Citrus Sinensis ID: 030902

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------17
Protein Sequence
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHcccEEEcccccccccccccccEEccccccccEEccccccccccccccHHHHHHccccccccccccccccccHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHccEEEEcHcccccccccccEEEEEcccccccHHHccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mgfpvgytevflpKFFVHTLSFLGFIRNIIICLFRYlglsdfletdviwpdnsptripenapvSARLIREILpvikfqdlemvngdppencAVCLyefeggeeirwlRNCKHIfhracldpwmdhdqktcplcrtpfvpdeMQEEFNQRLWAASGvddlfseyssvpel
Flexible Loop (DISEMBL)
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL
Low Complexity Region (SEG)
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL
Disordered region (IsUnstruct)
***PVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLF*********
Disordered Region (DISOPRED)
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDF****************************ILPVIKFQDLE****DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV*******************************
Disordered Region (DISEMBL)
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFS********
Disordered Region (DISPRO)
*GFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSD*********************VSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE****************************
Transmembrane Helix (TMHMM)
ooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL
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	169	2.2.26 [Sep-21-2011]
Q9SUS5	157	E3 ubiquitin-protein liga	no	no	0.857	0.923	0.374	2e-22
Q9SUS4	159	RING-H2 zinc finger prote	no	no	0.893	0.949	0.353	1e-21
Q9P7E1	583	Uncharacterized RING fing	yes	no	0.372	0.108	0.470	2e-12
O54965	381	E3 ubiquitin-protein liga	yes	no	0.378	0.167	0.428	6e-11
Q90972	381	E3 ubiquitin-protein liga	yes	no	0.378	0.167	0.428	6e-11
Q66HG0	380	E3 ubiquitin-protein liga	yes	no	0.378	0.168	0.428	7e-11
Q0VD51	380	E3 ubiquitin-protein liga	yes	no	0.378	0.168	0.428	7e-11
Q5RCV8	381	E3 ubiquitin-protein liga	yes	no	0.378	0.167	0.428	8e-11
O43567	381	E3 ubiquitin-protein liga	yes	no	0.378	0.167	0.428	8e-11
Q9ZU51	147	Probable E3 ubiquitin-pro	no	no	0.337	0.387	0.431	9e-11

>sp|Q9SUS5|RHA1B_ARATH E3 ubiquitin-protein ligase RHA1B OS=Arabidopsis thaliana GN=RHA1B PE=2 SV=1

 Score =  105 bits (261), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 89/155 (57%), Gaps = 10/155 (6%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MG P  + E+ +P + + TL  +GF R+++  L  Y+GL  FL+ +     + PTR+  +
Sbjct: 1   MGLPTDFKELQIPGYVLKTLYVIGFFRDMVDALCPYIGLPSFLDHNET-SRSDPTRLALS 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
              SA L  E++PV++F DL     DP + C VCL +F   ++IR L  C H+FH  CLD
Sbjct: 60  T--SATLANELIPVVRFSDLLT---DPEDCCTVCLSDFVSDDKIRQLPKCGHVFHHRCLD 114

Query: 121 PWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAAS 154
            W+ D ++ TCP+CR  F+P+E    F+   W  S
Sbjct: 115 RWIVDCNKITCPICRNRFLPEEKSTPFD---WGTS 146

Possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q9SUS4|RHA1A_ARATH RING-H2 zinc finger protein RHA1a OS=Arabidopsis thaliana GN=RHA1A PE=2 SV=1

 Score =  102 bits (254), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 58/164 (35%), Positives = 92/164 (56%), Gaps = 13/164 (7%)

Query: 1   MGFPVGY-TEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPE 59
           MG P  + TE+ +P + +  L  +GF R+I+  L  Y+GL  FL+ +     ++P     
Sbjct: 1   MGLPEDFITELQIPSYILKILYVIGFFRDIVDALCPYIGLPRFLDHNET---SAPDLTRH 57

Query: 60  NAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACL 119
               SA L  E++PV++F DL     DP + C VCL +FE  +++R L  C H+FH  CL
Sbjct: 58  ALSTSASLANELIPVVRFSDLPT---DPEDCCTVCLSDFESDDKVRQLPKCGHVFHHYCL 114

Query: 120 DPWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSE 162
           D W+ D+++  CP+CR  F+P   +E++ Q  W +    D FS+
Sbjct: 115 DRWIVDYNKMKCPVCRHRFLP---KEKYTQSDWGSGS--DWFSD 153

Arabidopsis thaliana (taxid: 3702)

>sp|Q9P7E1|YOF7_SCHPO Uncharacterized RING finger protein P4H10.07 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBP4H10.07 PE=1 SV=1

 Score = 72.0 bits (175), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/68 (47%), Positives = 38/68 (55%), Gaps = 5/68 (7%)

Query: 73  PVIKFQDLEMVNGDPP-----ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ 127
           PV   +DLE   G  P     E C VCL  FE  +E R L+ C H FHR C+D W+   Q
Sbjct: 502 PVASQKDLEKAGGVFPFSGTDERCLVCLSNFELNDECRRLKQCNHFFHRECIDQWLTSSQ 561

Query: 128 KTCPLCRT 135
            +CPLCRT
Sbjct: 562 NSCPLCRT 569

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

>sp|O54965|RNF13_MOUSE E3 ubiquitin-protein ligase RNF13 OS=Mus musculus GN=Rnf13 PE=1 SV=2

 Score = 66.6 bits (161), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLEEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q90972|RNF13_CHICK E3 ubiquitin-protein ligase RNF13 OS=Gallus gallus GN=RNF13 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLDEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase. May play a role in controlling cell proliferation, including that of muscle cells.

Gallus gallus (taxid: 9031)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q66HG0|RNF13_RAT E3 ubiquitin-protein ligase RNF13 OS=Rattus norvegicus GN=Rnf13 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLEEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q0VD51|RNF13_BOVIN E3 ubiquitin-protein ligase RNF13 OS=Bos taurus GN=RNF13 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLDEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5RCV8|RNF13_PONAB E3 ubiquitin-protein ligase RNF13 OS=Pongo abelii GN=RNF13 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLDEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O43567|RNF13_HUMAN E3 ubiquitin-protein ligase RNF13 OS=Homo sapiens GN=RNF13 PE=1 SV=1

 Score = 66.6 bits (161), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 44/70 (62%), Gaps = 6/70 (8%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct: 226 LPVHKFK-----KGDEYDVCAICLDEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 279

Query: 132 LCRTPFVPDE 141
           +C+   VP +
Sbjct: 280 VCKQKVVPSQ 289

E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9ZU51|RHA2B_ARATH Probable E3 ubiquitin-protein ligase RHA2B OS=Arabidopsis thaliana GN=RHA2B PE=1 SV=2

 Score = 66.2 bits (160), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ 143
           +   +C VCL + + GEE+R L +C+H+FH+ CL+ W+ H    CPLCR+P +P   Q
Sbjct: 69  NAASDCIVCLSKLKTGEEVRKL-DCRHVFHKQCLEGWLQHLNFNCPLCRSPLLPHHHQ 125

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	169
338190109	171	ubiquitin-protein ligase E3 [Jatropha cu	0.994	0.982	0.779	1e-68
15233117	170	brassinosteroid-responsive RING-H2 [Arab	0.940	0.935	0.777	1e-66
225454353	167	PREDICTED: E3 ubiquitin-protein ligase R	0.988	1.0	0.733	2e-66
255541660	171	zinc finger protein, putative [Ricinus c	0.994	0.982	0.744	2e-66
224067916	165	predicted protein [Populus trichocarpa]	0.952	0.975	0.740	3e-63
224130340	165	predicted protein [Populus trichocarpa]	0.952	0.975	0.715	8e-61
255537543	164	zinc finger protein, putative [Ricinus c	0.970	1.0	0.650	9e-59
388517185	167	unknown [Lotus japonicus]	0.934	0.946	0.656	1e-54
388501000	163	unknown [Medicago truncatula]	0.923	0.957	0.645	3e-54
217075440	163	unknown [Medicago truncatula]	0.923	0.957	0.639	1e-53

>gi|338190109|gb|AEI84328.1| ubiquitin-protein ligase E3 [Jatropha curcas]

 Score =  263 bits (673), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 134/172 (77%), Positives = 145/172 (84%), Gaps = 4/172 (2%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTEVFLPK FVHTLS LGFIR++I+CLF YLGLSDFLETD IWPDN PTRI  +
Sbjct: 1   MGFPVGYTEVFLPKLFVHTLSLLGFIRSLILCLFNYLGLSDFLETDNIWPDN-PTRIHSH 59

Query: 61  APVSARLIREILPVIKFQDL--EMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRAC 118
            PVSA LIREILPVIKF+DL      GD PE+CAVCLYEF+G +EIRWL+NCKHIFHRAC
Sbjct: 60  PPVSATLIREILPVIKFEDLVPGAGEGDLPESCAVCLYEFDGEDEIRWLKNCKHIFHRAC 119

Query: 119 LDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDL-FSEYSSVPEL 169
           LD WMDHD+ TCPLCRT FVPDEMQEEFNQRL AAS   D  +SEYSSVP L
Sbjct: 120 LDRWMDHDRNTCPLCRTSFVPDEMQEEFNQRLLAASDNSDFYYSEYSSVPVL 171

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15233117|ref|NP_191705.1| brassinosteroid-responsive RING-H2 [Arabidopsis thaliana] gi|297820998|ref|XP_002878382.1| brassinosteroid-responsive ring-H2 [Arabidopsis lyrata subsp. lyrata] gi|4689366|gb|AAD27870.1|AF134155_1 BRH1 RING finger protein [Arabidopsis thaliana] gi|6850837|emb|CAB71076.1| RING finger protein [Arabidopsis thaliana] gi|17644157|gb|AAL38776.1| putative RING finger protein [Arabidopsis thaliana] gi|21436189|gb|AAM51382.1| putative RING finger protein [Arabidopsis thaliana] gi|21554590|gb|AAM63625.1| RING finger protein [Arabidopsis thaliana] gi|297324220|gb|EFH54641.1| brassinosteroid-responsive ring-H2 [Arabidopsis lyrata subsp. lyrata] gi|332646687|gb|AEE80208.1| brassinosteroid-responsive RING-H2 [Arabidopsis thaliana]

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 126/162 (77%), Positives = 136/162 (83%), Gaps = 3/162 (1%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNS--PTRIP 58
           MGFPVGYTEVFLPK FV TLS LGFIR I+  +FR+LGLSDFLE D  WPD +  PTRIP
Sbjct: 1   MGFPVGYTEVFLPKLFVQTLSILGFIRTIVFSIFRFLGLSDFLEMDQTWPDYTSYPTRIP 60

Query: 59  EN-APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRA 117
           E  +P SA LIREILPVIKF++L     D PENCAVCLYEFEG +EIRWLRNC+HIFHR+
Sbjct: 61  ETRSPFSALLIREILPVIKFEELTNSGEDLPENCAVCLYEFEGEQEIRWLRNCRHIFHRS 120

Query: 118 CLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDL 159
           CLD WMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGV D 
Sbjct: 121 CLDRWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVHDF 162

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454353|ref|XP_002278353.1| PREDICTED: E3 ubiquitin-protein ligase RHA1B [Vitis vinifera]

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/169 (73%), Positives = 140/169 (82%), Gaps = 2/169 (1%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTEVFLPK F+HTLSFLGFIR +I  LF +LGLSDFLETDV W +    ++PE 
Sbjct: 1   MGFPVGYTEVFLPKLFLHTLSFLGFIRKLIFSLFHFLGLSDFLETDVSWSETQ-AQVPEY 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
            PVSA LIREILPV+KF +  +  GD PE+CAVCLY+FE GEEIR L NCKHIFHR+CLD
Sbjct: 60  PPVSAVLIREILPVMKFGE-AVCGGDAPESCAVCLYDFEVGEEIRRLTNCKHIFHRSCLD 118

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL 169
            WMDHDQKTCPLCRTPFVPDEMQ+EFNQRLWAASG+ D +SEY +V  L
Sbjct: 119 RWMDHDQKTCPLCRTPFVPDEMQDEFNQRLWAASGITDFYSEYGTVSGL 167

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541660|ref|XP_002511894.1| zinc finger protein, putative [Ricinus communis] gi|223549074|gb|EEF50563.1| zinc finger protein, putative [Ricinus communis]

 Score =  256 bits (654), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 128/172 (74%), Positives = 142/172 (82%), Gaps = 4/172 (2%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTEVFLPK FVHTLSFLGFIRNII+C F +LGLSDFLETD IWP+N P R   +
Sbjct: 1   MGFPVGYTEVFLPKLFVHTLSFLGFIRNIILCFFNFLGLSDFLETDNIWPEN-PIRNYTH 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
            PVSA LIREILPVIK++DL   + + PE+CAVCLYEFE   EIRWL+NCKHIFHRACLD
Sbjct: 60  PPVSATLIREILPVIKYEDLVAGDAELPESCAVCLYEFEREAEIRWLKNCKHIFHRACLD 119

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDD---LFSEYSSVPEL 169
            WMDHD+ TCPLCRT FVPDEMQEEFNQRL AA+  +D    +SEYSSVP L
Sbjct: 120 RWMDHDRNTCPLCRTSFVPDEMQEEFNQRLLAAAADNDGDFFYSEYSSVPVL 171

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067916|ref|XP_002302597.1| predicted protein [Populus trichocarpa] gi|222844323|gb|EEE81870.1| predicted protein [Populus trichocarpa]

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 123/166 (74%), Positives = 137/166 (82%), Gaps = 5/166 (3%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGY+EVFLPK FVH LSFLGFIRN+I+CLF YLGLS FLETD IWPDN P R+   
Sbjct: 1   MGFPVGYSEVFLPKLFVHILSFLGFIRNLILCLFNYLGLSGFLETDNIWPDN-PIRMSCY 59

Query: 61  APVSARLIREILPVIKFQDLEMVNG---DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRA 117
            P+SA L+REILPVIKF+DL   +G   D PE+CAVCLYEFEG +EIRWL+NCKHIFHR 
Sbjct: 60  PPLSAALLREILPVIKFEDLVTGDGGCCDLPESCAVCLYEFEGEDEIRWLKNCKHIFHRT 119

Query: 118 CLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASG-VDDLFSE 162
           CLD WMDHD+KTCPLCR  FVPDEMQEEFNQRLWAA+  V D + E
Sbjct: 120 CLDRWMDHDRKTCPLCRNSFVPDEMQEEFNQRLWAANNDVSDFYCE 165

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130340|ref|XP_002320813.1| predicted protein [Populus trichocarpa] gi|222861586|gb|EEE99128.1| predicted protein [Populus trichocarpa]

 Score =  238 bits (606), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 118/165 (71%), Positives = 132/165 (80%), Gaps = 4/165 (2%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGY+EV LPK FVH LS LGFIR +++CLF Y+GLSDFLETD IWPD  PTR    
Sbjct: 1   MGFPVGYSEVLLPKLFVHALSLLGFIRGLVLCLFTYVGLSDFLETDNIWPD-YPTRTSFY 59

Query: 61  APVSARLIREILPVIKFQDLEMVNG---DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRA 117
             +SA LIREILPVIKF+DL   +G   D PE+CAVCLYEFEG +EIRWL+NCKHIFHRA
Sbjct: 60  PSLSAALIREILPVIKFEDLLGGDGGCCDLPESCAVCLYEFEGEDEIRWLKNCKHIFHRA 119

Query: 118 CLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSE 162
           CLD WMDHD+ TCPLCRT FVPDEMQ EFNQRLWAA+  D  F +
Sbjct: 120 CLDRWMDHDRNTCPLCRTSFVPDEMQGEFNQRLWAANSDDSDFYD 164

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537543|ref|XP_002509838.1| zinc finger protein, putative [Ricinus communis] gi|223549737|gb|EEF51225.1| zinc finger protein, putative [Ricinus communis]

 Score =  231 bits (588), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 110/169 (65%), Positives = 133/169 (78%), Gaps = 5/169 (2%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTE+ LPK  +HTLS LGFIR +I  LFRYLGL DFLE D+ WP+ +P+R+PE 
Sbjct: 1   MGFPVGYTELLLPKLLIHTLSILGFIRKLINTLFRYLGLPDFLEPDISWPE-TPSRVPEF 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
              SA LIREILPV+KF DL     DPP++CAVCLYEFE  +EIR L NC+HIFH+ACLD
Sbjct: 60  YSASAVLIREILPVVKFSDLV----DPPDSCAVCLYEFEDHDEIRRLTNCRHIFHKACLD 115

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYSSVPEL 169
            W+ +DQKTCPLCRTP +PD+MQE FN+RLWAASG+ D + +YS +  L
Sbjct: 116 RWVGYDQKTCPLCRTPVIPDDMQEAFNERLWAASGIPDFYGDYSQIGAL 164

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388517185|gb|AFK46654.1| unknown [Lotus japonicus]

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 107/163 (65%), Positives = 124/163 (76%), Gaps = 5/163 (3%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTE   PK  +  LS LGFIR ++  LFRYLGL DFLE D++WPDNS TRIPE 
Sbjct: 1   MGFPVGYTEFLFPKLVLQILSLLGFIRKLVCTLFRYLGLPDFLEPDIVWPDNS-TRIPEF 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
             VSA LIREILPV+KF++L     DPPE+C VCL EFE  +EIR L NC+HIFHRACLD
Sbjct: 60  ESVSALLIREILPVVKFREL----VDPPESCVVCLSEFEESDEIRRLANCRHIFHRACLD 115

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEY 163
            W+ +DQ TCPLCRTP +PDEMQ  FN+RLWAASG+ +   EY
Sbjct: 116 RWVGYDQSTCPLCRTPLIPDEMQGAFNERLWAASGIPEFPPEY 158

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501000|gb|AFK38566.1| unknown [Medicago truncatula]

 Score =  216 bits (549), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 104/161 (64%), Positives = 124/161 (77%), Gaps = 5/161 (3%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTE+  PK  +H LS   FIR +I  +FRY+GL DF+E D+IWP+NS TRIPE 
Sbjct: 1   MGFPVGYTELLFPKLVLHLLSIFTFIRKLINTIFRYMGLPDFIEPDIIWPENS-TRIPEF 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
             VSA LIREILPV+KF +L     DPPE+CAVCL EFE  +EIR L NC+HIFHR CLD
Sbjct: 60  ESVSALLIREILPVVKFMEL----VDPPESCAVCLTEFEENDEIRRLANCRHIFHRGCLD 115

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFS 161
            WM +DQ+TCPLCRTPF+PDE+Q  FN+RLWAASG+ +  S
Sbjct: 116 RWMGYDQRTCPLCRTPFIPDELQSAFNERLWAASGIPEFHS 156

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075440|gb|ACJ86080.1| unknown [Medicago truncatula]

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 103/161 (63%), Positives = 124/161 (77%), Gaps = 5/161 (3%)

Query: 1   MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
           MGFPVGYTE+  PK  +H LS   FIR +I  +FRY+GL DF+E D+IWP+NS TRIPE 
Sbjct: 1   MGFPVGYTELLFPKLVLHLLSIFTFIRKLINTIFRYMGLPDFIEPDIIWPENS-TRIPEF 59

Query: 61  APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
             VSA LIREILPV+KF +L     DPPE+CAVCL EFE  +EIR L NC++IFHR CLD
Sbjct: 60  ESVSALLIREILPVVKFMEL----VDPPESCAVCLTEFEENDEIRRLANCRYIFHRGCLD 115

Query: 121 PWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFS 161
            WM +DQ+TCPLCRTPF+PDE+Q  FN+RLWAASG+ +  S
Sbjct: 116 RWMGYDQRTCPLCRTPFIPDELQSAFNERLWAASGIPEFHS 156

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	169
TAIR|locus:2082757	170	BRH1 "brassinosteroid-responsi	0.934	0.929	0.782	8.2e-67
TAIR|locus:2195498	166	AT1G63840 [Arabidopsis thalian	0.940	0.957	0.529	5.7e-43
TAIR|locus:2177931	176	AT5G41400 [Arabidopsis thalian	0.911	0.875	0.532	4.2e-40
TAIR|locus:2128293	157	RHA1B "RING-H2 finger A1B" [Ar	0.857	0.923	0.374	2e-24
TAIR|locus:2128303	159	RHA1A "RING-H2 finger A1A" [Ar	0.893	0.949	0.365	8.7e-24
TAIR|locus:505006414	126	AT4G00305 [Arabidopsis thalian	0.408	0.547	0.541	1.7e-20
TAIR|locus:2102311	167	AT3G43430 [Arabidopsis thalian	0.656	0.664	0.363	7.7e-16
UNIPROTKB|F1NA38	380	RNF13 "E3 ubiquitin-protein li	0.378	0.168	0.428	9.6e-14
TAIR|locus:505006623	176	AT5G20885 "AT5G20885" [Arabido	0.449	0.431	0.406	1e-13
TAIR|locus:2059793	162	XERICO [Arabidopsis thaliana (	0.485	0.506	0.373	1e-13

TAIR|locus:2082757 BRH1 "brassinosteroid-responsive RING-H2" [Arabidopsis thaliana (taxid:3702)]

 Score = 679 (244.1 bits), Expect = 8.2e-67, P = 8.2e-67
 Identities = 126/161 (78%), Positives = 136/161 (84%)

Query:     1 MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNS--PTRIP 58
             MGFPVGYTEVFLPK FV TLS LGFIR I+  +FR+LGLSDFLE D  WPD +  PTRIP
Sbjct:     1 MGFPVGYTEVFLPKLFVQTLSILGFIRTIVFSIFRFLGLSDFLEMDQTWPDYTSYPTRIP 60

Query:    59 EN-APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRA 117
             E  +P SA LIREILPVIKF++L     D PENCAVCLYEFEG +EIRWLRNC+HIFHR+
Sbjct:    61 ETRSPFSALLIREILPVIKFEELTNSGEDLPENCAVCLYEFEGEQEIRWLRNCRHIFHRS 120

Query:   118 CLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDD 158
             CLD WMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGV D
Sbjct:   121 CLDRWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVHD 161

GO:0005634 "nucleus" evidence=ISM

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

GO:0009741 "response to brassinosteroid stimulus" evidence=IEP

GO:0010200 "response to chitin" evidence=IEP

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0070838 "divalent metal ion transport" evidence=RCA

TAIR|locus:2195498 AT1G63840 [Arabidopsis thaliana (taxid:3702)]

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 91/172 (52%), Positives = 115/172 (66%)

Query:     1 MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVI---WPDNSPTRI 57
             MGFPVGY+E+ LPK F + LSFLG IR +I  +F+ +GL DFLE + +   WPD  PT  
Sbjct:     1 MGFPVGYSELLLPKIFFYLLSFLGLIRKLISTMFKIIGLPDFLEPEPVSTSWPDPPPTLT 60

Query:    58 -PENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHR 116
              P++A +   L  E+LPV++F D   +N    E CAVCLY+FE  +EIR L NC+HIFHR
Sbjct:    61 KPDSAAI---LAGEMLPVVRFSD---INRPESECCAVCLYDFENDDEIRRLTNCRHIFHR 114

Query:   117 ACLDPWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGV--DDLFSEYSS 165
              CLD WM  ++Q TCPLCRT F+PD +Q EFNQRLW+ S      L  E SS
Sbjct:   115 GCLDRWMMGYNQMTCPLCRTQFIPDHLQLEFNQRLWSQSSAVSSQLLDESSS 166

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

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

GO:0007165 "signal transduction" evidence=RCA

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

GO:0009611 "response to wounding" evidence=RCA

GO:0009723 "response to ethylene stimulus" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=RCA

GO:0009753 "response to jasmonic acid stimulus" evidence=RCA

GO:0042538 "hyperosmotic salinity response" evidence=RCA

TAIR|locus:2177931 AT5G41400 [Arabidopsis thaliana (taxid:3702)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 90/169 (53%), Positives = 113/169 (66%)

Query:     1 MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVI-----W--PDNS 53
             MG+PVGYTE+ LP+ F+H LS LG IR +I   FR LGL DFLE+D +     W  P   
Sbjct:     1 MGYPVGYTELLLPRIFLHLLSLLGLIRTLIDTGFRILGLPDFLESDPVSSSSSWLEPPYM 60

Query:    54 PTRI---PENA---PVSARLIREILPVIKFQDLEMVN-GDPPENCAVCLYEFEGGEEIRW 106
              T      E++   PV+ARL  EILPVI+F +L     G   + CAVCL+EFE  +EIR 
Sbjct:    61 STAAHHHQESSFFFPVAARLAGEILPVIRFSELTRPGFGSGSDCCAVCLHEFENDDEIRR 120

Query:   107 LRNCKHIFHRACLDPWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAAS 154
             L NC+HIFHR+CLD WM  ++Q TCPLCRTPF+ DE+Q  FNQR+W+ S
Sbjct:   121 LTNCQHIFHRSCLDRWMMGYNQMTCPLCRTPFISDELQVAFNQRVWSES 169

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2128293 RHA1B "RING-H2 finger A1B" [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 58/155 (37%), Positives = 89/155 (57%)

Query:     1 MGFPVGYTEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPEN 60
             MG P  + E+ +P + + TL  +GF R+++  L  Y+GL  FL+ +     + PTR+  +
Sbjct:     1 MGLPTDFKELQIPGYVLKTLYVIGFFRDMVDALCPYIGLPSFLDHNET-SRSDPTRLALS 59

Query:    61 APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD 120
                SA L  E++PV++F DL     DP + C VCL +F   ++IR L  C H+FH  CLD
Sbjct:    60 T--SATLANELIPVVRFSDLLT---DPEDCCTVCLSDFVSDDKIRQLPKCGHVFHHRCLD 114

Query:   121 PWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAAS 154
              W+ D ++ TCP+CR  F+P+E    F+   W  S
Sbjct:   115 RWIVDCNKITCPICRNRFLPEEKSTPFD---WGTS 146

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:0046686 "response to cadmium ion" evidence=IEP

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2128303 RHA1A "RING-H2 finger A1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 60/164 (36%), Positives = 93/164 (56%)

Query:     1 MGFPVGY-TEVFLPKFFVHTLSFLGFIRNIIICLFRYLGLSDFLETDVIWPDNSPTRIPE 59
             MG P  + TE+ +P + +  L  +GF R+I+  L  Y+GL  FL+ +     ++P     
Sbjct:     1 MGLPEDFITELQIPSYILKILYVIGFFRDIVDALCPYIGLPRFLDHN---ETSAPDLTRH 57

Query:    60 NAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACL 119
                 SA L  E++PV++F DL     DP + C VCL +FE  +++R L  C H+FH  CL
Sbjct:    58 ALSTSASLANELIPVVRFSDLPT---DPEDCCTVCLSDFESDDKVRQLPKCGHVFHHYCL 114

