Identities=23%  Similarity=0.619  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ....|+||++.|.+.   .++| |||.||..||..|+..+.+||+||..+.
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            346899999998663   4688 9999999999999999999999999874

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

Probab=99.61  E-value=2.8e-16  Score=102.91  Aligned_cols=46  Identities=39%  Similarity=0.943  Sum_probs=41.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ..|+||++.|.++   ..+| |||.||..||..|+..+.+||+||+++..
T Consensus        54 ~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             CCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            4799999998653   6789 99999999999999999999999998753

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

Probab=99.60  E-value=3.8e-16  Score=101.24  Aligned_cols=51  Identities=31%  Similarity=0.690  Sum_probs=44.8

Q ss_pred             ccccccccccccCC----CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSG----DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~----~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +..|+||++.|.+.    +.++.++ |||.||.+||+.|++.+.+||+||+.+..+
T Consensus         7 ~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            7 TVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             SCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            46899999999764    5667888 999999999999999999999999988653

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

Probab=99.60  E-value=1.1e-15  Score=89.07  Aligned_cols=48  Identities=23%  Similarity=0.574  Sum_probs=41.3

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC--CCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE--FTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~  146 (148)
                      ..+|+||.+.+..++...  . |+|.||..||++||+.+  .+||+||++...
T Consensus        15 i~~C~IC~~~i~~g~~C~--~-C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           15 VKICNICHSLLIQGQSCE--T-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SCBCSSSCCBCSSSEECS--S-SCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             CCcCcchhhHcccCCccC--C-CCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            478999999998775444  4 99999999999999987  789999998654

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

Probab=99.59  E-value=1.8e-15  Score=90.83  Aligned_cols=49  Identities=27%  Similarity=0.583  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC------CCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD------EFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~~~~~  147 (148)
                      +...|+||++.|.+.   .++| |||.||..||..|+..      +.+||+||..+..+
T Consensus        18 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            346899999998765   4788 9999999999999987      66799999988754

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

Probab=99.58  E-value=1.7e-15  Score=89.70  Aligned_cols=48  Identities=23%  Similarity=0.463  Sum_probs=41.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      ...|+||++.|.+.   .+++ |||.||..||..|+.. +.+||+||.++..+
T Consensus         8 ~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            8 YFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             cCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            47899999998764   5678 9999999999999987 78899999988653

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens}

Probab=99.58  E-value=4.1e-16  Score=92.56  Aligned_cols=49  Identities=29%  Similarity=0.560  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-------CCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-------EFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~~~~~  147 (148)
                      ++..|+||++.|.+.   ..+| |||.||.+||..|+..       +.+||+||..+..+
T Consensus        11 ~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           11 EEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            347899999999764   4578 9999999999999987       56799999988653

>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=99.58  E-value=6.2e-16  Score=95.90  Aligned_cols=49  Identities=29%  Similarity=0.734  Sum_probs=41.1

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-CCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  147 (148)
                      ...|+||++.|.+  .+..++ |||.||..||..|+..+ .+||+||.++..+
T Consensus        22 ~~~C~IC~~~~~~--p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           22 VFRCFICMEKLRD--ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCccCCccccC--ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            3689999999965  333378 99999999999999987 6899999988653

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

Probab=99.57  E-value=2.1e-15  Score=86.31  Aligned_cols=51  Identities=20%  Similarity=0.456  Sum_probs=41.5

Q ss_pred             ccccccccc-cccCCCee-eecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           96 TSECVICLE-EFVSGDLF-RILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~-~~~~~~~v-r~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      +..|+||++ .|.+.... ..++ |||.||..||+.|+.. +.+||+||..+..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            368999999 77776543 4567 9999999999999765 56799999998764

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=2e-15  Score=90.56  Aligned_cols=48  Identities=31%  Similarity=0.670  Sum_probs=41.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC------CCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD------EFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~~~~~  147 (148)
                      ...|+||++.|.+.   ..+| |||.||.+|+..|+..      +.+||+||..+..+
T Consensus        19 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           19 EVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            46899999998764   5678 9999999999999987      77899999988754

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

Probab=99.56  E-value=9.7e-16  Score=99.31  Aligned_cols=52  Identities=31%  Similarity=0.644  Sum_probs=44.8

Q ss_pred             CccccccccccccCC----CeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSG----DLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~----~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      +...|+||++.|.+.    ..+..++ |||.||..||++|++.+.+||+||+++..+
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            347899999999763    3456778 999999999999999999999999998764

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

Probab=99.56  E-value=1.8e-15  Score=93.63  Aligned_cols=48  Identities=33%  Similarity=0.670  Sum_probs=40.8

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ...|+||++.|.+.  +..++ |||.||..||..|+..+.+||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNIA--MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCCc--CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            36899999998763  33347 99999999999999999999999998764

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

Probab=99.55  E-value=8.2e-15  Score=83.25  Aligned_cols=42  Identities=29%  Similarity=0.657  Sum_probs=36.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHh---CCCCCccc
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---DEFTCPIC  140 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---~~~~CP~C  140 (148)
                      ++..|+||++.|.+.   .++| |||.||..||..|++   .+.+||+|
T Consensus        19 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            347899999998764   5678 999999999999998   46689998

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=6.6e-15  Score=82.20  Aligned_cols=42  Identities=36%  Similarity=1.051  Sum_probs=35.5

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHh---CCCCCccc
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---DEFTCPIC  140 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---~~~~CP~C  140 (148)
                      +...|+||++.+.+.   ..++ |||.||.+||..|+.   .+.+||+|
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            346899999999775   5578 999999999999954   56789998

>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=99.53  E-value=5.2e-15  Score=92.92  Aligned_cols=48  Identities=29%  Similarity=0.730  Sum_probs=41.3

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      +..|+||++.|.+  .+..++ |||.||..||..|+..+.+||+||..+..
T Consensus        15 ~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           15 HLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             GTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             cCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCccccc
Confidence            3689999999865  344448 99999999999999999999999998864

>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=99.51  E-value=1.7e-14  Score=97.02  Aligned_cols=72  Identities=22%  Similarity=0.451  Sum_probs=50.4

Q ss_pred             CCCHHHHhcCCCccccCCcc-----CCCCCccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCC
Q 045986           71 LRHQRVIEKLPPAEKYDGHL-----HNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSI  144 (148)
Q Consensus        71 ~~~~~~i~~lp~~~~~~~~~-----~~~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~  144 (148)
                      +++...+.+.+......+..     ....+...|+||++.|.+  .+..+| |||.||..||..|+.. +.+||+||..+
T Consensus        24 ~l~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~  100 (165)
T 2ckl_B           24 ELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKL  100 (165)
T ss_dssp             CCCHHHHHCCCCCCCCSCCEEC----CCHHHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBC
T ss_pred             cCCHHHHhcCchhhhccccccccchhhCCCCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcC
Confidence            45555555555433333221     111234689999999875  344458 9999999999999997 78899999988


Q ss_pred             C
Q 045986          145 Y  145 (148)
Q Consensus       145 ~  145 (148)
                      .
T Consensus       101 ~  101 (165)
T 2ckl_B          101 V  101 (165)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing, mRNA splicing; NMR {Homo sapiens}

Probab=99.51  E-value=2.3e-14  Score=87.39  Aligned_cols=47  Identities=26%  Similarity=0.645  Sum_probs=39.7

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC--CCCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE--FTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~  144 (148)
                      ++..|+||++.|.+.   ..+|.|||.||..||..|+..+  .+||+||..+
T Consensus        12 ~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           12 DELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             TTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             cCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            347899999999764   5677699999999999999753  5899999987

>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=99.50  E-value=1.1e-14  Score=93.53  Aligned_cols=47  Identities=28%  Similarity=0.598  Sum_probs=40.2

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC-CCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF-TCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~  146 (148)
                      ...|+||++.|.+.   ..+| |||.||..||..|+..+. +||+||..+..
T Consensus        52 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            36799999998754   5678 999999999999998644 89999998865

>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=99.49  E-value=1.3e-14  Score=91.49  Aligned_cols=47  Identities=28%  Similarity=0.754  Sum_probs=40.2

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC---CCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF---TCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~~~~~  147 (148)
                      ..|+||++.|.+.   ..+| |||.||..||..|+..+.   +||+||..+..+
T Consensus        22 ~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            5799999998764   4578 999999999999998754   899999988654

>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=99.47  E-value=6.6e-15  Score=93.56  Aligned_cols=47  Identities=28%  Similarity=0.631  Sum_probs=40.5

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ...|+||++.+.+.   ..++ |||.||..||..|+.. +.+||+||.++..
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            36899999998654   4578 9999999999999987 7789999998764

>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=99.47  E-value=2e-14  Score=91.63  Aligned_cols=48  Identities=29%  Similarity=0.582  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC-CCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF-TCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~  146 (148)
                      +...|+||++.+.+.   ..++ |||.||..||..|+..+. +||+||.++..
T Consensus        17 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           17 SKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            347899999998764   5678 999999999999998765 89999998865

>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=99.45  E-value=4.4e-14  Score=93.57  Aligned_cols=48  Identities=27%  Similarity=0.574  Sum_probs=41.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC-CCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF-TCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~~~  147 (148)
                      ...|+||++.|.+.   .++| |||.||..||..|+.... +||+||.++..+
T Consensus        78 ~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            36899999998664   5588 999999999999998754 899999998754

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

Probab=99.44  E-value=1.1e-13  Score=81.75  Aligned_cols=51  Identities=27%  Similarity=0.449  Sum_probs=40.0

Q ss_pred             CccccccccccccCCC-eeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ++.+|+||++.+...+ .+..++ |||.||..|+..++.. +..||+||+++..
T Consensus        10 ~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~   62 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   62 (78)
T ss_dssp             CCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSS
T ss_pred             cCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCC
Confidence            3478999999986543 233356 9999999999999854 6679999998765

>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=99.44  E-value=1.2e-13  Score=85.40  Aligned_cols=50  Identities=14%  Similarity=0.075  Sum_probs=43.8

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .+...|+||++-|.+.   .++| |||.|+..||..|+..+.+||+||.++..+
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             cHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            4457899999998775   6788 999999999999999999999999988654

>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=99.43  E-value=1.5e-14  Score=91.75  Aligned_cols=46  Identities=30%  Similarity=0.758  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~  145 (148)
                      +..|+||++.|.+.   ..+| |||.||..||..|+.. +.+||+||..+.
T Consensus        15 ~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           15 ECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            46899999998764   5678 9999999999999977 678999999874

