Citrus Sinensis ID: 045579

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100----
Protein Sequence
KRNRNHNHNPDRDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHccEEEccccccccccccccccccccccccEEEcccccccccccccHHHHHccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHHHcccccccHHHHHHccEEEEccccccccccEEEEEEcccccccEEEEcccccccccHHHHHHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
krnrnhnhnpdrdvndsdlevgerqglgdealeqlmpcvnysdqemtpssnycviclenfvdgescrlfpVCYRIFHSVCIDQWLkehltcpvcriscidieny
Flexible Loop (DISEMBL)
krnrnhnhnpdrdvndsdleVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY
Low Complexity Region (SEG)
KrnrnhnhnpdrdvndSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY
Disordered region (IsUnstruct)
**********************************LMPCVNYS******SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI***
Disordered Region (DISOPRED)
*******************************LEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI*****
Disordered Region (DISEMBL)
***********RDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY
Disordered Region (DISPRO)
*******************E***RQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
KRNRNHNHNPDRDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY
Positional Conservation
no confident homologs detected

---

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	104	2.2.26 [Sep-21-2011]
Q9C919	178	Putative RING-H2 finger p	yes	no	0.711	0.415	0.45	7e-15
Q94BY6	226	RING-H2 finger protein AT	no	no	0.673	0.309	0.472	8e-13
P0C034	251	RING-H2 finger protein AT	no	no	0.673	0.278	0.486	2e-12
Q9LS99	220	RING-H2 finger protein AT	no	no	0.721	0.340	0.454	2e-12
Q8RXX9	398	E3 ubiquitin-protein liga	no	no	0.644	0.168	0.442	3e-12
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.673	0.311	0.486	3e-12
Q9LZV8	159	RING-H2 finger protein AT	no	no	0.769	0.503	0.407	3e-12
Q8LGA5	368	E3 ubiquitin-protein liga	no	no	0.673	0.190	0.432	3e-11
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.846	0.5	0.380	4e-11
Q8W571	323	RING-H2 finger protein AT	no	no	0.692	0.222	0.413	1e-10

>sp|Q9C919|ATL19_ARATH Putative RING-H2 finger protein ATL19 OS=Arabidopsis thaliana GN=ATL19 PE=3 SV=1

 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 36/80 (45%), Positives = 50/80 (62%), Gaps = 6/80 (7%)

Query: 22  GERQGLGDEALEQLMPCV------NYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRI 75
           G+++GL    +E L+P +      +  D+E +  S  C ICL  +V  E CR+FPVC  I
Sbjct: 93  GKKRGLKQSVIETLLPKLLVGQGNHEEDEEKSLESRECAICLSGYVVNEECRVFPVCRHI 152

Query: 76  FHSVCIDQWLKEHLTCPVCR 95
           +H++CID WLK HLTCP CR
Sbjct: 153 YHALCIDAWLKNHLTCPTCR 172

Arabidopsis thaliana (taxid: 3702)

>sp|Q94BY6|ATL75_ARATH RING-H2 finger protein ATL75 OS=Arabidopsis thaliana GN=ATL75 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 47/72 (65%), Gaps = 2/72 (2%)

Query: 25  QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
           +G+  +AL ++ P V+YS +   P     CVICL +FV GE  R+ P C+  FH  CID+
Sbjct: 108 KGINKKAL-RMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDK 166

Query: 84  WLKEHLTCPVCR 95
           WL++HLTCP CR
Sbjct: 167 WLQQHLTCPKCR 178

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 47/72 (65%), Gaps = 2/72 (2%)

Query: 25  QGLGDEALEQLMPCVNYSDQEMTPSSNY-CVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
           +G+  +AL ++ P V+YS +   P  +  CVICL +FV GE  RL P C   FH  CID+
Sbjct: 107 KGIKKKAL-RMFPVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDK 165

Query: 84  WLKEHLTCPVCR 95
           WL++HLTCP CR
Sbjct: 166 WLQQHLTCPKCR 177

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 48/77 (62%), Gaps = 2/77 (2%)

Query: 25  QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
           +G+  +AL +++P VNYS +   P     CVICL +FV GE  R+ P C   FH  CID+
Sbjct: 102 KGIKKKAL-KMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDK 160

Query: 84  WLKEHLTCPVCRISCID 100
           WL +H+TCP CR   +D
Sbjct: 161 WLTQHMTCPKCRHCLVD 177

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RXX9|ATL6_ARATH E3 ubiquitin-protein ligase ATL6 OS=Arabidopsis thaliana GN=ATL6 PE=1 SV=2

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/70 (44%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 29  DEALEQLMPCVNYSD---QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL 85
           D ++ +  P   YSD   Q++      C ICL  F D E+ RL P C  +FH  CID WL
Sbjct: 101 DVSVVETFPTFLYSDVKTQKLGKGELECAICLNEFEDDETLRLLPKCDHVFHPHCIDAWL 160

Query: 86  KEHLTCPVCR 95
           + H+TCPVCR
Sbjct: 161 EAHVTCPVCR 170

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro. May be involved in the plant C/N response and the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6NML0|ATL76_ARATH E3 ubiquitin-protein ligase ATL76 OS=Arabidopsis thaliana GN=ATL76 PE=1 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/72 (48%), Positives = 45/72 (62%), Gaps = 2/72 (2%)

Query: 25  QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
           +G+  +AL ++ P V+YS +   P     CVICL +FV GE  RL P C   FH  CID+
Sbjct: 107 KGIKKKAL-RMFPVVSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDK 165

Query: 84  WLKEHLTCPVCR 95
           WL+ HLTCP CR
Sbjct: 166 WLQHHLTCPKCR 177

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 70.1 bits (170), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/81 (40%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 21  VGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVC 80
           V +R GL    L++  P   Y   E+  ++  C ICL  F DGE  R+ P C   FH  C
Sbjct: 74  VADRAGLKKRELKKF-PVAEYGSGEVKIAATECAICLGEFADGERVRVLPPCNHSFHMSC 132

Query: 81  IDQWLKEHLTCPVCRISCIDI 101
           ID WL  H +CP CR S I++
Sbjct: 133 IDTWLVSHSSCPNCRHSLIEV 153

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LGA5|ATL31_ARATH E3 ubiquitin-protein ligase ATL31 OS=Arabidopsis thaliana GN=ATL31 PE=1 SV=2

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 25  QGLGDEALEQLMPCVNYSD---QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCI 81
           +GL  E +E   P   YS+   Q++   +  C ICL  F D E+ RL P C  +FH  CI
Sbjct: 94  RGLDAETIETF-PTFVYSEVKTQKIGKGALECAICLNEFEDDETLRLLPKCDHVFHPHCI 152

Query: 82  DQWLKEHLTCPVCR 95
             WL+ H+TCPVCR
Sbjct: 153 GAWLQGHVTCPVCR 166

E3 ubiquitin-protein ligase that is required for the plant C/N response during seedling growth transition. May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9FLC6|ATL73_ARATH RING-H2 finger protein ATL73 OS=Arabidopsis thaliana GN=ATL73 PE=2 SV=1

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 4/92 (4%)

Query: 9   NPDRDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRL 68
            P+ D  D++  V   +G+   AL +++P  +YS  E+   +  C+ICL +FV+GE+ R+
Sbjct: 73  TPNEDPVDTNANVA--KGIKKRAL-KVIPVDSYS-PELKMKATECLICLGDFVEGETVRV 128

Query: 69  FPVCYRIFHSVCIDQWLKEHLTCPVCRISCID 100
            P C   FH  CID WL  H +CP CR S ++
Sbjct: 129 LPKCNHGFHVKCIDTWLLSHSSCPTCRQSLLE 160

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W571|ATL32_ARATH RING-H2 finger protein ATL32 OS=Arabidopsis thaliana GN=ATL32 PE=2 SV=3

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/75 (41%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 24  RQGLGDEALEQLMPCVNYS---DQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVC 80
           R+G  D A+ +  P   YS   + ++      C ICL    D E+ RL P+C  +FH  C
Sbjct: 92  RRGGLDNAVVESFPVFAYSSVKESKIGSKDLECAICLNELEDHETVRLLPICNHLFHIDC 151

Query: 81  IDQWLKEHLTCPVCR 95
           ID WL  H TCPVCR
Sbjct: 152 IDTWLYSHATCPVCR 166

Arabidopsis thaliana (taxid: 3702)

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	104
297847686	177	zinc finger family protein [Arabidopsis	0.711	0.418	0.462	1e-13
15219164	178	putative RING-H2 finger protein ATL19 [A	0.711	0.415	0.45	3e-13
255581815	150	protein with unknown function [Ricinus c	0.653	0.453	0.536	4e-13
302756931	1406	hypothetical protein SELMODRAFT_403293 [	0.730	0.054	0.381	2e-11
297810639	178	zinc finger family protein [Arabidopsis	0.865	0.505	0.402	2e-11
15222068	226	RING-H2 finger protein ATL75 [Arabidopsi	0.673	0.309	0.472	3e-11
414869199	377	TPA: putative RING zinc finger domain su	0.644	0.177	0.432	4e-11
212721568	377	uncharacterized protein LOC100192844 pre	0.644	0.177	0.432	4e-11
226493615	393	uncharacterized LOC100274267 precursor [	0.730	0.193	0.405	4e-11
168028079	122	predicted protein [Physcomitrella patens	0.701	0.598	0.461	5e-11