Query:   120 DPWM-DHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSE 162
             D W+ D+++  CP+CR  F+P   +E++ Q  W  SG  D FS+
Sbjct:   115 DRWIVDYNKMKCPVCRHRFLP---KEKYTQSDWG-SG-SDWFSD 153

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009723 "response to ethylene stimulus" evidence=RCA

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

 Score = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 39/72 (54%), Positives = 54/72 (75%)

Query:    70 EILPVIKFQDLEM-VNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQK 128
             ++LP  KF+D+   VN  PPE+C +C  EF+GG+E+R LRNC H++H+ C+D W+  D+ 
Sbjct:    51 DMLPATKFEDISSRVN--PPESCRICQDEFDGGDEVRCLRNCVHVYHKTCIDRWIQDDKM 108

Query:   129 TCPLCRTPFVPD 140
             TCPLCRTP VPD
Sbjct:   109 TCPLCRTPIVPD 120

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2102311 AT3G43430 [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 44/121 (36%), Positives = 66/121 (54%)

Query:    52 NSPTRIPENAPVSARLIREILPVIKFQD-LEMVNGDPPENCAVCLYEFEGGEEIRWLRNC 110
             +S ++   +  +S++ I+E L V  F+D +E       + CAVCL + E  +EIR LRNC
Sbjct:    43 SSSSQSSSSPSISSQTIKESLAVSAFRDAVERSPAAINDMCAVCLGDLEDEDEIRELRNC 102

Query:   111 KHIFHRACLDPWMDHD--------QKTCPLCRTPFVPDEMQ-EEFNQRLWAASGVDDLFS 161
              H+FHR C+D W+D++         +TCPLCRTP +P         Q  WA   +  LF 
Sbjct:   103 THVFHRDCIDRWLDYECCGGDDDNHRTCPLCRTPLLPSFTDYSTVTQTSWAVERLLYLFG 162

Query:   162 E 162
             +
Sbjct:   163 D 163

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

UNIPROTKB|F1NA38 RNF13 "E3 ubiquitin-protein ligase RNF13" [Gallus gallus (taxid:9031)]

 Score = 163 (62.4 bits), Expect = 9.6e-14, Sum P(2) = 9.6e-14
 Identities = 30/70 (42%), Positives = 44/70 (62%)

Query:    72 LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
             LPV KF+      GD  + CA+CL E+E G+++R L  C H +H  C+DPW+   +KTCP
Sbjct:   225 LPVHKFK-----KGDEYDVCAICLDEYEDGDKLRILP-CSHAYHCKCVDPWLTKTKKTCP 278

Query:   132 LCRTPFVPDE 141
             +C+   VP +
Sbjct:   279 VCKQKVVPSQ 288

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005765 "lysosomal membrane" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=IEA

TAIR|locus:505006623 AT5G20885 "AT5G20885" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 37/91 (40%), Positives = 53/91 (58%)

Query:    63 VSARLIREILPVIKFQDL-EMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDP 121
             +S++ I+E L V  F+D  E       + CAVCL + E G+E+R LRNC H+FHR C+D 
Sbjct:    53 ISSQAIKESLSVTTFRDAAERSPAMINDTCAVCLGDLEDGDEVRELRNCSHMFHRECIDR 112

Query:   122 WMDHD--------------QKTCPLCRTPFV 138
             W+D++               +TCPLCRTP +
Sbjct:   113 WLDYECCGGDENNEGEEDNHRTCPLCRTPLL 143

GO:0008150 "biological_process" evidence=ND

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2059793 XERICO [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 31/83 (37%), Positives = 46/83 (55%)

Query:    69 REILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQK 128
             R   P ++F+ L          C+VCL +F+G  EI  L+ C H+FH+ CL+ W+D+   
Sbjct:    81 RNRTPTLRFESLCRCKKQADNECSVCLSKFQGDSEINKLK-CGHLFHKTCLEKWIDYWNI 139

Query:   129 TCPLCRTPFVPDEMQEEFNQRLW 151
             TCPLCRTP V      + +  +W
Sbjct:   140 TCPLCRTPLVVVPEDHQLSSNVW 162

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

GO:0005515 "protein binding" evidence=IPI

GO:0006970 "response to osmotic stress" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

GO:0010200 "response to chitin" evidence=IEP

GO:0009687 "abscisic acid metabolic process" evidence=IMP

GO:0009739 "response to gibberellin stimulus" evidence=IEP

---

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	BRH1	BRH1 (BRASSINOSTEROID-RESPONSIVE RING-H2); protein binding / zinc ion binding; Encodes a novel ring finger protein and forms an N-terminal hydrophobic domain and a C-terminal RING-H2 signature. Expression is down regulated by brassinolide. (170 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	CUL4	CUL4 (CULLIN4); protein binding / ubiquitin-protein ligase; Arabidopsis CULLIN4 (CUL4) forms an [...] (792 aa)							•		0.931
	HTB2	HTB2; DNA binding; Encodes a histone 2B (H2B) protein. This protein can be ubiquitinated in pla [...] (145 aa)							•		0.866
	HTB4	HTB4; DNA binding; HTB4; FUNCTIONS IN- DNA binding; INVOLVED IN- nucleosome assembly; LOCATED I [...] (150 aa)							•		0.865
	HTB11	HTB11; DNA binding; HTB11; FUNCTIONS IN- DNA binding; INVOLVED IN- nucleosome assembly; LOCATED [...] (145 aa)							•		0.865
	HTB9	HTB9; DNA binding; Encodes a histone 2B (H2B) protein. This protein can be ubiquitinated in pla [...] (150 aa)							•		0.865
	AT2G37470	histone H2B, putative; histone H2B, putative; FUNCTIONS IN- DNA binding; INVOLVED IN- nucleosom [...] (138 aa)							•		0.865
	RBX1	RBX1 (RING-BOX 1); protein binding; Encodes a ring-box 1 like protein and component of the SCF [...] (142 aa)							•		0.742
	UBQ9	UBQ9; protein binding; polyubiquitin gene with 4 ubiquitin repeats. The first ubiquitin repeat [...] (322 aa)							•		0.718
	AT5G24240	phosphatidylinositol 3- and 4-kinase family protein / ubiquitin family protein; phosphatidylino [...] (574 aa)							•		0.718
	UBQ3	UBQ3 (POLYUBIQUITIN 3); protein binding; encodes ubiquitin that is attached to proteins destine [...] (306 aa)							•		0.718

---

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	169
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-12
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-08
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-07
smart00184	40	smart00184, RING, Ring finger	1e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	7e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	8e-04
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	8e-04
PHA02926	242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.001
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.002

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

 Score = 60.5 bits (147), Expect = 3e-13
 Identities = 25/48 (52%), Positives = 31/48 (64%), Gaps = 2/48 (4%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTP 136
           + C +CL EFE GEE+  L  C H+FH+ CLD W+     TCPLCR P
Sbjct: 1   DECPICLDEFEPGEEVVVL-PCGHVFHKECLDKWLRS-SNTCPLCRAP 46

Length = 46

>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 = 58.6 bits (142), Expect = 1e-12
 Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 3/47 (6%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           C +CL EF    E   L  C H+F R+C+D W+   + TCPLCRTP 
Sbjct: 2   CPICLEEFR---EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 54.2 bits (130), Expect = 3e-09
 Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP 139
           CA+C+  F   + +R L  C H FH  C+D W+      CP+CRT   P
Sbjct: 326 CAICMSNFIKNDRLRVL-PCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373

Length = 374

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

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 12/56 (21%)

Query: 89  ENCAVCLYEFEG--------GEE--IRWLRNCKHIFHRACLDPWMDHDQKTCPLCR 134
           + CA+C   F+G        G++  + W   C H FH  C+  W+   + TCPLCR
Sbjct: 20  DVCAICRNHFDGTCPECKSPGDDCPVVWGE-CGHAFHLHCISRWL-KTRNTCPLCR 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|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 48.4 bits (115), Expect = 4e-07
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 12/70 (17%)

Query: 81  EMVNGDPPENCAVCLYE-FEGGEEIRWLRN--------CKHIFHRACLDPWMDHDQKTCP 131
           ++ N D    C +C+ E F    E              C HI H  CL  W++  Q+TCP
Sbjct: 282 QLTNSD--RTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER-QQTCP 338

Query: 132 LCRTPFVPDE 141
           +CR P + D+
Sbjct: 339 ICRRPVIFDQ 348

Length = 491

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

 Score = 42.9 bits (101), Expect = 1e-06
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC 133
           C +CL E+   ++   L  C H F R+C+  W++    TCP+C
Sbjct: 1   CPICLEEYL--KDPVIL-PCGHTFCRSCIRKWLESGNNTCPIC 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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 44.0 bits (104), Expect = 7e-06
 Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 13/58 (22%)

Query: 89  ENCAVCL---YEFEGGEEIR-----WLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV 138
           + CA+C+   Y+    +EI+      L NC H+F   C+D W   ++ TCP+CRTPF+
Sbjct: 175 KECAICMEKVYD----KEIKNMYFGILSNCNHVFCIECIDIW-KKEKNTCPVCRTPFI 227

Length = 238

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

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC 133
           C +CL E +   +   +  C H+F   C+  W++    TCPLC
Sbjct: 1   CPICLEEPK---DPVTILPCGHLFCSKCILSWLESGNVTCPLC 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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 36.4 bits (84), Expect = 8e-04
 Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 15/65 (23%)

Query: 87  PPENCAVCLYEFEG-----------GEE--IRWLRNCKHIFHRACLDPWMDHDQKTCPLC 133
           P + CA+C     G           G+E  + W   C H FH  C+  W+D  +  CPL 
Sbjct: 19  PIDVCAICRNHIMGTCPECQFGMTPGDECPVVW-GVCNHAFHDHCIYRWLD-TKGVCPLD 76

Query: 134 RTPFV 138
           R  +V
Sbjct: 77  RQTWV 81

Length = 88

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

 Score = 35.5 bits (82), Expect = 8e-04
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 4/45 (8%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT 135
           C +CL       +   L  C H+F R C+  ++    K CP+CRT
Sbjct: 5   CPICLDLLR---DPVVLTPCGHVFCRECILRYLKKKSK-CPICRT 45

Length = 45

>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 34/124 (27%), Positives = 56/124 (45%), Gaps = 18/124 (14%)

Query: 28  NIIICLFRYLGLSDFLETDVIWPDNSPTRIPENAPVSARLIRE--ILPVI-KFQDLEMVN 84
           N++I     + +   L   V W   + T  P N P +   I E  I+ ++ K++D+  V+
Sbjct: 110 NVVIDWITDVIVQSILRGLVNWYIANNTYTP-NTPNNTTTISELDIIKILDKYEDVYRVS 168

Query: 85  GDPPENCAVCLYE------FEGGEEIRWLRNCKHIFHRACLDPWMDHDQKT-----CPLC 133
            +  + C +C YE       E       L +C HIF   C++ W    ++T     CP+C
Sbjct: 169 KE--KECGIC-YEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPIC 225

Query: 134 RTPF 137
           RT F
Sbjct: 226 RTRF 229

Length = 242

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

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 13/62 (20%)

Query: 89  ENCAVCLYEFEG--------GEE--IRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRTP 136
           + C +C   F+G        G++  + W   CKH FH  C+  W+  +  +  CP+CR  
Sbjct: 22  DVCGICRVSFDGTCPQCKFPGDDCPLVW-GKCKHNFHMHCILKWLATETSKGLCPMCRQT 80

Query: 137 FV 138
           FV
Sbjct: 81  FV 82

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	169
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.73
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.54
PHA02929	238	N1R/p28-like protein; Provisional	99.4
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.36
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.33
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.26
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.11
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.09
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.06
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.05
PHA02926	242	zinc finger-like protein; Provisional	99.04
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.02
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.95
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.93
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.91
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.89
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.83
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.77
PF14634	44	zf-RING_5: zinc-RING finger domain	98.74
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.72
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.7
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.66
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.61
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.59
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.49
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.39
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.38
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.35
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.35
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.31
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.3
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.27
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.27
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.19
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.11
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.03
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.03
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.89
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.86
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.74
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.7
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.54
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.48
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.42
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.23
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.12
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.01
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.97
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.97
KOG1940	276	consensus Zn-finger protein [General function pred	96.96
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.9
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.81
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.81
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.74
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.72
PHA02862	156	5L protein; Provisional	96.63
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.57
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.55
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.54
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.44
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.39
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.39
COG5152	259	Uncharacterized conserved protein, contains RING a	96.31
PHA03096	284	p28-like protein; Provisional	96.23
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.22
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.01
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.99
KOG2660	331	consensus Locus-specific chromosome binding protei	95.97
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.85
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.71
PF04641	260	Rtf2: Rtf2 RING-finger	95.65
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.57
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.44
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.42
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.33
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.23
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.77
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.76
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.69
KOG4739	233	consensus Uncharacterized protein involved in syna	94.62
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	94.48
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	94.38
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	94.09
COG5236	493	Uncharacterized conserved protein, contains RING Z	93.97
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.42
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	93.25
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	92.75
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	92.36
KOG1001	674	consensus Helicase-like transcription factor HLTF/	91.69
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	91.33
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	90.18
KOG0298	1394	consensus DEAD box-containing helicase-like transc	90.14
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	90.0
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	89.1
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	88.3
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.67
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	87.63
KOG1609	323	consensus Protein involved in mRNA turnover and st	86.49
KOG3899	381	consensus Uncharacterized conserved protein [Funct	86.1
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	85.94
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	85.74
KOG3002	299	consensus Zn finger protein [General function pred	85.73
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	85.73
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	85.55
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	85.54
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	84.03
KOG1829	580	consensus Uncharacterized conserved protein, conta	83.68
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	82.73
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	82.44
KOG3113	293	consensus Uncharacterized conserved protein [Funct	82.43
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	81.42
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	81.16
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	80.99
KOG0269	839	consensus WD40 repeat-containing protein [Function	80.28

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

Probab=99.73  E-value=2e-18  Score=142.36  Aligned_cols=76  Identities=34%  Similarity=0.882  Sum_probs=63.2

Q ss_pred             CCCCHHHHHhhCCCcccccccccCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           61 APVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        61 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      ..+.++.+++ +|...|.+.....+.  +.|+||+|+|+.+++++.| ||+|.||..||+.|+.+.+..||+||..+...
T Consensus       205 ~r~~k~~l~~-~p~~~f~~~~~~~~~--~~CaIClEdY~~GdklRiL-PC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  205 NRLIKRLLKK-LPVRTFTKGDDEDAT--DTCAICLEDYEKGDKLRIL-PCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhHHHHHhh-CCcEEeccccccCCC--ceEEEeecccccCCeeeEe-cCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            4456666655 899999888743332  6999999999999999999 89999999999999998556699999987653

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

Probab=99.54  E-value=2e-15  Score=89.81  Aligned_cols=44  Identities=45%  Similarity=1.275  Sum_probs=39.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCR  134 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr  134 (169)
                      ++|+||++++..++.+..+ +|+|.||.+|+.+|++. +.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~~~-~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWLKR-NNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHHHH-SSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHHHh-CCcCCccC
Confidence            4799999999998899999 79999999999999997 77999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.40  E-value=2.9e-13  Score=107.26  Aligned_cols=75  Identities=29%  Similarity=0.727  Sum_probs=54.0

Q ss_pred             CCCHHHHHhhCCCcccccccccCCCccccccccccccccCc----eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           62 PVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGE----EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        62 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      +.++..+ +.+|.+..+-......+.+.+|+||++.+..+.    .+..+++|+|.||..||.+|+.. +.+||+||.++
T Consensus       149 ~~~~~~i-~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-~~tCPlCR~~~  226 (238)
T PHA02929        149 KNYKKFL-KTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-KNTCPVCRTPF  226 (238)
T ss_pred             chhHHHH-HhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-CCCCCCCCCEe
Confidence            3344444 447877655433223345679999999987543    23456689999999999999986 88999999876


Q ss_pred             C
Q 030902          138 V  138 (169)
Q Consensus       138 ~  138 (169)
                      .
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=99.36  E-value=4.1e-13  Score=108.12  Aligned_cols=53  Identities=38%  Similarity=0.928  Sum_probs=47.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ....+|+|||++|..+++++.+ ||.|.||..|+++|+...+..||+||.++++
T Consensus       321 ~~GveCaICms~fiK~d~~~vl-PC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVL-PCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEe-ccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            3446999999999999999999 8999999999999998547789999999986

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

Probab=99.33  E-value=9.4e-13  Score=86.59  Aligned_cols=46  Identities=43%  Similarity=1.092  Sum_probs=35.3

Q ss_pred             cccccccccccccc----------CceeeEcCCCCCcchHhhHHHHHhcCCCCCCccC
Q 030902           87 PPENCAVCLYEFEG----------GEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCR  134 (169)
Q Consensus        87 ~~~~C~ICl~~~~~----------~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr  134 (169)
                      .++.|+||++.+..          +..+.. ++|+|.||..||.+|++. +.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~-~~C~H~FH~~Ci~~Wl~~-~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVW-GPCGHIFHFHCISQWLKQ-NNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEE-ETTSEEEEHHHHHHHHTT-SSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEe-cccCCCEEHHHHHHHHhc-CCcCCCCC
Confidence            35579999999932          223333 489999999999999987 77999997

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 ....

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

Probab=99.26  E-value=1.2e-11  Score=102.23  Aligned_cols=68  Identities=31%  Similarity=0.807  Sum_probs=50.9

Q ss_pred             HHHHhhCCCcccccccccCCCccccccccccc-cccC---------ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           66 RLIREILPVIKFQDLEMVNGDPPENCAVCLYE-FEGG---------EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        66 ~~i~~~l~~~~~~~~~~~~~~~~~~C~ICl~~-~~~~---------~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      +++.+.+|+.+.++..    .+|..|.|||++ ++.+         .+-.+| +|||.+|.+|+..|+.+ +++||+||.
T Consensus       269 kdl~~~~~t~t~eql~----n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrL-pCGHilHl~CLknW~ER-qQTCPICr~  342 (491)
T COG5243         269 KDLNAMYPTATEEQLT----NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRL-PCGHILHLHCLKNWLER-QQTCPICRR  342 (491)
T ss_pred             hHHHhhcchhhhhhhc----CCCCeEEEecccccCCCCccCcccccCCcccc-cccceeeHHHHHHHHHh-ccCCCcccC
Confidence            3445557776665553    456689999999 4443         133456 89999999999999997 899999999


Q ss_pred             CCCC
Q 030902          136 PFVP  139 (169)
Q Consensus       136 ~~~~  139 (169)
                      ++.-
T Consensus       343 p~if  346 (491)
T COG5243         343 PVIF  346 (491)
T ss_pred             cccc
Confidence            9643

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.11  E-value=2.5e-11  Score=92.91  Aligned_cols=60  Identities=18%  Similarity=0.580  Sum_probs=46.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---------------CCCCCCccCCCCCCChHHHHHHHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---------------DQKTCPLCRTPFVPDEMQEEFNQR  149 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---------------~~~~CP~Cr~~~~~~~~~~~~~~~  149 (169)
                      .++.+|+||++.++.+..+    +|||.||+.||..|+..               ++..||+||..+...++...+.+-
T Consensus        16 ~~~~~CpICld~~~dPVvT----~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygrg   90 (193)
T PLN03208         16 GGDFDCNICLDQVRDPVVT----LCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGRG   90 (193)
T ss_pred             CCccCCccCCCcCCCcEEc----CCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeeccC
Confidence            4567999999998766433    89999999999999852               134799999999877666554443

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

Probab=99.09  E-value=2e-11  Score=95.13  Aligned_cols=66  Identities=23%  Similarity=0.514  Sum_probs=50.5

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC--CCCCCccCCCCCCChHHHHHHHHHHHhc
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRTPFVPDEMQEEFNQRLWAAS  154 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~~~~~~~~~~~~~~~  154 (169)
                      +....+|.|||+.-+++  |..  .|||.||+.||.+|++..  .+.||+|+..+..++++..|.+-....+
T Consensus        44 ~~~~FdCNICLd~akdP--VvT--lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~~  111 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP--VVT--LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSKKPS  111 (230)
T ss_pred             CCCceeeeeeccccCCC--EEe--ecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCCCCC
Confidence            46677999999996555  433  599999999999999763  3459999999988887776655444333

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

Probab=99.06  E-value=8.3e-11  Score=94.33  Aligned_cols=51  Identities=31%  Similarity=0.855  Sum_probs=44.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ..+..|.+|||..+++..+    ||||+||+.||..|... +..||+||....+..
T Consensus       237 ~a~~kC~LCLe~~~~pSaT----pCGHiFCWsCI~~w~~e-k~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNPSAT----PCGHIFCWSCILEWCSE-KAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCCCCCcC----cCcchHHHHHHHHHHcc-ccCCCcccccCCCcc
Confidence            4456899999999998888    99999999999999986 778999999987654

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

Probab=99.05  E-value=1.3e-10  Score=77.76  Aligned_cols=52  Identities=31%  Similarity=0.928  Sum_probs=39.9

Q ss_pred             cccccccccccccc--------Cc--eeeEcCCCCCcchHhhHHHHHhcC--CCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEG--------GE--EIRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~--------~~--~~~~l~~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~  139 (169)
                      .++.|.||+..|+.        ++  .+. ...|+|.||..||.+|+...  +..||+||.+...
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv-~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLV-WGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCcee-eccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            47799999999973        22  222 33899999999999999852  5679999997643

>PHA02926 zinc finger-like protein; Provisional

Probab=99.04  E-value=8.3e-11  Score=91.40  Aligned_cols=54  Identities=28%  Similarity=0.727  Sum_probs=41.5

Q ss_pred             CCcccccccccccccc-----CceeeEcCCCCCcchHhhHHHHHhcC-----CCCCCccCCCCC
Q 030902           85 GDPPENCAVCLYEFEG-----GEEIRWLRNCKHIFHRACLDPWMDHD-----QKTCPLCRTPFV  138 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~-----~~~~~~l~~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~  138 (169)
                      .+.+.+|+||+|..-.     +..-..|++|+|.||..||..|...+     ..+||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            3556799999998633     22356778999999999999999752     235999998763

>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=99.02  E-value=3e-10  Score=66.37  Aligned_cols=45  Identities=47%  Similarity=1.212  Sum_probs=35.7

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      .|+||++.+..  .+... +|+|.||..|+..|+..+...||.|+..+
T Consensus         1 ~C~iC~~~~~~--~~~~~-~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE--PVVLL-PCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC--ceEec-CCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            58999999833  33333 79999999999999986566899998753

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

Probab=98.95  E-value=5.7e-10  Score=83.87  Aligned_cols=57  Identities=19%  Similarity=0.606  Sum_probs=45.4

Q ss_pred             cCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           83 VNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        83 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      ..+.+...|+|||+.+.+...+  -+.|||+||+.||..-+.. ...||+|+..+..+.+
T Consensus       126 ~~~~~~~~CPiCl~~~sek~~v--sTkCGHvFC~~Cik~alk~-~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEKVPV--STKCGHVFCSQCIKDALKN-TNKCPTCRKKITHKQF  182 (187)
T ss_pred             cccccccCCCceecchhhcccc--ccccchhHHHHHHHHHHHh-CCCCCCcccccchhhh
Confidence            3445567899999999876543  2389999999999999986 7799999987765543

>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=98.93  E-value=5.7e-10  Score=67.91  Aligned_cols=46  Identities=30%  Similarity=0.875  Sum_probs=37.0

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      +..|.||++...+   +..+ +|||. |+..|+.+|+.. ...||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~~-pCgH~~~C~~C~~~~~~~-~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLL-PCGHLCFCEECAERLLKR-KKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEE-TTCEEEEEHHHHHHHHHT-TSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEe-CCCChHHHHHHhHHhccc-CCCCCcCChhhc
Confidence            4689999998554   4444 89999 999999999985 889999999874

...