>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=99.43  E-value=5.5e-14  Score=80.06  Aligned_cols=46  Identities=28%  Similarity=0.522  Sum_probs=39.0

Q ss_pred             ccccccccccccCCCeeee--cCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRI--LPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~--lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +.+|+||++.+.+.   ..  +| |||. |+.+|+..|.+.+.+||+||+++.
T Consensus         8 ~~~C~IC~~~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPKNG---CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCSCE---EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             cCCCCcCCCCCCCE---EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            46899999986543   33  49 9999 899999999999999999999874

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.41  E-value=4.4e-14  Score=78.36  Aligned_cols=45  Identities=31%  Similarity=0.663  Sum_probs=38.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ...|+||++.|.+.   ++|| |||.||..|+..|   ..+||+||+.+..+
T Consensus         6 ~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            6 FLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            46899999999765   7789 9999999999884   67899999988654

>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=99.40  E-value=1.2e-13  Score=78.47  Aligned_cols=48  Identities=25%  Similarity=0.450  Sum_probs=39.1

Q ss_pred             ccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ...|+||++...+. .+..+| |||. |+.+|+..|.+.+.+||+||+++.
T Consensus         7 ~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            46899999986443 122349 9998 999999999988889999999874

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus}

Probab=99.39  E-value=2.2e-13  Score=81.82  Aligned_cols=48  Identities=17%  Similarity=0.061  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      +...|+||++-|.+.   .+++ |||.|+..||..|+..+.+||+||.++..
T Consensus        13 ~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           13 DEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             TTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             hheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            357899999998775   6788 99999999999999988999999998764

>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=99.38  E-value=2.3e-13  Score=101.81  Aligned_cols=46  Identities=33%  Similarity=0.779  Sum_probs=40.5

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHh-CCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS-DEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  146 (148)
                      .+|+||++.+.+   +..+| |||.||..|+..|+. .+.+||+||+++..
T Consensus       333 ~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          333 QLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            689999999754   57789 999999999999999 78899999998753

>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=99.36  E-value=7.9e-13  Score=81.42  Aligned_cols=49  Identities=20%  Similarity=0.152  Sum_probs=42.9

Q ss_pred             CccccccccccccCCCeeeecCCCC-ccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCK-HVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ++..|+||++-|.+.   .+++ || |.|+..||..|+..+.+||+||.++..+
T Consensus        21 ~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           21 DEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             HhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            357899999998775   5688 99 9999999999999999999999988654

>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=99.34  E-value=2.3e-13  Score=89.25  Aligned_cols=47  Identities=21%  Similarity=0.378  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC-CCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF-TCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~~~  145 (148)
                      +...|+||++.+.+.   ..++ |||.||..||..|+.... +||+||.++.
T Consensus        30 ~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           30 AKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             cCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            347899999998765   4578 999999999999998654 8999999753

>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=99.32  E-value=3e-13  Score=86.02  Aligned_cols=44  Identities=23%  Similarity=0.691  Sum_probs=38.3

Q ss_pred             cccccccccccCCCeeeec-CCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRIL-PFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~l-p~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ..|+||++.|.+.   ..+ + |||.||..||..|+.  .+||+||..+..
T Consensus        23 ~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           23 LRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             TSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             CCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            6899999999764   555 7 999999999999987  789999998754

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=99.31  E-value=1.3e-12  Score=73.16  Aligned_cols=47  Identities=28%  Similarity=0.603  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCeeeecCCCC--c---cchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCK--H---VYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~--H---~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      ++..|.||+++.  ++.+ ++| |+  |   .||.+|++.|+..  +.+||+||..+.
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            457899999983  3344 688 75  4   9999999999975  678999999875

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

Probab=99.31  E-value=4.4e-13  Score=98.15  Aligned_cols=52  Identities=23%  Similarity=0.531  Sum_probs=40.1

Q ss_pred             CCccccccccccccCCCee----eecCCCCccchHHhHHHHHhCC-----------CCCcccCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLF----RILPFCKHVYHSHCIIRWFSDE-----------FTCPICRSSIY  145 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~v----r~lp~C~H~FH~~Ci~~Wl~~~-----------~~CP~CR~~~~  145 (148)
                      +...+|+||++.+.++..+    ...+.|||.||..|+.+||+..           .+||+||+++.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            3457999999999873322    2223499999999999999752           46999999875

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.28  E-value=5.6e-13  Score=78.01  Aligned_cols=41  Identities=27%  Similarity=0.728  Sum_probs=35.8

Q ss_pred             cccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ..|+||++.+.+   ...+| |||. |+..|+..|    .+||+||+++.
T Consensus        25 ~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~   66 (74)
T 4ic3_A           25 KLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVIT   66 (74)
T ss_dssp             TBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCS
T ss_pred             CCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCcc
Confidence            579999998754   46789 9999 999999999    78999999874

>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=99.24  E-value=2.9e-12  Score=86.45  Aligned_cols=49  Identities=29%  Similarity=0.620  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-CCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  147 (148)
                      +...|+||++.|.+.   ..++ |||.|+..||..|+..+ .+||+||.++..+
T Consensus        17 ~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            347899999998765   4578 99999999999999864 4899999988653

>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=99.21  E-value=5.3e-12  Score=77.16  Aligned_cols=50  Identities=22%  Similarity=0.657  Sum_probs=42.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhC--------CCCCcc--cCCC--CCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--------EFTCPI--CRSS--IYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~--~~~  146 (148)
                      ..+|+||++++...+.++.++ |||.|+.+|+..++..        ..+||.  |+..  +.+
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            468999999998887777778 9999999999999864        236999  9988  543

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=2.1e-11  Score=70.09  Aligned_cols=43  Identities=30%  Similarity=0.792  Sum_probs=35.9

Q ss_pred             CccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +...|.||++...   .+..+| |||. |+..|+..    ..+||+||+++.
T Consensus        14 ~~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~   57 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQ   57 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETT-TTBCCSCTTHHHH----CSSCTTTCCCCC
T ss_pred             CCCCCCCcCcCCC---CEEEEC-CCChhhhHHHHhc----CCCCCCCCcchh
Confidence            3478999999854   457899 9999 99999984    578999999874

>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=99.15  E-value=1.3e-11  Score=75.45  Aligned_cols=45  Identities=27%  Similarity=0.514  Sum_probs=37.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC------CCCcc--cCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE------FTCPI--CRSS  143 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~------~~CP~--CR~~  143 (148)
                      ...|+||++.|.+.   .++|.|||.|+..||..|+..+      .+||+  |+..
T Consensus         7 ~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            7 GFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             CCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             EeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            46899999998764   4553499999999999999764      48999  9865

>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=99.14  E-value=2.1e-11  Score=87.90  Aligned_cols=49  Identities=18%  Similarity=0.099  Sum_probs=41.5

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      .....|+||++-|.++   .++| |||.|+..||..|+.. +.+||+||.++..
T Consensus       206 ~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          206 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            3457899999998765   6788 9999999999999986 4459999998864

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=1.9e-11  Score=71.63  Aligned_cols=42  Identities=26%  Similarity=0.732  Sum_probs=34.9

Q ss_pred             cccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ..|+||++.+.+   +..+| |||. |+..|+..    ...||+||.++..
T Consensus        26 ~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           26 KLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            579999999755   46689 9999 99999964    4789999998753

>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=99.06  E-value=2.1e-11  Score=72.09  Aligned_cols=41  Identities=32%  Similarity=0.800  Sum_probs=34.9

Q ss_pred             cccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ..|+||++.+.+   +..+| |||. |+..|+..|    ..||+||+++.
T Consensus        19 ~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           19 MLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             TBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            579999998644   57789 9999 999999987    38999999774

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.04  E-value=9.5e-11  Score=79.29  Aligned_cols=49  Identities=18%  Similarity=0.082  Sum_probs=41.4

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-CCCcccCCCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYL  146 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~  146 (148)
                      .....||||++-|.++   .++| |||.|...||..|+..+ .+||+||.++..
T Consensus       104 p~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            4458899999998764   6678 99999999999999864 469999998764

>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=98.94  E-value=2.4e-10  Score=64.13  Aligned_cols=47  Identities=11%  Similarity=0.196  Sum_probs=40.6

Q ss_pred             cccccccccccCCCeeeec-CCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRIL-PFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~l-p~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ..|+|+++-+.+.   .++ + +||.|..+||.+|++.+.+||+.+.++..+
T Consensus         4 ~~CpIs~~~m~dP---V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             EEecCCCCCCCCC---EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            4799999999754   455 6 999999999999999988999999988654

>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=98.89  E-value=2.4e-10  Score=84.92  Aligned_cols=42  Identities=33%  Similarity=0.811  Sum_probs=36.2

Q ss_pred             ccccccccccccCCCeeeecCCCCcc-chHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHV-YHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +..|+||++.+.+   +..+| |||. ||..|+..|    ..||+||.++.
T Consensus       295 ~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          295 ERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             TCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             CCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            3689999999754   46779 9999 999999998    68999999874

>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=98.86  E-value=1.3e-09  Score=77.44  Aligned_cols=48  Identities=19%  Similarity=0.472  Sum_probs=39.2

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC--CCCcc--cCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE--FTCPI--CRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--~~CP~--CR~~~~~  146 (148)
                      ...||||++.|.++  |+.+. |||.|++.||..|+..+  .+||+  ||..+..
T Consensus       181 el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          181 ELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             CSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             eeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            46899999999554  55456 99999999999999864  46999  9987654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.69  E-value=1.6e-08  Score=61.18  Aligned_cols=45  Identities=29%  Similarity=0.575  Sum_probs=37.1

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIY  145 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~  145 (148)
                      .|++|--++  ....|..| |+|+|+.+|+..|.++ ..+||+|+.++.
T Consensus         3 fC~~C~~Pi--~iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPI--KVYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBC--SEEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCe--EEEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            477786655  44679999 9999999999999865 678999999874

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

Probab=98.38  E-value=3e-07  Score=64.93  Aligned_cols=47  Identities=23%  Similarity=0.588  Sum_probs=37.9

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC--CCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF--TCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~--~CP~CR~~~~  145 (148)
                      ...|+||.+-...|...  -. |+|.||..|++.|++.+.  +||.|+...+
T Consensus       180 i~~C~iC~~iv~~g~~C--~~-C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~  228 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSC--ET-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWP  228 (238)
T ss_dssp             CCBCTTTCSBCSSCEEC--SS-SCCEECHHHHHHHTTTCSSCBCTTTCCBCC
T ss_pred             CCcCcchhhHHhCCccc--Cc-cChHHHHHHHHHHHHhCCCCCCCCCCCCCC
Confidence            47899999988776322  23 999999999999998754  8999998754