>gi|297847686|ref|XP_002891724.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297337566|gb|EFH67983.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 50/80 (62%), Gaps = 6/80 (7%)

Query: 22  GERQGLGDEALEQLMPCVNYS------DQEMTPSSNYCVICLENFVDGESCRLFPVCYRI 75
           G+++GL   A+E L+P +         D+E +  S  C ICL  +V  E CR+FPVC  I
Sbjct: 92  GKKRGLKQSAIETLLPKLLVGQGNHEDDKERSLESRECAICLSGYVINEECRVFPVCRHI 151

Query: 76  FHSVCIDQWLKEHLTCPVCR 95
           +H++CID WLK HLTCP CR
Sbjct: 152 YHALCIDTWLKNHLTCPTCR 171

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219164|ref|NP_175709.1| putative RING-H2 finger protein ATL19 [Arabidopsis thaliana] gi|75308900|sp|Q9C919.1|ATL19_ARATH RecName: Full=Putative RING-H2 finger protein ATL19 gi|12324634|gb|AAG52270.1|AC019018_7 hypothetical protein; 116909-117445 [Arabidopsis thaliana] gi|332194755|gb|AEE32876.1| putative RING-H2 finger protein ATL19 [Arabidopsis thaliana]

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 36/80 (45%), Positives = 50/80 (62%), Gaps = 6/80 (7%)

Query: 22  GERQGLGDEALEQLMPCV------NYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRI 75
           G+++GL    +E L+P +      +  D+E +  S  C ICL  +V  E CR+FPVC  I
Sbjct: 93  GKKRGLKQSVIETLLPKLLVGQGNHEEDEEKSLESRECAICLSGYVVNEECRVFPVCRHI 152

Query: 76  FHSVCIDQWLKEHLTCPVCR 95
           +H++CID WLK HLTCP CR
Sbjct: 153 YHALCIDAWLKNHLTCPTCR 172

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581815|ref|XP_002531708.1| protein with unknown function [Ricinus communis] gi|223528651|gb|EEF30667.1| protein with unknown function [Ricinus communis]

 Score = 78.6 bits (192), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 37/69 (53%), Positives = 47/69 (68%), Gaps = 1/69 (1%)

Query: 28  GDEALEQLMPCVNYSDQEM-TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK 86
           G  A++ L+P V Y D EM  P    CVICLE+++D E CR+ P C  +FHS CI+QWLK
Sbjct: 78  GQYAIDNLLPTVIYGDNEMKIPEFEVCVICLEDYMDRELCRILPSCRHMFHSHCIEQWLK 137

Query: 87  EHLTCPVCR 95
            +LTCP CR
Sbjct: 138 WNLTCPTCR 146

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 41/76 (53%)

Query: 25   QGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW 84
            +GL    ++ L+P   Y  +    ++  C +CL  F DGE  RL P C   FH+ CID W
Sbjct: 1189 KGLDQGVIDSLLPAFVYGKEGYVGATTECAVCLSEFEDGERGRLLPKCNHAFHAGCIDMW 1248

Query: 85   LKEHLTCPVCRISCID 100
             + H TCP+CR   +D
Sbjct: 1249 FQSHATCPICRSPVVD 1264

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297810639|ref|XP_002873203.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297319040|gb|EFH49462.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score = 72.8 bits (177), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/92 (40%), Positives = 54/92 (58%), Gaps = 2/92 (2%)

Query: 9   NPDRDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRL 68
            PD D  D++  V   +G+   AL +L+P  +YS  E+   +  C+ICL +FV+GE+ R+
Sbjct: 73  TPDEDPVDTNANVNVAKGIKKRAL-KLIPVDSYS-LELKMKATECLICLGDFVEGETVRV 130

Query: 69  FPVCYRIFHSVCIDQWLKEHLTCPVCRISCID 100
            P C   FH  CID WL  H +CP CR S ++
Sbjct: 131 LPKCNHGFHVKCIDTWLLSHSSCPTCRQSLLE 162

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222068|ref|NP_175346.1| RING-H2 finger protein ATL75 [Arabidopsis thaliana] gi|68565250|sp|Q94BY6.1|ATL75_ARATH RecName: Full=RING-H2 finger protein ATL75 gi|14517432|gb|AAK62606.1| At1g49200/F27J15_35 [Arabidopsis thaliana] gi|20147327|gb|AAM10377.1| At1g49200/F27J15_35 [Arabidopsis thaliana] gi|332194283|gb|AEE32404.1| RING-H2 finger protein ATL75 [Arabidopsis thaliana]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 47/72 (65%), Gaps = 2/72 (2%)

Query: 25  QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
           +G+  +AL ++ P V+YS +   P     CVICL +FV GE  R+ P C+  FH  CID+
Sbjct: 108 KGINKKAL-RMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDK 166

Query: 84  WLKEHLTCPVCR 95
           WL++HLTCP CR
Sbjct: 167 WLQQHLTCPKCR 178

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414869199|tpg|DAA47756.1| TPA: putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 29/67 (43%), Positives = 38/67 (56%)

Query: 29  DEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH 88
           D A+    P + Y+D      +  C +CL  F DG++ RL P C   FH+ CID WL  H
Sbjct: 103 DRAVLDSFPTMAYADVRAHKGALECAVCLSEFDDGDTLRLLPRCAHAFHTDCIDAWLASH 162

Query: 89  LTCPVCR 95
           +TCPVCR
Sbjct: 163 VTCPVCR 169

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|212721568|ref|NP_001131506.1| uncharacterized protein LOC100192844 precursor [Zea mays] gi|194691718|gb|ACF79943.1| unknown [Zea mays]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 29/67 (43%), Positives = 38/67 (56%)

Query: 29  DEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH 88
           D A+    P + Y+D      +  C +CL  F DG++ RL P C   FH+ CID WL  H
Sbjct: 103 DRAVLDSFPTMAYADVRAHKGALECAVCLSEFDDGDTLRLLPRCAHAFHTDCIDAWLASH 162

Query: 89  LTCPVCR 95
           +TCPVCR
Sbjct: 163 VTCPVCR 169

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226493615|ref|NP_001142103.1| uncharacterized LOC100274267 precursor [Zea mays] gi|194707124|gb|ACF87646.1| unknown [Zea mays] gi|414589721|tpg|DAA40292.1| TPA: putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/79 (40%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 24  RQGLGDEALEQLMPCVNYSDQEMTPSSN---YCVICLENFVDGESCRLFPVCYRIFHSVC 80
           RQ   DEA+ +  P + Y+D +   +      C +CL  F D E+ RL P C  +FH  C
Sbjct: 103 RQRGLDEAVLESFPTMAYADVKAHKAGKGALECAVCLSEFDDDETLRLLPKCSHVFHPDC 162

Query: 81  IDQWLKEHLTCPVCRISCI 99
           ID WL  H+TCPVCR + +
Sbjct: 163 IDTWLASHVTCPVCRANLV 181

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168028079|ref|XP_001766556.1| predicted protein [Physcomitrella patens subsp. patens] gi|162682201|gb|EDQ68621.1| predicted protein [Physcomitrella patens subsp. patens]

 Score = 71.6 bits (174), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 45/78 (57%), Gaps = 5/78 (6%)

Query: 23  ERQGLGDEALEQLMPCVNYSDQEMTPS-----SNYCVICLENFVDGESCRLFPVCYRIFH 77
           ER+   D+++ + +P V YS   +  S      N CV+CL  FV+GE  RL P C   FH
Sbjct: 44  EREKGLDKSVIEALPVVAYSPDSIKSSFDPSGENDCVVCLSGFVEGEKVRLLPHCKHGFH 103

Query: 78  SVCIDQWLKEHLTCPVCR 95
            VCID WL  H TCPVCR
Sbjct: 104 LVCIDTWLLSHTTCPVCR 121

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

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	104
TAIR|locus:2011491	178	AT1G53010 [Arabidopsis thalian	0.711	0.415	0.462	2.7e-18
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.701	0.323	0.460	8.8e-15
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.701	0.290	0.473	1.4e-14
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.721	0.340	0.467	2.3e-14
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.701	0.324	0.473	4.9e-14
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.769	0.503	0.407	4.4e-13
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.778	0.460	0.385	3.9e-12
TAIR|locus:2019110	223	AT1G74410 [Arabidopsis thalian	0.692	0.322	0.397	5e-12
TAIR|locus:2096309	398	ATL6 "Arabidopsis toxicos en l	0.673	0.175	0.445	7.6e-12
UNIPROTKB|K7GLM9	238	LOC100519887 "Uncharacterized	0.692	0.302	0.350	8.2e-12