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

Probab=98.91  E-value=1.1e-09  Score=63.22  Aligned_cols=39  Identities=28%  Similarity=0.945  Sum_probs=31.8

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~C  133 (169)
                      |+||++.+.++  +..+ +|||.|+..|+.+|++. +..||+|
T Consensus         1 C~iC~~~~~~~--~~~~-~CGH~fC~~C~~~~~~~-~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDP--VVVT-PCGHSFCKECIEKYLEK-NPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSE--EEEC-TTSEEEEHHHHHHHHHC-TSB-TTT
T ss_pred             CCCCCCcccCc--CEEC-CCCCchhHHHHHHHHHC-cCCCcCC
Confidence            88999998773  3344 99999999999999997 7899998

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

Probab=98.89  E-value=3.8e-10  Score=99.58  Aligned_cols=62  Identities=35%  Similarity=0.758  Sum_probs=48.3

Q ss_pred             CccccccccccccccCce--eeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHHHHHHH
Q 030902           86 DPPENCAVCLYEFEGGEE--IRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQR  149 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~--~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~~~~  149 (169)
                      ..+..|+||+|.+..+..  ...+ +|+|.||..|+.+|+++ +++||+||..+...........+
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er-~qtCP~CR~~~~~~~~~~~~~~~  352 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFER-QQTCPTCRTVLYDYVLWQIAALQ  352 (543)
T ss_pred             hcCCeeeeechhhcccccccccee-ecccchHHHHHHHHHHH-hCcCCcchhhhhccccccccCCc
Confidence            446789999999988644  5566 89999999999999997 89999999966554443333333

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

Probab=98.83  E-value=2.1e-09  Score=63.11  Aligned_cols=39  Identities=33%  Similarity=0.853  Sum_probs=30.3

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC---CCCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ---KTCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~---~~CP~C  133 (169)
                      |+||++.|.++..+    +|||.|+..||.+|....+   ..||.|
T Consensus         1 CpiC~~~~~~Pv~l----~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSL----PCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-----SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCcccc----CCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999998776    9999999999999997633   359987

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

Probab=98.77  E-value=3.9e-09  Score=61.37  Aligned_cols=40  Identities=43%  Similarity=1.053  Sum_probs=33.6

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHHHHh-cCCCCCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD-HDQKTCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~~CP~C  133 (169)
                      |+||++.+..+.  ..+ +|+|.|+..|+.+|+. .+...||.|
T Consensus         1 C~iC~~~~~~~~--~~~-~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILL-PCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EET-TTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEe-cCCCcchHHHHHHHHHhcCCccCCcC
Confidence            889999987765  344 9999999999999998 446679988

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

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.74  E-value=9.6e-09  Score=60.84  Aligned_cols=44  Identities=30%  Similarity=0.831  Sum_probs=35.6

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      .|.||.+++.+......+ +|||.|+..|+..+.. ....||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~-~CgH~~C~~C~~~~~~-~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLT-SCGHIFCEKCLKKLKG-KSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEc-ccCCHHHHHHHHhhcC-CCCCCcCCCC
Confidence            489999999555455555 9999999999999883 3668999974

>smart00184 RING Ring finger

Probab=98.72  E-value=1.1e-08  Score=57.63  Aligned_cols=39  Identities=38%  Similarity=1.098  Sum_probs=31.3

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~C  133 (169)
                      |+||++...   ....+ +|+|.||..|++.|+...+..||.|
T Consensus         1 C~iC~~~~~---~~~~~-~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVL-PCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEe-cCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789998833   34445 8999999999999998546679987

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)

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

Probab=98.70  E-value=3.3e-08  Score=84.50  Aligned_cols=52  Identities=38%  Similarity=0.933  Sum_probs=40.9

Q ss_pred             ccccccccccccc-----Cc--------eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEG-----GE--------EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~-----~~--------~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ..+|+|||.++.-     +.        .-.+++||.|+||..|+.+|....+-.||+||.++++
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            4589999999742     11        1135679999999999999998546689999999875

>smart00504 Ubox Modified RING finger domain

Probab=98.70  E-value=1.4e-08  Score=64.17  Aligned_cols=51  Identities=14%  Similarity=0.361  Sum_probs=42.7

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQE  144 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  144 (169)
                      ..|+||.+.+.++...    +|||+|+..||.+|+.. +.+||.|+.++...++..
T Consensus         2 ~~Cpi~~~~~~~Pv~~----~~G~v~~~~~i~~~~~~-~~~cP~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKDPVIL----PSGQTYERRAIEKWLLS-HGTDPVTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCCCEEC----CCCCEEeHHHHHHHHHH-CCCCCCCcCCCChhhcee
Confidence            3699999999887433    89999999999999986 779999999886655544

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

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

Probab=98.66  E-value=3.6e-08  Score=76.87  Aligned_cols=74  Identities=28%  Similarity=0.677  Sum_probs=59.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc-------CCCCCCccCCCCCC---------ChHHHHHHHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH-------DQKTCPLCRTPFVP---------DEMQEEFNQR  149 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-------~~~~CP~Cr~~~~~---------~~~~~~~~~~  149 (169)
                      +.+..|..|-..+..++.++..  |-|.||++|+++|..+       ....||.|..++.+         +.+.+...+.
T Consensus        48 DY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qv  125 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQV  125 (299)
T ss_pred             CCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhh
Confidence            4566899999999999887655  9999999999999865       23569999888865         4567789999


Q ss_pred             HHHhcCCCchhc
Q 030902          150 LWAASGVDDLFS  161 (169)
Q Consensus       150 ~~~~~~~~~~~~  161 (169)
                      +|+|+++-....
T Consensus       126 NWaRagLGLpll  137 (299)
T KOG3970|consen  126 NWARAGLGLPLL  137 (299)
T ss_pred             hHHhhccCCccc
Confidence            999998755443

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

Probab=98.61  E-value=2.6e-08  Score=65.35  Aligned_cols=48  Identities=35%  Similarity=0.931  Sum_probs=36.0

Q ss_pred             ccccccccccc-----------cCc--eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           89 ENCAVCLYEFE-----------GGE--EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        89 ~~C~ICl~~~~-----------~~~--~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      +.|+||+..+-           +++  .+..- -|.|.||.+||.+|+.. +..||++|....
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG-~CnHaFH~HCI~rWL~T-k~~CPld~q~w~   81 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWG-VCNHAFHDHCIYRWLDT-KGVCPLDRQTWV   81 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEE-ecchHHHHHHHHHHHhh-CCCCCCCCceeE
Confidence            57778777653           222  22222 69999999999999997 889999998764

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.59  E-value=1.9e-08  Score=85.23  Aligned_cols=48  Identities=27%  Similarity=0.611  Sum_probs=40.6

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ....|+||++.|..+...    +|+|.||..||..|+.. ...||+|+..+..
T Consensus        25 ~~l~C~IC~d~~~~Pvit----pCgH~FCs~CI~~~l~~-~~~CP~Cr~~~~~   72 (397)
T TIGR00599        25 TSLRCHICKDFFDVPVLT----SCSHTFCSLCIRRCLSN-QPKCPLCRAEDQE   72 (397)
T ss_pred             cccCCCcCchhhhCccCC----CCCCchhHHHHHHHHhC-CCCCCCCCCcccc
Confidence            345999999999877533    99999999999999986 6689999998754

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

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

Probab=98.49  E-value=7.1e-08  Score=76.76  Aligned_cols=51  Identities=33%  Similarity=0.693  Sum_probs=42.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHH-HHhcCCCC-CCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDP-WMDHDQKT-CPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~-wl~~~~~~-CP~Cr~~~~~~~  141 (169)
                      ..+..|.||++..+.+...    +|||+||+.||-. |-.+ +.. ||+||+...++.
T Consensus       213 ~~d~kC~lC~e~~~~ps~t----~CgHlFC~~Cl~~~~t~~-k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCT----PCGHLFCLSCLLISWTKK-KYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCcccc----cccchhhHHHHHHHHHhh-ccccCchhhhhccchh
Confidence            4477899999998777666    8999999999999 8776 444 999999886654

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

Probab=98.39  E-value=7.1e-08  Score=77.01  Aligned_cols=52  Identities=29%  Similarity=0.671  Sum_probs=42.4

Q ss_pred             CccccccccccccccCc-------eeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGE-------EIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~-------~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~  138 (169)
                      .++..|+||-..+....       ++..| .|+|+||..||+.|-..+ +++||-|+..+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            45669999998886554       67788 899999999999998653 678999987663

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

Probab=98.38  E-value=4.6e-08  Score=63.70  Aligned_cols=53  Identities=34%  Similarity=0.948  Sum_probs=38.0

Q ss_pred             Ccccccccccccccc--------Ccee-eEcCCCCCcchHhhHHHHHhc--CCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEG--------GEEI-RWLRNCKHIFHRACLDPWMDH--DQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~--------~~~~-~~l~~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~~  138 (169)
                      ..++.|-||+-.|..        +|.. ..+..|.|.||..||.+|+..  ++..||+||..+.
T Consensus        18 ~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   18 APDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            345589999988863        2211 123369999999999999965  2456999998653

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.35  E-value=3.2e-07  Score=75.20  Aligned_cols=53  Identities=21%  Similarity=0.571  Sum_probs=39.6

Q ss_pred             cccccccccc-cccCc-eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           88 PENCAVCLYE-FEGGE-EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        88 ~~~C~ICl~~-~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      +..|++|..+ +-+++ .+.+- +|||.||..|++..+..+...||.|+..+...+
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            4589999996 33443 33333 799999999999977655678999998876544

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).

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

Probab=98.35  E-value=2.5e-07  Score=63.63  Aligned_cols=50  Identities=28%  Similarity=0.747  Sum_probs=37.4

Q ss_pred             Cccccccccccccc--------------cCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           86 DPPENCAVCLYEFE--------------GGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~--------------~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      -.-+.|+||+.-+-              ++-.+..- -|.|.||..||.+|++. ++.||+|....
T Consensus        44 i~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG-~CNHaFH~hCisrWlkt-r~vCPLdn~eW  107 (114)
T KOG2930|consen   44 IVVDNCAICRNHIMDLCIECQANQSATSEECTVAWG-VCNHAFHFHCISRWLKT-RNVCPLDNKEW  107 (114)
T ss_pred             eeechhHHHHHHHHHHHHhhccCCCCCCCceEEEee-ecchHHHHHHHHHHHhh-cCcCCCcCcce
Confidence            34568999987651              11233334 79999999999999997 88999997654

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

Probab=98.31  E-value=2.5e-07  Score=84.41  Aligned_cols=53  Identities=30%  Similarity=0.768  Sum_probs=40.9

Q ss_pred             CccccccccccccccCc---eeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGE---EIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~---~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~  138 (169)
                      ++.++|+||...+..-+   .-.+.+.|.|.||..|+.+|+... ..+||+||..++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            67789999998876211   223445799999999999999763 567999998764

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

Probab=98.30  E-value=3e-07  Score=75.58  Aligned_cols=51  Identities=20%  Similarity=0.600  Sum_probs=43.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQE  144 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  144 (169)
                      -.|.||.|.|..+..+    ||+|.||.-||+..|.. +..||.|+.++.+..+..
T Consensus        24 LRC~IC~eyf~ip~it----pCsHtfCSlCIR~~L~~-~p~CP~C~~~~~Es~Lr~   74 (442)
T KOG0287|consen   24 LRCGICFEYFNIPMIT----PCSHTFCSLCIRKFLSY-KPQCPTCCVTVTESDLRN   74 (442)
T ss_pred             HHHhHHHHHhcCceec----cccchHHHHHHHHHhcc-CCCCCceecccchhhhhh
Confidence            3899999999777555    99999999999999986 889999999887655444

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

Probab=98.27  E-value=4.9e-07  Score=53.25  Aligned_cols=39  Identities=31%  Similarity=0.751  Sum_probs=21.9

Q ss_pred             ccccccccccCcee-eEcCCCCCcchHhhHHHHHhcC---CCCCC
Q 030902           91 CAVCLYEFEGGEEI-RWLRNCKHIFHRACLDPWMDHD---QKTCP  131 (169)
Q Consensus        91 C~ICl~~~~~~~~~-~~l~~C~H~fh~~Ci~~wl~~~---~~~CP  131 (169)
                      |+||.| |..++.. ..| +|||+|+.+|+.+++..+   ...||
T Consensus         1 CpIc~e-~~~~~n~P~~L-~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVL-PCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE--SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEE-eCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 7654433 456 799999999999999853   33476

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

Probab=98.27  E-value=8.4e-07  Score=53.75  Aligned_cols=43  Identities=30%  Similarity=0.855  Sum_probs=31.5

Q ss_pred             cccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcC-CCCCCccC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHD-QKTCPLCR  134 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr  134 (169)
                      .|.||++...++ ..... ||.     |.+|..|+.+|+... +.+||+|+
T Consensus         1 ~CrIC~~~~~~~-~~l~~-PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEG-DPLVS-PCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCC-CeeEe-ccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            489999833333 33455 786     889999999999753 44799995

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

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

Probab=98.24  E-value=5.2e-07  Score=77.64  Aligned_cols=51  Identities=25%  Similarity=0.656  Sum_probs=39.1

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC----CCCCCccCCCCCCChH
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD----QKTCPLCRTPFVPDEM  142 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~~~~~~  142 (169)
                      +..|+||++....+...    .|||+||..||-+.+...    ...||+||..+-.+++
T Consensus       186 ~~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl  240 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDL  240 (513)
T ss_pred             CCcCCcccCCCCccccc----ccCceeeHHHHHHHHhhhcccCCccCCchhhhccccce
Confidence            77999999985544333    799999999998777553    3469999998866443

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

Probab=98.19  E-value=7.3e-07  Score=58.41  Aligned_cols=53  Identities=15%  Similarity=0.388  Sum_probs=40.7

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHH
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQE  144 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  144 (169)
                      ...|+|+.+-|.++..+    ++||.|.+.+|..|+..++.+||.|+.++...++..
T Consensus         4 ~f~CpIt~~lM~dPVi~----~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~p   56 (73)
T PF04564_consen    4 EFLCPITGELMRDPVIL----PSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIP   56 (73)
T ss_dssp             GGB-TTTSSB-SSEEEE----TTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE
T ss_pred             ccCCcCcCcHhhCceeC----CcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceE
Confidence            45899999999998766    899999999999999876778999999887655543

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 ....

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

Probab=98.11  E-value=5.5e-07  Score=58.60  Aligned_cols=51  Identities=25%  Similarity=0.606  Sum_probs=23.9

Q ss_pred             cccccccccccccCce--eeEc--CCCCCcchHhhHHHHHhc---CC-------CCCCccCCCCC
Q 030902           88 PENCAVCLYEFEGGEE--IRWL--RNCKHIFHRACLDPWMDH---DQ-------KTCPLCRTPFV  138 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~--~~~l--~~C~H~fh~~Ci~~wl~~---~~-------~~CP~Cr~~~~  138 (169)
                      +.+|.||++.+..++.  ....  ..|+..||..|+.+|+..   .+       ..||.|+.++.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            3589999998762222  2222  379999999999999964   11       24999998763

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

Probab=98.03  E-value=2e-06  Score=69.50  Aligned_cols=46  Identities=26%  Similarity=0.590  Sum_probs=39.7

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ..|.||.+.+..+...    +|||.||.-||...|.. +..||+||.+...
T Consensus        26 lrC~IC~~~i~ip~~T----tCgHtFCslCIR~hL~~-qp~CP~Cr~~~~e   71 (391)
T COG5432          26 LRCRICDCRISIPCET----TCGHTFCSLCIRRHLGT-QPFCPVCREDPCE   71 (391)
T ss_pred             HHhhhhhheeecceec----ccccchhHHHHHHHhcC-CCCCccccccHHh
Confidence            4899999998776655    99999999999999985 8899999987643

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

Probab=98.03  E-value=1.5e-06  Score=73.70  Aligned_cols=48  Identities=35%  Similarity=0.841  Sum_probs=37.9

Q ss_pred             cccccccccccccCce-eeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEE-IRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~-~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      -..|+||||.+..... ++.. .|.|.||..|+..|-   ..+||+||.-..+
T Consensus       175 LPTCpVCLERMD~s~~gi~t~-~c~Hsfh~~cl~~w~---~~scpvcR~~q~p  223 (493)
T KOG0804|consen  175 LPTCPVCLERMDSSTTGILTI-LCNHSFHCSCLMKWW---DSSCPVCRYCQSP  223 (493)
T ss_pred             CCCcchhHhhcCccccceeee-ecccccchHHHhhcc---cCcChhhhhhcCc
Confidence            4589999999976542 2333 799999999999995   4499999987763

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

Probab=97.95  E-value=3.7e-06  Score=66.93  Aligned_cols=45  Identities=36%  Similarity=0.769  Sum_probs=38.1

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      .+...|+||++.|..+   ..+ +|+|.||..|+..+.. ....||.||.
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l-~C~H~~c~~C~~~~~~-~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLL-PCGHNFCRACLTRSWE-GPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHhhcC---ccc-cccchHhHHHHHHhcC-CCcCCcccCC
Confidence            3455899999999998   444 8999999999999987 4678999993

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

Probab=97.94  E-value=4.1e-06  Score=70.07  Aligned_cols=50  Identities=30%  Similarity=0.878  Sum_probs=37.0

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC--CCCCccCCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ--KTCPLCRTPFV  138 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~  138 (169)
                      ..|.||-+-+-....+.....|||+||..|+.+|+....  .+||+|+-.+.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            489999444444556666645999999999999998743  47999984443

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

Probab=97.89  E-value=6.1e-06  Score=68.87  Aligned_cols=52  Identities=31%  Similarity=0.832  Sum_probs=40.6

Q ss_pred             CccccccccccccccCc----eeeEcCCCCCcchHhhHHHHHhcCC------CCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGE----EIRWLRNCKHIFHRACLDPWMDHDQ------KTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~----~~~~l~~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~~~  137 (169)
                      ..+..|.||++..-...    ..+++++|.|.||..||+.|-...+      ..||.||...
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            44679999999975443    2456679999999999999995533      5699998854

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

Probab=97.86  E-value=5e-06  Score=52.70  Aligned_cols=49  Identities=27%  Similarity=0.735  Sum_probs=24.3

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHH
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQE  144 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~  144 (169)
                      .|++|.+-++++..+   +.|+|.|+..|+..-+.   ..||+|+.+....+++-
T Consensus         9 rCs~C~~~l~~pv~l---~~CeH~fCs~Ci~~~~~---~~CPvC~~Paw~qD~~~   57 (65)
T PF14835_consen    9 RCSICFDILKEPVCL---GGCEHIFCSSCIRDCIG---SECPVCHTPAWIQDIQI   57 (65)
T ss_dssp             S-SSS-S--SS-B------SSS--B-TTTGGGGTT---TB-SSS--B-S-SS---
T ss_pred             CCcHHHHHhcCCcee---ccCccHHHHHHhHHhcC---CCCCCcCChHHHHHHHh
Confidence            799999998877443   38999999999988543   36999998876666543

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

Probab=97.74  E-value=3.4e-05  Score=65.03  Aligned_cols=63  Identities=27%  Similarity=0.773  Sum_probs=44.5

Q ss_pred             ccccccccccccc-Cc-eeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCCCChHHHHHHHHHH
Q 030902           88 PENCAVCLYEFEG-GE-EIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFVPDEMQEEFNQRLW  151 (169)
Q Consensus        88 ~~~C~ICl~~~~~-~~-~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~~~~~~~~~~~  151 (169)
                      ...|+||++.+.. ++ .+..+ .|||.|-..||++|+.+. ...||.|...-....+..++..+.+
T Consensus         4 g~tcpiclds~~~~g~hr~vsl-~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~alR~q   69 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSL-QCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEYALRVQ   69 (463)
T ss_pred             cccCceeeeeeeecCceEEeee-cccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHHHHHHH
Confidence            4589999999874 33 44455 999999999999999531 3459999776555555554444433

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

Probab=97.73  E-value=7.4e-06  Score=50.12  Aligned_cols=46  Identities=24%  Similarity=0.586  Sum_probs=34.3

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      +++|.||+|.-.+....    -|||. .+-+|..+..+..+..||+||+++
T Consensus         7 ~dECTICye~pvdsVlY----tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi   53 (62)
T KOG4172|consen    7 SDECTICYEHPVDSVLY----TCGHMCMCYACGLRLKKALHGCCPICRAPI   53 (62)
T ss_pred             ccceeeeccCcchHHHH----HcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence            46999999974443222    69994 788887766654588999999986

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

Probab=97.70  E-value=2.1e-05  Score=63.93  Aligned_cols=50  Identities=28%  Similarity=0.588  Sum_probs=41.4

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ..+|+||+.+..-+..   + .|+|.||.-||..-...++.+|++||.++...-
T Consensus         7 ~~eC~IC~nt~n~Pv~---l-~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    7 KKECLICYNTGNCPVN---L-YCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             CCcceeeeccCCcCcc---c-cccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            4589999999766633   3 899999999999877776778999999997643

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

Probab=97.66  E-value=6.4e-06  Score=68.16  Aligned_cols=50  Identities=24%  Similarity=0.556  Sum_probs=42.0

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .+..|+|||+-++....+.   .|.|.||..||..-+..+...||.||..+..
T Consensus        42 ~~v~c~icl~llk~tmttk---eClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   42 IQVICPICLSLLKKTMTTK---ECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhccHHHHHHHHhhcccH---HHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            3558999999987765443   8999999999999998878899999987753

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

Probab=97.66  E-value=3e-05  Score=64.33  Aligned_cols=47  Identities=28%  Similarity=0.750  Sum_probs=37.3

Q ss_pred             ccccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ...+|.|||.+-.+   +..| ||.|. .|..|.+...-+ +..||+||.++.
T Consensus       289 ~gkeCVIClse~rd---t~vL-PCRHLCLCs~Ca~~Lr~q-~n~CPICRqpi~  336 (349)
T KOG4265|consen  289 SGKECVICLSESRD---TVVL-PCRHLCLCSGCAKSLRYQ-TNNCPICRQPIE  336 (349)
T ss_pred             CCCeeEEEecCCcc---eEEe-cchhhehhHhHHHHHHHh-hcCCCccccchH
Confidence            35689999998544   4455 99995 999999987654 778999999873

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

Probab=97.54  E-value=3e-05  Score=63.03  Aligned_cols=54  Identities=30%  Similarity=0.774  Sum_probs=43.1

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc----------------------CCCCCCccCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH----------------------DQKTCPLCRTPFVP  139 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----------------------~~~~CP~Cr~~~~~  139 (169)
                      ......|.|||--|..++..... .|.|.||..|+.+.++.                      -+..||+||.++..
T Consensus       112 n~p~gqCvICLygfa~~~~ft~T-~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  112 NHPNGQCVICLYGFASSPAFTVT-ACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCCCceEEEEEeecCCCceeee-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            35567999999999999877777 89999999999877633                      02349999988754

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

Probab=97.48  E-value=4e-05  Score=68.93  Aligned_cols=49  Identities=24%  Similarity=0.753  Sum_probs=39.5

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .|++|-...++-..+    .|+|+||..|+..-+..++..||.|...+-+.++
T Consensus       645 kCs~Cn~R~Kd~vI~----kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  645 KCSVCNTRWKDAVIT----KCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             eCCCccCchhhHHHH----hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            799998665443333    7999999999999998778889999998866554

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

Probab=97.42  E-value=1.8e-05  Score=71.33  Aligned_cols=48  Identities=27%  Similarity=0.550  Sum_probs=36.8

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .|++|+..+..+...... +|+|.||..|+..|-.. .++||+||..+-.
T Consensus       125 ~CP~Ci~s~~DqL~~~~k-~c~H~FC~~Ci~sWsR~-aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  125 QCPNCLKSCNDQLEESEK-HTAHYFCEECVGSWSRC-AQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhHHHHHHHHHhhcccc-ccccccHHHHhhhhhhh-cccCchhhhhhhe
Confidence            466666666554444444 89999999999999986 8899999987643

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

Probab=97.23  E-value=0.00022  Score=60.82  Aligned_cols=50  Identities=32%  Similarity=0.631  Sum_probs=43.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      ..+.+|.||..-+.++...    +|||.|+..|+.+-+.+ ...||.||..+...
T Consensus        82 ~sef~c~vc~~~l~~pv~t----pcghs~c~~Cl~r~ld~-~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPPVVT----PCGHSFCLECLDRSLDQ-ETECPLCRDELVEL  131 (398)
T ss_pred             cchhhhhhhHhhcCCCccc----cccccccHHHHHHHhcc-CCCCcccccccccc
Confidence            5567999999999888776    99999999999997774 67799999999753

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

Probab=97.12  E-value=0.00019  Score=60.61  Aligned_cols=50  Identities=30%  Similarity=0.800  Sum_probs=38.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      +.-..|.||-|.   +..+.+- ||||..|..|+..|-... .++||.||..+..
T Consensus       367 sTFeLCKICaen---dKdvkIE-PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  367 STFELCKICAEN---DKDVKIE-PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             chHHHHHHhhcc---CCCcccc-cccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            445679999775   3345555 899999999999998553 6789999987754

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

Probab=97.01  E-value=0.00022  Score=53.33  Aligned_cols=30  Identities=37%  Similarity=0.886  Sum_probs=27.1

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHR  116 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~  116 (169)
                      ....+|.||||+++.++.+.+| ||-.+||+
T Consensus       175 ddkGECvICLEdL~~GdtIARL-PCLCIYHK  204 (205)
T KOG0801|consen  175 DDKGECVICLEDLEAGDTIARL-PCLCIYHK  204 (205)
T ss_pred             ccCCcEEEEhhhccCCCceecc-ceEEEeec
Confidence            4456999999999999999999 89999996

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

Probab=96.97  E-value=0.00049  Score=58.78  Aligned_cols=53  Identities=25%  Similarity=0.607  Sum_probs=43.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      ..+..|++|+..+..+...  . .|||.||..|+..|+.. +..||.|+..+...+.
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~-~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSN-HQKCPVCRQELTQAEE   71 (391)
T ss_pred             cccccCccccccccCCCCC--C-CCCCcccccccchhhcc-CcCCcccccccchhhc
Confidence            4456899999999888763  2 89999999999999997 8899999887754433

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

Probab=96.97  E-value=0.00035  Score=43.57  Aligned_cols=43  Identities=23%  Similarity=0.617  Sum_probs=27.9

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc-CCCCCCc
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH-DQKTCPL  132 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-~~~~CP~  132 (169)
                      -...|+|.+..|+++  ++.. .|+|.|-+..|.+|+.. +...||+
T Consensus        10 ~~~~CPiT~~~~~~P--V~s~-~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP--VKSK-KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE--EEES-SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC--cCcC-CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            345899999998876  4444 89999999999999943 2445998

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

Probab=96.96  E-value=0.00085  Score=54.49  Aligned_cols=78  Identities=18%  Similarity=0.258  Sum_probs=59.6

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHHHHHHHHHHhcCCCchhcccC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLWAASGVDDLFSEYS  164 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (169)
                      ......|+||.+.+-.........+|||..|..|....... ..+||+|.+ +.+........+..-+++++++.+++..
T Consensus       155 ~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-~y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~y~~~~  232 (276)
T KOG1940|consen  155 RSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-GYTCPICSK-PGDMSHYFRKLDKELAGSPMPEEYKNKT  232 (276)
T ss_pred             hcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-CCCCCcccc-hHHHHHHHHHHHHHHhcCCCCchhhchh
Confidence            34455699999997655544433399999999999999886 499999988 7677777777777778888887766653

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

Probab=96.90  E-value=0.00035  Score=58.87  Aligned_cols=46  Identities=33%  Similarity=0.813  Sum_probs=36.5

Q ss_pred             cccccccccccc-cCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCccC
Q 030902           88 PENCAVCLYEFE-GGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCR  134 (169)
Q Consensus        88 ~~~C~ICl~~~~-~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr  134 (169)
                      .-.|..|-|.+. .++.+.-| ||.|+||..|+...+.++ ..+||.||
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqAL-pCsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQAL-PCSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             hhhhhhhhhhhcCCccccccc-chhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            347999988875 34456666 899999999999998653 45799998

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

Probab=96.81  E-value=0.00089  Score=40.16  Aligned_cols=46  Identities=24%  Similarity=0.683  Sum_probs=22.8

Q ss_pred             ccccccccccCc-eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           91 CAVCLYEFEGGE-EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        91 C~ICl~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      |++|.+++...+ ...-. +|++..+..|...-+......||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            788999984433 44434 78899999998887764467899999864

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

Probab=96.81  E-value=0.00065  Score=62.01  Aligned_cols=50  Identities=22%  Similarity=0.718  Sum_probs=41.5

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC------CCCCccCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ------KTCPLCRT  135 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~------~~CP~Cr~  135 (169)
                      ....+|.||.+.+.....+-....|-|+||..||..|.....      -.||.|+.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            556799999999998888877778889999999999996522      24999984

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

Probab=96.74  E-value=0.0021  Score=54.57  Aligned_cols=67  Identities=25%  Similarity=0.634  Sum_probs=49.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc----C---CCCCCc--cCCCCCCChHHHHHHHHHHHh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH----D---QKTCPL--CRTPFVPDEMQEEFNQRLWAA  153 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~---~~~CP~--Cr~~~~~~~~~~~~~~~~~~~  153 (169)
                      .....|.||.++.....-...+ ||+|+||+.|+...+..    +   .-.||-  |....++..+.+.......+|
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~l-pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~ar  257 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFL-PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFAR  257 (445)
T ss_pred             hhcccceeeehhhcCcceeeec-ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHH
Confidence            3456899999998777778788 89999999999988854    1   234754  455566666666666666665

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.72  E-value=0.0016  Score=48.58  Aligned_cols=49  Identities=27%  Similarity=0.776  Sum_probs=35.1