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=97.44  E-value=0.00013  Score=41.13  Aligned_cols=46  Identities=20%  Similarity=0.503  Sum_probs=34.3

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~~~  145 (148)
                      ...|.||.+.   ++.+.--. |...||..|+++.|....    .||.|++...
T Consensus        12 ~~~C~vC~~~---~~ll~Cd~-C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C           12 GARCGVCGDG---TDVLRCTH-CAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             TCCCTTTSCC---TTCEECSS-SCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCcCCCCCC---CeEEECCC-CCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            4679999754   55555444 899999999999887643    4999987543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.69  E-value=0.00095  Score=40.51  Aligned_cols=33  Identities=15%  Similarity=0.402  Sum_probs=26.1

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHH
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRW  130 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~W  130 (148)
                      ..|+||++++.......-++ |+|.|+..|+..+
T Consensus         4 ~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            4 VLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            57999998764444444488 9999999999983

>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=96.14  E-value=0.0067  Score=35.31  Aligned_cols=35  Identities=26%  Similarity=0.598  Sum_probs=23.4

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHH
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRW  130 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~W  130 (148)
                      .+++.|.||- .|..++...-=- |+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~pCRv-C~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFPCRV-CTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSSCSS-SSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceecccc-ccccccHhhcccc
Confidence            3457899994 344443222222 7899999999996

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=95.86  E-value=0.0046  Score=34.03  Aligned_cols=44  Identities=23%  Similarity=0.625  Sum_probs=31.3

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      ++..|.+|...   ++.+.--. |...||..|+++=+....    .||.|+.
T Consensus        10 ~~~~C~vC~~~---g~ll~CD~-C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQG---GEIILCDT-CPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSCC---SSEEECSS-SSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCCC---CcEEECCC-CChhhhhhccCCCCCCCCCCceECccccc
Confidence            34789999874   55554443 888999999998654322    3999975

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=95.38  E-value=0.004  Score=34.29  Aligned_cols=47  Identities=26%  Similarity=0.614  Sum_probs=32.0

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSSI  144 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~~  144 (148)
                      .++..|.||-+.   ++.+.--. |...||..|+.+=|....    .||.|+...
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~-C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GELLCCDT-CPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSS-SCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CCEEEcCC-CCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            345689999863   44444333 788999999987554422    399998754

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=95.23  E-value=0.0051  Score=41.47  Aligned_cols=46  Identities=24%  Similarity=0.586  Sum_probs=33.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~~  144 (148)
                      +++.|.+|.+.   |+.+.--. |.-.||..|+++-+...+    .||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~-C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEK-CPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSS-SSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---CeeeecCC-CCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            34689999865   55444333 889999999988766532    399998754

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=95.15  E-value=0.0096  Score=31.37  Aligned_cols=44  Identities=20%  Similarity=0.563  Sum_probs=29.5

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      .|.||...-..++.+.--. |...||..|+++=+...+    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~-C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDE-CNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTT-TCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCC-CChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            4888987644444444343 889999999986444322    3999975

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=95.12  E-value=0.0083  Score=40.50  Aligned_cols=47  Identities=23%  Similarity=0.477  Sum_probs=34.0

Q ss_pred             cccccccccccCCC----eeeecCCCCccchHHhHHH------HHh-----CCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGD----LFRILPFCKHVYHSHCIIR------WFS-----DEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~----~vr~lp~C~H~FH~~Ci~~------Wl~-----~~~~CP~CR~~~  144 (148)
                      ..|+||...|.+++    .|.--. |...||..|+.-      -+.     ..-.||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~-C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGK-CDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTT-TCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCC-CCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            46999999998876    444444 899999999732      111     146799998754

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.07  E-value=0.0024  Score=34.55  Aligned_cols=44  Identities=27%  Similarity=0.644  Sum_probs=31.1

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      ++..|.+|...   ++.+.--. |...||..|+++=|...+    .||.|+.
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~-C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---GQLLMCDT-CSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---SCCEECSS-SSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---CeEEEcCC-CCcceECccCCCCcCCCCCCceEChhhhC
Confidence            34689999875   55554444 889999999997554432    3998864

>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=94.99  E-value=0.0051  Score=34.10  Aligned_cols=48  Identities=19%  Similarity=0.511  Sum_probs=33.4

Q ss_pred             CccccccccccccCC-CeeeecCCCCccchHHhHHHHHh-----CCCCCcccCCC
Q 045986           95 FTSECVICLEEFVSG-DLFRILPFCKHVYHSHCIIRWFS-----DEFTCPICRSS  143 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~-~~vr~lp~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~  143 (148)
                      ++..|++|...+.++ ..|.--. |...||..|+..-..     ..-.||.|+..
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~-C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDL-CEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSS-SCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccC-CCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            346799999988643 4555454 899999999864321     23459999654

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=94.95  E-value=0.0056  Score=42.12  Aligned_cols=45  Identities=27%  Similarity=0.584  Sum_probs=31.9

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSS  143 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  143 (148)
                      +++.|.+|-..   |+.+. --.|...||..|+++-+...+    .||.|+..
T Consensus         6 ~~~~C~~C~~~---g~ll~-Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            6 NEDWCAVCQNG---GDLLC-CEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             SCSSBTTTCCC---EEEEE-CSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCC---CceEE-cCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            45789999854   44333 333889999999988765533    49999864

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.67  E-value=0.019  Score=33.96  Aligned_cols=46  Identities=24%  Similarity=0.621  Sum_probs=32.5

Q ss_pred             CCccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCC
Q 045986           94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSS  143 (148)
Q Consensus        94 ~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  143 (148)
                      .++..|.+|...   ++.+.--. |.-.||..|+++=|..-+    .||.|+..
T Consensus        23 ~n~~~C~vC~~~---g~LL~CD~-C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---GDLVMCNQ-CEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---SCCEECTT-SSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---CCEEECCC-CCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            345789999875   55444333 788899999987665423    39999754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=94.64  E-value=0.004  Score=34.83  Aligned_cols=44  Identities=23%  Similarity=0.576  Sum_probs=31.0

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      ++..|.||.+.   ++.+.--. |.-.||..|+.+=|...+    .||.|..
T Consensus         7 ~~~~C~vC~~~---g~ll~CD~-C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            7 NEDECAVCRDG---GELICCDG-CPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             CCCSBSSSSCC---SSCEECSS-CCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCccCCCC---CCEEEcCC-CChhhcccccCCCcCcCCCCCeECccccC
Confidence            45789999864   55554444 888999999987554422    3999965

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.60  E-value=0.011  Score=33.82  Aligned_cols=49  Identities=20%  Similarity=0.375  Sum_probs=33.1

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC----CCCCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD----EFTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~  144 (148)
                      +...|.||-.....+..|.--- |.-.||..|+..-...    .-.||.|+..+
T Consensus        17 ~~~~C~~C~~~~~~~~mi~CD~-C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~   69 (75)
T 2k16_A           17 QIWICPGCNKPDDGSPMIGCDD-CDDWYHWPCVGIMAAPPEEMQWFCPKCANKI   69 (75)
T ss_dssp             EEECBTTTTBCCSSCCEEECSS-SSSEEEHHHHTCSSCCCSSSCCCCTTTHHHH
T ss_pred             CCcCCCCCCCCCCCCCEEEcCC-CCcccccccCCCCccCCCCCCEEChhccCch
Confidence            3467999988764333444444 8899999999765433    23499997654

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=94.11  E-value=0.014  Score=35.98  Aligned_cols=37  Identities=22%  Similarity=0.349  Sum_probs=26.2

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHh
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS  132 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~  132 (148)
                      +++.|.||.+.=+..+.+.=-. |+..||..|++..+.
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~-C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTT-CGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSS-SCCEECTTTTTCCCC
T ss_pred             CCCCCcCCCCCCCCcCCeECCC-CCCCcChHHhCCccc
Confidence            4578999987732222344444 899999999988764

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=94.09  E-value=0.041  Score=34.93  Aligned_cols=47  Identities=26%  Similarity=0.652  Sum_probs=31.4

Q ss_pred             CCCccccccccccccCCCeeeecCCCCccchHHhHHHHH------hC-----CCCCcccCCC
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF------SD-----EFTCPICRSS  143 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl------~~-----~~~CP~CR~~  143 (148)
                      +.+++.|.||-+.   ++.+---. |-..||.+||++=+      +.     .=.|++|+..
T Consensus        54 Dg~~~~C~vC~dG---G~LlcCd~-Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           54 DGMDEQCRWCAEG---GNLICCDF-CHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             TSCBSSCTTTCCC---SEEEECSS-SSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCCCcCeecCCC---CeeEecCC-CchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            3445789999876   54433333 78999999999752      11     2249999653

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=94.06  E-value=0.096  Score=33.77  Aligned_cols=47  Identities=26%  Similarity=0.690  Sum_probs=34.0

Q ss_pred             CCCccccccccccccCCCeeeecCCCCccchHHhHHHHHh---------C--CCCCcccCCC
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---------D--EFTCPICRSS  143 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---------~--~~~CP~CR~~  143 (148)
                      +.+++.|.+|-+.   |+.+---. |-..||..||++=+.         .  .=.||+|+..
T Consensus        60 Dg~~d~C~vC~~G---G~LlcCD~-Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GNLICCDF-CHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC---SSEEECSS-SCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC---CcEEeCCC-CCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            3445789999886   66555444 889999999997653         1  2249999753

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=93.65  E-value=0.0078  Score=32.93  Aligned_cols=44  Identities=27%  Similarity=0.646  Sum_probs=31.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSS  143 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  143 (148)
                      +..|.+|...   ++.+.--. |.-.||..|+++=+...+    .||.|+..
T Consensus         5 ~~~C~vC~~~---g~ll~Cd~-C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   52 (60)
T 2puy_A            5 EDFCSVCRKS---GQLLMCDT-CSRVYHLDCLDPPLKTIPKGMWICPRCQDQ   52 (60)
T ss_dssp             CSSCTTTCCC---SSCEECSS-SSCEECGGGSSSCCSSCCCSCCCCHHHHHH
T ss_pred             CCCCcCCCCC---CcEEEcCC-CCcCEECCcCCCCcCCCCCCceEChhccCh
Confidence            4689999874   55555444 889999999997554422    39998653