TAIR|locus:2011491 AT1G53010 [Arabidopsis thaliana (taxid:3702)]

 Score = 205 (77.2 bits), Expect = 2.7e-18, Sum P(2) = 2.7e-18
 Identities = 37/80 (46%), Positives = 51/80 (63%)

Query:    22 GERQGLGDEALEQLMPCV-----NYS-DQEMTPSSNYCVICLENFVDGESCRLFPVCYRI 75
             G+++GL    +E L+P +     N+  D+E +  S  C ICL  +V  E CR+FPVC  I
Sbjct:    93 GKKRGLKQSVIETLLPKLLVGQGNHEEDEEKSLESRECAICLSGYVVNEECRVFPVCRHI 152

Query:    76 FHSVCIDQWLKEHLTCPVCR 95
             +H++CID WLK HLTCP CR
Sbjct:   153 YHALCIDAWLKNHLTCPTCR 172

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

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

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 35/76 (46%), Positives = 49/76 (64%)

Query:    25 QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
             +G+  +AL ++ P V+YS +   P     CVICL +FV GE  R+ P C+  FH  CID+
Sbjct:   108 KGINKKAL-RMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDK 166

Query:    84 WLKEHLTCPVCRISCI 99
             WL++HLTCP CR  C+
Sbjct:   167 WLQQHLTCPKCR-HCL 181

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

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

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 36/76 (47%), Positives = 49/76 (64%)

Query:    25 QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
             +G+  +AL ++ P V+YS +   P     CVICL +FV GE  RL P C   FH  CID+
Sbjct:   107 KGIKKKAL-RMFPVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDK 165

Query:    84 WLKEHLTCPVCRISCI 99
             WL++HLTCP CR +C+
Sbjct:   166 WLQQHLTCPKCR-NCL 180

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

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

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 36/77 (46%), Positives = 47/77 (61%)

Query:    25 QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
             +G+  +AL+ L P VNYS +   P     CVICL +FV GE  R+ P C   FH  CID+
Sbjct:   102 KGIKKKALKML-PVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDK 160

Query:    84 WLKEHLTCPVCRISCID 100
             WL +H+TCP CR   +D
Sbjct:   161 WLTQHMTCPKCRHCLVD 177

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

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

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 36/76 (47%), Positives = 47/76 (61%)

Query:    25 QGLGDEALEQLMPCVNYSDQEMTPS-SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ 83
             +G+  +AL ++ P V+YS +   P     CVICL +FV GE  RL P C   FH  CID+
Sbjct:   107 KGIKKKAL-RMFPVVSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDK 165

Query:    84 WLKEHLTCPVCRISCI 99
             WL+ HLTCP CR  C+
Sbjct:   166 WLQHHLTCPKCR-HCL 180

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/81 (40%), Positives = 43/81 (53%)

Query:    21 VGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVC 80
             V +R GL    L++  P   Y   E+  ++  C ICL  F DGE  R+ P C   FH  C
Sbjct:    74 VADRAGLKKRELKKF-PVAEYGSGEVKIAATECAICLGEFADGERVRVLPPCNHSFHMSC 132

Query:    81 IDQWLKEHLTCPVCRISCIDI 101
             ID WL  H +CP CR S I++
Sbjct:   133 IDTWLVSHSSCPNCRHSLIEV 153

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

TAIR|locus:2153554 DAF "DEFECTIVE IN ANTHER DEHISCENCE1- ( DAD1-) Activating Factor" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 32/83 (38%), Positives = 48/83 (57%)

Query:    18 DLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFH 77
             D      +G+   AL+ ++P  +YS  E+   +  C+ICL +FV+GE+ R+ P C   FH
Sbjct:    80 DTNANVAKGIKKRALK-VIPVDSYSP-ELKMKATECLICLGDFVEGETVRVLPKCNHGFH 137

Query:    78 SVCIDQWLKEHLTCPVCRISCID 100
               CID WL  H +CP CR S ++
Sbjct:   138 VKCIDTWLLSHSSCPTCRQSLLE 160

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

TAIR|locus:2019110 AT1G74410 [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 29/73 (39%), Positives = 42/73 (57%)

Query:    23 ERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCID 82
             E +GL  ++L +L PC   S + +     +C ICL++   GE  R  P C   FH VC+D
Sbjct:   147 EARGLSGDSLRKL-PCYIMSSEMVRRQVTHCTICLQDIKTGEITRSLPKCDHTFHLVCVD 205

Query:    83 QWLKEHLTCPVCR 95
             +WL  H +CP+CR
Sbjct:   206 KWLIRHGSCPICR 218

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

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2096309 ATL6 "Arabidopsis toxicos en levadura 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 7.6e-12, P = 7.6e-12
 Identities = 33/74 (44%), Positives = 43/74 (58%)

Query:    25 QGLGDEALEQLMPCVNYSD---QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCI 81
             +GL D ++ +  P   YSD   Q++      C ICL  F D E+ RL P C  +FH  CI
Sbjct:    98 RGL-DVSVVETFPTFLYSDVKTQKLGKGELECAICLNEFEDDETLRLLPKCDHVFHPHCI 156

Query:    82 DQWLKEHLTCPVCR 95
             D WL+ H+TCPVCR
Sbjct:   157 DAWLEAHVTCPVCR 170

GO:0005576 "extracellular region" evidence=ISM

GO:0008270 "zinc ion binding" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

GO:0009814 "defense response, incompatible interaction" evidence=IEP

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IMP

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

GO:0035556 "intracellular signal transduction" evidence=RCA

UNIPROTKB|K7GLM9 LOC100519887 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 27/77 (35%), Positives = 46/77 (59%)

Query:    27 LGD---EALEQLMP-CVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCID 82
             LGD   +A+ +L    V   D+E  P  ++C +C+E++   +  R+ P C  +FH  C+D
Sbjct:    88 LGDAAKKAISKLTTRTVKKGDKETDPDFDHCAVCIESYKQNDVVRILP-CKHVFHKSCVD 146

Query:    83 QWLKEHLTCPVCRISCI 99
              WL EH TCP+C+++ +
Sbjct:   147 PWLSEHCTCPMCKLNIL 163

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh2_kg.1__4375__AT1G53010.1 annotation not avaliable (177 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	104
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	7e-10
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	5e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-06
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	2e-05
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	0.001
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	0.003

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

 Score = 49.7 bits (119), Expect = 7e-10
 Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 1/43 (2%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C ICL+ F  GE   + P C  +FH  C+D+WL+   TCP+CR
Sbjct: 3  CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 51.5 bits (123), Expect = 5e-09
 Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 53  CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-LTCPVCR 95
           C IC+ NF+  +  R+ P C   FH  C+D+WL  +   CPVCR
Sbjct: 326 CAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 40.9 bits (96), Expect = 4e-06
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 9/52 (17%)

Query: 53 CVICLENFVD--------GESCRL-FPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C IC  +F          G+ C + +  C   FH  CI +WLK   TCP+CR
Sbjct: 22 CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

>gnl|CDD|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 = 40.1 bits (94), Expect = 4e-06
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISC 98
          C ICLE F +     +   C  +F   CID+WLK    TCP+CR   
Sbjct: 2  CPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 53  CVICLENFVDGESCRLF----PVCYRIFHSVCIDQWLKEHLTCPVCR 95
           C IC+E   D E   ++      C  +F   CID W KE  TCPVCR
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 32  LEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFP---------VCYRIFHSVCID 82
           L  + P    +++++T S   C IC++     +   L            C  I H  C+ 
Sbjct: 271 LNAMYPTA--TEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLK 328

Query: 83  QWLKEHLTCPVCRISCI 99
            WL+   TCP+CR   I
Sbjct: 329 NWLERQQTCPICRRPVI 345

Length = 491

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

 Score = 33.6 bits (77), Expect = 0.001
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
              C ICL+   D     +   C  +F   CI ++LK+   CP+CR
Sbjct: 1  EELECPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