Q ss_pred             CccccccccccccccCceeeEcCCCCC-----cchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKH-----IFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H-----~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      ..+..|-||.++-.  +...   ||..     ..|.+|+.+|+..+ ...|++|+.++.-
T Consensus         6 ~~~~~CRIC~~~~~--~~~~---PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          6 LMDKCCWICKDEYD--VVTN---YCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCeeEecCCCCC--CccC---CcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            44568999998843  2222   5553     56999999999763 4469999887643

>PHA02862 5L protein; Provisional

Probab=96.63  E-value=0.0011  Score=48.55  Aligned_cols=49  Identities=22%  Similarity=0.652  Sum_probs=35.8

Q ss_pred             cccccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcC-CCCCCccCCCCCCCh
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHD-QKTCPLCRTPFVPDE  141 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~~  141 (169)
                      ++.|-||+++-++  .+.   ||.     ...|.+|+.+|+... +..|++|+.++.-+.
T Consensus         2 ~diCWIC~~~~~e--~~~---PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~   56 (156)
T PHA02862          2 SDICWICNDVCDE--RNN---FCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKK   56 (156)
T ss_pred             CCEEEEecCcCCC--Ccc---cccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEE
Confidence            3589999998433  333   555     579999999999763 446999999875433

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

Probab=96.57  E-value=0.0019  Score=38.59  Aligned_cols=41  Identities=32%  Similarity=0.919  Sum_probs=26.9

Q ss_pred             ccccccccccCceeeEcCCCC--C---cchHhhHHHHHhc-CCCCCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCK--H---IFHRACLDPWMDH-DQKTCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~--H---~fh~~Ci~~wl~~-~~~~CP~C  133 (169)
                      |-||+++-.....+ .. ||.  -   ..|..|+.+|+.. ++.+|++|
T Consensus         1 CrIC~~~~~~~~~l-i~-pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPL-IS-PCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-E-E--SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCce-ec-ccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            77999987665522 22 555  3   7899999999975 34569887

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

Probab=96.55  E-value=0.0021  Score=62.02  Aligned_cols=66  Identities=24%  Similarity=0.581  Sum_probs=48.4

Q ss_pred             CCCcccccccccCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC---------CCCCCccCCCCCC
Q 030902           72 LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD---------QKTCPLCRTPFVP  139 (169)
Q Consensus        72 l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---------~~~CP~Cr~~~~~  139 (169)
                      +|-...++.... .+.++.|.||..+--.......| .|+|.||..|.+.-+.++         -..||+|+.++..
T Consensus      3471 LPCl~Cdks~tk-QD~DDmCmICFTE~L~AAP~IqL-~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3471 LPCLHCDKSATK-QDADDMCMICFTEALSAAPAIQL-DCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             ccccccChhhhh-cccCceEEEEehhhhCCCcceec-CCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            565554444432 25577999999887666677778 899999999998777652         1359999998865

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

Probab=96.54  E-value=0.0027  Score=51.21  Aligned_cols=52  Identities=31%  Similarity=0.549  Sum_probs=39.7

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      ...+.+|++|-+.-..+....   +|+|+||-.|+..-..-. ..+||.|..+..+
T Consensus       236 ~t~~~~C~~Cg~~PtiP~~~~---~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIPHVIG---KCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccCCceeeccCCCCCCCeeec---cccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            356779999999866665552   699999999998765431 3589999887754

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.44  E-value=0.0028  Score=50.52  Aligned_cols=57  Identities=14%  Similarity=0.297  Sum_probs=49.7

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ  143 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  143 (169)
                      +....|+||.+.+.+......|.+|||+|...|.++.+.. -..||+|..++.+.++.
T Consensus       219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~-D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK-DMVDPVTDKPLKDRDII  275 (303)
T ss_pred             ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc-cccccCCCCcCcccceE
Confidence            3567899999999999988899999999999999999875 67899999988876654

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

Probab=96.39  E-value=0.0018  Score=56.64  Aligned_cols=50  Identities=26%  Similarity=0.637  Sum_probs=38.6

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc----CCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH----DQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~~~~CP~Cr~~~~~  139 (169)
                      .+..+|.+|.+.-+.....    .|.|.||+-|+.+++..    .+.+||+|-..+.-
T Consensus       534 k~~~~C~lc~d~aed~i~s----~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi  587 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIES----SCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI  587 (791)
T ss_pred             cCceeecccCChhhhhHhh----hhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence            3456899999986665555    89999999999877743    35689999877643

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

Probab=96.39  E-value=0.0014  Score=47.59  Aligned_cols=35  Identities=14%  Similarity=0.588  Sum_probs=28.0

Q ss_pred             cccccccccccccCceeeEcCCCC------CcchHhhHHHHH
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCK------HIFHRACLDPWM  123 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~------H~fh~~Ci~~wl  123 (169)
                      ..+|+||++.+.+.+-+..+ .|+      |.||.+|+.+|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHH
Confidence            45999999999884555555 455      899999999994

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

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

Probab=96.31  E-value=0.0016  Score=50.24  Aligned_cols=44  Identities=20%  Similarity=0.488  Sum_probs=37.5

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      ..|.||-++|+.+...    .|||.||..|...-.+. ...|-+|.+..
T Consensus       197 F~C~iCKkdy~spvvt----~CGH~FC~~Cai~~y~k-g~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYESPVVT----ECGHSFCSLCAIRKYQK-GDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccchhhh----hcchhHHHHHHHHHhcc-CCcceecchhh
Confidence            3899999999998777    89999999999887764 66899997654

>PHA03096 p28-like protein; Provisional

Probab=96.23  E-value=0.0024  Score=52.22  Aligned_cols=47  Identities=28%  Similarity=0.559  Sum_probs=35.1

Q ss_pred             ccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcC--CCCCCccCC
Q 030902           89 ENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRT  135 (169)
Q Consensus        89 ~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~  135 (169)
                      ..|.||++.....    ..-..|+.|.|.|+..|+..|....  ...||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5899999997643    3455778999999999999999653  234555544

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

Probab=96.22  E-value=0.0017  Score=44.85  Aligned_cols=33  Identities=21%  Similarity=0.590  Sum_probs=26.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD  120 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~  120 (169)
                      .++..|++|...+.++ ..... ||||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~~-~f~~~-p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNS-VFVVF-PCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCc-eEEEe-CCCeEEeccccc
Confidence            3456899999999774 55566 899999999975

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 [].

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.01  E-value=0.0039  Score=51.85  Aligned_cols=56  Identities=16%  Similarity=0.437  Sum_probs=38.1

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      +++++.|+.|+|++...++--.--+||-..|.-|...--+.-+..||.||....+.
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            44555699999999876643322289987777776554433355899999876553

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

Probab=95.99  E-value=0.017  Score=47.85  Aligned_cols=58  Identities=19%  Similarity=0.343  Sum_probs=43.7

Q ss_pred             CCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHHH
Q 030902           84 NGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEE  145 (169)
Q Consensus        84 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~  145 (169)
                      .......|++|+....++..+.   --|-+||..|+...+.. ++.||+=..+..-.++...
T Consensus       296 l~~~~~~CpvClk~r~Nptvl~---vSGyVfCY~Ci~~Yv~~-~~~CPVT~~p~~v~~l~rl  353 (357)
T KOG0826|consen  296 LPPDREVCPVCLKKRQNPTVLE---VSGYVFCYPCIFSYVVN-YGHCPVTGYPASVDHLIRL  353 (357)
T ss_pred             CCCccccChhHHhccCCCceEE---ecceEEeHHHHHHHHHh-cCCCCccCCcchHHHHHHH
Confidence            3345568999999998887663   34899999999999985 8899987666554444443

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

Probab=95.97  E-value=0.0017  Score=53.57  Aligned_cols=48  Identities=25%  Similarity=0.653  Sum_probs=39.9

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ....|.+|-..|.+...+.   -|-|.||+.||...+.. ...||.|...+-
T Consensus        14 ~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~-~~~CP~C~i~ih   61 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEE-SKYCPTCDIVIH   61 (331)
T ss_pred             cceehhhccceeecchhHH---HHHHHHHHHHHHHHHHH-hccCCccceecc
Confidence            4558999999987765553   79999999999999997 889999977553

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

Probab=95.85  E-value=0.0042  Score=51.91  Aligned_cols=62  Identities=16%  Similarity=0.332  Sum_probs=45.3

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHHHHHHHHH
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQRLW  151 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~~~~~~  151 (169)
                      ++++..|+||...-.+..    ..||+|.-|..||.+.+.+ .+.|=.|+..+.+..+......+.|
T Consensus       419 ~sEd~lCpICyA~pi~Av----f~PC~H~SC~~CI~qHlmN-~k~CFfCktTv~~~~ld~~~~~~~d  480 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPINAV----FAPCSHRSCYGCITQHLMN-CKRCFFCKTTVIDVILDKEEEEEED  480 (489)
T ss_pred             CcccccCcceecccchhh----ccCCCCchHHHHHHHHHhc-CCeeeEecceeeehhcccccccccc
Confidence            367789999987633332    2399999999999999986 8899999998876544443333333

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

Probab=95.71  E-value=0.0057  Score=51.10  Aligned_cols=47  Identities=28%  Similarity=0.554  Sum_probs=34.4

Q ss_pred             cCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           83 VNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        83 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      ..++..+.|.||+++.++-..+    +|||.-+  |..--.+  ...||+||..+
T Consensus       300 ~~~~~p~lcVVcl~e~~~~~fv----pcGh~cc--ct~cs~~--l~~CPvCR~rI  346 (355)
T KOG1571|consen  300 RELPQPDLCVVCLDEPKSAVFV----PCGHVCC--CTLCSKH--LPQCPVCRQRI  346 (355)
T ss_pred             cccCCCCceEEecCCccceeee----cCCcEEE--chHHHhh--CCCCchhHHHH
Confidence            3445667999999998886666    9999866  6554332  34599999876

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.65  E-value=0.014  Score=47.23  Aligned_cols=53  Identities=30%  Similarity=0.646  Sum_probs=43.0

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ......|+|...+|........+.+|||+|-..++.+.-  ....||+|..++..
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--KSKKCPVCGKPFTE  162 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--ccccccccCCcccc
Confidence            355678999999997777777777999999999999973  25579999888654

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

Probab=95.57  E-value=0.0043  Score=50.58  Aligned_cols=45  Identities=20%  Similarity=0.394  Sum_probs=38.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ..|-||...|..+...    .|+|.||..|...-++. ...|++|.....
T Consensus       242 f~c~icr~~f~~pVvt----~c~h~fc~~ca~~~~qk-~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVT----KCGHYFCEVCALKPYQK-GEKCYVCSQQTH  286 (313)
T ss_pred             ccccccccccccchhh----cCCceeehhhhcccccc-CCcceecccccc
Confidence            4699999999998777    89999999999887764 678999977664

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

Probab=95.44  E-value=0.0018  Score=54.52  Aligned_cols=60  Identities=20%  Similarity=0.546  Sum_probs=48.5

Q ss_pred             cccccccccccccC-ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChHHHHHHHH
Q 030902           88 PENCAVCLYEFEGG-EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFNQR  149 (169)
Q Consensus        88 ~~~C~ICl~~~~~~-~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~~~~~~~  149 (169)
                      ...|+||-+.++.. +++..+ .|||.+|..|+.+|+.. ...||.|++.++...+..+.+..
T Consensus       196 v~sl~I~~~slK~~y~k~~~~-~~g~~~~~~kL~k~L~~-~~kl~~~~rel~~~~~e~k~A~~  256 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAI-VCGHIYHHGKLSKWLAT-KRKLPSCRRELPKNGFEEKLAFF  256 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHH-hhcccchhhHHHHHHHH-HHHhHHHHhhhhhhhHHHHHHHH
Confidence            45899999999876 556566 89999999999999987 77899999999876665554333

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

Probab=95.42  E-value=0.0092  Score=48.90  Aligned_cols=44  Identities=20%  Similarity=0.544  Sum_probs=36.0

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      -.|+.|..-+.++.+.   +-|+|.||..||..-|......||+|..
T Consensus       275 LkCplc~~Llrnp~kT---~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKT---PCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccC---ccccchHHHHHHhhhhhhccccCCCccc
Confidence            4799999988887665   3799999999999877655778999944

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

Probab=95.33  E-value=0.011  Score=54.18  Aligned_cols=42  Identities=24%  Similarity=0.656  Sum_probs=33.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      ..|..|-..++-+..-  . .|||.||.+|.+.    +...||.|+...
T Consensus       841 skCs~C~~~LdlP~Vh--F-~CgHsyHqhC~e~----~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLPFVH--F-LCGHSYHQHCLED----KEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccceee--e-ecccHHHHHhhcc----CcccCCccchhh
Confidence            5899999998877432  3 6999999999982    466899998744

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

Probab=95.23  E-value=0.021  Score=46.66  Aligned_cols=48  Identities=25%  Similarity=0.739  Sum_probs=39.3

Q ss_pred             ccccccccccccCc--ee-eEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           89 ENCAVCLYEFEGGE--EI-RWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        89 ~~C~ICl~~~~~~~--~~-~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      ..|-||-++|+..+  .+ +.| .|||.++..|+...+......||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVL-KCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCccc-ccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            47999999998653  33 344 89999999999999887666799999984

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

Probab=94.77  E-value=0.031  Score=47.13  Aligned_cols=28  Identities=25%  Similarity=0.803  Sum_probs=21.8

Q ss_pred             CcchHhhHHHHHhcC------------CCCCCccCCCCCC
Q 030902          112 HIFHRACLDPWMDHD------------QKTCPLCRTPFVP  139 (169)
Q Consensus       112 H~fh~~Ci~~wl~~~------------~~~CP~Cr~~~~~  139 (169)
                      -.+|.+|+.+|+..+            +-.||+||+.++-
T Consensus       313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            467899999999652            3459999998864

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

>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=94.76  E-value=0.019  Score=33.64  Aligned_cols=42  Identities=24%  Similarity=0.690  Sum_probs=22.1

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCC-CCCcc
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQK-TCPLC  133 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~-~CP~C  133 (169)
                      |.+|.+-.-.+..-..- .|+-.+|..|+..++..... .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            56676665555443222 58889999999999976333 59987

; PDB: 3NW0_A 2CT0_A.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.69  E-value=0.019  Score=35.32  Aligned_cols=44  Identities=32%  Similarity=0.688  Sum_probs=29.8

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .|-.|...-..+   ..+ +|+|..+..|...+-   -+.||.|..++...
T Consensus         9 ~~~~~~~~~~~~---~~~-pCgH~I~~~~f~~~r---YngCPfC~~~~~~~   52 (55)
T PF14447_consen    9 PCVFCGFVGTKG---TVL-PCGHLICDNCFPGER---YNGCPFCGTPFEFD   52 (55)
T ss_pred             eEEEcccccccc---ccc-cccceeeccccChhh---ccCCCCCCCcccCC
Confidence            455554442222   233 999999999987752   44799999988654

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

Probab=94.62  E-value=0.016  Score=45.99  Aligned_cols=44  Identities=25%  Similarity=0.682  Sum_probs=31.5

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .|..|...-. ++..... .|+|+||..|...-.   ...||+|+.++-
T Consensus         5 hCn~C~~~~~-~~~f~LT-aC~HvfC~~C~k~~~---~~~C~lCkk~ir   48 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLT-ACRHVFCEPCLKASS---PDVCPLCKKSIR   48 (233)
T ss_pred             EeccccccCC-CCceeee-echhhhhhhhcccCC---ccccccccceee
Confidence            4777755544 6666666 999999999976521   238999998764

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

Probab=94.48  E-value=0.034  Score=42.41  Aligned_cols=50  Identities=26%  Similarity=0.653  Sum_probs=32.0

Q ss_pred             cccccccccccc---CceeeEcCCCCCcchHhhHHHHHhc----CC------CCCCccCCCCC
Q 030902           89 ENCAVCLYEFEG---GEEIRWLRNCKHIFHRACLDPWMDH----DQ------KTCPLCRTPFV  138 (169)
Q Consensus        89 ~~C~ICl~~~~~---~~~~~~l~~C~H~fh~~Ci~~wl~~----~~------~~CP~Cr~~~~  138 (169)
                      ..|-||...--.   ++.+..-.+|+.-||.-|+..|+..    ++      ..||.|..++-
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            356666543221   2222222289999999999999954    11      34999988764

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=94.38  E-value=0.049  Score=33.43  Aligned_cols=35  Identities=29%  Similarity=0.674  Sum_probs=30.0

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHH
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDP  121 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~  121 (169)
                      ....|.+|-+.|.+++.+...+.|+-.+|++|.+.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            34589999999998888888889999999999544

>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=94.09  E-value=0.048  Score=44.45  Aligned_cols=49  Identities=18%  Similarity=0.451  Sum_probs=39.1

Q ss_pred             ccccccccc-ccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           90 NCAVCLYEF-EGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        90 ~C~ICl~~~-~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .|++|..+. -+++......+|+|..|.+|.+..+..+...||-|...+-
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence            588888763 4555555555999999999999999988888999977654

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

Probab=93.97  E-value=0.056  Score=45.28  Aligned_cols=52  Identities=29%  Similarity=0.439  Sum_probs=36.3

Q ss_pred             cCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHh-cCCCCCCccCCCCC
Q 030902           83 VNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD-HDQKTCPLCRTPFV  138 (169)
Q Consensus        83 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~-~~~~~CP~Cr~~~~  138 (169)
                      ..+.++..|.||-+.+.-   +..+ ||+|..|-.|.-+.-. ..+..||+||....
T Consensus        56 dtDEen~~C~ICA~~~TY---s~~~-PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          56 DTDEENMNCQICAGSTTY---SARY-PCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccccccceeEEecCCceE---EEec-cCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            345567789999887432   3334 9999999999765432 24678999998653

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.42  E-value=0.037  Score=44.40  Aligned_cols=52  Identities=29%  Similarity=0.842  Sum_probs=35.3

Q ss_pred             CccccccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcCC-------CCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHDQ-------KTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~~-------~~CP~Cr~~~  137 (169)
                      ..+..|-||.+.=++.......-||.     |..|..|+..|+..++       ..||.|+...
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            34568999998855443221122453     8999999999996522       2499998865

>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=93.25  E-value=0.09  Score=39.31  Aligned_cols=58  Identities=22%  Similarity=0.491  Sum_probs=37.5

Q ss_pred             cccccccccccccCceeeEc---CC-----CCC-cchHhhHHHHHhc------------------------------CCC
Q 030902           88 PENCAVCLYEFEGGEEIRWL---RN-----CKH-IFHRACLDPWMDH------------------------------DQK  128 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l---~~-----C~H-~fh~~Ci~~wl~~------------------------------~~~  128 (169)
                      +..|+||||--.+...+.-.   .+     |+. .-|..|+++.-+.                              .+-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L   81 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPEL   81 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccc
Confidence            56899999985554322110   01     342 4588899987643                              023


Q ss_pred             CCCccCCCCCCChHHHH
Q 030902          129 TCPLCRTPFVPDEMQEE  145 (169)
Q Consensus       129 ~CP~Cr~~~~~~~~~~~  145 (169)
                      .||+||..+..+..++.
T Consensus        82 ~CPLCRG~V~GWtvve~   98 (162)
T PF07800_consen   82 ACPLCRGEVKGWTVVEP   98 (162)
T ss_pred             cCccccCceeceEEchH
Confidence            59999999988776664

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.

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

Probab=92.75  E-value=0.02  Score=46.79  Aligned_cols=41  Identities=27%  Similarity=0.724  Sum_probs=29.3

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      +..|+||++.   +.....| +|||. -|..|...     -+.||+||..+
T Consensus       300 ~~LC~ICmDa---P~DCvfL-eCGHmVtCt~CGkr-----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFL-ECGHMVTCTKCGKR-----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcC---CcceEEe-ecCcEEeehhhccc-----cccCchHHHHH
Confidence            5679999986   4455667 89994 55666443     34899999765

>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=92.36  E-value=0.042  Score=32.73  Aligned_cols=44  Identities=27%  Similarity=0.779  Sum_probs=24.5

Q ss_pred             cccccccccccCceeeEcCCCC-CcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCK-HIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .|.-|.-.  +...+    .|. |..+..|+...+.. ...||+|..++|.+
T Consensus         4 nCKsCWf~--~k~Li----~C~dHYLCl~CLt~ml~~-s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFA--NKGLI----KCSDHYLCLNCLTLMLSR-SDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S----SSEE----E-SS-EEEHHHHHHT-SS-SSEETTTTEE----
T ss_pred             cChhhhhc--CCCee----eecchhHHHHHHHHHhcc-ccCCCcccCcCccc
Confidence            45555533  34445    677 99999999999875 66899999988753

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.

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

Probab=91.69  E-value=0.048  Score=49.76  Aligned_cols=51  Identities=24%  Similarity=0.580  Sum_probs=37.2

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCC-CCCccCCCCCCChHHH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQK-TCPLCRTPFVPDEMQE  144 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~-~CP~Cr~~~~~~~~~~  144 (169)
                      ..|.+|++ ....   ... +|+|.|+..|+..-+...+. .||.||..+..+.+.+
T Consensus       455 ~~c~ic~~-~~~~---~it-~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD-LDSF---FIT-RCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc-cccc---eee-cccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            68999999 2222   222 79999999999988765433 4999998876655544

>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=91.33  E-value=0.088  Score=42.01  Aligned_cols=47  Identities=23%  Similarity=0.544  Sum_probs=36.1

Q ss_pred             ccccccccccc-ccCc-eeeEcCCCCCcchHhhHHHHHhcCCCCCC--ccC
Q 030902           88 PENCAVCLYEF-EGGE-EIRWLRNCKHIFHRACLDPWMDHDQKTCP--LCR  134 (169)
Q Consensus        88 ~~~C~ICl~~~-~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP--~Cr  134 (169)
                      +..|+||..+- -+++ ++.+-|.|-|..|.+|.++-+..+...||  -|.
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            45899999884 3444 44444449999999999999998788899  664

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

Probab=90.18  E-value=0.19  Score=46.06  Aligned_cols=40  Identities=28%  Similarity=0.816  Sum_probs=27.6

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCc
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPL  132 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~  132 (169)
                      .|+||.-.+.....+.  ..|+|+.|.+|...|+.. ...||.
T Consensus      1030 ~C~~C~l~V~gss~~C--g~C~Hv~H~sc~~eWf~~-gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNFC--GTCGHVGHTSCMMEWFRT-GDVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccchhh--ccccccccHHHHHHHHhc-CCcCCC
Confidence            4666655443333322  269999999999999987 657874

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

Probab=90.14  E-value=0.11  Score=50.02  Aligned_cols=45  Identities=24%  Similarity=0.627  Sum_probs=37.1

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      ....|.||++.+.+...+.   .|||.++..|...|+.+ +..||+|+.
T Consensus      1152 ~~~~c~ic~dil~~~~~I~---~cgh~~c~~c~~~~l~~-~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIA---GCGHEPCCRCDELWLYA-SSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHhcCCee---eechhHhhhHHHHHHHH-hccCcchhh
Confidence            3448999999998443332   79999999999999997 889999974

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

Probab=90.00  E-value=0.17  Score=47.00  Aligned_cols=36  Identities=28%  Similarity=0.582  Sum_probs=27.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWM  123 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl  123 (169)
                      .+++.|.+|.-.+.... -... +|||.||++|+.+-.
T Consensus       815 ep~d~C~~C~~~ll~~p-F~vf-~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIKP-FYVF-PCGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcCc-ceee-eccchHHHHHHHHHH
Confidence            55679999998876553 2233 899999999998765

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

Probab=89.10  E-value=0.17  Score=45.65  Aligned_cols=42  Identities=21%  Similarity=0.479  Sum_probs=31.4

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      .|.||+..|......-....|||..|..|......   .+|| |+.
T Consensus        13 ~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn---~scp-~~~   54 (861)
T KOG3161|consen   13 LCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN---ASCP-TKR   54 (861)
T ss_pred             hchHHHHHHHHHhcCcccccccchHHHHHHHhHhh---ccCC-CCc
Confidence            79999888865543333338999999999988654   4899 644

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

Probab=88.30  E-value=0.2  Score=41.44  Aligned_cols=42  Identities=31%  Similarity=0.678  Sum_probs=26.4

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      -|--|--.+  ...=|.+ +|+|+||.+|...-   .-+.||.|-.++
T Consensus        92 fCd~Cd~PI--~IYGRmI-PCkHvFCl~CAr~~---~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPI--AIYGRMI-PCKHVFCLECARSD---SDKICPLCDDRV  133 (389)
T ss_pred             eecccCCcc--eeeeccc-ccchhhhhhhhhcC---ccccCcCcccHH
Confidence            455553332  2223344 99999999997652   244799996554

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

Probab=87.67  E-value=0.26  Score=42.16  Aligned_cols=38  Identities=26%  Similarity=0.714  Sum_probs=28.4

Q ss_pred             ccccccccc-cccccCceeeEcCCCCCcchHhhHHHHHhc
Q 030902           87 PPENCAVCL-YEFEGGEEIRWLRNCKHIFHRACLDPWMDH  125 (169)
Q Consensus        87 ~~~~C~ICl-~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~  125 (169)
                      ....|.||. +........... .|+|.|+.+|..+.+..
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhh
Confidence            456899999 554443444444 89999999999988864

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

Probab=87.63  E-value=0.26  Score=38.60  Aligned_cols=39  Identities=28%  Similarity=0.797  Sum_probs=28.1

Q ss_pred             ccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCC
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      |..|.+.   +..|..+ ||.|. +|..|-..     -..||+|+....
T Consensus       161 Cr~C~~~---~~~Vlll-PCrHl~lC~~C~~~-----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGER---EATVLLL-PCRHLCLCGICDES-----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcC---CceEEee-cccceEeccccccc-----CccCCCCcChhh
Confidence            8788665   5567777 89984 77888554     336999987653

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

Probab=86.49  E-value=0.51  Score=38.44  Aligned_cols=52  Identities=27%  Similarity=0.706  Sum_probs=35.2

Q ss_pred             cccccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      ...|.||+++...........+|.     +..|..|+..|+... ...|.+|......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN  135 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence            468999999865443111122565     467999999999742 4469999875543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.10  E-value=0.43  Score=39.19  Aligned_cols=30  Identities=30%  Similarity=0.790  Sum_probs=23.1

Q ss_pred             CCCcchHhhHHHHHhc------------CCCCCCccCCCCCC
Q 030902          110 CKHIFHRACLDPWMDH------------DQKTCPLCRTPFVP  139 (169)
Q Consensus       110 C~H~fh~~Ci~~wl~~------------~~~~CP~Cr~~~~~  139 (169)
                      |.-.+|.+|+.+|+..            ++-+||+||+.++-
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            4467889999999854            23569999998764

>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=85.94  E-value=0.9  Score=27.56  Aligned_cols=43  Identities=26%  Similarity=0.572  Sum_probs=22.4

Q ss_pred             ccccccccccC------ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccC
Q 030902           91 CAVCLYEFEGG------EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCR  134 (169)
Q Consensus        91 C~ICl~~~~~~------~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr  134 (169)
                      |.-|+..|..+      ......+.|++.|+.+|=. .+...-.+||-|.
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~-fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDV-FIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHH-TTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcCh-hhhccccCCcCCC
Confidence            56677777664      2456667999999999943 2322234699884

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.