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=93.42  E-value=0.036  Score=33.42  Aligned_cols=44  Identities=20%  Similarity=0.400  Sum_probs=31.2

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC---CCCCcccCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD---EFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR~  142 (148)
                      ..| ||-.....+..|.--. |.-.||..|+..=+..   .-.||.|+.
T Consensus        29 vrC-iC~~~~~~~~mi~Cd~-C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           29 TRC-ICGFTHDDGYMICCDK-CSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CCC-TTSCCSCSSCEEEBTT-TCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             EEe-ECCCccCCCcEEEcCC-CCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            567 8988776676666555 8899999998753222   224999974

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=93.28  E-value=0.11  Score=29.88  Aligned_cols=47  Identities=19%  Similarity=0.514  Sum_probs=31.9

Q ss_pred             cccccccccccc-CCCeeeecCCCCccchHHhHHHHHh-----CCCCCcccCCCC
Q 045986           96 TSECVICLEEFV-SGDLFRILPFCKHVYHSHCIIRWFS-----DEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~-~~~~vr~lp~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~~  144 (148)
                      ...| ||-..+. .+..|.--- |...||..|+.---.     ..-.||.|+..-
T Consensus        12 ~~~C-~C~~~~d~~~~MIqCd~-C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           12 PVYC-LCRQPYNVNHFMIECGL-CQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTT-TCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             ccEE-EcCCccCCCCceEEcCC-CCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            3567 9998875 445566555 899999999842211     234599998754

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=92.90  E-value=0.038  Score=31.30  Aligned_cols=48  Identities=19%  Similarity=0.465  Sum_probs=30.2

Q ss_pred             Cccccccccccc-cCCCeeeecCCCCccchHHhHHHHHhCC--CCCcccCC
Q 045986           95 FTSECVICLEEF-VSGDLFRILPFCKHVYHSHCIIRWFSDE--FTCPICRS  142 (148)
Q Consensus        95 ~~~~C~ICl~~~-~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~  142 (148)
                      ++..|.||.+.- .+++.+..=-.|.-.||..|+..=..-.  =.||.|+.
T Consensus        15 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           15 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             SSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            346899998763 2233333333488999999998532111  13888864

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=92.77  E-value=0.021  Score=38.66  Aligned_cols=43  Identities=26%  Similarity=0.678  Sum_probs=30.4

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  143 (148)
                      +.|.+|...   |+.+.--. |...||..|+++=+....    .||.|+..
T Consensus         3 ~~C~~C~~~---g~ll~Cd~-C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~   49 (189)
T 2ro1_A            3 TICRVCQKP---GDLVMCNQ-CEFCFHLDCHLPALQDVPGEEWSCSLCHVL   49 (189)
T ss_dssp             CCBTTTCCC---SSCCCCTT-TCCBCCSTTSTTCCSSCCCTTCCTTTTSCS
T ss_pred             CcCccCCCC---CceeECCC-CCchhccccCCCCcccCCCCCCCCcCccCC
Confidence            579999865   55444444 788999999987554322    39999864

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=92.50  E-value=0.025  Score=33.47  Aligned_cols=50  Identities=18%  Similarity=0.432  Sum_probs=31.2

Q ss_pred             Cccccccccccc-cCCCeeeecCCCCccchHHhHHHHHhC--CCCCcccCCCC
Q 045986           95 FTSECVICLEEF-VSGDLFRILPFCKHVYHSHCIIRWFSD--EFTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~-~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~  144 (148)
                      ++..|.||...- .+++.+..-..|.-.||..|+.+=+..  .=.||.|....
T Consensus        24 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~   76 (88)
T 2l43_A           24 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHT
T ss_pred             CCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCcc
Confidence            457899998753 122233333348889999999863321  12399996543

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.40  E-value=0.014  Score=34.87  Aligned_cols=46  Identities=22%  Similarity=0.475  Sum_probs=31.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      ...|.||...-..+..+.--. |...||..|+.+=|...+    .||.|+.
T Consensus        16 ~~~C~vC~~~~~~~~ll~CD~-C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           16 SYICQVCSRGDEDDKLLFCDG-CDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCSSSCCSGGGGGCEECTT-TCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCccCCCcCCCCCEEEcCC-CCchhccccCCCCcccCCCCCcCCccCcC
Confidence            467999988754333444333 889999999985443322    3999964

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=92.39  E-value=0.12  Score=28.66  Aligned_cols=32  Identities=22%  Similarity=0.457  Sum_probs=23.6

Q ss_pred             ccccccccccccCCCeeeecC-CCCccchHHhH
Q 045986           96 TSECVICLEEFVSGDLFRILP-FCKHVYHSHCI  127 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp-~C~H~FH~~Ci  127 (148)
                      ...|++|..++..++....-- .|.-.||..|+
T Consensus         8 ~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cv   40 (65)
T 2vpb_A            8 VYPCGICTNEVNDDQDAILCEASCQKWFHRICT   40 (65)
T ss_dssp             -CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHH
T ss_pred             cCcCccCCCccCCCCCeEecccCccccCchhcc
Confidence            367999999987665433332 48899999997

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=92.20  E-value=0.037  Score=34.16  Aligned_cols=45  Identities=22%  Similarity=0.465  Sum_probs=29.4

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      .|.||...=.+++.+..=-.|...||..|+++=|...+    .||.||.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            68888864222233333333889999999987665422    4999975

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=92.02  E-value=0.065  Score=30.61  Aligned_cols=47  Identities=19%  Similarity=0.472  Sum_probs=32.7

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHH---------HhCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRW---------FSDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~W---------l~~~~~CP~CR~~~  144 (148)
                      ...| ||-..+..+..|.--. |...||..|+.--         ....-.||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~MI~Cd~-C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCEE-ECCCccCCCCEEEeCC-CCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            3567 8998876556666555 8999999998421         12456799997643

>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=91.84  E-value=0.13  Score=42.88  Aligned_cols=50  Identities=16%  Similarity=0.037  Sum_probs=41.7

Q ss_pred             CCCccccccccccccCCCeeeecCCCC-ccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCK-HVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      .++...|||=++-+.++   .++| -| +.|-...|..||..+.+||+=|.++..
T Consensus       888 iP~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             SCGGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CcHHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            34457899999888665   6788 76 689999999999999999999988764

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=91.74  E-value=0.14  Score=28.89  Aligned_cols=46  Identities=20%  Similarity=0.552  Sum_probs=27.5

Q ss_pred             CccccccccccccCCCeeeecC-CCC-ccchHHhHHHHHhCC----CCCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILP-FCK-HVYHSHCIIRWFSDE----FTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp-~C~-H~FH~~Ci~~Wl~~~----~~CP~CR~~~  144 (148)
                      +...| ||-.... ++.|.-=- .|. ..||..|+.  |...    -.||.|+..-
T Consensus        15 ~~~~C-~C~~~~~-g~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           15 EPTYC-LCHQVSY-GEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             SCCCS-TTCCCSC-SSEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCEE-ECCCCCC-CCEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            34567 8987642 44333111 133 689999997  4432    2399998653

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=91.40  E-value=0.21  Score=26.22  Aligned_cols=43  Identities=14%  Similarity=0.327  Sum_probs=28.3

Q ss_pred             ccccccccccCCC-eeeec-CCCCccchHHhHHHH----HhCCCCCcccC
Q 045986           98 ECVICLEEFVSGD-LFRIL-PFCKHVYHSHCIIRW----FSDEFTCPICR  141 (148)
Q Consensus        98 ~C~ICl~~~~~~~-~vr~l-p~C~H~FH~~Ci~~W----l~~~~~CP~CR  141 (148)
                      .|.+|...+.+++ .|.-- . |.--||..|+.--    ...+-.||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~-C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGG-CDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTT-TCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCC-CCccCcccccCCCccccCCCCEECCCCC
Confidence            4778988886544 44433 4 8889999997421    12456699985

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=90.98  E-value=0.041  Score=30.85  Aligned_cols=45  Identities=24%  Similarity=0.592  Sum_probs=30.8

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHh---CCCCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---DEFTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  142 (148)
                      ...| ||-..+..+..|.--. |...||..|+..--.   ..-.||.|+.
T Consensus        19 ~~~C-iC~~~~~~~~MIqCd~-C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           19 LVTC-FCMKPFAGRPMIECNE-CHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             CCCS-TTCCCCTTCCEEECTT-TCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             ceEe-ECCCcCCCCCEEECCC-CCccccccccCcCcccCCCcEECCCCCC
Confidence            4678 9988776444666555 899999999864221   2335999975

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=90.79  E-value=0.033  Score=32.08  Aligned_cols=44  Identities=23%  Similarity=0.513  Sum_probs=27.1

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-----CCCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-----FTCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~  142 (148)
                      .|.||-..-..++.+. =-.|...||..|+++=|...     =.||.|++
T Consensus        28 ~C~vC~~~~d~~~ll~-CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQDPDKQLM-CDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCSCGGGEEE-CTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCCCCcceeE-eCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            4666665533333333 22378999999999766542     25999986

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=90.04  E-value=0.19  Score=30.77  Aligned_cols=44  Identities=23%  Similarity=0.522  Sum_probs=28.2

Q ss_pred             CccccccccccccCCCeeeec-CCCCccchHHhHHHHHhCCC----CCcccCCC
Q 045986           95 FTSECVICLEEFVSGDLFRIL-PFCKHVYHSHCIIRWFSDEF----TCPICRSS  143 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~l-p~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  143 (148)
                      +++.|.+|.+.   ++.+.-- +.|-..||..|+.  |...+    .||-|+..
T Consensus        14 ~~~~C~~C~~~---G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~   62 (107)
T 4gne_A           14 HEDYCFQCGDG---GELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCD   62 (107)
T ss_dssp             SCSSCTTTCCC---SEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCT
T ss_pred             CCCCCCcCCCC---CcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCC
Confidence            34689999843   5444332 0277899999998  54422    28877654

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=89.84  E-value=0.27  Score=29.13  Aligned_cols=47  Identities=19%  Similarity=0.512  Sum_probs=27.8

Q ss_pred             CccccccccccccCCCeeeecC-CCC-ccchHHhHHHHHhC----CCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILP-FCK-HVYHSHCIIRWFSD----EFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp-~C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~~~  145 (148)
                      +...| ||-.... ++.|.--- .|. ..||..|+.  |..    +-.||.|+..-.
T Consensus        35 e~~yC-iC~~~~~-g~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCBCS-TTCCBCC-SCCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCcEE-ECCCCCC-CCEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            34567 9987643 43333111 133 679999997  333    224999987543