>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 = 33.7 bits (77), Expect = 0.003
 Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 53 CVICLENFVDGESCRL-FPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C  C      G+ C + + VC   FH  CI +WL     CP+ R
Sbjct: 34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	104
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.82
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.81
PHA02929	238	N1R/p28-like protein; Provisional	99.68
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.68
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.61
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.56
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.55
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.54
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.54
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.52
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.5
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.49
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.46
PHA02926	242	zinc finger-like protein; Provisional	99.46
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.43
PF14634	44	zf-RING_5: zinc-RING finger domain	99.4
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.37
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.37
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.36
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.28
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.26
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.19
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.18
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.18
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.17
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	99.08
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.06
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.96
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.96
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.93
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.93
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.92
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.9
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.88
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.87
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.83
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.82
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.82
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.79
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.73
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.71
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.65
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.64
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.62
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.57
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.53
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.51
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.44
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.42
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.36
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.22
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.21
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.08
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	98.04
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.99
KOG2660	331	consensus Locus-specific chromosome binding protei	97.95
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.91
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.9
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.9
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.86
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.84
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.8
PHA02862	156	5L protein; Provisional	97.79
PHA03096	284	p28-like protein; Provisional	97.72
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.69
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.67
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.63
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.58
COG5152	259	Uncharacterized conserved protein, contains RING a	97.52
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.44
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.37
PF04641	260	Rtf2: Rtf2 RING-finger	97.29
KOG4739	233	consensus Uncharacterized protein involved in syna	97.27
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.25
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	97.09
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	97.05
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	97.02
KOG1940	276	consensus Zn-finger protein [General function pred	96.98
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.97
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.94
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.86
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.83
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.79
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.77
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.76
KOG3053	293	consensus Uncharacterized conserved protein [Funct	96.73
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.7
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.7
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.52
KOG0298	1394	consensus DEAD box-containing helicase-like transc	96.4
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.4
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	96.33
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	96.13
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.93
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.78
KOG3002	299	consensus Zn finger protein [General function pred	95.78
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG3899	381	consensus Uncharacterized conserved protein [Funct	95.55
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.36
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	95.3
KOG1609	323	consensus Protein involved in mRNA turnover and st	95.06
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	94.96
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.84
KOG4367	699	consensus Predicted Zn-finger protein [Function un	94.64
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	94.63
KOG0825	1134	consensus PHD Zn-finger protein [General function	94.18
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.02
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	93.81
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	93.14
KOG1829	580	consensus Uncharacterized conserved protein, conta	92.94
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	92.75
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	92.54
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	92.43
KOG0269	839	consensus WD40 repeat-containing protein [Function	92.33
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	92.17
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	91.93
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.84
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	91.78
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	91.27
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	91.2
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	90.72
KOG2807	378	consensus RNA polymerase II transcription initiati	90.67
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	90.49
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	90.34
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	89.97
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	89.95
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.14
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.96
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	88.69
KOG2068	327	consensus MOT2 transcription factor [Transcription	88.34
cd00065	57	FYVE FYVE domain; Zinc-binding domain; targets pro	88.12
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	88.09
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	87.32
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	86.52
KOG3005	276	consensus GIY-YIG type nuclease [General function	84.99
smart00064	68	FYVE Protein present in Fab1, YOTB, Vac1, and EEA1	84.84
COG5109	396	Uncharacterized conserved protein, contains RING Z	83.23
smart00647	64	IBR In Between Ring fingers. the domains occurs be	82.85
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	82.3
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	82.18
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	81.55
KOG3039	303	consensus Uncharacterized conserved protein [Funct	80.97
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	80.39

>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=99.82  E-value=6e-21  Score=96.48  Aligned_cols=44  Identities=52%  Similarity=1.208  Sum_probs=40.3

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      ..|+||+++|..++.++.++ |||+||.+||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            36999999999999999999 999999999999999999999997

...

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

Probab=99.81  E-value=1.9e-20  Score=128.89  Aligned_cols=76  Identities=30%  Similarity=0.741  Sum_probs=62.6

Q ss_pred             CCCCHHHHHhhCCccccCCCCCCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC-CCccccccccCCC
Q 045579           25 QGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCRISCIDIE  102 (104)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~-~CP~CR~~~~~~~  102 (104)
                      ..+.+..+.+ +|...+...........|+||||+|..++++++|| |+|.||..||++||.... .||+|++++....
T Consensus       205 ~r~~k~~l~~-~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  205 NRLIKRLLKK-LPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             hhhHHHHHhh-CCcEEeccccccCCCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            3445555655 68888887776544479999999999999999999 999999999999997664 5999999987554

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.68  E-value=3e-17  Score=108.71  Aligned_cols=76  Identities=32%  Similarity=0.612  Sum_probs=53.7

Q ss_pred             CCCCHHHHHhhCCccccCCCC--CCCCccccccccccccCCC----cEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           25 QGLGDEALEQLMPCVNYSDQE--MTPSSNYCVICLENFVDGE----SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~C~ICl~~~~~~~----~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      .+.....+.. +|.+......  ....+.+|+||++.+..+.    .+.+++.|+|.||..||.+|+..+.+||+||..+
T Consensus       148 ~~~~~~~i~~-lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        148 GKNYKKFLKT-IPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             cchhHHHHHh-cchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            3444555554 5666433221  2245789999999987643    1334545999999999999999999999999988


Q ss_pred             cCC
Q 045579           99 IDI  101 (104)
Q Consensus        99 ~~~  101 (104)
                      ..+
T Consensus       227 ~~v  229 (238)
T PHA02929        227 ISV  229 (238)
T ss_pred             eEE
Confidence            643

>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=99.68  E-value=3.1e-17  Score=91.10  Aligned_cols=45  Identities=47%  Similarity=0.947  Sum_probs=35.7

Q ss_pred             ccccccccccccCC----------CcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           50 SNYCVICLENFVDG----------ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        50 ~~~C~ICl~~~~~~----------~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      +..|+||++.|...          -.+...+ |||.||..||.+||+.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            44699999999422          2444455 999999999999999999999998

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

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

Probab=99.61  E-value=4.1e-16  Score=105.16  Aligned_cols=52  Identities=37%  Similarity=0.875  Sum_probs=47.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~~  101 (104)
                      .+.+|+|||+.|..++.++++| |.|.||..|+.+|+. -+..||+||..+++.
T Consensus       322 ~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPPp  374 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPPP  374 (374)
T ss_pred             CCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCCC
Confidence            4688999999999999999999 999999999999996 677899999998753

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

Probab=99.56  E-value=2.5e-15  Score=77.68  Aligned_cols=47  Identities=36%  Similarity=0.799  Sum_probs=39.6

Q ss_pred             ccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      +..|.||++.+..   ++.+| |||. ||..|+.+|+.....||+||+++..
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            5689999998644   77788 9999 9999999999999999999999864

...

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

Probab=99.55  E-value=3.5e-15  Score=103.15  Aligned_cols=52  Identities=35%  Similarity=0.883  Sum_probs=44.0

Q ss_pred             CCCccccccccccc-cCCC---------cEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           47 TPSSNYCVICLENF-VDGE---------SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        47 ~~~~~~C~ICl~~~-~~~~---------~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ..++..|.|||+++ +.+.         ....|| |||+||.+|+.-|+.++.+||+||.+++
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            45688999999994 4431         445788 9999999999999999999999999965

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

Probab=99.54  E-value=5.8e-15  Score=92.87  Aligned_cols=53  Identities=28%  Similarity=0.601  Sum_probs=44.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ++...|+|||+.+.....+.  .+|||+||..||...++....||+||+.|...+
T Consensus       129 ~~~~~CPiCl~~~sek~~vs--TkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVPVS--TKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             ccccCCCceecchhhccccc--cccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            56789999999987765432  359999999999999999999999999876543

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

Probab=99.54  E-value=4e-15  Score=99.68  Aligned_cols=50  Identities=34%  Similarity=0.714  Sum_probs=43.1

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .....|.|||+..+.   ...+| |||+||+.||..|...+..||+||..+..-
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            567899999998766   45577 999999999999999999999999988643

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

Probab=99.52  E-value=1.1e-14  Score=71.56  Aligned_cols=39  Identities=38%  Similarity=0.995  Sum_probs=32.8

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~C   94 (104)
                      |+||++.+.+  .+++++ |||+||.+||.+|+..+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998876  456777 99999999999999888899998

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

Probab=99.50  E-value=1.5e-14  Score=81.41  Aligned_cols=52  Identities=29%  Similarity=0.610  Sum_probs=38.9

Q ss_pred             CccccccccccccCC--------C-cEEecCCCCCcccHHhHHHHHhc---CCCCccccccccC
Q 045579           49 SSNYCVICLENFVDG--------E-SCRLFPVCYRIFHSVCIDQWLKE---HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~--------~-~~~~lp~C~H~fh~~Ci~~wl~~---~~~CP~CR~~~~~  100 (104)
                      .++.|.||...|...        + -..++..|+|.||..||.+||..   +.+||+||++..-
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            377899999888721        1 12233349999999999999964   4679999998753

>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=99.49  E-value=3.2e-14  Score=71.21  Aligned_cols=44  Identities=50%  Similarity=1.116  Sum_probs=36.5

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISC   98 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~   98 (104)
                      .|+||++.+  ...+.+++ |||.||..|+..|+.. ...||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  33455555 9999999999999986 77899999864

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.46  E-value=5.3e-14  Score=90.23  Aligned_cols=49  Identities=29%  Similarity=0.645  Sum_probs=39.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----------------CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----------------HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----------------~~~CP~CR~~~~~  100 (104)
                      .++..|+||++.+..+   ++++ |||+||..||..|+..                ...||+||..+..
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            3578899999987653   4466 9999999999999842                2479999998854

>PHA02926 zinc finger-like protein; Provisional

Probab=99.46  E-value=3.9e-14  Score=92.16  Aligned_cols=52  Identities=29%  Similarity=0.668  Sum_probs=40.4