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

Probab=85.74  E-value=0.47  Score=44.00  Aligned_cols=51  Identities=27%  Similarity=0.666  Sum_probs=36.7

Q ss_pred             ccccccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      ++..|.||+.+=..++.+-.  ||+     ...|.+|+-+|+.-+ ...|-+|..++.-
T Consensus        11 d~~~CRICr~e~~~d~pLfh--PCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F   67 (1175)
T COG5183          11 DKRSCRICRTEDIRDDPLFH--PCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF   67 (1175)
T ss_pred             cchhceeecCCCCCCCcCcc--cccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence            34689999988655554432  455     368999999999753 3459999887644

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

Probab=85.73  E-value=0.66  Score=38.38  Aligned_cols=45  Identities=22%  Similarity=0.459  Sum_probs=33.4

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .--+|+||.+.+..+..-.   +=||.-|..|-.+    ....||.||.++.
T Consensus        47 ~lleCPvC~~~l~~Pi~QC---~nGHlaCssC~~~----~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSPPIFQC---DNGHLACSSCRTK----VSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCcccceec---CCCcEehhhhhhh----hcccCCccccccc
Confidence            3458999999998875331   3358998888654    2558999999886

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

Probab=85.73  E-value=0.67  Score=39.45  Aligned_cols=46  Identities=20%  Similarity=0.368  Sum_probs=37.0

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC--CCCCccC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ--KTCPLCR  134 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~--~~CP~Cr  134 (169)
                      -..|+|=.+.-.++..-..| .|||+..++-+++..+.+.  ..||-|=
T Consensus       334 vF~CPVlKeqtsdeNPPm~L-~CGHVISkdAlnrLS~ng~~sfKCPYCP  381 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMML-ICGHVISKDALNRLSKNGSQSFKCPYCP  381 (394)
T ss_pred             eeecccchhhccCCCCCeee-eccceecHHHHHHHhhCCCeeeeCCCCC
Confidence            34899988777666666677 8999999999999988765  4699993

>TIGR00622 ssl1 transcription factor ssl1

Probab=85.55  E-value=1.3  Score=31.28  Aligned_cols=47  Identities=21%  Similarity=0.328  Sum_probs=33.2

Q ss_pred             cccccccccccccC----------ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCC
Q 030902           88 PENCAVCLYEFEGG----------EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT  135 (169)
Q Consensus        88 ~~~C~ICl~~~~~~----------~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~  135 (169)
                      ...|.-|+..|..+          ......+.|++.|+.+|-..+-.. -.+||-|..
T Consensus        55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~-Lh~CPGC~~  111 (112)
T TIGR00622        55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES-LHCCPGCIH  111 (112)
T ss_pred             CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh-ccCCcCCCC
Confidence            45799999988643          122345689999999997665543 457999953

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

>smart00249 PHD PHD zinc finger

Probab=85.54  E-value=0.33  Score=27.57  Aligned_cols=30  Identities=37%  Similarity=0.879  Sum_probs=20.8

Q ss_pred             ccccccccccCceeeEcCCCCCcchHhhHHH
Q 030902           91 CAVCLYEFEGGEEIRWLRNCKHIFHRACLDP  121 (169)
Q Consensus        91 C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~  121 (169)
                      |.+|......+ .+.....|...||..|+..
T Consensus         2 C~~C~~~~~~~-~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        2 CSVCGKPDDGG-ELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             cccCCCcCCCC-CEEECCCCCchhhhhhCCC
Confidence            67887766333 3444447999999999754

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

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

Probab=84.03  E-value=1.3  Score=27.26  Aligned_cols=45  Identities=22%  Similarity=0.640  Sum_probs=31.8

Q ss_pred             cccccccccccCceeeEcCCCC--CcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCK--HIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~--H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .|--|-.++..+..-..+  |+  ..|+.+|.+..+..   .||.|...+..
T Consensus         7 nCE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l~~---~CPNCgGelv~   53 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI--CSFECTFCADCAETMLNG---VCPNCGGELVR   53 (57)
T ss_pred             CccccCCCCCCCCCcceE--EeEeCcccHHHHHHHhcC---cCcCCCCcccc
Confidence            677777887765522222  44  57999999998743   99999877654

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

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

Probab=83.68  E-value=0.4  Score=42.97  Aligned_cols=41  Identities=32%  Similarity=0.772  Sum_probs=28.0

Q ss_pred             cccccccccc-----cccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCcc
Q 030902           88 PENCAVCLYE-----FEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC  133 (169)
Q Consensus        88 ~~~C~ICl~~-----~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~C  133 (169)
                      ...|.+|...     |+ .+.++....|+++||..|...    ....||.|
T Consensus       511 gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r----~s~~CPrC  556 (580)
T KOG1829|consen  511 GFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR----KSPCCPRC  556 (580)
T ss_pred             eeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc----cCCCCCch
Confidence            4578888433     33 345555558999999999765    34459999

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=82.73  E-value=1.7  Score=28.67  Aligned_cols=52  Identities=21%  Similarity=0.503  Sum_probs=22.4

Q ss_pred             ccccccccccccc---cCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFE---GGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~---~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ....|.||-+++.   +++...-...|+--.++.|.+-=.+.+.+.||.|+.+..
T Consensus         8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~yk   62 (80)
T PF14569_consen    8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYK   62 (80)
T ss_dssp             SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred             CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcc
Confidence            3458999999874   333322222566778999988666666889999987653

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=82.44  E-value=0.91  Score=37.20  Aligned_cols=34  Identities=24%  Similarity=0.551  Sum_probs=29.5

Q ss_pred             cccccccccccccCceeeEcCCCC----CcchHhhHHHHHhc
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCK----HIFHRACLDPWMDH  125 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~----H~fh~~Ci~~wl~~  125 (169)
                      .-.|.+|.|.+++..-|    +|-    |.||..|-++-+++
T Consensus       268 pLcCTLC~ERLEDTHFV----QCPSVp~HKFCFPCSResIK~  305 (352)
T KOG3579|consen  268 PLCCTLCHERLEDTHFV----QCPSVPSHKFCFPCSRESIKQ  305 (352)
T ss_pred             ceeehhhhhhhccCcee----ecCCCcccceecccCHHHHHh
Confidence            35899999999998888    675    99999999988876

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.43  E-value=1.4  Score=35.52  Aligned_cols=50  Identities=22%  Similarity=0.421  Sum_probs=38.6

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ....|+|---+|...-....+.+|||+|-...+.+-   +..+|++|.+.+..
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei---kas~C~~C~a~y~~  159 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI---KASVCHVCGAAYQE  159 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh---hhccccccCCcccc
Confidence            345799987777776666677799999988887774   35589999987754

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

Probab=81.42  E-value=1  Score=35.40  Aligned_cols=46  Identities=24%  Similarity=0.723  Sum_probs=35.7

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF  137 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~  137 (169)
                      -..|.+|.+-.-.+..   ...|+=.+|..|+...++. ...||.|..-+
T Consensus       181 lk~Cn~Ch~LvIqg~r---Cg~c~i~~h~~c~qty~q~-~~~cphc~d~w  226 (235)
T KOG4718|consen  181 LKNCNLCHCLVIQGIR---CGSCNIQYHRGCIQTYLQR-RDICPHCGDLW  226 (235)
T ss_pred             HHHHhHhHHHhheeec---cCcccchhhhHHHHHHhcc-cCcCCchhccc
Confidence            3489999988655532   3378888999999999986 77899995544

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

Probab=81.16  E-value=0.4  Score=43.63  Aligned_cols=52  Identities=27%  Similarity=0.735  Sum_probs=39.6

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC--CCCCCccCCCCCCChHHH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRTPFVPDEMQE  144 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~~~~~  144 (169)
                      .+|.||.+.+..+..+    .|.|.|+..|+..-+...  ...||+|++.+...+..+
T Consensus        22 lEc~ic~~~~~~p~~~----kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~~E   75 (684)
T KOG4362|consen   22 LECPICLEHVKEPSLL----KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSLRE   75 (684)
T ss_pred             ccCCceeEEeeccchh----hhhHHHHhhhhhceeeccCccccchhhhhhhhhhhccc
Confidence            4899999999887444    899999999998666442  346999998776555444

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

Probab=80.99  E-value=1.7  Score=31.73  Aligned_cols=53  Identities=21%  Similarity=0.419  Sum_probs=35.1

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHH-HHHhc-CCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD-PWMDH-DQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~-~wl~~-~~~~CP~Cr~~~~~  139 (169)
                      .-.+|.||.|.-.++.-+..-.-||-..|-.|-. -|-.- -+..||+|+.++..
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs  133 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS  133 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence            5679999999854433222222489888888765 44432 24579999988754

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

Probab=80.28  E-value=1.5  Score=40.41  Aligned_cols=41  Identities=24%  Similarity=0.548  Sum_probs=29.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCc
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPL  132 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~  132 (169)
                      ..|.+|.-.+..- .+. ...|+|.-|..|+.+|+.. ...||.
T Consensus       780 ~~CtVC~~vi~G~-~~~-c~~C~H~gH~sh~~sw~~~-~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRGV-DVW-CQVCGHGGHDSHLKSWFFK-ASPCAK  820 (839)
T ss_pred             cCceeecceeeee-Eee-cccccccccHHHHHHHHhc-CCCCcc
Confidence            3688886654332 222 3379999999999999985 667765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	169
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-08
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		3e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		5e-05
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		1e-04
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-04

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV 138
           D    CAVCL E E GEE R+L  C H FH  C+D W+     TCPLCR   V
Sbjct: 3   DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLG-SHSTCPLCRLTVV 54

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 90  NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRT 135
            C +CL   E GE++R L  C H+FH+ C+D W+  ++K CP+CR 
Sbjct: 16  KCTICLSILEEGEDVRRL-PCMHLFHQVCVDQWLITNKK-CPICRV 59

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV 138
           E CAVCL +F+  +E+  +  CKH FHR CL  W++  +K CPLC  P +
Sbjct: 16  ELCAVCLEDFKPRDEL-GICPCKHAFHRKCLIKWLE-VRKVCPLCNMPVL 63

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE 141
           C VC+ +FE  + +R L  C H FH  C+D W+  + +TCP+CR    P  
Sbjct: 26  CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN-RTCPICRADSGPSS 74

>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 = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 4/49 (8%)
Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD-HDQKTCPLCRTPFV 138
           C VC  ++  GE +R L  C H+FH +C+ PW++ HD  +CP+CR    
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHD--SCPVCRKSLT 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	169
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	1e-19
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	5e-19
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-18
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-17
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-16
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	8e-15
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	7e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	9e-12
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	7e-11
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	4e-10
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	7e-10
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	6e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-08
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-07
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	6e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-06
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-06
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	5e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	7e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	8e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-04
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	4e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	4e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	5e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	7e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	2e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-04
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-04

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

 Score = 77.4 bits (191), Expect = 1e-19
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCP 131
           LP  +F      +      C VC+ +FE  + +R L  C H FH  C+D W+    +TCP
Sbjct: 9   LPSYRFNPNNHQSEQ--TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWL-KANRTCP 64

Query: 132 LCRTPFVPD 140
           +CR    P 
Sbjct: 65  ICRADSGPS 73

>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 = 75.5 bits (186), Expect = 5e-19
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 75  IKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCR 134
           +K    E    D  E C +CL   E GE++R L  C H+FH+ C+D W+    K CP+CR
Sbjct: 1   MKQDGEEGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWL-ITNKKCPICR 58

Query: 135 TPFVPD 140
                 
Sbjct: 59  VDIEAQ 64

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

 Score = 74.2 bits (183), Expect = 1e-18
 Identities = 28/54 (51%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 85  GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV 138
            D  E CAVCL E E GEE R+L  C H FH  C+D W+     TCPLCR   V
Sbjct: 3   DDGVE-CAVCLAELEDGEEARFLPRCGHGFHAECVDMWL-GSHSTCPLCRLTVV 54

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

 Score = 72.8 bits (179), Expect = 1e-17
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD-HDQKTC 130
           LP I   + +         C +C  E+  G+    L  C H FH+ C+  W+      TC
Sbjct: 25  LPEILVTE-DHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSG--TC 80

Query: 131 PLCRTPFVP 139
           P+CR  F P
Sbjct: 81  PVCRCMFPP 89

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

 Score = 69.4 bits (170), Expect = 1e-16
 Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 85  GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP 139
            +  E CAVCL +F+  +E+     CKH FHR CL  W++  +K CPLC  P + 
Sbjct: 12  LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLE-VRKVCPLCNMPVLQ 64

>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 = 67.1 bits (164), Expect = 1e-15
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE 141
           C VC  ++  GE +R L  C H+FH +C+ PW++    +CP+CR       
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQH-DSCPVCRKSLTGQN 66

>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 = 64.2 bits (157), Expect = 8e-15
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
             C +CL +      +  +  C H+ HR C +  +      CPLC  P 
Sbjct: 6   SGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKE-GYRCPLCSGPS 53

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

 Score = 62.6 bits (152), Expect = 7e-14
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           + C  C  E +  + +     C H FH  C+  W+  +   CPLC+  +V   +
Sbjct: 27  DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNN-RCPLCQQDWVVQRI 79

>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 = 9e-12
 Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
              E C +CL +         L  C H F   C+  W+     TCPLC+ P 
Sbjct: 3   TVAERCPICLEDPS--NYSMAL-PCLHAFCYVCITRWIRQ-NPTCPLCKVPV 50

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

 Score = 54.3 bits (131), Expect = 7e-11
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 6/48 (12%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTP 136
           E C +C+     G     L  C H F + C+D W D   + CP+CR  
Sbjct: 16  EECCICM----DGRADLIL-PCAHSFCQKCIDKWSDR-HRNCPICRLQ 57

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

 Score = 52.2 bits (125), Expect = 4e-10
 Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLR---NCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
               +C +C+  +    +   L     C H+F   CL   + +   TCP CR   
Sbjct: 13  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKI 66

>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 = 51.9 bits (124), Expect = 7e-10
 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 5/61 (8%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPW-MDHDQKTCPLCRTPFVPDEMQE 144
           D  + C +C      G+       C    H  C+  +   + +  CP C   + P E+ +
Sbjct: 13  DAVKICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW-PHEIPK 68

Query: 145 E 145
            
Sbjct: 69  S 69

>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 = 51.8 bits (123), Expect = 2e-09
 Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 18/76 (23%)

Query: 80  LEMVNGDPPENCAVCLYEFE--------------GGEEIRWLRNCKHIFHRACLDPWMDH 125
            E +   P E+C +C+ +                G   +  L  C H FH  CL     +
Sbjct: 17  TEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCN 76

Query: 126 DQK----TCPLCRTPF 137
             K     CP C+T +
Sbjct: 77  GNKDGSLQCPSCKTIY 92

>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 = 51.4 bits (122), Expect = 2e-09
 Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 1/57 (1%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           D    C          E       C H FH  C+  W+   ++ CPL    +   + 
Sbjct: 49  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWL-KTRQVCPLDNREWEFQKY 104

>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 = 49.5 bits (118), Expect = 5e-09
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 4/60 (6%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLR---NCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
               +C +C+  +    +   L     C H+F   CL   + +   TCP CR        
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY 66

>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 = 50.6 bits (120), Expect = 6e-09
 Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 1/57 (1%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           D    C          E       C H FH  C+  W+   ++ CPL    +   + 
Sbjct: 60  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWL-KTRQVCPLDNREWEFQKY 115

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

 Score = 48.6 bits (116), Expect = 8e-09
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 4/56 (7%)

Query: 90  NCAVCLYEFEGGEEIRWLR---NCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           +C +C+  +    +   L     C H+F   CL   + +   TCP CR        
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY 59

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

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           C +C+ +     + R   +C  +   +C+  W+   +  CP CR P    E+
Sbjct: 25  CFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL 73

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

 Score = 49.0 bits (116), Expect = 1e-07
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPW-MDHDQKTCPLCRTPFVPDEMQE 144
           D  + C +C      G+       C    H  C+  +   + +  CP C   + P E+ +
Sbjct: 178 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYW-PHEIPK 233

Query: 145 EFNQR 149
            F+  
Sbjct: 234 VFDPE 238

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

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 5/52 (9%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD 140
             CA+CL        +     CKH+F   C+        K C LCR     D
Sbjct: 16  PECAICLQTCVHPVSL----PCKHVFCYLCVKGASWL-GKRCALCRQEIPED 62

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

 Score = 48.7 bits (115), Expect = 2e-07
 Identities = 13/80 (16%), Positives = 21/80 (26%), Gaps = 14/80 (17%)

Query: 72  LPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLR----NCKHIFHRACLDPWM---- 123
           +P            +    C +C      G E+  +      C    H  CL+ W     
Sbjct: 292 MPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLM 351

Query: 124 ------DHDQKTCPLCRTPF 137
                 +     CP C+   
Sbjct: 352 DGKTFLEVSFGQCPFCKAKL 371

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

 Score = 44.4 bits (105), Expect = 4e-07
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 4/51 (7%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTP 136
            P   C++C        +   +  C H F ++C+     +    CP C   
Sbjct: 13  TPYILCSICKGYLI---DATTITECLHTFCKSCIVRHFYY-SNRCPKCNIV 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 = 47.5 bits (112), Expect = 5e-07
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE 141
           + C +C    +   +++    C H+   +CL  W + + + CP CR      E
Sbjct: 333 QLCKICAENDK---DVKIE-PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 381

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

 Score = 44.3 bits (104), Expect = 6e-07
 Identities = 13/60 (21%), Positives = 21/60 (35%)

Query: 84  NGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ 143
             + P  C +C+   E  +   +   C +   R C       +   CP CR P+  D   
Sbjct: 7   AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV 66

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

 Score = 42.5 bits (100), Expect = 2e-06
 Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 5/51 (9%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTP 136
           + P  C +C   F+     +    C+H F  +C         + C +C  P
Sbjct: 13  EIPFRCFICRQAFQNPVVTK----CRHYFCESCALEHFRATPR-CYICDQP 58

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

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 12/39 (30%), Positives = 19/39 (48%)

Query: 109 NCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEFN 147
           +CKH+F R C+   +      CP CR P  P +++    
Sbjct: 40  SCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVK 78

>2d8s_A Cellular modulator of immune recognition; C-MIR, march8, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 41.8 bits (98), Expect = 5e-06
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDH-DQKTCPLCRTPF 137
              + C +C  E +       +  C      H  H+ACL  W+   D + C LC+  F
Sbjct: 13  SSQDICRICHCEGDDES--PLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEF 68

>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 = 42.7 bits (100), Expect = 7e-06
 Identities = 17/76 (22%), Positives = 22/76 (28%), Gaps = 9/76 (11%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD-EMQEEFNQR 149
           C  C               C H   + CL         +CP CR     +  M    N+ 
Sbjct: 81  CVCCQELVYQPVTT----ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIP--NEI 134

Query: 150 LWAASGVDDLFSEYSS 165
           L     +D  F  YS 
Sbjct: 135 LQTL--LDLFFPGYSK 148

>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 = 42.3 bits (99), Expect = 8e-06
 Identities = 11/50 (22%), Positives = 14/50 (28%), Gaps = 4/50 (8%)

Query: 90  NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP 139
            C  C               C+H   + CLD        +CP CR     
Sbjct: 54  QCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGR 99

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

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 8/33 (24%), Positives = 14/33 (42%)

Query: 110 CKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           C H F  +C+   +      C  C+   V D++
Sbjct: 33  CGHRFCESCMAALLSSSSPKCTACQESIVKDKV 65

>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 = 40.2 bits (94), Expect = 3e-05
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           C +C   F    +   +  C H F + C+  +++   K CP+C    
Sbjct: 18  CVLCGGYFI---DATTIIECLHSFCKTCIVRYLET-SKYCPICDVQV 60

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

 Score = 40.9 bits (95), Expect = 3e-05
 Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 4/69 (5%)

Query: 84  NGDPPENCAVCLYEFEGGEEIRWLR---NCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD 140
            G    +C +C+  +    +   L     C H+F   CL   + +   TCP CR      
Sbjct: 3   MGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKINHK 61

Query: 141 EMQEEFNQR 149
                +   
Sbjct: 62  RYHPIYIGS 70

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 1/49 (2%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
             C     E      +     C H+F   CL   + +   TCP CR   
Sbjct: 76  PICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-ANTCPTCRKKI 123

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

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           C +C   F     +    NC H F   C++ WM   +  CP+CR   
Sbjct: 67  CIICSEYFIEAVTL----NCAHSFCSYCINEWMKR-KIECPICRKDI 108

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

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 7/33 (21%), Positives = 15/33 (45%)

Query: 110 CKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           C H F +AC+   +      CP+     + +++
Sbjct: 36  CGHRFCKACIIKSIRDAGHKCPVDNEILLENQL 68

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

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 7/33 (21%), Positives = 15/33 (45%)

Query: 110 CKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           C H F +AC+   +      CP+     + +++
Sbjct: 36  CGHRFCKACIIKSIRDAGHKCPVDNEILLENQL 68

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 40.5 bits (94), Expect = 5e-05
 Identities = 11/80 (13%), Positives = 19/80 (23%), Gaps = 16/80 (20%)

Query: 79  DLEMVNGDPPEN--CAVCLYEFEGGEEIRWLRN-----CKHIFHRACLDPWMDHDQKTCP 131
              ++         C+ C            LR      C H +   CL   +    + C 
Sbjct: 20  SKTLLGTKLEAKYLCSACRN---------VLRRPFQAQCGHRYCSFCLASILSSGPQNCA 70

Query: 132 LCRTPFVPDEMQEEFNQRLW 151
            C    + +E          
Sbjct: 71  ACVHEGIYEEGISILESSSA 90

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

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 7/28 (25%), Positives = 10/28 (35%)

Query: 110 CKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           C H   + C    ++     CP CR   
Sbjct: 33  CNHTLCKPCFQSTVEKASLCCPFCRRRV 60

>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 Length = 117

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ 143
           C+ C        E   L  C+HIF   C+   +      CP+C TP    +++
Sbjct: 25  CSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG---TGCPVCYTPAWIQDLK 71

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 10/35 (28%), Positives = 13/35 (37%)

Query: 107 LRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE 141
            + C H F   C+   +    K CP CR   V   
Sbjct: 70  TKECLHRFCADCIITALRSGNKECPTCRKKLVSKR 104

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 89  ENCAVCLYEFEGGEEIRWLRN-CKHIFHRACLDPWMDHDQKTCPLCRTP 136
           + C  C         ++ + N C H    +C+D         CP C TP
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTP 52

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

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 2/50 (4%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKT--CPLCRTPFV 138
           C +C+  F   +    L +C H   R CL+  +        CP C     
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITR 67

>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 = 36.3 bits (84), Expect = 4e-04
 Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 4/52 (7%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDP-WMDHDQKTCPLCRTPFVPDE 141
           C +C        +   +  C + +   C+    ++ D+ TCP C    V  +
Sbjct: 18  CLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.68
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.61
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.56
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.55
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.52
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.51
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.51
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.48
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.42
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.42
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.39
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.39
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.39
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.34
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.33
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.33
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.33
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.3
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.28
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.28
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.28
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.26
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.25
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.25
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.24
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.23
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.23
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.2
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.17
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.16
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.15
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.15
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.14
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.14
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.13
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.13
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.12
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.11
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.09
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.06
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.02
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.92
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.91
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.9
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.89
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.87
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.85
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.85
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.8
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.8
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.78
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.78
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.77
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.74
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.73
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.72
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.68
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.64
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.54
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.46
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.36
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.29
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.2
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.16
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.04
3nw0_A	238	Non-structural maintenance of chromosomes element	97.8
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.9
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	94.89
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.37
1we9_A	64	PHD finger family protein; structural genomics, PH	93.89
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	92.1
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	91.21
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	91.06
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	90.42
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	89.72
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	89.21
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	88.73
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	88.36
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	88.2
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	88.16
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	87.98
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	87.91
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	87.74
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	87.35
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	85.97
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	85.78
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.58
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	85.14
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	84.45
1wem_A	76	Death associated transcription factor 1; structura	84.37
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	84.36
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	83.93
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	83.54
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	82.35
2yt5_A	66	Metal-response element-binding transcription facto	81.75
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	80.89
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	80.33
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	80.16

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

Probab=99.68  E-value=8.4e-17  Score=109.02  Aligned_cols=79  Identities=32%  Similarity=0.681  Sum_probs=64.6

Q ss_pred             CCCCCCCCHHHHHhhCCCcccccccccCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCC
Q 030902           57 IPENAPVSARLIREILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTP  136 (169)
Q Consensus        57 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~  136 (169)
                      .....+++++.+.+ +|...+.... .....+..|+||++.+..++.+..+ +|+|.||..||..|+.. +.+||+||..
T Consensus        11 ~~~~~~~s~~~i~~-lp~~~~~~~~-~~~~~~~~C~IC~~~~~~~~~~~~l-~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~   86 (91)
T 2l0b_A           11 MVANPPASKESIDA-LPEILVTEDH-GAVGQEMCCPICCSEYVKGDVATEL-PCHHYFHKPCVSIWLQK-SGTCPVCRCM   86 (91)
T ss_dssp             SSCCCCCCHHHHHT-SCEEECCTTC-SSSSSCSEETTTTEECCTTCEEEEE-TTTEEEEHHHHHHHHTT-TCBCTTTCCB
T ss_pred             CcCCCCCCHHHHHh-CCCeeecccc-cccCCCCCCcccChhhcCCCcEEec-CCCChHHHHHHHHHHHc-CCcCcCcCcc
Confidence            34556778888766 8988877654 2334567899999999999888888 79999999999999986 7799999998


Q ss_pred             CCC
Q 030902          137 FVP  139 (169)
Q Consensus       137 ~~~  139 (169)
                      +.+
T Consensus        87 ~~~   89 (91)
T 2l0b_A           87 FPP   89 (91)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

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

Probab=99.61  E-value=4e-16  Score=101.74  Aligned_cols=66  Identities=35%  Similarity=0.851  Sum_probs=54.7