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=89.83  E-value=0.034  Score=31.16  Aligned_cols=45  Identities=24%  Similarity=0.569  Sum_probs=28.3

Q ss_pred             cccccccccccCCCeeeec-CCCCccchHHhHHHHH---h-----CCCCCcccCC
Q 045986           97 SECVICLEEFVSGDLFRIL-PFCKHVYHSHCIIRWF---S-----DEFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~l-p~C~H~FH~~Ci~~Wl---~-----~~~~CP~CR~  142 (148)
                      ..| ||-.....+..|.-- +.|...||..|+.---   .     .+-.||.||.
T Consensus        11 v~C-~C~~~~~~g~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~   64 (68)
T 2rsd_A           11 VRC-ICSSTMVNDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRL   64 (68)
T ss_dssp             ECC-TTCCCSCCSCEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHH
T ss_pred             EEe-ECCCCcCCCCEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccC
Confidence            457 797766666665542 2388899999983210   0     1245999974

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.65  E-value=0.064  Score=30.84  Aligned_cols=45  Identities=22%  Similarity=0.507  Sum_probs=29.5

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CC---CCcccCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EF---TCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~---~CP~CR~  142 (148)
                      ..|.||...-..++.+.--. |...||..|+++=|..  ..   .||.|+.
T Consensus        27 c~C~vC~~~~~~~~ll~CD~-C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKHEPNMQLLCDE-CNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCCCSTTEEECSS-SCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcCCCCCEEEcCC-CCccccccccCCCccCCCCCCCcCCcCccC
Confidence            36889986533344443333 8899999999864433  22   4999975

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=89.54  E-value=0.15  Score=29.27  Aligned_cols=47  Identities=23%  Similarity=0.557  Sum_probs=31.5

Q ss_pred             ccccccccccccCCCeeeec--CCCCccchHHhHHHHH---------hCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGDLFRIL--PFCKHVYHSHCIIRWF---------SDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~l--p~C~H~FH~~Ci~~Wl---------~~~~~CP~CR~~~  144 (148)
                      ...| ||-.....+..|.--  - |...||..|+.-=-         ..+-.||.|+..-
T Consensus        16 ~~~C-iC~~~~~~g~MI~CD~~~-C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T 1wew_A           16 KVRC-VCGNSLETDSMIQCEDPR-CHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTT-TCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CEEe-ECCCcCCCCCEEEECCcc-CCccccCEEEccccccccccccCCCCEECCCCCccc
Confidence            4568 798875556555544  4 88999999985321         1244599997643

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=89.40  E-value=0.66  Score=28.43  Aligned_cols=32  Identities=22%  Similarity=0.467  Sum_probs=22.3

Q ss_pred             cccccccccc------cCCCeeeecCCCCccchHHhHHH
Q 045986           97 SECVICLEEF------VSGDLFRILPFCKHVYHSHCIIR  129 (148)
Q Consensus        97 ~~C~ICl~~~------~~~~~vr~lp~C~H~FH~~Ci~~  129 (148)
                      ..|.+|+..=      ..++.+.=-. |+..||..|++.
T Consensus         6 ~~C~~C~~~~~~~~~g~~~~Ll~C~~-C~~~~H~~Cl~~   43 (112)
T 3v43_A            6 PICSFCLGTKEQNREKKPEELISCAD-CGNSGHPSCLKF   43 (112)
T ss_dssp             SSBTTTCCCTTCCTTSCCCCCEECTT-TCCEECHHHHTC
T ss_pred             ccccccCCchhhCcCCCchhceEhhh-cCCCCCCchhcC
Confidence            5799998752      2224444444 999999999963

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=88.90  E-value=0.085  Score=29.72  Aligned_cols=45  Identities=22%  Similarity=0.465  Sum_probs=27.7

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CC---CCcccCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EF---TCPICRSS  143 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~---~CP~CR~~  143 (148)
                      .|.||...-..++.+. =-.|...||..|+++=|..  ..   .||.|+..
T Consensus        20 ~C~~C~~~~~~~~ll~-CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQDPDKQLM-CDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCSCGGGEEE-CTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcCCCCCEEE-cCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            4667775422333333 3338899999999864443  22   49999753

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=88.11  E-value=0.22  Score=27.37  Aligned_cols=50  Identities=24%  Similarity=0.541  Sum_probs=32.2

Q ss_pred             CccccccccccccC-CCeeeecCCCCccchHHhHHHHHh-------CCCCCcccCCCC
Q 045986           95 FTSECVICLEEFVS-GDLFRILPFCKHVYHSHCIIRWFS-------DEFTCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~-~~~vr~lp~C~H~FH~~Ci~~Wl~-------~~~~CP~CR~~~  144 (148)
                      ++..|.||...... +..+..=..|.-.||..|+.+=+.       ..=.||.|+...
T Consensus         5 ~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            34789999987533 223333334899999999886432       122499997543

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=87.21  E-value=0.12  Score=28.07  Aligned_cols=43  Identities=21%  Similarity=0.613  Sum_probs=25.7

Q ss_pred             ccccccccccccCCCeeeecC-CCC-ccchHHhHHHHHhCC----CCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILP-FCK-HVYHSHCIIRWFSDE----FTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp-~C~-H~FH~~Ci~~Wl~~~----~~CP~CR~  142 (148)
                      ...| ||-... .++.|.--. +|. ..||..|+.  |...    -.||.|+.
T Consensus         9 ~~yC-~C~~~~-~g~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            9 PTYC-LCHQVS-YGEMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CEET-TTTEEC-CSEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CcEE-ECCCCC-CCCeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            3567 898764 344333111 144 689999998  4432    24999965

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=87.14  E-value=0.3  Score=29.69  Aligned_cols=48  Identities=19%  Similarity=0.404  Sum_probs=30.9

Q ss_pred             cccccccccccCCCe-eeecCCCCccchHHhHHHH------H----hCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDL-FRILPFCKHVYHSHCIIRW------F----SDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~-vr~lp~C~H~FH~~Ci~~W------l----~~~~~CP~CR~~~  144 (148)
                      ..|.||...|.++.. +.--..|.-.||.+|+.-=      +    ..+-.||.|+..-
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            469999999866543 3322138889999998421      1    0233599997643

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=87.11  E-value=0.12  Score=34.17  Aligned_cols=45  Identities=29%  Similarity=0.576  Sum_probs=30.2

Q ss_pred             ccccccccccccCC-CeeeecCCCCccchHHhHHHHH-----hCCCCCcccCC
Q 045986           96 TSECVICLEEFVSG-DLFRILPFCKHVYHSHCIIRWF-----SDEFTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~-~~vr~lp~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~  142 (148)
                      ...| +|...+.++ ..+.--. |.-.||..|+..--     ...-.||.|+.
T Consensus         8 ~~~C-~C~~~~~~~~~mi~Cd~-C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~   58 (174)
T 2ri7_A            8 KLYC-ICKTPEDESKFYIGCDR-CQNWYHGRCVGILQSEAELIDEYVCPQCQS   58 (174)
T ss_dssp             CEET-TTTEECCTTSCEEECTT-TCCEEEHHHHTCCHHHHTTCSSCCCHHHHH
T ss_pred             CcEe-eCCCCCCCCCCEeECCC-CCchhChhhcCCchhhccCccCeecCCCcc
Confidence            4679 999887543 3455444 88999999995321     12445999975

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=86.76  E-value=0.099  Score=32.34  Aligned_cols=33  Identities=24%  Similarity=0.377  Sum_probs=23.0

Q ss_pred             cccccccccccC-------CCeeeecCCCCccchHHhHHHH
Q 045986           97 SECVICLEEFVS-------GDLFRILPFCKHVYHSHCIIRW  130 (148)
Q Consensus        97 ~~C~ICl~~~~~-------~~~vr~lp~C~H~FH~~Ci~~W  130 (148)
                      +.|.+|+..-..       ++.+.-.. |+..||..|++..
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~-C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCAD-CGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSS-SCCEECTTTTTCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCC-CCCccchhhCCCh
Confidence            469999876421       23444444 8999999999765

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=86.74  E-value=0.12  Score=28.14  Aligned_cols=43  Identities=21%  Similarity=0.627  Sum_probs=25.3

Q ss_pred             ccccccccccccCCCeeeecC-CCC-ccchHHhHHHHHhCC----CCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILP-FCK-HVYHSHCIIRWFSDE----FTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp-~C~-H~FH~~Ci~~Wl~~~----~~CP~CR~  142 (148)
                      ...| ||-... .++.|.--. .|. ..||..|+.  |...    -.||.|+.
T Consensus        10 ~~~C-~C~~~~-~g~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A           10 PTYC-LCHQVS-YGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CEET-TTTEEC-CSEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCEE-ECCCcC-CCCEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            3567 898764 243333111 133 679999998  4442    23999964

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=84.82  E-value=0.18  Score=27.59  Aligned_cols=43  Identities=23%  Similarity=0.675  Sum_probs=25.6

Q ss_pred             ccccccccccccCCCeeeecC-CCC-ccchHHhHHHHHhC----CCCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILP-FCK-HVYHSHCIIRWFSD----EFTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp-~C~-H~FH~~Ci~~Wl~~----~~~CP~CR~  142 (148)
                      ...| ||-... .++.|.--- .|. ..||..|+.  |..    +-.||.|+.
T Consensus        11 ~~yC-~C~~~~-~g~MI~CD~c~C~~~WfH~~Cvg--l~~~p~~~w~Cp~C~~   59 (62)
T 2g6q_A           11 PTYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRG   59 (62)
T ss_dssp             CEET-TTTEEC-CSEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHT
T ss_pred             CcEE-ECCCCC-CCCeeeeeCCCCCcccEecccCC--cCcCCCCCEECcCccc
Confidence            3567 898763 344333211 133 789999997  333    224999965

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=84.55  E-value=0.12  Score=31.76  Aligned_cols=44  Identities=20%  Similarity=0.465  Sum_probs=28.2

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      .|.+|-..-.+...+.--. |...||..|+++=|...+    .||.|+.
T Consensus        56 ~C~~C~~~~~~~~ll~Cd~-C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~  103 (111)
T 2ysm_A           56 VCQNCKQSGEDSKMLVCDT-CDKGYHTFCLQPVMKSVPTNGWKCKNCRI  103 (111)
T ss_dssp             CCTTTCCCSCCTTEEECSS-SCCEEEGGGSSSCCSSCCSSCCCCHHHHC
T ss_pred             cccccCccCCCCCeeECCC-CCcHHhHHhcCCccccCCCCCcCCcCCcC
Confidence            5777876533333344333 889999999987554322    3888865