Q ss_pred             CCccccccccccccCC-----CcEEecCCCCCcccHHhHHHHHhcC------CCCcccccccc
Q 045579           48 PSSNYCVICLENFVDG-----ESCRLFPVCYRIFHSVCIDQWLKEH------LTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~-----~~~~~lp~C~H~fh~~Ci~~wl~~~------~~CP~CR~~~~   99 (104)
                      +.+.+|+|||+.....     ....+|+.|+|.||..||..|...+      .+||+||..+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            4578999999986432     2345666699999999999999642      45999999875

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

Probab=99.43  E-value=1.3e-13  Score=90.02  Aligned_cols=51  Identities=29%  Similarity=0.548  Sum_probs=39.7

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCccccccccCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRISCIDI  101 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~~~~~  101 (104)
                      .....+|.|||+.-++  .|+ +. |||+||+.||.+||.   .+..||+|+..|...
T Consensus        44 ~~~~FdCNICLd~akd--PVv-Tl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD--PVV-TL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             CCCceeeeeeccccCC--CEE-ee-cccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            3567899999998544  344 44 999999999999995   344699999988643

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.40  E-value=2.4e-13  Score=68.44  Aligned_cols=44  Identities=32%  Similarity=0.810  Sum_probs=37.8

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      .|+||++.|.......+++ |||+||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4899999996566777787 9999999999998866778999985

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

Probab=99.37  E-value=4.3e-13  Score=66.80  Aligned_cols=38  Identities=39%  Similarity=0.939  Sum_probs=28.2

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHhcC----CCCccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH----LTCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~----~~CP~C   94 (104)
                      |+||++.|..   .+.|+ |||.|+..||.+|.+..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999977   45566 99999999999999533    469987

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

Probab=99.37  E-value=1.8e-13  Score=100.37  Aligned_cols=52  Identities=38%  Similarity=0.962  Sum_probs=45.1

Q ss_pred             CCccccccccccccCCCc--EEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGES--CRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~--~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ..+..|+||++.+..+..  ...+| |+|+||..|+..|++++.+||+||..+..
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            347899999999988755  56788 99999999999999999999999995543

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

Probab=99.36  E-value=4.1e-13  Score=66.53  Aligned_cols=39  Identities=44%  Similarity=1.096  Sum_probs=33.0

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHh--cCCCCccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~C   94 (104)
                      |+||++.+..+  +.+++ |||.||..||.+|+.  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998664  35677 999999999999997  55679998

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 ....

>smart00184 RING Ring finger

Probab=99.28  E-value=3.8e-12  Score=61.50  Aligned_cols=38  Identities=45%  Similarity=1.116  Sum_probs=31.9

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~C   94 (104)
                      |+||++..   ..+..++ |||.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            78998883   3466677 999999999999997 66779987

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

>smart00504 Ubox Modified RING finger domain

Probab=99.26  E-value=8e-12  Score=67.17  Aligned_cols=45  Identities=29%  Similarity=0.457  Sum_probs=39.4

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ..|+||++.|..+   ++++ |||+|+..||.+|+..+.+||+|+..+.
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence            4699999998774   4567 9999999999999988889999998874

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

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

Probab=99.19  E-value=1.6e-11  Score=67.80  Aligned_cols=29  Identities=38%  Similarity=0.895  Sum_probs=27.2

Q ss_pred             CCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           71 VCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        71 ~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .|.|.||..||.+||..+..||++|++..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            49999999999999999999999999874

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.18  E-value=1.7e-11  Score=86.66  Aligned_cols=50  Identities=32%  Similarity=0.616  Sum_probs=42.2

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ......|+||++.|..+   ++++ |||.||..||..|+.....||+||..+..
T Consensus        23 Le~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        23 LDTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            34677999999998664   3567 99999999999999888899999998753

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

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

Probab=99.18  E-value=2.4e-12  Score=70.52  Aligned_cols=51  Identities=29%  Similarity=0.699  Sum_probs=37.7

Q ss_pred             CccccccccccccCC---------CcEEecCCCCCcccHHhHHHHHh---cCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDG---------ESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~---------~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~~~   99 (104)
                      ++++|.||...|...         +-..++..|.|.||..||.+|+.   ++..||+||+...
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            455899999888631         22223334999999999999994   4456999999864

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

Probab=99.17  E-value=1.3e-11  Score=82.04  Aligned_cols=51  Identities=27%  Similarity=0.628  Sum_probs=41.4

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHH-HHhcCCC-CccccccccCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ-WLKEHLT-CPVCRISCIDIE  102 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~-wl~~~~~-CP~CR~~~~~~~  102 (104)
                      ..+..|+||++..+.   ...++ |||+||..||.. |-.++.. ||+||+.+...+
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            458889999988655   55566 999999999999 9866655 999999887543

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

Probab=99.08  E-value=1e-10  Score=59.99  Aligned_cols=42  Identities=31%  Similarity=0.862  Sum_probs=32.4

Q ss_pred             ccccccccccCCCcEEecCCCC-----CcccHHhHHHHHhc--CCCCcccc
Q 045579           52 YCVICLENFVDGESCRLFPVCY-----RIFHSVCIDQWLKE--HLTCPVCR   95 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~-----H~fh~~Ci~~wl~~--~~~CP~CR   95 (104)
                      .|.||++ ...++...++| |.     |.||..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 33444555778 84     89999999999954  44899995

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

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

Probab=99.06  E-value=1.5e-10  Score=57.69  Aligned_cols=38  Identities=32%  Similarity=0.817  Sum_probs=22.2

Q ss_pred             cccccccccC-CCcEEecCCCCCcccHHhHHHHHhcC----CCCc
Q 045579           53 CVICLENFVD-GESCRLFPVCYRIFHSVCIDQWLKEH----LTCP   92 (104)
Q Consensus        53 C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl~~~----~~CP   92 (104)
                      |+||++ |.. ....++|+ |||+|+.+||.+++..+    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 755 34567788 99999999999999643    3576

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

Probab=98.96  E-value=2.4e-10  Score=81.80  Aligned_cols=52  Identities=38%  Similarity=0.802  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCC--------------cEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGE--------------SCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~--------------~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      .....|+|||.++..-.              ..+++| |.|+||..|+.+|+. .+..||+||..+++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            45678999998865211              233567 999999999999998 55689999999875

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

Probab=98.96  E-value=1.8e-10  Score=77.01  Aligned_cols=51  Identities=25%  Similarity=0.643  Sum_probs=42.9

Q ss_pred             CCccccccccccccCCC-------cEEecCCCCCcccHHhHHHHH--hcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGE-------SCRLFPVCYRIFHSVCIDQWL--KEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~-------~~~~lp~C~H~fh~~Ci~~wl--~~~~~CP~CR~~~~   99 (104)
                      ..+..|+||-..+....       .+..|. |+|+||..||.-|-  .++.+||.|+..+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            56778999988876554       667787 99999999999996  67889999998764

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.93  E-value=7.6e-10  Score=75.78  Aligned_cols=51  Identities=16%  Similarity=0.410  Sum_probs=37.6

Q ss_pred             Ccccccccccc-ccCCC-cEEecCCCCCcccHHhHHHHH-hcCCCCccccccccC
Q 045579           49 SSNYCVICLEN-FVDGE-SCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~-~~~~~-~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~~~  100 (104)
                      ++..||||+.. +..+. .+.+.+ |||.||.+||...+ .....||.|+..+..
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            35689999995 33333 334445 99999999999966 555689999987754

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).

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

Probab=98.93  E-value=5.3e-10  Score=80.25  Aligned_cols=47  Identities=32%  Similarity=0.535  Sum_probs=36.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-----CCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-----HLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-----~~~CP~CR~~~~~  100 (104)
                      +..|||||+....+   ..+. |||+||..||.+++..     -..||+||..|..
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            77899999875443   2333 9999999999998743     3469999998865

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

Probab=98.92  E-value=4.2e-10  Score=77.51  Aligned_cols=48  Identities=31%  Similarity=0.697  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .-..|.||.+.|..   .+++| |+|.||.-||..+|..+..||.|+.++.+
T Consensus        22 ~lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   22 DLLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             HHHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccch
Confidence            45679999999877   45567 99999999999999999999999998764

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

Probab=98.90  E-value=2.8e-10  Score=62.62  Aligned_cols=50  Identities=30%  Similarity=0.687  Sum_probs=23.1

Q ss_pred             cccccccccccc-CCCc-EEec--CCCCCcccHHhHHHHHhc---C--------CCCcccccccc
Q 045579           50 SNYCVICLENFV-DGES-CRLF--PVCYRIFHSVCIDQWLKE---H--------LTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~-~~~~-~~~l--p~C~H~fh~~Ci~~wl~~---~--------~~CP~CR~~~~   99 (104)
                      +..|.||+..+. .+.. ..+-  +.|+..||..||.+||..   .        .+||.|+.+|.
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            457999999865 3222 2222  259999999999999942   1        25999999874

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

Probab=98.88  E-value=1.1e-09  Score=63.44  Aligned_cols=51  Identities=29%  Similarity=0.657  Sum_probs=37.6