Q ss_pred             hCCCcccccccccCCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           71 ILPVIKFQDLEMVNGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        71 ~l~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .+|..+++...  ...++..|+||++++..++.++.+ +|+|.||..|+.+|+.. +.+||+||+.+.+.
T Consensus         8 ~lp~~~~~~~~--~~~~~~~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            8 QLPSYRFNPNN--HQSEQTLCVVCMCDFESRQLLRVL-PCNHEFHAKCVDKWLKA-NRTCPICRADSGPS   73 (75)
T ss_dssp             SCCCEEBCSSS--CSSSCCEETTTTEECCBTCEEEEE-TTTEEEETTHHHHHHHH-CSSCTTTCCCCCCC
T ss_pred             hCCcEEecCcc--ccCCCCCCeECCcccCCCCeEEEE-CCCCHhHHHHHHHHHHc-CCcCcCcCCcCCCC
Confidence            36777776543  334567899999999999888888 79999999999999987 77999999988653

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

Probab=99.56  E-value=1.6e-15  Score=92.94  Aligned_cols=51  Identities=51%  Similarity=1.067  Sum_probs=45.1

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ++.+|+||++++..++.+..+++|+|.||..|+.+|+.. +.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~-~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc-CCcCcCCCCEeE
Confidence            356899999999998888888559999999999999986 789999998864

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

Probab=99.55  E-value=6.3e-15  Score=94.37  Aligned_cols=53  Identities=42%  Similarity=1.043  Sum_probs=46.5

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ...+..|+||++.+..+..+..+ +|+|.||..|+..|+.. +.+||+||..+..
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRL-PCMHLFHQVCVDQWLIT-NKKCPICRVDIEA   63 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEEC-TTSCEEEHHHHHHHHHH-CSBCTTTCSBSCS
T ss_pred             CCCCCCCeeCCccccCCCcEEEe-CCCCHHHHHHHHHHHHc-CCCCcCcCccccC
Confidence            35566899999999888888888 89999999999999987 7789999998754

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

Probab=99.52  E-value=7.8e-15  Score=95.18  Aligned_cols=52  Identities=44%  Similarity=0.999  Sum_probs=46.6

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ..+..|+||++.+..+..+..+ +|+|.||..|+.+|+.. +.+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGIC-PCKHAFHRKCLIKWLEV-RKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEE-TTTEEEEHHHHHHHHHH-CSBCTTTCCBCSS
T ss_pred             CCCCCCcCCCcccCCCCcEEEc-CCCCEecHHHHHHHHHc-CCcCCCcCccccc
Confidence            4466899999999999888888 89999999999999987 6799999998864

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

Probab=99.51  E-value=9.8e-15  Score=95.64  Aligned_cols=54  Identities=33%  Similarity=0.979  Sum_probs=47.6

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ..+..|+||++.|..+..+..+ +|+|.||..||.+|+.. +.+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQL-PCNHLFHDSCIVPWLEQ-HDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEEC-TTSCEEETTTTHHHHTT-TCSCTTTCCCCCCSC
T ss_pred             CCCCCCeeCCccccCCCCEEEe-CCCCeecHHHHHHHHHc-CCcCcCcCCccCCcc
Confidence            4466899999999998888888 89999999999999986 779999999987654

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

Probab=99.51  E-value=8.5e-15  Score=97.09  Aligned_cols=53  Identities=26%  Similarity=0.782  Sum_probs=42.0

Q ss_pred             cccccccccccccc-----------CceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           87 PPENCAVCLYEFEG-----------GEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        87 ~~~~C~ICl~~~~~-----------~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      +++.|+||+++|..           ++.++.+++|+|.||..||.+|+.. +.+||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ-NNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTT-CCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHh-CCCCCCcCCCcchh
Confidence            34568888777753           4556677579999999999999986 77999999987643

>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=99.48  E-value=2.6e-14  Score=87.33  Aligned_cols=50  Identities=28%  Similarity=0.747  Sum_probs=42.0

Q ss_pred             ccccccccccccccCc-eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGE-EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .+..|+||++.+.+++ .+..+ +|+|.||..|+.+|+.. +.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVL-PCGHLLHRTCYEEMLKE-GYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEEC-TTSCEEETTHHHHHHHH-TCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEec-CCCCcccHHHHHHHHHc-CCcCCCCCCcCC
Confidence            4568999999997654 45555 89999999999999997 689999999874

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

Probab=99.42  E-value=1.3e-13  Score=96.46  Aligned_cols=53  Identities=28%  Similarity=0.642  Sum_probs=41.4

Q ss_pred             ccccccccccccccCc---------------eeeEcCCCCCcchHhhHHHHHhc----CCCCCCccCCCCCCC
Q 030902           87 PPENCAVCLYEFEGGE---------------EIRWLRNCKHIFHRACLDPWMDH----DQKTCPLCRTPFVPD  140 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~---------------~~~~l~~C~H~fh~~Ci~~wl~~----~~~~CP~Cr~~~~~~  140 (169)
                      .++.|+||++.|..+.               .+..+ +|+|.||..||..|+..    .+.+||+||+.+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLT-KCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEES-SSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecC-CCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3568999999997653               23345 89999999999999952    356899999987543

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

Probab=99.42  E-value=8.6e-14  Score=89.26  Aligned_cols=55  Identities=24%  Similarity=0.576  Sum_probs=45.1

Q ss_pred             CccccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .++..|+||++.+.++    ..+..+ +|||.||..|+.+|+.. +.+||+||..+...++
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~   66 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY   66 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEEC-TTSCEEEHHHHHHHHHH-CSBCTTTCCBCCCCSC
T ss_pred             CCCCCCcccChhhhccccccCCeEeC-CCCChHhHHHHHHHHHc-CCCCCCCCCccChhhe
Confidence            4466899999999764    344555 89999999999999987 7799999999876543

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

Probab=99.39  E-value=2.1e-13  Score=86.80  Aligned_cols=52  Identities=25%  Similarity=0.605  Sum_probs=42.8

Q ss_pred             CccccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .+...|+||++.+.++    ..+..+ +|+|.||..|+..|+.. +.+||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKN-ANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEEC-SSSCEEEHHHHHHHHHH-CSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeC-CCCChhcHHHHHHHHHc-CCCCCCCCCccCc
Confidence            4456899999999764    233455 89999999999999987 7799999998753

>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=99.39  E-value=2e-13  Score=94.98  Aligned_cols=51  Identities=27%  Similarity=0.705  Sum_probs=42.2

Q ss_pred             CccccccccccccccCc---------------eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGE---------------EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~---------------~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ..++.|+||++.|..+.               .+..+ +|+|.||..||..|+.. +.+||+||+.+.
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~-~C~H~FH~~Ci~~Wl~~-~~~CP~Cr~~~~  100 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWG-VCNHAFHFHCISRWLKT-RQVCPLDNREWE  100 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEE-TTSCEEEHHHHHHHHTT-CSBCSSSCSBCC
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeec-ccCcEECHHHHHHHHHc-CCcCcCCCCcce
Confidence            45678999999998541               24555 89999999999999986 889999999864

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

Probab=99.39  E-value=1.5e-13  Score=86.16  Aligned_cols=53  Identities=25%  Similarity=0.592  Sum_probs=43.7

Q ss_pred             ccccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           87 PPENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ++..|+||++.+..+    ..+..+ +|||.||..|+.+|+.. +.+||+||.++...+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEE-TTSCEEEHHHHHHHHHH-CSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeC-CCCCchhHHHHHHHHHc-CCCCCCCCccCCccc
Confidence            356899999999764    334455 89999999999999987 779999999987654

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

Probab=99.34  E-value=1.1e-12  Score=83.25  Aligned_cols=52  Identities=19%  Similarity=0.574  Sum_probs=43.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      .++..|+||++.+.++..+    +|||.||..|+..|+......||+||..+..++
T Consensus        13 ~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSPKQT----ECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCEECTTTCCEESSCCCC----SSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CcCCCCCCCChHhcCeeEC----CCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            3456899999999877654    899999999999999644678999999987554

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

Probab=99.33  E-value=7.5e-13  Score=87.59  Aligned_cols=54  Identities=26%  Similarity=0.766  Sum_probs=43.6

Q ss_pred             CCccccccccccccccCceeeEcCCCC-----CcchHhhHHHHHhcCC-CCCCccCCCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCK-----HIFHRACLDPWMDHDQ-KTCPLCRTPFVPD  140 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~-----H~fh~~Ci~~wl~~~~-~~CP~Cr~~~~~~  140 (169)
                      ..++..|.||++++..++.+ .+ +|.     |.||..||++|+..+. .+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~-pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-IT-PCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-EC-SSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Ee-ccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            34456899999999877665 46 796     9999999999998632 5899999988643

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

Probab=99.33  E-value=7.7e-13  Score=83.65  Aligned_cols=55  Identities=20%  Similarity=0.529  Sum_probs=43.8

Q ss_pred             ccccccccc-ccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           88 PENCAVCLY-EFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        88 ~~~C~ICl~-~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      +..|+||++ .+.++.....+.+|||.||..|+.+|+..+...||+||..+...++
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            458999999 7877764433338999999999999987656789999999876543

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

Probab=99.33  E-value=3.4e-13  Score=86.83  Aligned_cols=51  Identities=31%  Similarity=0.528  Sum_probs=42.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      .++..|+||++.+.++..   + +|+|.||..|+..|+.. +..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~---~-~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           13 LTVPECAICLQTCVHPVS---L-PCKHVFCYLCVKGASWL-GKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSCCBCSSSSSBCSSEEE---E-TTTEEEEHHHHHHCTTC-SSBCSSSCCBCCHHH
T ss_pred             CCCCCCccCCcccCCCEE---c-cCCCHHHHHHHHHHHHC-CCcCcCcCchhCHhh
Confidence            445689999999877643   3 89999999999999986 679999999886433

>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=99.30  E-value=2.7e-13  Score=95.88  Aligned_cols=52  Identities=25%  Similarity=0.544  Sum_probs=1.6

Q ss_pred             CccccccccccccccCc--------------eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGE--------------EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~--------------~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ..++.|+||+++|..+.              ....+++|+|.||..||.+|+.. +.+||+||+++.
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~-~~~CP~Cr~~~~  111 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDNREWE  111 (117)
T ss_dssp             CCC----------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc-CCcCCCCCCeee
Confidence            45679999999997532              12232389999999999999987 789999999763

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

Probab=99.28  E-value=3e-12  Score=85.19  Aligned_cols=55  Identities=22%  Similarity=0.553  Sum_probs=44.3

Q ss_pred             CccccccccccccccCce-eeEcCCCCCcchHhhHHHHHhcC--CCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEE-IRWLRNCKHIFHRACLDPWMDHD--QKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~-~~~l~~C~H~fh~~Ci~~wl~~~--~~~CP~Cr~~~~~~~  141 (169)
                      .+...|+||++.+...+. ...+ +|||.||..|+..|+..+  ...||+||..+...+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLL-HCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEEC-SSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             cCCCCCccCCccccccCCCeEEC-CCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            345689999999987654 4455 899999999999999863  368999999876543

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

Probab=99.28  E-value=2.4e-12  Score=82.98  Aligned_cols=52  Identities=19%  Similarity=0.499  Sum_probs=42.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      .++..|+||++.+.++..   +++|+|.||..||..|+.. +..||+||..+...+
T Consensus        13 ~~~~~C~IC~~~~~~p~~---~~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           13 TPYILCSICKGYLIDATT---ITECLHTFCKSCIVRHFYY-SNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CGGGSCTTTSSCCSSCEE---CSSSCCEECHHHHHHHHHH-CSSCTTTCCCCCSSC
T ss_pred             CCCCCCCCCChHHHCcCE---ECCCCCHHHHHHHHHHHHc-CCcCCCcCcccCccc
Confidence            345689999999877532   2389999999999999986 779999999987654

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

Probab=99.28  E-value=1.6e-12  Score=82.71  Aligned_cols=49  Identities=33%  Similarity=0.798  Sum_probs=41.1

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .+..|+||++.+.++  +..+ +|||.||..|+..|+.. +.+||+||.++..
T Consensus         4 ~~~~C~IC~~~~~~~--~~~~-~C~H~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNY--SMAL-PCLHAFCYVCITRWIRQ-NPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEET-TTTEEESTTHHHHHHHH-SCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCC--cEec-CCCCeeHHHHHHHHHhC-cCcCcCCChhhHh
Confidence            356899999998754  3455 89999999999999986 7799999998853

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

Probab=99.26  E-value=3.5e-12  Score=82.14  Aligned_cols=52  Identities=23%  Similarity=0.553  Sum_probs=42.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc--CCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH--DQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~~~~~  141 (169)
                      ..+..|+||++.+.++..   + +|||.||..|+..|+..  ++..||+||..+...+
T Consensus        18 ~~~~~C~IC~~~~~~~~~---~-~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDILQKPVT---I-DCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBCSSEEE---C-TTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCcccCCeEE---c-CCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            345689999999886544   3 89999999999999963  3568999999986544

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

Probab=99.25  E-value=7.6e-13  Score=84.75  Aligned_cols=49  Identities=31%  Similarity=0.846  Sum_probs=41.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .++..|+||++.+..    ..+ +|+|.||..|+..|+.. +.+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~----~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LIL-PCAHSFCQKCIDKWSDR-HRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEE-TTTEEECHHHHHHSSCC-CSSCHHHHHCTTCC
T ss_pred             CCCCCCeeCCcCccC----ccc-CCCCcccHHHHHHHHHC-cCcCCCcCCcccCC
Confidence            345689999999876    345 89999999999999985 88999999988654

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

Probab=99.25  E-value=4.8e-12  Score=83.35  Aligned_cols=48  Identities=23%  Similarity=0.573  Sum_probs=40.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .....|+||++.+..+.   .+ +|+|.||..|+..|+.. ...||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p~---~~-~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNPV---VT-KCRHYFCESCALEHFRA-TPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSEE---EC-TTSCEEEHHHHHHHHHH-CSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCee---Ec-cCCCHhHHHHHHHHHHC-CCcCCCcCcccc
Confidence            34568999999997754   34 89999999999999986 779999999875

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

Probab=99.24  E-value=5e-12  Score=82.01  Aligned_cols=51  Identities=18%  Similarity=0.430  Sum_probs=41.2

Q ss_pred             CccccccccccccccCceeeEcCC-CCCcchHhhHHHHHhcC-CCCCCccCCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRN-CKHIFHRACLDPWMDHD-QKTCPLCRTPFVPD  140 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~-C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~~  140 (169)
                      ..+..|+||++.+.++..   + + |||.||..||..|+... ...||+||.++...
T Consensus        13 ~~~~~C~IC~~~~~~p~~---~-~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2yur_A           13 PDELLCLICKDIMTDAVV---I-PCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   65 (74)
T ss_dssp             CGGGSCSSSCCCCTTCEE---C-SSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCT
T ss_pred             CCCCCCcCCChHHhCCeE---c-CCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCc
Confidence            345689999999987654   4 7 99999999999999862 25899999976543

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

Probab=99.23  E-value=4.1e-12  Score=82.98  Aligned_cols=52  Identities=17%  Similarity=0.436  Sum_probs=43.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      .++..|+||++.+.++..+    +|||.||..||..|+..++.+||+||.++...+
T Consensus         6 ~~~~~C~IC~~~~~~Pv~~----~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            6 PEYFRCPISLELMKDPVIV----STGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSSEEEE----TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             cccCCCCCccccccCCEEc----CCCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            3456899999999887544    899999999999999865778999999886543

>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=99.23  E-value=2.8e-12  Score=87.98  Aligned_cols=52  Identities=21%  Similarity=0.667  Sum_probs=42.3

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ++..|+||++.+..+..  .+ +|||.||..||..|+...+..||+||.++...+
T Consensus        21 ~~~~C~IC~~~~~~p~~--~~-~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           21 EVFRCFICMEKLRDARL--CP-HCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHTBCTTTCSBCSSEEE--CT-TTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCccCCccccCccc--cC-CCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            34589999999976533  14 899999999999999874468999999986544

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

Probab=99.20  E-value=5.5e-12  Score=91.30  Aligned_cols=47  Identities=32%  Similarity=0.820  Sum_probs=40.4

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|+||++.+..+..   + +|||.||..||..|+.. +.+||+||.++..
T Consensus        53 ~~~C~iC~~~~~~~~~---~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIEAVT---L-NCAHSFCSYCINEWMKR-KIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSSEEE---E-TTSCEEEHHHHHHHTTT-CSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCCceE---C-CCCCCccHHHHHHHHHc-CCcCCCCCCcCCC
Confidence            3479999999977643   4 89999999999999986 7899999999864

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

Probab=99.17  E-value=7.8e-12  Score=81.60  Aligned_cols=53  Identities=21%  Similarity=0.603  Sum_probs=43.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC------CCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD------QKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~------~~~CP~Cr~~~~~~~~  142 (169)
                      .++..|+||++.+.++..+    +|||.||..|+..|+...      ...||+||..+...++
T Consensus        10 ~~~~~C~IC~~~~~~p~~l----~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   68 (79)
T 2egp_A           10 QEEVTCPICLELLTEPLSL----DCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHL   68 (79)
T ss_dssp             CCCCEETTTTEECSSCCCC----SSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGG
T ss_pred             ccCCCCcCCCcccCCeeEC----CCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhC
Confidence            3456899999999876554    899999999999999752      5679999999876554

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

Probab=99.16  E-value=1.4e-11  Score=87.61  Aligned_cols=53  Identities=25%  Similarity=0.596  Sum_probs=43.7

Q ss_pred             ccccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           87 PPENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      ++..|+||++.+.++    ..+..+ +|||.||..||.+|+.. +.+||+||..+....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEE-TTCCEEEHHHHHHHHTT-CSBCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEec-CCCChhhHHHHHHHHHh-CCCCCCCCCcCcccc
Confidence            456899999999765    334555 89999999999999986 779999999887544

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

Probab=99.15  E-value=2.7e-11  Score=75.86  Aligned_cols=44  Identities=27%  Similarity=0.622  Sum_probs=36.5

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc--CCCCCCcc
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH--DQKTCPLC  133 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~~CP~C  133 (169)
                      .++..|+||++.+.++..+    +|||.||..||.+|+..  ++..||+|
T Consensus        18 ~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQKPVTI----DCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSSCEEC----TTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCCeEEe----CCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3456899999999876444    89999999999999984  35689998

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

Probab=99.15  E-value=2.8e-11  Score=79.69  Aligned_cols=51  Identities=27%  Similarity=0.702  Sum_probs=42.0

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-----CCCCCccCCCCCCCh
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-----QKTCPLCRTPFVPDE  141 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-----~~~CP~Cr~~~~~~~  141 (169)
                      .+..|+||++.+..+.   .+ +|+|.||..|+..|+...     ...||.||..+...+
T Consensus        18 ~~~~C~IC~~~~~~p~---~~-~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           18 EEVTCPICLELLKEPV---SA-DCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             TTTSCTTTCSCCSSCE---EC-TTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             cCCCCcCCChhhCcce---eC-CCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            4568999999998765   34 899999999999999862     567999999987543

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

Probab=99.14  E-value=3.4e-11  Score=78.33  Aligned_cols=51  Identities=20%  Similarity=0.572  Sum_probs=41.5

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      +..+.|+||++.+..++...   .|+|.||..||.+|++.. +.+||+||..+..
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            34568999999998765443   799999999999999862 2689999998753

>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=99.14  E-value=2e-11  Score=86.64  Aligned_cols=48  Identities=23%  Similarity=0.423  Sum_probs=41.0

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|+||++.+..+..+    +|||.||..|+..|+..+...||+||..+..
T Consensus        52 ~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSEEEC----TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCcEEe----eCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45899999999876444    8999999999999998645589999998865

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

Probab=99.13  E-value=3.7e-11  Score=73.79  Aligned_cols=44  Identities=32%  Similarity=0.838  Sum_probs=36.1

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc--CCCCCCcc
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH--DQKTCPLC  133 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~~CP~C  133 (169)
                      .+...|+||++.+.++..+    +|+|.||..|+.+|+..  .+..||+|
T Consensus        13 ~~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEPVII----ECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSCCCC----SSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCccEeC----CCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            3456899999999887443    89999999999999653  46789998

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

Probab=99.13  E-value=8e-11  Score=79.09  Aligned_cols=48  Identities=19%  Similarity=0.444  Sum_probs=40.0

Q ss_pred             CccccccccccccccCceeeEcCC-CCCcchHhhHHHHHhcC-CCCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRN-CKHIFHRACLDPWMDHD-QKTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~-C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~  137 (169)
                      .++..|+||++.|.++..+    + |||.||..||..|+... ...||+||..+
T Consensus        11 ~~~~~C~IC~~~~~~p~~~----~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           11 PDELLCLICKDIMTDAVVI----PCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CTTTEETTTTEECSSCEEC----TTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             CcCCCCCCCChhhcCceEC----CCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            3456899999999877544    7 99999999999999752 36899999987

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

Probab=99.12  E-value=5.1e-11  Score=78.39  Aligned_cols=51  Identities=27%  Similarity=0.755  Sum_probs=42.2

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc-----CCCCCCccCCCCCCCh
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH-----DQKTCPLCRTPFVPDE  141 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~-----~~~~CP~Cr~~~~~~~  141 (169)
                      +...|+||++.+..+..+    +|+|.||..|+..|+..     +...||.||..+...+
T Consensus        18 ~~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           18 EEVTCPICLELLTQPLSL----DCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCTTTCSCCSSCBCC----SSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             CCCCCCCCCcccCCceeC----CCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            456899999999876544    89999999999999975     2568999999987644

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

Probab=99.11  E-value=2.2e-11  Score=83.05  Aligned_cols=48  Identities=21%  Similarity=0.591  Sum_probs=40.4

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ...|+||++.+..+..+   ++|||.||..|+..|+.. +..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p~~~---~~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNIAMII---PQCSHNYCSLCIRKFLSY-KTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSSEEEC---TTTCCEEEHHHHHHHHTT-CCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCCcCEE---CCCCCHhhHHHHHHHHHC-CCCCCCCCCcCCh
Confidence            45899999999765322   389999999999999986 7799999998864

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

Probab=99.09  E-value=2.8e-11  Score=85.96  Aligned_cols=55  Identities=24%  Similarity=0.576  Sum_probs=44.5

Q ss_pred             CccccccccccccccC----ceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGG----EEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~----~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .....|+||++.+..+    .....+ +|||.||..|+++|+.. +.+||+||..+..+++
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~  128 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVST-ECGHVFCSQCLRDSLKN-ANTCPTCRKKINHKRY  128 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEE-TTSBEEEHHHHHHHHHH-CSBCTTTCCBCCGGGE
T ss_pred             CCCCCCCCCCCccccccccCcceEeC-CCCChhhHHHHHHHHHc-CCCCCCCCCcCChhcc
Confidence            3456899999999764    233445 89999999999999997 7799999999976553

>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=99.06  E-value=3.2e-11  Score=84.55  Aligned_cols=50  Identities=30%  Similarity=0.694  Sum_probs=42.1

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      +..|+||++.+.++..   + +|||.||..|+..|+......||+||.++...+
T Consensus        23 ~~~C~IC~~~~~~p~~---~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           23 SISCQICEHILADPVE---T-SCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HTBCTTTCSBCSSEEE---C-TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcHhcCcEE---c-CCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            4589999999977644   3 899999999999999865668999999986544

>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=99.06  E-value=7e-11  Score=83.19  Aligned_cols=52  Identities=19%  Similarity=0.555  Sum_probs=42.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      .++..|+||++.+..+..   + +|||.||..|+..|+..+..+||+||.++...+
T Consensus        16 ~~~~~C~IC~~~~~~p~~---~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           16 ESKYECPICLMALREAVQ---T-PCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CGGGBCTTTCSBCSSEEE---C-TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCcCChhhcCeEE---C-CcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            445689999999987633   4 899999999999999874459999999987543

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

Probab=99.05  E-value=1.1e-10  Score=76.75  Aligned_cols=56  Identities=23%  Similarity=0.564  Sum_probs=42.4

Q ss_pred             CccccccccccccccCc-eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGE-EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~-~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .++..|+||++.+...+ .+..+ +|||.||..|+..+.......||.||.++....+
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~-~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPC-TCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSS-TTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCcccccccccc-CCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            34568999999986443 22223 5999999999999886556789999999876543

>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=99.05  E-value=7.2e-11  Score=81.92  Aligned_cols=49  Identities=24%  Similarity=0.689  Sum_probs=40.5

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC--CCCCccCCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ--KTCPLCRTPFVPD  140 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~  140 (169)
                      ...|+||++.+..+..+    +|||.||..|+..|+..+.  ..||+||..+...
T Consensus        21 ~~~C~IC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKEPVST----KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSSCCBC----TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcCeEEC----CCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            45899999999877554    8999999999999998522  4799999988653

>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=99.05  E-value=8.8e-11  Score=81.34  Aligned_cols=50  Identities=24%  Similarity=0.638  Sum_probs=41.4

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .+..|+||++.+.++  +... +|||.||..|+..|+.. ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~-~CgH~fC~~Ci~~~~~~-~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA--TTII-ECLHSFCKTCIVRYLET-SKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE--EEET-TTCCEEEHHHHHHHHTS-CSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc--CEeC-CCCChhhHHHHHHHHHh-CCcCcCCCcccccc
Confidence            355899999999764  3334 89999999999999986 68999999988653

>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=99.05  E-value=8.3e-11  Score=86.44  Aligned_cols=49  Identities=20%  Similarity=0.411  Sum_probs=41.6

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      ...|+||++.+..+..   + +|||.||..||..|+..+...||+||..+...
T Consensus        78 ~~~C~IC~~~~~~pv~---~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQPVT---T-ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSEEE---C-TTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCCEE---c-CCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4589999999987655   3 89999999999999986455899999998754

>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=99.05  E-value=9.4e-11  Score=87.06  Aligned_cols=50  Identities=26%  Similarity=0.606  Sum_probs=41.5

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ....|+||++.+.++  +..+ +|||.||..|+..|+..++..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~p--~~~~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKNT--MTTK-ECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSSE--EEET-TTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhCc--CEeC-CCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            345899999999864  3334 8999999999999998657789999998853

>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=99.02  E-value=2.7e-11  Score=84.79  Aligned_cols=48  Identities=19%  Similarity=0.621  Sum_probs=40.9

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ++..|+||++.+..+..+    +|||.||..|+..|+..++..||+||..+.
T Consensus        14 ~~~~C~iC~~~~~~p~~~----~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           14 SECQCGICMEILVEPVTL----PCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHBCTTTCSBCSSCEEC----TTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCccCCcccCceeEc----CCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            356899999999876544    899999999999999765678999999875

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

Probab=98.92  E-value=4.1e-10  Score=75.00  Aligned_cols=52  Identities=8%  Similarity=0.013  Sum_probs=44.5