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=83.76  E-value=0.21  Score=34.68  Aligned_cols=45  Identities=22%  Similarity=0.444  Sum_probs=25.0

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhC--CC---CCcccCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD--EF---TCPICRSS  143 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~--~~---~CP~CR~~  143 (148)
                      .|.+|...=..++.+.-- .|...||..|+++=|..  ..   .||.|+..
T Consensus       176 ~C~vC~~~~~~~~lL~CD-~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          176 ACHLCGGRQDPDKQLMCD-ECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             SCSSSCCCCC--CCEECS-SSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCcCCCCCCCCCCeEEcC-CCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            578887643233333323 38899999999965443  22   39999753

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=83.65  E-value=0.14  Score=26.97  Aligned_cols=42  Identities=26%  Similarity=0.580  Sum_probs=27.2

Q ss_pred             cccccccCCCeeeecCCCCccchHHhHHHHHh---CCCCCcccCCC
Q 045986          101 ICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS---DEFTCPICRSS  143 (148)
Q Consensus       101 ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~  143 (148)
                      ||-.....+..|.--. |+--||..|+.-=-.   ..-.||.|+.+
T Consensus         8 ~C~~~~~~~~MI~Cd~-C~~W~H~~Cvgi~~~~~~~~~~C~~C~~S   52 (52)
T 3o7a_A            8 FCMKPFAGRPMIECNE-CHTWIHLSCAKIRKSNVPEVFVCQKCRDS   52 (52)
T ss_dssp             TTCCBCTTCCEEECTT-TCCEEETTTTTCCGGGCCSSCCCHHHHTC
T ss_pred             EeCCcCCCCCEEEcCC-CCccccccccCCCcccCCCcEECcCCCCc
Confidence            6766655445566555 889999999853221   23459999753

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=83.03  E-value=1.2  Score=25.56  Aligned_cols=39  Identities=15%  Similarity=0.223  Sum_probs=29.8

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      ....|.+|.+.+++.--|.--..=.|-|+-.|-+..+++
T Consensus        14 a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           14 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            346899999999888766622212799999999999876

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=82.91  E-value=0.21  Score=30.35  Aligned_cols=21  Identities=29%  Similarity=0.635  Sum_probs=14.1

Q ss_pred             CCccchHHhHHHHHhCCCCCcccCCC
Q 045986          118 CKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus       118 C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      ||+.|     ..=+.....||.|++.
T Consensus        73 CG~~F-----~~~~~kPsrCP~CkSe   93 (105)
T 2gmg_A           73 CGFVF-----KAEINIPSRCPKCKSE   93 (105)
T ss_dssp             TCCBC-----CCCSSCCSSCSSSCCC
T ss_pred             CcCee-----cccCCCCCCCcCCCCC
Confidence            89999     1112345679999874

>1wee_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=82.74  E-value=0.17  Score=28.48  Aligned_cols=47  Identities=21%  Similarity=0.366  Sum_probs=31.7

Q ss_pred             ccccccccccccCCC-eeeecCCCCccchHHhHHHHH----hCCCCCcccCCCC
Q 045986           96 TSECVICLEEFVSGD-LFRILPFCKHVYHSHCIIRWF----SDEFTCPICRSSI  144 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~~Wl----~~~~~CP~CR~~~  144 (148)
                      ...| ||-..+..++ .|.--. |...||..|+.---    ...-.||.|+..-
T Consensus        16 ~~~C-~C~~~~~~g~~mI~Cd~-C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           16 KVDC-KCGTKDDDGERMLACDG-CGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             EECC-TTCCCSCCSSCEEECSS-SCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             ceEe-eCCCccCCCCcEEECCC-CCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            3568 7988776654 555555 89999999986431    1234599997643

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=82.36  E-value=0.8  Score=24.78  Aligned_cols=42  Identities=21%  Similarity=0.631  Sum_probs=28.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHH-hCCCCCccc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPIC  140 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl-~~~~~CP~C  140 (148)
                      ..|--|...|.+.... .=|.|++.|+.+| |..+ +.-.+||-|
T Consensus        16 ~~C~~C~~~~~~~~~y-~C~~C~~~FC~dC-D~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQHVY-VCAVCQNVFCVDC-DVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSEEE-CCTTTTCCBCHHH-HHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCCccE-ECCccCcCcccch-hHHHHhhccCCcCC
Confidence            3699999998543223 3455999999999 3333 234569988

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=81.33  E-value=1.1  Score=33.35  Aligned_cols=48  Identities=21%  Similarity=0.542  Sum_probs=30.9

Q ss_pred             cccccccccccCCCeeeecCCCCcc--chHHhHHHHHhC--CCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV--YHSHCIIRWFSD--EFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~--FH~~Ci~~Wl~~--~~~CP~CR~~~~~~  147 (148)
                      ..|++=...+.  ..+|-.. |.|.  |-.+=+-..-.+  .-.||+|...+.++
T Consensus       250 L~CPlS~~ri~--~PvRg~~-C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~  301 (371)
T 3i2d_A          250 LQCPISYTRMK--YPSKSIN-CKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALE  301 (371)
T ss_dssp             SBCTTTSSBCS--SEEEETT-CCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGG
T ss_pred             ecCCCcccccc--ccCcCCc-CCCcceECHHHHHHHhhcCCceeCCCCCcccCHH
Confidence            56887777653  4578777 9998  654433333222  33599999887654

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=81.07  E-value=1.2  Score=33.12  Aligned_cols=48  Identities=15%  Similarity=0.452  Sum_probs=31.4

Q ss_pred             cccccccccccCCCeeeecCCCCcc--chHHhHHHHHhCC--CCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHV--YHSHCIIRWFSDE--FTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~--FH~~Ci~~Wl~~~--~~CP~CR~~~~~~  147 (148)
                      ..|++=...+.  ..+|-.. |.|.  |-..=+-....+.  -.||+|...+.++
T Consensus       216 L~CPlS~~ri~--~P~Rg~~-C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~  267 (360)
T 4fo9_A          216 LMCPLGKMRLT--IPCRAVT-CTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYE  267 (360)
T ss_dssp             SBCTTTCSBCS--SEEEETT-CCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGG
T ss_pred             eeCCCccceec--cCCcCCC-CCCCccCCHHHHHHHHhhCCCeECCCCCcccCHH
Confidence            46887776653  4577777 9998  6644433333333  3499999987654

---

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	148
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-16
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-07
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-07
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-07
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	4e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-05
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	5e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.003

>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 = 66.4 bits (162), Expect = 2e-16
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
           EC +CL E   G+  R LP C H +H+ C+  W     TCP+CR ++
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 52.6 bits (126), Expect = 6e-11
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
            C ICLE+  +      LP C H +   CI RW     TCP+C+  +
Sbjct: 7   RCPICLEDPSNYS--MALP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50

>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 = 48.5 bits (115), Expect = 3e-09
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 5/62 (8%)

Query: 84  EKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPICRS 142
           E+Y+ +         C IC E        +I P C H+  + C+  W  S+   CP CR 
Sbjct: 11  EQYELYCEMGSTFQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCRC 66

Query: 143 SI 144
            I
Sbjct: 67  EI 68

>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 = 46.4 bits (110), Expect = 1e-08
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 7/51 (13%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLDA 148
            C  C  E       ++LP C H   S C+         CPIC++   L A
Sbjct: 8   RCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA 51

>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 = 44.0 bits (103), Expect = 1e-07
 Identities = 9/50 (18%), Positives = 15/50 (30%), Gaps = 2/50 (4%)

Query: 97  SECVICLEEFVSGDLFRILPF-CKHVYHSHCIIRWFSD-EFTCPICRSSI 144
             C  C          +++   C H     C+   F      CP C + +
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 43.2 bits (101), Expect = 2e-07
 Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSI 144
           EC +C+E     D+      C +     C  R  +DE   CP CR   
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>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 = 43.6 bits (102), Expect = 3e-07
 Identities = 13/59 (22%), Positives = 17/59 (28%), Gaps = 14/59 (23%)

Query: 98  ECVICLEEFVSGDLFRILPF--------------CKHVYHSHCIIRWFSDEFTCPICRS 142
            C IC    +   +                    C H +H HCI RW      CP+   
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>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 = 44.3 bits (103), Expect = 3e-07
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 19/66 (28%)

Query: 98  ECVICLEEFVS--------------GDLFRILPFCKHVYHSHCIIRWFS-----DEFTCP 138
           +C+IC+E+                   +   L  C H +H  C++  +          CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 139 ICRSSI 144
            C++  
Sbjct: 87  SCKTIY 92

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score = 43.5 bits (102), Expect = 4e-07
 Identities = 10/54 (18%), Positives = 22/54 (40%), Gaps = 9/54 (16%)

Query: 96  TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF--------SDEFTCPICR 141
           +S C +CL E+    +  I   C+ ++ + C+ ++             +CP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 38.7 bits (90), Expect = 2e-05
 Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPICRSSIY 145
           C IC           +   CKH++   CI+R        CP CR   +
Sbjct: 26  CQICEHILA----DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF---SDEFTCPICRSSI 144
           EC ICLE             C H++   C+++          CP+C++ I
Sbjct: 23  ECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>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 = 37.1 bits (85), Expect = 5e-05
 Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 3/47 (6%)

Query: 99  CVICLEEFVSGDL-FRILPFCKHVYHSHCIIRWFS--DEFTCPICRS 142
           C IC EE  +               H  C+  W +      C IC  
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGV 55

>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 = 37.1 bits (85), Expect = 1e-04
 Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 98  ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD 147
            C  C            L  C+H++ S+C+         CP+C +  ++ 
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ 68

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

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]

 Score = 32.4 bits (73), Expect = 0.003
 Identities = 6/49 (12%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 99  CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD 147
           C I  +         + P  + ++    + ++  D    PI    + ++
Sbjct: 3   CAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	148
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.9
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.78
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.78
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.77
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.74
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.71
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.69
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.65
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.61
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.56
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.55
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.41
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.37
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.36
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.28
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.18
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.83
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	96.28
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	95.99
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	95.98
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	95.68
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.56
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	92.88
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	92.35
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	90.35
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	89.89
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	89.27
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	88.3
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	87.47
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	86.99
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	83.58
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	83.32
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	83.19
d2co8a2	36	Nedd9 interacting protein with calponin homology,	82.29
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	80.94
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	80.02