Q ss_pred             CCcccccccccccc-------------CCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           48 PSSNYCVICLENFV-------------DGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        48 ~~~~~C~ICl~~~~-------------~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      ...+.|+||..-+-             ..+-.+.-..|.|.||..||.+||+.+..||+|.++-
T Consensus        44 i~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   44 IVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             eeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            34667998875431             2223333344999999999999999999999998764

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

Probab=98.87  E-value=7.1e-10  Score=78.55  Aligned_cols=49  Identities=29%  Similarity=0.681  Sum_probs=39.3

Q ss_pred             CCccccccccccccCCCc-EEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGES-CRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~-~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .+-.+|+|||+.|..... ++... |.|.||..|+.+|  ...+||+||-...
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            456789999999976653 33444 9999999999999  6678999997654

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

Probab=98.83  E-value=1.3e-09  Score=73.43  Aligned_cols=45  Identities=38%  Similarity=0.800  Sum_probs=39.1

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      .+...|+||++.|..+   .++| |+|.||..|+..++.....||.||.
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            4677899999999887   6777 9999999999999875567999993

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

Probab=98.82  E-value=1.2e-09  Score=83.25  Aligned_cols=52  Identities=23%  Similarity=0.660  Sum_probs=38.9

Q ss_pred             CCccccccccccccC-CC--cEEecCCCCCcccHHhHHHHHhc--CCCCcccccccc
Q 045579           48 PSSNYCVICLENFVD-GE--SCRLFPVCYRIFHSVCIDQWLKE--HLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~-~~--~~~~lp~C~H~fh~~Ci~~wl~~--~~~CP~CR~~~~   99 (104)
                      ++.++|+||...+.. ..  .-...++|.|.||..|+.+|++.  +++||+||.++.
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            678899999877651 11  11234459999999999999964  557999998774

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

Probab=98.82  E-value=3.8e-09  Score=58.53  Aligned_cols=48  Identities=23%  Similarity=0.363  Sum_probs=36.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      +...|+|+.+-|.+   .+++| +||+|...+|..|+.. ..+||+++..+..
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            46789999999977   44567 9999999999999987 8899999988754

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 ....

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

Probab=98.79  E-value=3e-09  Score=72.05  Aligned_cols=47  Identities=32%  Similarity=0.474  Sum_probs=39.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .-..|-||-+.|..+   ..++ |||.||.-||...|..+..||+||.+..
T Consensus        24 s~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          24 SMLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             hHHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHH
Confidence            355799999888663   3345 9999999999999999999999998764

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

Probab=98.73  E-value=8e-09  Score=71.50  Aligned_cols=49  Identities=31%  Similarity=0.669  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      +...+|.|||.+-.+   +.+|| |.|. .|.+|.+...-..+.||+||+.+.+
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            457799999987544   78899 9996 9999999976678889999998853

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

Probab=98.71  E-value=7.5e-10  Score=75.09  Aligned_cols=56  Identities=29%  Similarity=0.602  Sum_probs=45.7

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-----------------------cCCCCccccccccCCC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-----------------------EHLTCPVCRISCIDIE  102 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-----------------------~~~~CP~CR~~~~~~~  102 (104)
                      ...+...|+|||-.|..+..+.+++ |-|.||..|+.++|.                       .+..||+||..|...+
T Consensus       111 nn~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  111 NNHPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCCCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            3356778999999999999888998 999999999998761                       1235999999886443

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

Probab=98.70  E-value=7.1e-09  Score=72.26  Aligned_cols=52  Identities=29%  Similarity=0.752  Sum_probs=40.5

Q ss_pred             CCccccccccccccCCC----cEEecCCCCCcccHHhHHHHH--hc-----CCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGE----SCRLFPVCYRIFHSVCIDQWL--KE-----HLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~----~~~~lp~C~H~fh~~Ci~~wl--~~-----~~~CP~CR~~~~   99 (104)
                      ..+..|.|||+......    ...++|+|.|.||..||..|-  .+     ...||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            35789999999875543    234567899999999999997  33     467999998753

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

Probab=98.65  E-value=1.2e-08  Score=71.36  Aligned_cols=49  Identities=29%  Similarity=0.781  Sum_probs=36.5

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc---CCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE---HLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~---~~~CP~CR~~~   98 (104)
                      ...|.||-+.+.....+.....|||+||..|+..|+..   ...||+|+-.+
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            45799996666555555555459999999999999953   25799999443

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

Probab=98.64  E-value=2.6e-09  Score=73.85  Aligned_cols=50  Identities=26%  Similarity=0.471  Sum_probs=40.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      ..+..|+|||+-+...   +..+.|.|.||.+||..-|+ ..++||.||+.+..
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            4578899999988663   33445999999999999985 56789999998864

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

Probab=98.62  E-value=1.7e-08  Score=75.88  Aligned_cols=53  Identities=25%  Similarity=0.382  Sum_probs=43.8

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .....|++|+..+.........+ |+|.||..||..|-+...+||+||..+..+
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            34567999998887665554555 999999999999999999999999988654

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

Probab=98.57  E-value=5.2e-08  Score=68.63  Aligned_cols=50  Identities=30%  Similarity=0.803  Sum_probs=37.6

Q ss_pred             CccccccccccccC-CCcEEecCCCCCcccHHhHHHHHh--cCCCCccccccc
Q 045579           49 SSNYCVICLENFVD-GESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~~   98 (104)
                      ...+|+|||+.+.- ++..++.+.|||.|-.+||++||.  ....||.|..+.
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            35689999998864 344444445999999999999994  234699997653

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

Probab=98.53  E-value=1.3e-08  Score=54.41  Aligned_cols=46  Identities=28%  Similarity=0.594  Sum_probs=23.0

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      -..|++|.+-|..+..   +.+|.|+||..||..-+.  ..||+|+.+.-.
T Consensus         7 lLrCs~C~~~l~~pv~---l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~   52 (65)
T PF14835_consen    7 LLRCSICFDILKEPVC---LGGCEHIFCSSCIRDCIG--SECPVCHTPAWI   52 (65)
T ss_dssp             TTS-SSS-S--SS-B------SSS--B-TTTGGGGTT--TB-SSS--B-S-
T ss_pred             hcCCcHHHHHhcCCce---eccCccHHHHHHhHHhcC--CCCCCcCChHHH
Confidence            3579999998877532   234999999999988543  359999988743

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

Probab=98.51  E-value=1.6e-08  Score=52.17  Aligned_cols=47  Identities=34%  Similarity=0.623  Sum_probs=34.9

Q ss_pred             ccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHh-cCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      +.+|.||++.-.+.  |..  .|||. .|.+|..+.++ .+..||+||+++.+
T Consensus         7 ~dECTICye~pvds--VlY--tCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDS--VLY--TCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchH--HHH--HcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            47899998764332  222  39995 89999877655 78899999998854

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

Probab=98.44  E-value=9.1e-08  Score=65.09  Aligned_cols=48  Identities=27%  Similarity=0.550  Sum_probs=38.2

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      ...+|+||+....-+   +.|+ |+|.||.-||.--.. ...+|++||.+|.+
T Consensus         6 ~~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             cCCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            356899999886554   5566 999999999988764 45569999999864

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

Probab=98.42  E-value=1.9e-07  Score=66.35  Aligned_cols=49  Identities=27%  Similarity=0.615  Sum_probs=42.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ..+..|.||+.-+..   .+++| |||.||..||.+-+.....||+||..+..
T Consensus        82 ~sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            568899999888766   45567 99999999999988888889999998874

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

Probab=98.36  E-value=1.5e-07  Score=66.36  Aligned_cols=51  Identities=31%  Similarity=0.778  Sum_probs=40.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh--cCCCCccccccccCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVCRISCIDIE  102 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~~~~~~  102 (104)
                      ..-.-|.||-+.   ...|.+-| |||..|..|+..|-.  ...+||.||.+|...|
T Consensus       367 sTFeLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  367 STFELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             chHHHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            345679999764   44577888 999999999999973  3568999999997655

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

Probab=98.22  E-value=3.3e-07  Score=68.72  Aligned_cols=49  Identities=18%  Similarity=0.471  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH-hcCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~~~~  101 (104)
                      +-..|++|-..+.+   ++++ +|||+||..||.+-+ .+...||.|-+.|..-
T Consensus       642 ~~LkCs~Cn~R~Kd---~vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD---AVIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             hceeCCCccCchhh---HHHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            35689999865433   3333 499999999999988 4677899998887643

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

Probab=98.21  E-value=6.8e-07  Score=63.72  Aligned_cols=53  Identities=28%  Similarity=0.561  Sum_probs=44.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIEN  103 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  103 (104)
                      ..+..|+||+..+..+...  +. |||.||..|+..|+..+..||.|+..+...+.
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--TT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             cccccCccccccccCCCCC--CC-CCCcccccccchhhccCcCCcccccccchhhc
Confidence            5678999999998776443  33 99999999999999998999999988865543