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .....|+||++.|.++..+    +|||.|++.||..|+.. +.+||.||.++...++
T Consensus        12 p~~~~CpI~~~~m~dPV~~----~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~~l   63 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDPVRL----PSGTVMDRSIILRHLLN-SPTDPFNRQMLTESML   63 (85)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHH-CSBCTTTCCBCCGGGC
T ss_pred             chheECcccCchhcCCeEC----CCCCEECHHHHHHHHhc-CCCCCCCcCCCChHhc
Confidence            3456899999999988665    89999999999999986 7899999998876443

>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=98.91  E-value=2.2e-10  Score=83.38  Aligned_cols=49  Identities=16%  Similarity=0.435  Sum_probs=41.1

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .++..|+||++.+.++..   + +|||.||..||..|+..+...||+||.++.
T Consensus        29 ~~~~~C~IC~~~~~~pv~---~-~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           29 EAKYLCSACRNVLRRPFQ---A-QCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CGGGBCTTTCSBCSSEEE---C-TTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CcCcCCCCCChhhcCcEE---C-CCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            456689999999988744   3 899999999999999864558999999763

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

Probab=98.90  E-value=7.2e-10  Score=92.59  Aligned_cols=50  Identities=22%  Similarity=0.628  Sum_probs=41.0

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      ....|+||++.+..+..   + +|||.||..|+..|+......||+||.++...
T Consensus       331 ~~~~C~ICle~~~~pv~---l-pCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKI---E-PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSSBCTTTSSSBCCEEE---E-TTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCccCcCCCCeEE---e-CCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            34689999999866533   3 89999999999999984477899999988643

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

Probab=98.89  E-value=4.4e-10  Score=68.99  Aligned_cols=46  Identities=24%  Similarity=0.558  Sum_probs=37.7

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      .+...|+||++.+..+..+    +|||.||..|+..|    ...||+||..+..
T Consensus         4 ~~~~~C~IC~~~~~~p~~l----~CgH~fC~~Ci~~~----~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLL----PCLHTLCSGCLEAS----GMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCS----TTSCCSBTTTCSSS----SSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCCeEEc----CCCCcccHHHHccC----CCCCCcCCcEeec
Confidence            4456899999999887444    89999999998873    5689999998753

>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=98.87  E-value=5e-10  Score=76.88  Aligned_cols=52  Identities=10%  Similarity=0.034  Sum_probs=44.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .....|+||++.|.++..+    +|||.|++.||..|+.. +.+||.||.++...++
T Consensus        27 p~~~~CpI~~~~m~dPV~~----~cGhtf~r~~I~~~l~~-~~~cP~~~~~l~~~~L   78 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDPVRL----PSGTIMDRSIILRHLLN-SPTDPFNRQTLTESML   78 (100)
T ss_dssp             STTTBCTTTCSBCSSEEEE----TTTEEEEHHHHHHHTTS-CSBCSSSCCBCCTTSS
T ss_pred             cHhhCCcCccCcccCCeEC----CCCCEEchHHHHHHHHc-CCCCCCCCCCCChhhc
Confidence            4456899999999998766    89999999999999985 7899999999876544

>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=98.85  E-value=9.4e-10  Score=75.25  Aligned_cols=52  Identities=12%  Similarity=0.073  Sum_probs=44.3

Q ss_pred             CccccccccccccccCceeeEcCCCC-CcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCK-HIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .+...|+||++.|.++..+    +|| |.|++.||..|+.. +.+||.||.++...++
T Consensus        20 p~~~~CpI~~~~m~dPV~~----~cG~htf~r~cI~~~l~~-~~~cP~~~~~l~~~~L   72 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDPVVL----PSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTTTS
T ss_pred             cHhcCCcCccccccCCeEC----CCCCeEECHHHHHHHHHh-CCCCCCCCCCCChhhc
Confidence            3456899999999988665    899 99999999999986 7799999999876443

>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=98.85  E-value=1.3e-09  Score=68.80  Aligned_cols=50  Identities=26%  Similarity=0.541  Sum_probs=39.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .++..|.||++...+.. +..+ +|||. |+..|+..|... +..||+||.++.
T Consensus         6 ~~~~~C~IC~~~~~~~~-~~~~-pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   56 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGC-IVHG-KTGHLMACFTCAKKLKKR-NKPCPVCRQPIQ   56 (64)
T ss_dssp             GGGSCCTTTSSSCSCEE-EEET-TEEEEEECHHHHHHHHHT-TCCCTTTCCCCC
T ss_pred             CCcCCCCcCCCCCCCEE-EECC-CCCChhhHHHHHHHHHHc-CCcCCCcCcchh
Confidence            34568999999865442 2234 89999 899999999985 778999999874

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.80  E-value=2.4e-09  Score=67.30  Aligned_cols=50  Identities=18%  Similarity=0.414  Sum_probs=39.2

Q ss_pred             CccccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      .....|.||++...+.. +..+ ||||. |+..|+..|... ...||+||.++.
T Consensus         5 ~~~~~C~IC~~~~~~~~-~~~~-pCgH~~~C~~C~~~~~~~-~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGN-IIHG-RTGHLVTCFHCARRLKKA-GASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSCEE-EEET-TEEEEEECHHHHHHHHHT-TCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCCeE-EEec-CCCCHhHHHHHHHHHHHh-CCcCCCcCchhh
Confidence            34568999999864432 2234 89998 999999999876 678999999874

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

Probab=98.80  E-value=2.2e-09  Score=79.89  Aligned_cols=51  Identities=20%  Similarity=0.555  Sum_probs=42.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .+...|+||++.+.++..   + +|||.||..|+..|+..+..+||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~pv~---~-~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALREAVQ---T-PCGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSSEEE---C-TTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcCcEE---C-CCCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            456689999999988743   4 89999999999999986455999999998754

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.78  E-value=3.2e-09  Score=71.64  Aligned_cols=56  Identities=23%  Similarity=0.606  Sum_probs=43.3

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc----C---CCCCCc--cCCC--CCCChHH
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH----D---QKTCPL--CRTP--FVPDEMQ  143 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~----~---~~~CP~--Cr~~--~~~~~~~  143 (169)
                      ....|+||++++..++.+... +|+|.||..|+..++..    +   ...||.  |+..  +.+....
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~-~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~   70 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIA-QCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIE   70 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEET-TTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHH
T ss_pred             CCcCCcccCcccccccceEcC-CCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHH
Confidence            355899999999877666555 89999999999999864    1   236999  9998  6654443

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.78  E-value=2.5e-09  Score=84.67  Aligned_cols=53  Identities=8%  Similarity=0.105  Sum_probs=44.5

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .....|+||++.|.++..+    +|||.|+..||..|+..++.+||+||.++...++
T Consensus       206 ~~~~~c~i~~~~~~dPv~~----~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l  258 (281)
T 2c2l_A          206 PDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQL  258 (281)
T ss_dssp             CSTTBCTTTCSBCSSEEEC----SSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGC
T ss_pred             CcccCCcCcCCHhcCCeEC----CCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcC
Confidence            4566899999999988665    8999999999999998655569999999875443

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

Probab=98.77  E-value=9.2e-10  Score=90.27  Aligned_cols=54  Identities=22%  Similarity=0.572  Sum_probs=40.9

Q ss_pred             CCccccccccccccccCcee----eEcCCCCCcchHhhHHHHHhcCC----------CCCCccCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEI----RWLRNCKHIFHRACLDPWMDHDQ----------KTCPLCRTPFV  138 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~----~~l~~C~H~fh~~Ci~~wl~~~~----------~~CP~Cr~~~~  138 (169)
                      +....+|+||++.+..+..+    ...++|+|.||..|+.+|+....          .+||.||+++.
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            35667899999998873333    22237999999999999997511          36999999875

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.74  E-value=1.5e-09  Score=76.16  Aligned_cols=46  Identities=26%  Similarity=0.609  Sum_probs=38.3

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ...|+||++.+..+..+   ++|||.||..||..|+.   ..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~pv~~---~~CgH~fC~~Ci~~~~~---~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCSRCTNILREPVCL---GGCEHIFCSNCVSDCIG---TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCSSSCSCCSSCBCC---CSSSCCBCTTTGGGGTT---TBCSSSCCBCSC
T ss_pred             CCCCCCCChHhhCccEe---CCCCCHHHHHHHHHHhc---CCCcCCCCcCcc
Confidence            45899999999776433   27999999999999986   589999998854

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=98.73  E-value=2.1e-09  Score=69.63  Aligned_cols=43  Identities=21%  Similarity=0.529  Sum_probs=35.7

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|.||++.+.+...   + +|||. ||..|+..|     ..||+||..+..
T Consensus        24 ~~~C~iC~~~~~~~~~---~-pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           24 EKLCKICMDRNIAIVF---V-PCGHLVTCKQCAEAV-----DKCPMCYTVITF   67 (74)
T ss_dssp             HTBCTTTSSSBCCEEE---E-TTCCBCCCHHHHTTC-----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCCCEEE---c-CCCChhHHHHhhhcC-----ccCCCcCcCccC
Confidence            4589999998766543   4 89999 999999988     589999998753

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=98.72  E-value=1.2e-08  Score=63.51  Aligned_cols=49  Identities=24%  Similarity=0.664  Sum_probs=36.9

Q ss_pred             CccccccccccccccCceeeEcCCCC--C---cchHhhHHHHHhc-CCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCK--H---IFHRACLDPWMDH-DQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~--H---~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  138 (169)
                      ++...|.||+++..+  .+ .+ ||.  +   .||..|+.+|+.. ++.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~--~l-~~-PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGN--ER-FR-ACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSC--CC-CC-SCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCC--ce-ec-CcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            455689999998432  33 34 655  4   9999999999975 3568999998875

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.68  E-value=8.7e-09  Score=69.69  Aligned_cols=50  Identities=14%  Similarity=0.383  Sum_probs=39.8

Q ss_pred             CccccccccccccccCceeeEcCC-CCCcchHhhHHHHHhcC-----CCCCCc--cCCC-CCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRN-CKHIFHRACLDPWMDHD-----QKTCPL--CRTP-FVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~-C~H~fh~~Ci~~wl~~~-----~~~CP~--Cr~~-~~~  139 (169)
                      .....|+||++.|.++..+    + |||.|++.||..|+..+     ..+||+  |+.. +..
T Consensus         5 ~~~~~CPI~~~~~~dPV~~----~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPVKN----KVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SSCCBCTTTCSBCSSEEEE----SSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             CcEeECcCcCchhcCCEEc----CCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            3456899999999887554    5 99999999999999752     248999  9865 543

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.64  E-value=8.4e-09  Score=77.78  Aligned_cols=53  Identities=9%  Similarity=0.108  Sum_probs=44.2

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .....|+||++.|.++..+    +|||.|+..||..|+..+..+||.|+.++...++
T Consensus       104 p~~f~CPI~~elm~DPV~~----~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L  156 (179)
T 2f42_A          104 PDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQL  156 (179)
T ss_dssp             CGGGBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             cHhhcccCccccCCCCeEC----CCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhC
Confidence            4566899999999988665    8999999999999998644479999998876444

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.54  E-value=2.3e-08  Score=64.68  Aligned_cols=43  Identities=21%  Similarity=0.547  Sum_probs=34.9

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|+||++.+.+...+    +|||. ||..|+..     ...||+||.++..
T Consensus        25 ~~~C~IC~~~~~~~~~~----pCgH~~~C~~C~~~-----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRNIAIVFV----PCGHLVTCKQCAEA-----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSCCCBCCS----SSCCCCBCHHHHHH-----CSBCTTTCCBCCC
T ss_pred             CCCCCcCCCCCCCEEEe----cCCCHHHHHHHhhC-----CCCCccCCceecC
Confidence            45899999998765444    89999 99999964     4589999998854

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.46  E-value=9.5e-08  Score=60.83  Aligned_cols=45  Identities=24%  Similarity=0.635  Sum_probs=35.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      ..+..|.||++...+   +..+ ||+|. |+..|+..     ...||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~-pCgH~~~C~~C~~~-----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLL-PCRHTCLCDGCVKY-----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEET-TTTBCCSCTTHHHH-----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCCC---EEEE-CCCChhhhHHHHhc-----CCCCCCCCcchhc
Confidence            445689999998644   3445 99999 99999984     4589999998854

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.36  E-value=5.9e-08  Score=63.58  Aligned_cols=43  Identities=26%  Similarity=0.603  Sum_probs=34.4

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|.||++.+.+.   ..+ +|||. |+..|+..|     ..||+||.++..
T Consensus        18 ~~~C~IC~~~~~~~---v~~-pCgH~~~C~~C~~~~-----~~CP~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEINS---TFC-PCGHTVCCESCAAQL-----QSCPVCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCCE---EEE-TTCBCCBCHHHHTTC-----SBCTTTCCBCCE
T ss_pred             CCEeEEeCcccCcE---EEE-CCCCHHHHHHHHHhc-----CcCCCCCchhhC
Confidence            44899999987554   334 89999 999999875     399999998754

>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=98.29  E-value=2e-07  Score=73.95  Aligned_cols=54  Identities=17%  Similarity=0.438  Sum_probs=42.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCc--cCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPL--CRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~--Cr~~~~~~~~  142 (169)
                      .....|+||++.|..+..  .. .|||.|++.||..|+..+ ...||+  |+..+...++
T Consensus       179 ~~el~CPIcl~~f~DPVt--s~-~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          179 KIELTCPITCKPYEAPLI--SR-KCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             BCCSBCTTTSSBCSSEEE--ES-SSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGE
T ss_pred             ceeeECcCccCcccCCee--eC-CCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhC
Confidence            345589999999977743  33 799999999999999752 346999  9997765443

>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=98.20  E-value=2.5e-07  Score=76.34  Aligned_cols=43  Identities=26%  Similarity=0.620  Sum_probs=35.8

Q ss_pred             cccccccccccccCceeeEcCCCCCc-chHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHI-FHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~-fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +..|+||++.+.....+    +|||. ||..|+..|     ..||+||.++..
T Consensus       295 ~~~C~IC~~~~~~~v~l----pCgH~~fC~~C~~~~-----~~CP~CR~~i~~  338 (345)
T 3t6p_A          295 ERTCKVCMDKEVSVVFI----PCGHLVVCQECAPSL-----RKCPICRGIIKG  338 (345)
T ss_dssp             TCBCTTTSSSBCCEEEE----TTCCEEECTTTGGGC-----SBCTTTCCBCCE
T ss_pred             CCCCCccCCcCCceEEc----CCCChhHhHHHHhcC-----CcCCCCCCCccC
Confidence            45899999998765444    89999 999999987     489999998753

>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=98.16  E-value=5.2e-07  Score=56.20  Aligned_cols=50  Identities=16%  Similarity=0.296  Sum_probs=41.7

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      ..|+||++.+.++  +... ++||.|.+.||.+|+.. +.+||+.+.++...++
T Consensus         4 ~~CpIs~~~m~dP--V~~~-~sG~~yer~~I~~~l~~-~~~cP~t~~~L~~~~L   53 (61)
T 2bay_A            4 MLCAISGKVPRRP--VLSP-KSRTIFEKSLLEQYVKD-TGNDPITNEPLSIEEI   53 (61)
T ss_dssp             CCCTTTCSCCSSE--EEET-TTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGGGC
T ss_pred             EEecCCCCCCCCC--EEeC-CCCcEEcHHHHHHHHHh-CCCCcCCcCCCChhhc
Confidence            4799999999876  3332 79999999999999986 6689999999876665

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.04  E-value=4.4e-06  Score=56.68  Aligned_cols=47  Identities=28%  Similarity=0.543  Sum_probs=36.5

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      -|.+|--.+.  ...+.+ ||+|+|+.+|+..|..++.++||.|+.++..
T Consensus         3 fC~~C~~Pi~--iygRmI-PCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMI-PCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCS--EEEEEE-TTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeE--EEeeec-cccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            3666655543  345566 9999999999999987667899999998854

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

Probab=97.80  E-value=1.2e-05  Score=63.14  Aligned_cols=50  Identities=18%  Similarity=0.552  Sum_probs=39.6

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-CCCCCccCCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-QKTCPLCRTPFVP  139 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-~~~CP~Cr~~~~~  139 (169)
                      .-..|.||.+-...+...   +.|+|.||..|+..|+... +..||.|+..++.
T Consensus       179 ~i~~C~iC~~iv~~g~~C---~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             TCCBCTTTCSBCSSCEEC---SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCCcCcchhhHHhCCccc---CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            356899999998876333   3599999999999999752 3489999998754

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=94.90  E-value=0.019  Score=35.87  Aligned_cols=48  Identities=23%  Similarity=0.456  Sum_probs=33.8

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC---CCCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD---QKTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~~~  137 (169)
                      .....|.||.+.   ++ +.....|...||..|++..+...   .-.||.|.+..
T Consensus        10 ~~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            445679999753   33 44455899999999998877542   22599997643

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.37  E-value=0.018  Score=38.32  Aligned_cols=33  Identities=15%  Similarity=0.360  Sum_probs=25.8

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHH
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDP  121 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~  121 (169)
                      +..|.||.+++..+....-+ .|+|.|+..|+..
T Consensus         3 e~~C~~C~~~~~~~av~~C~-~C~~~~C~~Cl~~   35 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCV-TCEVSYCDECLKA   35 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEET-TTTEEECHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECC-cCChHHhHHHCHH
Confidence            45899999875444444446 8999999999998

>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=93.89  E-value=0.01  Score=36.57  Aligned_cols=51  Identities=22%  Similarity=0.434  Sum_probs=34.9

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHh----cCCCCCCccCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD----HDQKTCPLCRTP  136 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~----~~~~~CP~Cr~~  136 (169)
                      .+...|++|...+..+......-.|...||..|+.--..    .....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            445689999988765544544457889999999864321    135669999653

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=92.10  E-value=0.07  Score=32.53  Aligned_cols=47  Identities=36%  Similarity=0.815  Sum_probs=32.3

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRT  135 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~  135 (169)
                      +..+..|.+|...   + .+.....|...||..|+..-+..   +.-.||.|+.
T Consensus         8 ~~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             SCCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            4556689999873   3 34444478899999999875432   2235999964

>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=91.21  E-value=0.14  Score=31.67  Aligned_cols=36  Identities=28%  Similarity=0.697  Sum_probs=26.9

Q ss_pred             CCccccccccccccccCceeeEcC-CCCCcchHhhHH
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLR-NCKHIFHRACLD  120 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~-~C~H~fh~~Ci~  120 (169)
                      +.+...|.+|...+..+......- .|...||..|+.
T Consensus         5 ~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            5 SDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ----CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            345668999999987777777666 789999999974

>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=91.06  E-value=0.14  Score=38.30  Aligned_cols=51  Identities=16%  Similarity=0.374  Sum_probs=35.9

Q ss_pred             ccccccccccccCce---eeEcCCCCCcchHhhHHH------HHh----cCCCCCCccCCCCCC
Q 030902           89 ENCAVCLYEFEGGEE---IRWLRNCKHIFHRACLDP------WMD----HDQKTCPLCRTPFVP  139 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~---~~~l~~C~H~fh~~Ci~~------wl~----~~~~~CP~Cr~~~~~  139 (169)
                      ..|+||...+..++.   ......|...||..|..-      -+.    .....||.|+..-..
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~~   66 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPA   66 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSSC
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCCH
Confidence            369999999887762   555558889999999742      111    015689999876543

>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=90.42  E-value=0.2  Score=32.01  Aligned_cols=51  Identities=24%  Similarity=0.470  Sum_probs=33.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHh----cCCCCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD----HDQKTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~----~~~~~CP~Cr~~~  137 (169)
                      .....| ||.............-.|...||..|+.--..    .....||.|+...
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            444567 99888754444444447889999999852211    1355799997654

>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=89.72  E-value=0.094  Score=39.67  Aligned_cols=49  Identities=27%  Similarity=0.579  Sum_probs=34.3

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      +..++.|.+|...   + .+.....|...||..|+..-+..   +.-.||.|+..-
T Consensus         4 d~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            4 DPNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             CSSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            4456689999753   3 35555589999999999776543   223599997754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=89.21  E-value=0.28  Score=32.69  Aligned_cols=48  Identities=23%  Similarity=0.495  Sum_probs=31.9

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhc--CCCCCCccCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH--DQKTCPLCRTPF  137 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~--~~~~CP~Cr~~~  137 (169)
                      ...| ||......+..+ ....|...||..|+..-...  ....||.|+..-
T Consensus        28 ~vrC-iC~~~~~~~~mi-~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~~   77 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMI-CCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRN   77 (98)
T ss_dssp             BCCC-TTSCCSCSSCEE-EBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSSC
T ss_pred             CEEe-ECCCccCCCcEE-EcCCCCCcCcCcCCCCCccCCCCCEECCCCcCCC
Confidence            3467 898776555444 44488899999998753222  134699997543

>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=88.73  E-value=0.1  Score=31.77  Aligned_cols=49  Identities=31%  Similarity=0.647  Sum_probs=32.2

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      +..+..|.||.+.   ++.+ ....|...||..|+..-+..   +.-.||.|+...
T Consensus         6 d~~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GELL-CCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---SSCB-CCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC---CCEE-EcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            3456689999853   3333 33378889999999864432   123499997653

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=88.36  E-value=0.17  Score=31.88  Aligned_cols=52  Identities=21%  Similarity=0.419  Sum_probs=34.5

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      +.....|.||..... ++.....-.|...||..|+..-...   ..-.||.|+..+
T Consensus        15 ~~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~   69 (75)
T 2k16_A           15 GNQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKI   69 (75)
T ss_dssp             SCEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHH
T ss_pred             CCCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCch
Confidence            344567999987753 4344444578899999998754432   234599996543

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=88.20  E-value=0.83  Score=30.00  Aligned_cols=52  Identities=19%  Similarity=0.456  Sum_probs=36.8

Q ss_pred             ccccccccccccc---cCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFE---GGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~---~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ....|.||-+++.   +++...-...|+--.|+.|.+-=...+++.||.|+.++.
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            3458999999864   333222222566778999998766667889999998874

>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=88.16  E-value=0.15  Score=29.95  Aligned_cols=45  Identities=16%  Similarity=0.375  Sum_probs=30.1

Q ss_pred             cccccccccccCceeeEcC-CCCCcchHhhHHHHH---hcCCCCCCccC
Q 030902           90 NCAVCLYEFEGGEEIRWLR-NCKHIFHRACLDPWM---DHDQKTCPLCR  134 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~-~C~H~fh~~Ci~~wl---~~~~~~CP~Cr  134 (169)
                      .|.+|...+..+......- .|...||..|+.--.   ...+..||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4778888876555555554 588899999975211   12467799885

>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=87.98  E-value=0.12  Score=38.35  Aligned_cols=47  Identities=30%  Similarity=0.680  Sum_probs=32.7

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      .++.|.+|...   ++ +.....|...||..|+..-+..   +.-.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            35679999854   44 4444578899999998765543   223599997754

>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=87.91  E-value=0.25  Score=32.16  Aligned_cols=35  Identities=26%  Similarity=0.528  Sum_probs=24.1

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPW  122 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~w  122 (169)
                      ..++.|.||- .+..++...-- -|+-+||..|+.+.
T Consensus        13 ~~D~~C~VC~-~~t~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceeccc-cccccccHhhcccc
Confidence            3566899994 34444433222 58899999999986

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.74  E-value=0.22  Score=28.93  Aligned_cols=45  Identities=29%  Similarity=0.676  Sum_probs=29.5

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRT  135 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~  135 (169)
                      .|.||...-..+ .+.....|...||..|++.=+..   +.-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588888764333 34444488899999999754432   1234999965

>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=87.35  E-value=0.13  Score=37.55  Aligned_cols=49  Identities=20%  Similarity=0.506  Sum_probs=32.6

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHh----cCCCCCCccCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD----HDQKTCPLCRT  135 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~----~~~~~CP~Cr~  135 (169)
                      .....| +|......+........|...||..|+.--..    .....||.|+.
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~   58 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS   58 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcc
Confidence            345578 99988654444555557889999999852111    13557999965

>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=85.97  E-value=1.7  Score=28.08  Aligned_cols=40  Identities=18%  Similarity=0.298  Sum_probs=29.6

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH  125 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~  125 (169)
                      ...-.|.+|.|.+++..-|.--..=.|.||..|-...++.
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            3445899999999998888211112399999999988865

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=85.78  E-value=0.94  Score=32.34  Aligned_cols=48  Identities=21%  Similarity=0.496  Sum_probs=33.8

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHh----------cCCCCCCccCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD----------HDQKTCPLCRTP  136 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~----------~~~~~CP~Cr~~  136 (169)
                      +..++.|.+|.+.   ++ +.....|...||..|+..-+.          .+.=.||.|+..
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---GN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC---SS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC---Cc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            4566789999874   44 444447889999999997652          123359999753

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.58  E-value=0.93  Score=30.75  Aligned_cols=34  Identities=29%  Similarity=0.512  Sum_probs=24.3

Q ss_pred             cccccccccccc-----ccCceeeEcCCCCCcchHhhHH
Q 030902           87 PPENCAVCLYEF-----EGGEEIRWLRNCKHIFHRACLD  120 (169)
Q Consensus        87 ~~~~C~ICl~~~-----~~~~~~~~l~~C~H~fh~~Ci~  120 (169)
                      +...|.+|+..=     ..++.+..-..|+..||..|+.
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            345899998763     1233555556899999999995

>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=85.14  E-value=0.22  Score=33.72  Aligned_cols=39  Identities=28%  Similarity=0.473  Sum_probs=26.9

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHh
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMD  124 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~  124 (169)
                      +..++.|.||.+.-+..+ +.....|+..||..|+.....
T Consensus         4 ~~~~~~C~~C~~~g~~~~-ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLD-QFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTT-SEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCCcCCCCCCCCcC-CeECCCCCCCcChHHhCCccc
Confidence            345678999987633222 234448999999999987653

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.45  E-value=0.086  Score=31.48  Aligned_cols=47  Identities=28%  Similarity=0.731  Sum_probs=30.7

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRT  135 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~  135 (169)
                      +..+..|.+|...   ++ +.....|...||..|+..-+..   +.-.||.|..
T Consensus         6 ~~~~~~C~vC~~~---g~-ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SC-CEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---Ce-EEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3456689999874   33 4444488899999999864432   1223888743

>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=84.37  E-value=0.25  Score=31.18  Aligned_cols=47  Identities=21%  Similarity=0.485  Sum_probs=30.3

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHH--------hcCCCCCCccCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWM--------DHDQKTCPLCRTP  136 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl--------~~~~~~CP~Cr~~  136 (169)
                      ...| ||......+.-+ ..-.|...||..|+.--.        ......||.|+..
T Consensus        16 ~~~C-~C~~~~~~~~MI-~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMI-CCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCCSSCEE-ECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCEE-ECCCccCCCCEE-EeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            3467 898876544444 333788999999984211        1136789999653

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=84.36  E-value=0.38  Score=31.61  Aligned_cols=49  Identities=27%  Similarity=0.637  Sum_probs=33.5