>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=99.90  E-value=5.4e-25  Score=120.74  Aligned_cols=50  Identities=38%  Similarity=0.971  Sum_probs=46.6

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      +.+|+|||++|.+++.++.+|.|||.||.+||++|++++.+||+||++|.
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            46799999999999999888779999999999999999999999999885

>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=99.78  E-value=2.9e-20  Score=106.20  Aligned_cols=46  Identities=37%  Similarity=0.904  Sum_probs=41.3

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ++|+||++.|.+  .++.+| |||.||.+||..|++.+.+||+||+++.
T Consensus         6 d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           6 ERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            679999999864  467789 9999999999999999999999999874

>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=99.78  E-value=3.5e-20  Score=100.25  Aligned_cols=49  Identities=31%  Similarity=0.575  Sum_probs=41.9

Q ss_pred             ccccccccccCCCe-eeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           98 ECVICLEEFVSGDL-FRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        98 ~C~ICl~~~~~~~~-vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      +|+||+++|..++. ++.++ |||.||.+|++.|++. +.+||+||+++..|
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            79999999987764 45567 9999999999999986 55699999998764

>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=99.77  E-value=1.6e-19  Score=108.06  Aligned_cols=49  Identities=27%  Similarity=0.633  Sum_probs=41.9

Q ss_pred             ccccccccccccCCC---------------eeeecCCCCccchHHhHHHHHhCCCCCcccCCCCC
Q 045986           96 TSECVICLEEFVSGD---------------LFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY  145 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~---------------~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  145 (148)
                      ++.|+||++++.+..               .+..++ |||.||.+||++||+.+.+||+||++..
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            357999999886532               367788 9999999999999999999999999764

>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=99.74  E-value=9.2e-19  Score=98.91  Aligned_cols=51  Identities=18%  Similarity=0.399  Sum_probs=41.1

Q ss_pred             ccccccccccccCC-C-eeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCCC
Q 045986           96 TSECVICLEEFVSG-D-LFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYLD  147 (148)
Q Consensus        96 ~~~C~ICl~~~~~~-~-~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  147 (148)
                      +..|+||++++..+ + .+.+++ |||.||.+||..|+.+ +.+||+||+++..+
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            46899999986443 3 445677 9999999999999966 56799999998654

>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=99.71  E-value=3.3e-18  Score=107.11  Aligned_cols=50  Identities=24%  Similarity=0.740  Sum_probs=40.1

Q ss_pred             ccccccccccccC---------------CCeeeecCCCCccchHHhHHHHHhC-----CCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVS---------------GDLFRILPFCKHVYHSHCIIRWFSD-----EFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~---------------~~~vr~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~~~~  146 (148)
                      ++.|+||+++|..               ...+++++ |||.||.+||+.||+.     +.+||+||+.+..
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             cccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhcc
Confidence            3579999999854               23467788 9999999999999975     3479999987643

>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=99.69  E-value=7.3e-18  Score=98.71  Aligned_cols=46  Identities=33%  Similarity=0.763  Sum_probs=39.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ..|+||++.+.+   ++++| |||.||.+||..|+.. +.+||+||..|..
T Consensus        24 ~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~   70 (79)
T d1fbva4          24 QLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG   70 (79)
T ss_dssp             TBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCC
T ss_pred             CCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccC
Confidence            469999998754   57899 9999999999999985 5679999998864

>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=99.65  E-value=1.2e-17  Score=91.53  Aligned_cols=47  Identities=13%  Similarity=0.241  Sum_probs=40.7

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .|+||++.+++.   .+++.|||.||.+||.+||+++.+||+||+++..+
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            599999998654   45555999999999999999999999999998754

>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=99.61  E-value=4.6e-17  Score=88.83  Aligned_cols=44  Identities=32%  Similarity=0.695  Sum_probs=38.3

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      .+|+||++.|.+.   +++| |||.||.+||+.|   +.+||+||+++.++
T Consensus         7 l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           7 LRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             SSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            4899999999765   6789 9999999999876   67899999998764

>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=99.58  E-value=3.4e-16  Score=92.52  Aligned_cols=46  Identities=28%  Similarity=0.634  Sum_probs=39.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ..|+||++.|.+.   .+++ |||.|+..||..|++. +.+||+||.++.+
T Consensus        24 l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          24 ISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             TBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            5799999998653   6788 9999999999999975 5679999998764

>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=99.56  E-value=8.5e-16  Score=94.26  Aligned_cols=47  Identities=28%  Similarity=0.757  Sum_probs=39.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCC---CCCcccCCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE---FTCPICRSSIYLD  147 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~~  147 (148)
                      ..|+||++.|.+.   ..+| |||.||..||..|+..+   .+||+||.++..+
T Consensus        22 l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             cCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            4699999999764   5578 99999999999999764   3799999988654

>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=99.55  E-value=1.9e-15  Score=83.78  Aligned_cols=48  Identities=25%  Similarity=0.451  Sum_probs=37.1

Q ss_pred             CccccccccccccCCCeeeecC----CCCccchHHhHHHHHhC--CCCCcccCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILP----FCKHVYHSHCIIRWFSD--EFTCPICRSSIY  145 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp----~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  145 (148)
                      +...|.||++++.+.   .+.|    +|+|.||..||..|+..  +.+||+||+++.
T Consensus         5 d~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           5 DVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            457899999998654   2333    14599999999999954  568999999864

>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=99.41  E-value=1.4e-14  Score=87.75  Aligned_cols=45  Identities=20%  Similarity=0.642  Sum_probs=37.1

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  146 (148)
                      ..|+||++.|.++  +...+ |||.||.+||..|+.  .+||.||.++..
T Consensus        23 l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             CCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCch
Confidence            4799999999764  44456 999999999999984  459999987754

>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=99.37  E-value=3.3e-13  Score=78.37  Aligned_cols=49  Identities=22%  Similarity=0.419  Sum_probs=41.7

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC-CCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  147 (148)
                      ++..|+||++-|.+.   .+++ |||.|+..||..|++.+ .+||.|+.++..+
T Consensus         7 ~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           7 EYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            457899999999765   5678 99999999999999874 5699999988654

>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=99.36  E-value=1.8e-13  Score=79.90  Aligned_cols=48  Identities=19%  Similarity=0.106  Sum_probs=40.8

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhC-CCCCcccCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD-EFTCPICRSSIYL  146 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  146 (148)
                      ++..|+||++-|.+.   .+++ |||.|+..||..|+.. +.+||+||.++..
T Consensus         6 ~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           6 DYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             STTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             ccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            346899999999765   4688 9999999999999975 5679999998764

>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=99.28  E-value=2.4e-12  Score=77.76  Aligned_cols=50  Identities=20%  Similarity=0.148  Sum_probs=42.8

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccCCCCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYLD  147 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  147 (148)
                      ++..|+||++-|.+.   .++|.|||.|...||..||+.+.+||+||.++..+
T Consensus        21 ~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             HHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            357899999999775   67884456899999999999999999999998764

>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=99.18  E-value=5.4e-12  Score=75.64  Aligned_cols=46  Identities=22%  Similarity=0.627  Sum_probs=38.2

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHHhCC--------CCCcccCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE--------FTCPICRS  142 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~--------~~CP~CR~  142 (148)
                      ..+|+||++++..++.++.++ |+|.||.+|+..|++.+        -+||.|+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            468999999998878888778 99999999999999531        25998654

>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=96.83  E-value=0.00023  Score=36.56  Aligned_cols=44  Identities=20%  Similarity=0.563  Sum_probs=30.8

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRS  142 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  142 (148)
                      .|.||-..-..+..+.= -.|+..||..|+++-+...+    .||.||.
T Consensus         2 ~C~vC~~~~~~~~~i~C-d~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILC-DECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEEC-TTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEc-CCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            48888766444444433 33899999999998765533    3999985

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.28  E-value=0.00039  Score=37.11  Aligned_cols=46  Identities=26%  Similarity=0.623  Sum_probs=31.9

Q ss_pred             CccccccccccccCCCeeeecCCCCccchHHhHHHHHhCCC----CCcccCCCC
Q 045986           95 FTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEF----TCPICRSSI  144 (148)
Q Consensus        95 ~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~~  144 (148)
                      +++.|.+|.+.   ++.|.=-. |.-.||..|++.-+....    .||.|+..-
T Consensus         8 ~~~~C~~C~~~---g~lv~Cd~-C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG---GELLCCDT-CPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSS-SCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC---CeEEEeCC-CCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            34679999754   55444333 789999999987665422    499998653

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.99  E-value=0.0014  Score=35.78  Aligned_cols=43  Identities=26%  Similarity=0.658  Sum_probs=30.4

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCC----CcccCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFT----CPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~----CP~CR~~  143 (148)
                      ..|.+|.+.   ++.+.=-. |...||..|+.+.+...+.    ||.|+..
T Consensus         8 ~~C~~C~~~---~~ll~Cd~-C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~   54 (70)
T d1fp0a1           8 TICRVCQKP---GDLVMCNQ-CEFCFHLDCHLPALQDVPGEEWSCSLCHVL   54 (70)
T ss_dssp             SCCSSSCSS---SCCEECTT-SSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCCCCCc---CEEEECCC-CChhhccccCCCCcCcCCCCCEECcCCcCc
Confidence            467777643   55444333 8999999999988765433    9999764

>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=95.98  E-value=0.00046  Score=37.11  Aligned_cols=51  Identities=18%  Similarity=0.561  Sum_probs=34.4

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhHHHHH---h--CCCCCcccCCCCCC
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF---S--DEFTCPICRSSIYL  146 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl---~--~~~~CP~CR~~~~~  146 (148)
                      ...|.+|...+.+++....=-.|+..||..|+..=.   .  .+-.||.|+..-.|
T Consensus         6 ~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~~p   61 (64)
T d1we9a_           6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSGP   61 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTTCS
T ss_pred             CCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcCCC
Confidence            368999999887766433333499999999986321   1  13359999765433

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=95.68  E-value=0.002  Score=35.95  Aligned_cols=49  Identities=24%  Similarity=0.554  Sum_probs=32.2