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

Probab=98.08  E-value=1.8e-06  Score=45.50  Aligned_cols=42  Identities=31%  Similarity=0.494  Sum_probs=27.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh--cCCCCcc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPV   93 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~   93 (104)
                      ....|||-+..|.++  +.... |||+|-.+.|..||.  ....||+
T Consensus        10 ~~~~CPiT~~~~~~P--V~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP--VKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE--EEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC--cCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            467899999998774  55444 999999999999993  3446998

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

Probab=98.04  E-value=2.1e-06  Score=65.34  Aligned_cols=50  Identities=28%  Similarity=0.745  Sum_probs=39.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC-------CCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-------LTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~-------~~CP~CR~~   97 (104)
                      ....+|.||.+.+.....+-.-..|-|+||..||.+|.+..       -.||.|...
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            45778999999998777665544599999999999998432       149999843

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

Probab=98.01  E-value=8.6e-06  Score=55.03  Aligned_cols=51  Identities=24%  Similarity=0.403  Sum_probs=39.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh--cCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~~~~~  101 (104)
                      ..+.+|++|-+.-..+  -...+ |||+||.-||..-+.  ...+||.|-..+.+.
T Consensus       237 t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~l  289 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVEPL  289 (298)
T ss_pred             cCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCcch
Confidence            5688999998875554  33444 999999999998764  457899998887643

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

Probab=97.99  E-value=6.2e-06  Score=41.80  Aligned_cols=45  Identities=24%  Similarity=0.493  Sum_probs=23.0

Q ss_pred             cccccccccCCC-cEEecCCCCCcccHHhHHHHHh-cCCCCccccccc
Q 045579           53 CVICLENFVDGE-SCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISC   98 (104)
Q Consensus        53 C~ICl~~~~~~~-~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~   98 (104)
                      |++|.+++...+ .+.--+ ||+.+|..|...-+. ....||-||+++
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999984443 444344 899999999999775 577899999875

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

Probab=97.95  E-value=1.4e-06  Score=60.00  Aligned_cols=49  Identities=27%  Similarity=0.612  Sum_probs=41.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ...+|.+|-..|.....+.-   |-|.||..||.+.|....+||.|...+..
T Consensus        14 ~~itC~LC~GYliDATTI~e---CLHTFCkSCivk~l~~~~~CP~C~i~ih~   62 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATTITE---CLHTFCKSCIVKYLEESKYCPTCDIVIHK   62 (331)
T ss_pred             cceehhhccceeecchhHHH---HHHHHHHHHHHHHHHHhccCCccceeccC
Confidence            56689999888877655442   99999999999999999999999887753

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

Probab=97.92  E-value=9.6e-06  Score=53.53  Aligned_cols=52  Identities=25%  Similarity=0.680  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc--------CCCCccccccccCCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE--------HLTCPVCRISCIDIE  102 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~--------~~~CP~CR~~~~~~~  102 (104)
                      ....|..|-..+..++.++..  |-|+||.+|+..|...        ...||.|-.+|...-
T Consensus        49 Y~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             CCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            455799999999999988763  9999999999999732        346999999986543

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.91  E-value=1.2e-05  Score=53.76  Aligned_cols=54  Identities=11%  Similarity=0.365  Sum_probs=48.6

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ....|+||.+.+.+.....+|.+|||+|+.+|+++.+.....||+|-.++.+.+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            567899999999999988888779999999999999999999999998887654

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

Probab=97.90  E-value=1.9e-05  Score=55.22  Aligned_cols=49  Identities=22%  Similarity=0.506  Sum_probs=38.9

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHH--HhcCCCCccccccc
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW--LKEHLTCPVCRISC   98 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w--l~~~~~CP~CR~~~   98 (104)
                      ..++...|.||-+.+.-   +.++| |+|..|..|..+.  |-.+..||+||..-
T Consensus        57 tDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          57 TDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            33677889999877543   56788 9999999999764  46788899999864

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

Probab=97.90  E-value=3.7e-06  Score=52.80  Aligned_cols=41  Identities=34%  Similarity=0.829  Sum_probs=34.6

Q ss_pred             CccccCCCCCCCCccccccccccccCCCcEEecCCCCCcccH
Q 045579           37 PCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHS   78 (104)
Q Consensus        37 ~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~   78 (104)
                      |.+.|.+........+|.||||+++.++.+..|| |-.+||.
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            5556666666677889999999999999999999 9999985

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

Probab=97.86  E-value=4.9e-06  Score=58.77  Aligned_cols=47  Identities=34%  Similarity=0.786  Sum_probs=38.0

Q ss_pred             CccccccccccccC-CCcEEecCCCCCcccHHhHHHHHhcC--CCCccccc
Q 045579           49 SSNYCVICLENFVD-GESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCRI   96 (104)
Q Consensus        49 ~~~~C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl~~~--~~CP~CR~   96 (104)
                      -+..|..|=+.+.. ++.+-.|| |.|+||..|+...|.++  .+||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            36679999888754 45677788 99999999999999544  47999994

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

Probab=97.84  E-value=1.2e-05  Score=64.66  Aligned_cols=52  Identities=23%  Similarity=0.678  Sum_probs=40.9

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----------CCCCcccccccc
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----------HLTCPVCRISCI   99 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----------~~~CP~CR~~~~   99 (104)
                      ...++.|.||+.+--.....+.|. |+|+||..|...-|.+          -.+||+|+.+|.
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            356889999998876666777887 9999999999775532          236999998874

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

Probab=97.80  E-value=2.1e-05  Score=39.88  Aligned_cols=40  Identities=33%  Similarity=0.923  Sum_probs=26.7

Q ss_pred             cccccccccCCCcEEecCCCC--C---cccHHhHHHHHh--cCCCCccc
Q 045579           53 CVICLENFVDGESCRLFPVCY--R---IFHSVCIDQWLK--EHLTCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~--H---~fh~~Ci~~wl~--~~~~CP~C   94 (104)
                      |-||++.-.... ..+.| |+  =   ..|.+|+.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999876665 34455 63  2   689999999995  55679987

>PHA02862 5L protein; Provisional

Probab=97.79  E-value=1.6e-05  Score=49.07  Aligned_cols=45  Identities=22%  Similarity=0.625  Sum_probs=33.5

Q ss_pred             ccccccccccccCCCcEEecCCCC-----CcccHHhHHHHHh--cCCCCcccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCY-----RIFHSVCIDQWLK--EHLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~-----H~fh~~Ci~~wl~--~~~~CP~CR~~~~   99 (104)
                      +..|-||+++-.+.  +  -| |.     ...|.+|+.+|+.  ++..||+|+.++.
T Consensus         2 ~diCWIC~~~~~e~--~--~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          2 SDICWICNDVCDER--N--NF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CCEEEEecCcCCCC--c--cc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            45799999885332  2  34 53     4699999999995  4557999999875

>PHA03096 p28-like protein; Provisional

Probab=97.72  E-value=1.7e-05  Score=54.42  Aligned_cols=36  Identities=28%  Similarity=0.617  Sum_probs=29.1

Q ss_pred             cccccccccccCC----CcEEecCCCCCcccHHhHHHHHh
Q 045579           51 NYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLK   86 (104)
Q Consensus        51 ~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~   86 (104)
                      ..|.|||+.....    ....+|+.|.|.||..|+..|..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~  218 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMT  218 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHH
Confidence            6899999976532    24456788999999999999984

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

Probab=97.71  E-value=2.8e-05  Score=54.48  Aligned_cols=49  Identities=29%  Similarity=0.547  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .++..|+||...   +-..+..| |+|.-|..||.+.|.+...|=.|+..+.+
T Consensus       420 sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            678899999654   33455677 99999999999999999999999998874

>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=97.69  E-value=1.2e-05  Score=49.02  Aligned_cols=35  Identities=17%  Similarity=0.503  Sum_probs=28.8

Q ss_pred             ccccccccccccCCCcEEecCCCC------CcccHHhHHHHH
Q 045579           50 SNYCVICLENFVDGESCRLFPVCY------RIFHSVCIDQWL   85 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~------H~fh~~Ci~~wl   85 (104)
                      ..+|.||++.+.....++.++ ||      |.||.+|+.+|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            668999999998855666666 74      679999999994

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.