Q ss_pred             CCCccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCC
Q 030902           84 NGDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTP  136 (169)
Q Consensus        84 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~  136 (169)
                      .+..++.|.+|...   ++ +.....|.-.||..|+.+=+..   +.-.||.|+..
T Consensus        21 ~d~n~~~C~vC~~~---g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           21 LDDSATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             cCCCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            34556689999864   33 4444478889999999775543   12249999764

>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=83.93  E-value=0.55  Score=31.68  Aligned_cols=50  Identities=22%  Similarity=0.450  Sum_probs=34.2

Q ss_pred             cccccccccccccCceeeEcC-CCCCcchHhhHHHHH---h------cCCCCCCccCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLR-NCKHIFHRACLDPWM---D------HDQKTCPLCRTPF  137 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~-~C~H~fh~~Ci~~wl---~------~~~~~CP~Cr~~~  137 (169)
                      ...|.+|...+.........- .|...||..|+.---   .      ..+..||.|+...
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            457999999986655555553 688999999974211   0      0245699997654

>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=83.54  E-value=1.5  Score=30.70  Aligned_cols=47  Identities=21%  Similarity=0.509  Sum_probs=32.3

Q ss_pred             CCccccccccccccccCceeeEcCCCCCcchHhhHHHHH------h----cCCCCCCccCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWM------D----HDQKTCPLCRT  135 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl------~----~~~~~CP~Cr~  135 (169)
                      +..++.|.||-+.   + .+.....|...||..|+..-+      .    .+.=.|+.|+.
T Consensus        54 Dg~~~~C~vC~dG---G-~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           54 DGMDEQCRWCAEG---G-NLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             TSCBSSCTTTCCC---S-EEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCCcCeecCCC---C-eeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            4556689999864   3 344445788999999999752      1    12346999954

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=82.35  E-value=0.35  Score=32.95  Aligned_cols=46  Identities=24%  Similarity=0.647  Sum_probs=31.1

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRT  135 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~  135 (169)
                      .|.||.+.-.+++.+.....|...||..|++.-+..   +.-.||.|+.
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            688888653344455555589999999998765543   1235999974

>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=81.75  E-value=0.73  Score=28.04  Aligned_cols=51  Identities=22%  Similarity=0.581  Sum_probs=33.9

Q ss_pred             Cccccccccccccc-cCceeeEcCCCCCcchHhhHHHHHh------cCCCCCCccCCC
Q 030902           86 DPPENCAVCLYEFE-GGEEIRWLRNCKHIFHRACLDPWMD------HDQKTCPLCRTP  136 (169)
Q Consensus        86 ~~~~~C~ICl~~~~-~~~~~~~l~~C~H~fh~~Ci~~wl~------~~~~~CP~Cr~~  136 (169)
                      ..+..|.||..... ++..+.....|...||..|+..-+.      .+.-.||.|...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~   61 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFA   61 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCc
Confidence            45668999997643 3345555558999999999875331      123458888553

>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=80.89  E-value=1.1  Score=27.94  Aligned_cols=46  Identities=33%  Similarity=0.634  Sum_probs=28.4

Q ss_pred             ccccccccccccccCceeeEcCC--CC-CcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRN--CK-HIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~--C~-H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      +...| ||.... .+..+ ..-.  |. ..||..|+.  +..   ++-.||.|+..-
T Consensus        15 ~~~~C-~C~~~~-~g~MI-~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           15 EPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             SCCCS-TTCCCS-CSSEE-CCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCEE-ECCCCC-CCCEe-EeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            44567 898764 24433 2224  55 689999997  332   234599997643

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=80.33  E-value=0.22  Score=30.74  Aligned_cols=46  Identities=33%  Similarity=0.687  Sum_probs=31.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRT  135 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~  135 (169)
                      ..+..|.||...   ++ +.....|...||..|+..-+..   +.-.||.|..
T Consensus         6 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            6 KNEDECAVCRDG---GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             SCCCSBSSSSCC---SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCccCCCC---CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccC
Confidence            456689999864   33 4444478899999999854432   1224999954

>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=80.16  E-value=0.53  Score=32.14  Aligned_cols=34  Identities=26%  Similarity=0.392  Sum_probs=23.7

Q ss_pred             ccccccccccc------cCceeeEcCCCCCcchHhhHHHH
Q 030902           89 ENCAVCLYEFE------GGEEIRWLRNCKHIFHRACLDPW  122 (169)
Q Consensus        89 ~~C~ICl~~~~------~~~~~~~l~~C~H~fh~~Ci~~w  122 (169)
                      +.|.+|+..-.      .+..+.....|+..||..|+...
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh
Confidence            47999987642      12345555589999999998743

---

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	169
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	4e-16
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-12
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	6e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	7e-10
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	4e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-08
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	6e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	8e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	8e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	4e-04

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 66.4 bits (162), Expect = 4e-16
 Identities = 26/48 (54%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV 138
           CAVCL E E GEE R+L  C H FH  C+D W+     TCPLCR   V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWL-GSHSTCPLCRLTVV 54

>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 = 55.5 bits (133), Expect = 7e-12
 Identities = 12/50 (24%), Positives = 19/50 (38%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD 140
           C +C+   E  +   +   C +   R C       +   CP CR P+  D
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 53.2 bits (127), Expect = 6e-11
 Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 1/59 (1%)

Query: 89  ENCAVCLYEFEGGEEIRWLRN-CKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQEEF 146
           + C  C         ++ + N C H    +C+D         CP C TP      + + 
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQL 62

>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 = 1e-10
 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 4/49 (8%)

Query: 89  ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           E C +CL +            C H F   C+  W+     TCPLC+ P 
Sbjct: 6   ERCPICLEDPS---NYSMALPCLHAFCYVCITRWIRQ-NPTCPLCKVPV 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 = 50.8 bits (121), Expect = 7e-10
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 85  GDPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPF 137
           G   + C +C    +   +++    C H+   +CL  W + + + CP CR   
Sbjct: 20  GSTFQLCKICAENDK---DVKIE-PCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 49.1 bits (117), Expect = 4e-09
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ 143
           C +C +            +CKH+F R C+   +      CP CR P  P +++
Sbjct: 26  CQICEHILA----DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

>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 = 48.2 bits (114), Expect = 1e-08
 Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 15/64 (23%)

Query: 89  ENCAVCLYEFEGGE--------------EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCR 134
           +NCA+C                             C H FH  C+  W+   ++ CPL  
Sbjct: 22  DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-RQVCPLDN 80

Query: 135 TPFV 138
             + 
Sbjct: 81  REWE 84

>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 = 48.5 bits (114), Expect = 1e-08
 Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 18/76 (23%)

Query: 80  LEMVNGDPPENCAVCLYEF--------------EGGEEIRWLRNCKHIFHRACLDPWMDH 125
            E +   P E+C +C+ +                G   +  L  C H FH  CL     +
Sbjct: 17  TEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCN 76

Query: 126 DQ----KTCPLCRTPF 137
                   CP C+T +
Sbjct: 77  GNKDGSLQCPSCKTIY 92

>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 = 47.2 bits (111), Expect = 1e-08
 Identities = 10/49 (20%), Positives = 15/49 (30%), Gaps = 2/49 (4%)

Query: 91  CAVCLYEFEGGEEIRW-LRNCKHIFHRACLDPWMDHD-QKTCPLCRTPF 137
           C +C  E                  HR+CL  W+       C +C   +
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVY 57

>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 = 42.2 bits (99), Expect = 6e-07
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 8/51 (15%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE 141
           C  C  E +     + L  C H     CL+         CP+C+ P+    
Sbjct: 9   CQQCQAEAK---CPKLL-PCLHTLCSGCLEAS----GMQCPICQAPWPLGA 51

>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 = 43.1 bits (101), Expect = 8e-07
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 72  LPVIKFQDLEMVNGDPPEN--CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQK- 128
           L  ++ ++++ V     +   C +CL   +     +    C HIF + C+   ++  +  
Sbjct: 3   LSALRVEEVQNVINAMQKILECPICLELIKEPVSTK----CDHIFCKFCMLKLLNQKKGP 58

Query: 129 -TCPLCRTPFVPDEMQ 143
             CPLC+       +Q
Sbjct: 59  SQCPLCKNDITKRSLQ 74

>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 = 37.8 bits (87), Expect = 8e-05
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ 143
           C+ C        E   L  C+HIF   C+   +      CP+C TP    +++
Sbjct: 25  CSRCTNILR---EPVCLGGCEHIFCSNCVSDCIGT---GCPVCYTPAWIQDLK 71

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 14/84 (16%), Positives = 26/84 (30%), Gaps = 20/84 (23%)

Query: 86  DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWM-------DHDQKTCPLCRTP-- 136
                C +CL E+   +    +  C+ IF   CL  ++            +CP    P  
Sbjct: 3   SGSSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ 61

Query: 137 ----------FVPDEMQEEFNQRL 150
                      V  E+ + + +  
Sbjct: 62  GHLQENEIECMVAAEIMQRYKKLQ 85

>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 = 34.7 bits (79), Expect = 4e-04
 Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 4/52 (7%)

Query: 91  CAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM 142
           CA+                 + IF ++ L+ ++  D    P+   P   +E+
Sbjct: 3   CAISGKVPR---RPVLSPKSRTIFEKSLLEQYV-KDTGNDPITNEPLSIEEI 50

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	169
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.69
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.58
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.48
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.45
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.44
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.38
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.38
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.27
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.22
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.19
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.16
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.15
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.06
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.02
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.96
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.63
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.59
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.81
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	93.75
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.75
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	91.2
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.14
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.07
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	88.99
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	88.37
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	85.97
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	83.65

>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=99.69  E-value=4.2e-18  Score=103.79  Aligned_cols=50  Identities=52%  Similarity=1.093  Sum_probs=45.5

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      +.+|+||+++|..++.+..+++|+|.||..|+.+|+.. +.+||+||+++.
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~-~~~CP~CR~~i~   54 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-HSTCPLCRLTVV   54 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-CCSCSSSCCCSC
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh-CCcCCCCCCEeE
Confidence            45799999999999999888789999999999999986 889999999874

>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=99.58  E-value=3e-16  Score=94.34  Aligned_cols=50  Identities=22%  Similarity=0.545  Sum_probs=42.3

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVP  139 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~  139 (169)
                      +|+||+++|..++.+..+.+|||.||..|+.+|++.++.+||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            79999999987766544448999999999999998656679999998864

>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=99.48  E-value=9.5e-15  Score=91.55  Aligned_cols=54  Identities=20%  Similarity=0.441  Sum_probs=42.1

Q ss_pred             ccccccccccccc-CceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCCh
Q 030902           88 PENCAVCLYEFEG-GEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDE  141 (169)
Q Consensus        88 ~~~C~ICl~~~~~-~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~  141 (169)
                      +..|+||++++.. ++....+++|||.||..||.+|+..++..||+||.++...+
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            5689999998643 33333334899999999999999765668999999886544

>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=99.45  E-value=1.6e-14  Score=91.21  Aligned_cols=48  Identities=33%  Similarity=0.812  Sum_probs=40.7

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ..+.|+||++.+.++  ++.+ +|+|.||..|+.+|++. +.+||+||.++.
T Consensus         4 ~~d~C~IC~~~~~~~--~~~~-~C~H~Fc~~Ci~~w~~~-~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMAL-PCLHAFCYVCITRWIRQ-NPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEET-TTTEEESTTHHHHHHHH-SCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccCC--cEEe-CCCCcCcHHHHHHHHHh-CCcCCCCCcchH
Confidence            345899999998654  3445 89999999999999997 789999999874

>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=99.44  E-value=3.5e-14  Score=94.02  Aligned_cols=51  Identities=27%  Similarity=0.705  Sum_probs=41.2

Q ss_pred             CccccccccccccccCc---------------eeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           86 DPPENCAVCLYEFEGGE---------------EIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~---------------~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ..+++|+||++.+....               .+..+ +|+|.||..||.+|+.. +.+||+||+++.
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~   84 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWG-VCNHAFHFHCISRWLKT-RQVCPLDNREWE   84 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEE-TTSCEEEHHHHHHHHTT-CSBCSSSCSBCC
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEc-cccCcccHHHHHHHHHH-CCcCCCCCCccc
Confidence            34567999999886432               24445 89999999999999997 789999999875

>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=99.38  E-value=1.4e-13  Score=89.37  Aligned_cols=49  Identities=22%  Similarity=0.656  Sum_probs=40.5

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      ...|+||++.+.+.   +.+ +|||.||..|+..|+..+..+||+||..+...
T Consensus        23 ~~~C~IC~~~~~~~---~~~-~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKDV---KIE-PCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCCE---ECS-SSCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCCe---EEe-CCCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            44799999987653   344 89999999999999986567899999998653

>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=99.38  E-value=1.6e-13  Score=94.68  Aligned_cols=55  Identities=27%  Similarity=0.641  Sum_probs=41.1

Q ss_pred             CccccccccccccccC--------------ceeeEcCCCCCcchHhhHHHHHhcC----CCCCCccCCCCCCC
Q 030902           86 DPPENCAVCLYEFEGG--------------EEIRWLRNCKHIFHRACLDPWMDHD----QKTCPLCRTPFVPD  140 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~--------------~~~~~l~~C~H~fh~~Ci~~wl~~~----~~~CP~Cr~~~~~~  140 (169)
                      ..++.|+||++++...              +.+..+++|+|.||..||..|+..+    +.+||+||+.+..+
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            3456899999998542              2233444999999999999999752    34799999987544

>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=99.27  E-value=8.6e-13  Score=86.80  Aligned_cols=50  Identities=30%  Similarity=0.715  Sum_probs=42.0

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      ..|+||++.+.++..+    +|||.||..||.+|++.++..||+||.++.+.++
T Consensus        24 l~C~IC~~~~~~pv~~----~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l   73 (86)
T d1rmda2          24 ISCQICEHILADPVET----SCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (86)
T ss_dssp             TBCTTTCSBCSSEEEC----TTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             cCCccCCcchhcceec----CCCChhhHHHHHHHHhhCCCcCcccCCCCChhhc
Confidence            4799999999876444    8999999999999998656689999998876553

>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=99.22  E-value=1.1e-12  Score=79.49  Aligned_cols=49  Identities=16%  Similarity=0.297  Sum_probs=41.4

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .|+||++.++++..+   +.|||.||.+||.+|+.+ +.+||+||.++..+++
T Consensus         2 ~C~Ic~~~~~~Pv~~---~~cGh~fc~~cI~~~l~~-~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKD-TGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSSEEEE---TTTTEEEEHHHHHHHHHH-HSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHhcCcc---CCCCCcccHHHHHHHHhh-ccCCCccCCcCCHHhc
Confidence            599999999876433   269999999999999997 7799999999876654

>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=99.19  E-value=7.1e-12  Score=76.83  Aligned_cols=54  Identities=19%  Similarity=0.428  Sum_probs=39.6

Q ss_pred             CCccccccccccccccCceee-EcCCCCCcchHhhHHHHHhc-CCCCCCccCCCCC
Q 030902           85 GDPPENCAVCLYEFEGGEEIR-WLRNCKHIFHRACLDPWMDH-DQKTCPLCRTPFV  138 (169)
Q Consensus        85 ~~~~~~C~ICl~~~~~~~~~~-~l~~C~H~fh~~Ci~~wl~~-~~~~CP~Cr~~~~  138 (169)
                      +++...|.||++++..+.... ...+|+|.||..|+.+|+.. ++.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            345568999999987654331 11134699999999999964 4568999999874

>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=99.16  E-value=7.6e-12  Score=84.70  Aligned_cols=49  Identities=24%  Similarity=0.708  Sum_probs=40.4

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCC--CCCCccCCCCCCCh
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQ--KTCPLCRTPFVPDE  141 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~--~~CP~Cr~~~~~~~  141 (169)
                      -.|+||++.+.++..+    +|||.||..||..|+...+  ..||.||.++...+
T Consensus        22 l~CpIC~~~~~~pv~~----~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          22 LECPICLELIKEPVST----KCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             TSCSSSCCCCSSCCBC----TTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             cCCCccCchhCCeEEc----CCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            3799999999887544    8999999999999997632  47999999886544

>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=99.15  E-value=3e-12  Score=77.55  Aligned_cols=45  Identities=24%  Similarity=0.606  Sum_probs=37.4

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      .-.|+||++.+.++..+    +|||.||..|+.+|    +.+||+||.++...
T Consensus         6 ~l~C~IC~~~~~~p~~l----pCgH~fC~~Ci~~~----~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAKCPKLL----PCLHTLCSGCLEAS----GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBCCSCS----TTSCCSBTTTCSSS----SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccCCCEEe----cCCCHHhHHHHHcC----CCcCcCCCCcccCC
Confidence            45899999999877544    89999999998764    55899999998654

>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=99.06  E-value=2e-11  Score=78.93  Aligned_cols=53  Identities=8%  Similarity=0.105  Sum_probs=44.4

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .++..|+||++.|.++..+    +|||.|+..||.+|+..++.+||.||.++...++
T Consensus         5 P~~l~CpIc~~l~~dPv~~----~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l   57 (80)
T d2c2la2           5 PDYLCGKISFELMREPCIT----PSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQL   57 (80)
T ss_dssp             CSTTBCTTTCSBCSSEEEC----SSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGC
T ss_pred             CccccCcCcCchhhhhccc----CCcCeecHHHHHHHHhcCCccCCCcccccccccc
Confidence            3456899999999888544    8999999999999998767789999998865444

>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=99.02  E-value=6.6e-11  Score=76.01  Aligned_cols=53  Identities=17%  Similarity=0.446  Sum_probs=44.2

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCChH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPDEM  142 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~  142 (169)
                      .++..|+||++.|.++..+    +|||.|++.||..|+..+...||.|+.++...++
T Consensus         6 P~~l~CpIc~~~m~dPV~~----~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l   58 (78)
T d1t1ha_           6 PEYFRCPISLELMKDPVIV----STGQTYERSSIQKWLDAGHKTCPKSQETLLHAGL   58 (78)
T ss_dssp             SSSSSCTTTSCCCSSEEEE----TTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCC
T ss_pred             CccCCCcCcCchhhCceEc----cCCCcchHHHHHHHHHHCCCCCCcccccCCcccc
Confidence            3456899999999888544    8999999999999998756789999998876443

>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=98.96  E-value=4.5e-11  Score=79.92  Aligned_cols=46  Identities=26%  Similarity=0.629  Sum_probs=37.7

Q ss_pred             ccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCCCC
Q 030902           89 ENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFVPD  140 (169)
Q Consensus        89 ~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~  140 (169)
                      -.|+||++.|..+..+   ++|||.||..||.+|+..   .||.||.++...
T Consensus        23 l~C~IC~~~~~~pv~~---~~CgH~fC~~Ci~~~~~~---~CP~Cr~~~~~~   68 (97)
T d1jm7b_          23 LRCSRCTNILREPVCL---GGCEHIFCSNCVSDCIGT---GCPVCYTPAWIQ   68 (97)
T ss_dssp             TSCSSSCSCCSSCBCC---CSSSCCBCTTTGGGGTTT---BCSSSCCBCSCS
T ss_pred             CCCccCCchhhcCcee---CCCCCchhHHHHHHHHhc---cccccCCcCchh
Confidence            3899999999877433   289999999999999853   699999877543

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=7.7e-09  Score=68.17  Aligned_cols=48  Identities=23%  Similarity=0.539  Sum_probs=37.7

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC-------CCCCCccC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD-------QKTCPLCR  134 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~-------~~~CP~Cr  134 (169)
                      ++...|+||++++...+.+..+ +|+|.||..|+..|+...       ...||.|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIA-QCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEET-TTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCCcCccCCCcccCCceEEEC-CCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            4466999999999777666666 899999999999999641       12599854

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=9.1e-09  Score=68.65  Aligned_cols=53  Identities=11%  Similarity=0.081  Sum_probs=43.6

Q ss_pred             CccccccccccccccCceeeEcCCCC-CcchHhhHHHHHhcCCCCCCccCCCCCCChHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCK-HIFHRACLDPWMDHDQKTCPLCRTPFVPDEMQ  143 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~-H~fh~~Ci~~wl~~~~~~CP~Cr~~~~~~~~~  143 (169)
                      .++..|+||++-|.++..+    +|+ |.|++.||..|+.. +..||.|+.++...++.
T Consensus        20 P~~f~CPI~~~lm~dPV~~----~~~~~ty~r~~I~~~l~~-~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDPVVL----PSSRVTVDRSTIARHLLS-DQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             CTTTBCTTTCSBCSSEEEC----TTTCCEEEHHHHHHHTTT-SCBCTTTCSBCCTTTSE
T ss_pred             cHHhCCcCchhHHHHHHhc----ccccchhhHHHHHHHHHh-cCCcccccccccchhhc
Confidence            4467899999999988655    666 57999999999986 77999999998765543

>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=94.81  E-value=0.0028  Score=37.65  Aligned_cols=51  Identities=24%  Similarity=0.507  Sum_probs=36.3

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHH---hc-CCCCCCccCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWM---DH-DQKTCPLCRTP  136 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl---~~-~~~~CP~Cr~~  136 (169)
                      .....|.+|.+....++.......|+..||..|+..-.   .. .+..||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            44568999998877766655566899999999986311   11 24569999654

>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=93.75  E-value=0.011  Score=33.34  Aligned_cols=45  Identities=29%  Similarity=0.654  Sum_probs=31.1

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHHHHHhcC---CCCCCccCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD---QKTCPLCRT  135 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~  135 (169)
                      .|.||...-..+ .+.....|...||..|++.-+...   .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588887664444 444455899999999998765431   224999975

>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=91.75  E-value=0.13  Score=31.41  Aligned_cols=48  Identities=21%  Similarity=0.407  Sum_probs=32.5

Q ss_pred             cccccccccccCceeeEcCCCCCcchHhhHH--HHH-hc-CCCCCCccCCCC
Q 030902           90 NCAVCLYEFEGGEEIRWLRNCKHIFHRACLD--PWM-DH-DQKTCPLCRTPF  137 (169)
Q Consensus        90 ~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~--~wl-~~-~~~~CP~Cr~~~  137 (169)
                      .+.||......+........|.-.||..|+.  ..- .. .+..||.|+...
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            3349988766555555556899999999985  222 11 246799997654

>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=91.20  E-value=0.017  Score=33.77  Aligned_cols=48  Identities=31%  Similarity=0.664  Sum_probs=32.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHHHhc---CCCCCCccCCCC
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDH---DQKTCPLCRTPF  137 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~---~~~~CP~Cr~~~  137 (169)
                      ..++.|.+|.+.   ++ +.....|...||..|+...+..   ..-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            445579999753   33 4444478899999998765542   133599997654

>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=90.14  E-value=0.17  Score=30.31  Aligned_cols=34  Identities=24%  Similarity=0.545  Sum_probs=28.7

Q ss_pred             cccccccccccccCceeeEcCCCC----CcchHhhHHHHHhc
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCK----HIFHRACLDPWMDH  125 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~----H~fh~~Ci~~wl~~  125 (169)
                      .-.|.+|.|.+++..-|    +|.    |.||..|-+..++.
T Consensus         8 ~l~CtlC~erLEdtHFV----QCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFV----QCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             SCCCSSSCSCCSSTTSE----ECSSCSSCEECHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceE----eCCCCcCCceeccccHHHHHh
Confidence            45899999999998877    564    99999999988865

>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=90.07  E-value=0.1  Score=32.25  Aligned_cols=35  Identities=29%  Similarity=0.590  Sum_probs=26.0

Q ss_pred             CccccccccccccccCceeeEcCCCCCcchHhhHHHH
Q 030902           86 DPPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPW  122 (169)
Q Consensus        86 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~w  122 (169)
                      ..+..|.|| +.+...+... ..-|+.+||..|+.+.
T Consensus        13 ~~D~mC~vC-~v~t~~~l~p-CRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceec-ceeecchhhHHHHHHh
Confidence            456689999 7776665552 2257899999999987

>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=88.99  E-value=0.065  Score=32.02  Aligned_cols=48  Identities=25%  Similarity=0.545  Sum_probs=31.9

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcC---CCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHD---QKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~---~~~CP~Cr~~~~  138 (169)
                      ....|.+|..   .++ +...-.|...||..|+...+...   .-.||.|+..-.
T Consensus         6 ~c~~C~~C~~---~~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           6 SATICRVCQK---PGD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSCCSSSCS---SSC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCC---cCE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            3456777764   344 44445899999999999776431   224999976443

>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=88.37  E-value=0.087  Score=30.52  Aligned_cols=45  Identities=20%  Similarity=0.437  Sum_probs=31.5

Q ss_pred             ccccccccccccccCceeeEcCCCCCcchHhhHHHHHhcCCCCCCcc
Q 030902           87 PPENCAVCLYEFEGGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLC  133 (169)
Q Consensus        87 ~~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~C  133 (169)
                      ....|.-|+..+... .+...+.|++.|+.+|-.- +...-.+||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~f-iHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVF-VHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHT-TTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchh-hhhhhcCCCCC
Confidence            345899999988654 4455669999999999433 32223469987

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=85.97  E-value=0.64  Score=28.74  Aligned_cols=52  Identities=19%  Similarity=0.456  Sum_probs=36.3

Q ss_pred             ccccccccccccc---cCceeeEcCCCCCcchHhhHHHHHhcCCCCCCccCCCCC
Q 030902           87 PPENCAVCLYEFE---GGEEIRWLRNCKHIFHRACLDPWMDHDQKTCPLCRTPFV  138 (169)
Q Consensus        87 ~~~~C~ICl~~~~---~~~~~~~l~~C~H~fh~~Ci~~wl~~~~~~CP~Cr~~~~  138 (169)
                      ....|.||-+++.   +++...-..-|+--.|+.|.+-=.+.+++.||.|+.++.
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Yk   69 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhh
Confidence            3458999999874   233222222566678999988666656889999998774

>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=83.65  E-value=0.38  Score=28.60  Aligned_cols=46  Identities=20%  Similarity=0.564  Sum_probs=29.2

Q ss_pred             cccccccccccccCceeeEcCCCCCcchHhhHH------HHH--hcCCCCCCccCC
Q 030902           88 PENCAVCLYEFEGGEEIRWLRNCKHIFHRACLD------PWM--DHDQKTCPLCRT  135 (169)
Q Consensus        88 ~~~C~ICl~~~~~~~~~~~l~~C~H~fh~~Ci~------~wl--~~~~~~CP~Cr~  135 (169)
                      ...| ||......+. +.....|.-.||..|+.      ...  ......||.|+.
T Consensus        16 ~~~C-iC~~~~~~~~-mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          16 ALYC-ICRQPHNNRF-MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             CCCS-TTCCCCCSSC-EEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             cCEE-ECCCccCCCe-EEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            3457 8987654443 44445788999999982      111  112468999954