Q ss_pred             cccccccccccCCCeeeec-CCCCccchHHhHHH----HHh-----CCCCCcccCCCCCC
Q 045986           97 SECVICLEEFVSGDLFRIL-PFCKHVYHSHCIIR----WFS-----DEFTCPICRSSIYL  146 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~l-p~C~H~FH~~Ci~~----Wl~-----~~~~CP~CR~~~~~  146 (148)
                      ..| ||-.....+..+..- ..|...||..|+.-    .-.     .+-.||.|+..-.|
T Consensus        17 ~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~p   75 (78)
T d1wewa_          17 VRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGP   75 (78)
T ss_dssp             CCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSC
T ss_pred             cEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCCC
Confidence            568 899887766655543 13999999999842    111     12459999765444

>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=95.56  E-value=0.0079  Score=33.40  Aligned_cols=36  Identities=28%  Similarity=0.642  Sum_probs=25.1

Q ss_pred             CCCccccccccccccCCCeeeecCCCCccchHHhHHHH
Q 045986           93 KKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRW  130 (148)
Q Consensus        93 ~~~~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~W  130 (148)
                      ..++..|.|| +.|..++..--- -|+-+||..|+.+-
T Consensus        12 v~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            3445789999 667665433111 17899999999986

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.88  E-value=0.22  Score=27.20  Aligned_cols=47  Identities=15%  Similarity=0.425  Sum_probs=30.0

Q ss_pred             ccccccccccCCC-eeeecCCCCccchHHhHH--HHHhC---CCCCcccCCCCC
Q 045986           98 ECVICLEEFVSGD-LFRILPFCKHVYHSHCII--RWFSD---EFTCPICRSSIY  145 (148)
Q Consensus        98 ~C~ICl~~~~~~~-~vr~lp~C~H~FH~~Ci~--~Wl~~---~~~CP~CR~~~~  145 (148)
                      .+-||...+..++ .|.=-. |+-.||..|+.  ..-..   +-.||.|+....
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~-C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGL-CQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTT-TCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCC-CCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            3349998776554 444333 88999999984  22222   345999987543

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.35  E-value=0.041  Score=29.79  Aligned_cols=44  Identities=23%  Similarity=0.641  Sum_probs=26.2

Q ss_pred             cccccccccccCCCeeeec-CCC-CccchHHhHHHHHhCC----CCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRIL-PFC-KHVYHSHCIIRWFSDE----FTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~l-p~C-~H~FH~~Ci~~Wl~~~----~~CP~CR~~~  144 (148)
                      .-| ||.... +++.+... ..| +..||..|+.  |...    -.||.|+..=
T Consensus        17 ~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~~   66 (71)
T d1wesa_          17 TYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGDS   66 (71)
T ss_dssp             CCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSCC
T ss_pred             CEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCcccc
Confidence            456 998764 33444432 124 4579999985  3332    2399998653

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.35  E-value=0.094  Score=27.05  Aligned_cols=42  Identities=21%  Similarity=0.545  Sum_probs=29.7

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHH-hCCCCCccc
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF-SDEFTCPIC  140 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl-~~~~~CP~C  140 (148)
                      ..|--|...+.+. .+..-|.|++.|+.+| |-.+ +.-.+||-|
T Consensus        16 ~~C~gC~~~l~~~-~~y~C~~C~~~FC~dC-D~fiHe~lh~CpgC   58 (59)
T d1z60a1          16 RFCYGCQGELKDQ-HVYVCAVCQNVFCVDC-DVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTS-EEECCTTTTCCBCHHH-HHTTTTTSCSSSTT
T ss_pred             CCccCCCCcCCCC-ceEECcCCCCcccccc-chhhhhhhcCCCCC
Confidence            5799999888654 3444566999999999 3333 234569988

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.89  E-value=0.087  Score=23.47  Aligned_cols=29  Identities=24%  Similarity=0.543  Sum_probs=24.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhH
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCI  127 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci  127 (148)
                      ..|+-|...+...|.|+.-  =+++||-+|.
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            4699999999999988764  3799999883

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.27  E-value=0.22  Score=26.79  Aligned_cols=46  Identities=22%  Similarity=0.585  Sum_probs=29.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHH------HHH---hCCCCCcccCCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCII------RWF---SDEFTCPICRSSI  144 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~------~Wl---~~~~~CP~CR~~~  144 (148)
                      ..| ||-.....+..|.=-. |.=.||..|+.      ...   ...-.||.|+..-
T Consensus        17 ~~C-iC~~~~~~~~mi~Cd~-C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          17 LYC-ICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCS-TTCCCCCSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CEE-ECCCccCCCeEEEECC-CCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            458 8987766555555444 78889999982      111   2245799997543

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.30  E-value=0.04  Score=25.30  Aligned_cols=26  Identities=31%  Similarity=0.754  Sum_probs=21.0

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHh
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHC  126 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~C  126 (148)
                      +.|++|-....+    |+|.+.|-.||..|
T Consensus         9 EkC~~C~~~I~d----riLrA~Gk~yHP~C   34 (35)
T d2dloa1           9 EKCATCSQPILD----RILRAMGKAYHPGC   34 (35)
T ss_dssp             CBCTTTCCBCCS----CCEEETTEEECTTT
T ss_pred             HHHHHhchHHHH----HHHHHhCCCCCCCC
Confidence            579999888776    46666788899887

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.47  E-value=0.034  Score=31.28  Aligned_cols=46  Identities=26%  Similarity=0.622  Sum_probs=28.9

Q ss_pred             cccccccccccC-CCeeeecCCCCccchHHhHHHHHh-----C---CCCCcccCC
Q 045986           97 SECVICLEEFVS-GDLFRILPFCKHVYHSHCIIRWFS-----D---EFTCPICRS  142 (148)
Q Consensus        97 ~~C~ICl~~~~~-~~~vr~lp~C~H~FH~~Ci~~Wl~-----~---~~~CP~CR~  142 (148)
                      ..|.||...... +..+..=-.|+..||..|+.+.+.     .   .-.||.|..
T Consensus        17 ~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~   71 (88)
T d1weva_          17 LACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTR   71 (88)
T ss_dssp             CSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHH
T ss_pred             CCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCc
Confidence            569999865432 223333333889999999875432     1   224999964

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {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 At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.99  E-value=0.057  Score=29.08  Aligned_cols=46  Identities=22%  Similarity=0.330  Sum_probs=29.5

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHh----CCCCCcccCCC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFS----DEFTCPICRSS  143 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~  143 (148)
                      ..| ||.....+++....=-.|.-.||..|+..=..    ..-.||.|+..
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            457 78877666654333333899999999854221    13349999654

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.58  E-value=0.25  Score=26.34  Aligned_cols=37  Identities=16%  Similarity=0.281  Sum_probs=28.9

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHhHHHHHhC
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD  133 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~  133 (148)
                      ..|.+|-+.+++.--|.--..=+|-|+-.|-+..+++
T Consensus         9 l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           9 LCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             eeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            5799999999887766522112799999999999876

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.32  E-value=0.36  Score=22.04  Aligned_cols=27  Identities=22%  Similarity=0.552  Sum_probs=18.8

Q ss_pred             cccccccccccCCCeeeecCCCCccchHHh
Q 045986           97 SECVICLEEFVSGDLFRILPFCKHVYHSHC  126 (148)
Q Consensus        97 ~~C~ICl~~~~~~~~vr~lp~C~H~FH~~C  126 (148)
                      +.|..|-...=.-|.+.  - =|+.||+.|
T Consensus         8 ~kC~~C~K~VY~~E~~~--a-~g~~~Hk~C   34 (35)
T d2d8ya1           8 ETCVECQKTVYPMERLL--A-NQQVFHISC   34 (35)
T ss_dssp             CBCTTTCCBCCTTSEEE--C-SSSEEETTT
T ss_pred             cccccCCCEEeeeeeEe--c-CCeehhhcc
Confidence            67999976654444333  1 489999998

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.19  E-value=0.053  Score=27.29  Aligned_cols=44  Identities=18%  Similarity=0.359  Sum_probs=26.9

Q ss_pred             ccccccccccCCCeeeecCCCCccchHHhHHHHHhCCCCCcccC
Q 045986           98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR  141 (148)
Q Consensus        98 ~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  141 (148)
                      .|.+|-..|..-..-..=..||.+|+.+|....-.....|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            48888888864332222333899999999765544445577774

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.29  E-value=0.48  Score=21.75  Aligned_cols=29  Identities=21%  Similarity=0.501  Sum_probs=19.0

Q ss_pred             ccccccccccccCCCeeeecCCCCccchHHhH
Q 045986           96 TSECVICLEEFVSGDLFRILPFCKHVYHSHCI  127 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C~H~FH~~Ci  127 (148)
                      .+.|.+|-...=.-|.+   .+=|+.||+.|.
T Consensus         8 ~~~C~~C~K~VY~~Erl---~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERL---CVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBC---CBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEE---EecCcEeccccC
Confidence            46899997654333332   215899999983

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=80.94  E-value=0.53  Score=21.60  Aligned_cols=25  Identities=32%  Similarity=0.754  Sum_probs=14.5

Q ss_pred             eeecCCCCccchHHhHHHHHhCCCCCcccCCC
Q 045986          112 FRILPFCKHVYHSHCIIRWFSDEFTCPICRSS  143 (148)
Q Consensus       112 vr~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  143 (148)
                      +-+-+.|||+.-.+       -...||+|.++
T Consensus         5 ~~vC~vCGyi~~g~-------~Pe~CPvCg~~   29 (36)
T d1yuza2           5 FHLCPICGYIHKGE-------DFEKCPICFRP   29 (36)
T ss_dssp             EEECSSSCCEEESS-------CCSBCTTTCCB
T ss_pred             EEECCCCCCEeeCC-------CCCcCCCCCCc
Confidence            33444488875421       24569999764

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=80.02  E-value=0.31  Score=21.62  Aligned_cols=27  Identities=19%  Similarity=0.648  Sum_probs=20.5

Q ss_pred             ccccccccccccCCCeeeecCCC-CccchHHh
Q 045986           96 TSECVICLEEFVSGDLFRILPFC-KHVYHSHC  126 (148)
Q Consensus        96 ~~~C~ICl~~~~~~~~vr~lp~C-~H~FH~~C  126 (148)
                      ...|..|....--.++|.    | |-.||+.|
T Consensus         7 g~kcg~c~ktvy~aeevq----c~g~sfhk~c   34 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEVQ----CEGSSFHKSC   34 (35)
T ss_dssp             CEECTTTCCEECSSCCEE----ETTEEECTTT
T ss_pred             CceeccccceEeeeeeee----ecCccccccc
Confidence            357999987766666776    7 67899988