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

Probab=97.67  E-value=1.5e-05  Score=46.73  Aligned_cols=33  Identities=27%  Similarity=0.667  Sum_probs=27.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCID   82 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~   82 (104)
                      .++..|++|-..+.. ..+.+.| |||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            557789999999877 4566778 99999999975

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

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.63  E-value=4.4e-05  Score=47.84  Aligned_cols=47  Identities=21%  Similarity=0.619  Sum_probs=34.2

Q ss_pred             CCccccccccccccCCCcEEecCCC--CC---cccHHhHHHHHhc--CCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVC--YR---IFHSVCIDQWLKE--HLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C--~H---~fh~~Ci~~wl~~--~~~CP~CR~~~~   99 (104)
                      ..+..|-||.++...  .  ..| |  ..   ..|.+|+.+|+..  ..+|++|+.++.
T Consensus         6 ~~~~~CRIC~~~~~~--~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          6 LMDKCCWICKDEYDV--V--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCCeeEecCCCCCC--c--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            457789999988432  1  234 5  34   5699999999954  456999998874

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

Probab=97.58  E-value=4.2e-05  Score=54.35  Aligned_cols=48  Identities=25%  Similarity=0.671  Sum_probs=37.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh--------cCCCCccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK--------EHLTCPVCRI   96 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~--------~~~~CP~CR~   96 (104)
                      ..-..|.||++.......+..+| |+|+||..|+..++.        +...||-+.-
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hhcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            44678999999886667888898 999999999999983        1234876654

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

Probab=97.52  E-value=3.6e-05  Score=49.98  Aligned_cols=45  Identities=22%  Similarity=0.459  Sum_probs=37.5

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      ...|.||-.+|..+   +++. |||.||..|.-+-++....|-+|-+..
T Consensus       196 PF~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            45899999999774   3344 999999999999888888999997654

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

Probab=97.44  E-value=4.8e-05  Score=51.96  Aligned_cols=47  Identities=23%  Similarity=0.414  Sum_probs=39.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ...|-||...|..+   +++. |+|.||..|..+-++....|++|-+.+..
T Consensus       241 Pf~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             Cccccccccccccc---hhhc-CCceeehhhhccccccCCcceeccccccc
Confidence            45699999999874   3344 99999999999999888999999887654

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

Probab=97.43  E-value=2.1e-05  Score=53.72  Aligned_cols=42  Identities=24%  Similarity=0.726  Sum_probs=32.4

Q ss_pred             ccccccccccccCCCcEEecCCCCC-cccHHhHHHHHhcCCCCcccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYR-IFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H-~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ..-|.|||+.-   .....|+ ||| +-|..|-.+-    +.||+||+.|+
T Consensus       300 ~~LC~ICmDaP---~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAP---RDCVFLE-CGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCC---cceEEee-cCcEEeehhhcccc----ccCchHHHHHH
Confidence            66799998763   4477788 999 4788887652    27999999875

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

Probab=97.37  E-value=0.00015  Score=50.71  Aligned_cols=45  Identities=31%  Similarity=0.693  Sum_probs=32.6

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .....|.||+++..+   ...+| |||+-|  |..-. +.-.+||+||+.+.
T Consensus       303 ~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            456789999998766   55677 999866  55543 23345999999874

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.37  E-value=0.00011  Score=38.16  Aligned_cols=48  Identities=21%  Similarity=0.414  Sum_probs=34.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCCC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIEN  103 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  103 (104)
                      ...|..|...   +..-.++| |||+.+..|..-+  +-+-||+|-+++...+.
T Consensus         7 ~~~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen    7 EQPCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             ceeEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccCCCC
Confidence            4456666432   33455677 9999999998864  66789999999876554

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.29  E-value=0.0004  Score=47.17  Aligned_cols=54  Identities=17%  Similarity=0.364  Sum_probs=42.1

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      ......|||....|......+.+-+|||+|-..+|..- .....||+|-.++...
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEE  163 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccC
Confidence            35678999999999665555555449999999999996 3456799999887643

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

Probab=97.27  E-value=7.2e-05  Score=49.74  Aligned_cols=45  Identities=22%  Similarity=0.479  Sum_probs=32.7

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .|--|.--- .++...++. |+|+||..|...-  ....||+|++.+..
T Consensus         5 hCn~C~~~~-~~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~   49 (233)
T KOG4739|consen    5 HCNKCFRFP-SQDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRI   49 (233)
T ss_pred             EeccccccC-CCCceeeee-chhhhhhhhcccC--Cccccccccceeee
Confidence            466665433 366777777 9999999999863  22389999998754

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

Probab=97.25  E-value=0.00012  Score=53.91  Aligned_cols=47  Identities=28%  Similarity=0.665  Sum_probs=36.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-----cCCCCccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-----EHLTCPVCRISC   98 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-----~~~~CP~CR~~~   98 (104)
                      .+...|.+|.++-+.   .+... |.|.||.-||..+..     .+.+||.|-..+
T Consensus       534 k~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L  585 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGL  585 (791)
T ss_pred             cCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence            567789999987544   34444 999999999988872     346899997665

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

Probab=97.09  E-value=0.00032  Score=48.23  Aligned_cols=48  Identities=25%  Similarity=0.610  Sum_probs=37.5

Q ss_pred             ccccccccccccCCC---cEEecCCCCCcccHHhHHHHHhc-CCCCccccccc
Q 045579           50 SNYCVICLENFVDGE---SCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~---~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~   98 (104)
                      ...|-||-++|...+   ..++|. |||.|+..|+.+.+.. ...||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            357999999998763   334555 9999999999998754 44699999984

>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=97.05  E-value=0.00031  Score=34.87  Aligned_cols=41  Identities=27%  Similarity=0.768  Sum_probs=22.5

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC--CCccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL--TCPVC   94 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~--~CP~C   94 (104)
                      |.+|.+-...+....... |+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            567777665554433223 888999999999996555  79987

; PDB: 3NW0_A 2CT0_A.

>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=97.02  E-value=0.00041  Score=34.87  Aligned_cols=43  Identities=21%  Similarity=0.528  Sum_probs=25.5

Q ss_pred             ccccccccccCCCcEEecCCC-CCcccHHhHHHHHhcCCCCccccccccC
Q 045579           52 YCVICLENFVDGESCRLFPVC-YRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C-~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .|--|+  |.....+.    | .|..|..|+..-|..+..||+|..+++.
T Consensus         4 nCKsCW--f~~k~Li~----C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCW--FANKGLIK----CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS---S--SSEEE-----SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             cChhhh--hcCCCeee----ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            466666  43443443    7 5999999999999999999999998864

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.

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

Probab=96.98  E-value=0.0002  Score=48.85  Aligned_cols=46  Identities=28%  Similarity=0.624  Sum_probs=37.0

Q ss_pred             ccccccccccccCCC-cEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           50 SNYCVICLENFVDGE-SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~-~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      ...||||.+.+.... .+..++ |||..|..|........-+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            444999999876655 444566 9999999999998876799999988

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

Probab=96.97  E-value=0.00036  Score=53.62  Aligned_cols=43  Identities=21%  Similarity=0.465  Sum_probs=33.6

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      ...|.+|-..++.+.  +-.. |||.||..|+.   .+...||-|+.++
T Consensus       840 ~skCs~C~~~LdlP~--VhF~-CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPF--VHFL-CGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccce--eeee-cccHHHHHhhc---cCcccCCccchhh
Confidence            468999988877653  3333 99999999999   4666799998754

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.94  E-value=0.0013  Score=34.16  Aligned_cols=35  Identities=26%  Similarity=0.650  Sum_probs=30.9

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ   83 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~   83 (104)
                      ....|++|-+.|..++.+++-|.||-.+|++|..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            35679999999998888888888999999999875

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

Probab=96.86  E-value=0.0007  Score=46.71  Aligned_cols=45  Identities=27%  Similarity=0.550  Sum_probs=35.2

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH-hcCCCCcccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRIS   97 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~   97 (104)
                      ...|+.|..-+.++..   +|.|+|.||.+||...| .....||.|-..
T Consensus       274 ~LkCplc~~Llrnp~k---T~cC~~~fc~eci~~al~dsDf~CpnC~rk  319 (427)
T COG5222         274 SLKCPLCHCLLRNPMK---TPCCGHTFCDECIGTALLDSDFKCPNCSRK  319 (427)
T ss_pred             cccCcchhhhhhCccc---CccccchHHHHHHhhhhhhccccCCCcccc
Confidence            3789999887766433   35699999999999887 456679999764

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.83  E-value=0.0011  Score=46.56  Aligned_cols=52  Identities=23%  Similarity=0.481  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCcEE-ecCCCCCcccHHhHHHHH-hcCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCR-LFPVCYRIFHSVCIDQWL-KEHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~-~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~~~~  101 (104)
                      +++.|+.|+++|...++-. -.| ||-..|.-|...-- .-+..||-||+.+.+.
T Consensus        13 eed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             ccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            4556999999998776433 345 89888888876543 2456899999987654

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

Probab=96.79  E-value=0.0017  Score=45.23  Aligned_cols=46  Identities=22%  Similarity=0.454  Sum_probs=37.4

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      .....|+||+-...++..+.+   =|-+||..||..++.+.+.||+=-.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT~~  343 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVTGY  343 (357)
T ss_pred             CccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCccCC
Confidence            456789999998877655443   6899999999999999999997543

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

Probab=96.77  E-value=6.2e-05  Score=53.26  Aligned_cols=52  Identities=21%  Similarity=0.448  Sum_probs=42.5

Q ss_pred             CCccccccccccccCC-CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDG-ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~-~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||.+.+... +.+..+- |||.+|.+||.+||.....||.|+..+.-
T Consensus       194 slv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  194 SLVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HHHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            3466899999988765 4455554 99999999999999888899999998753

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

Probab=96.76  E-value=0.0003  Score=53.50  Aligned_cols=45  Identities=24%  Similarity=0.639  Sum_probs=34.8

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhc--CCCCccccccccC
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE--HLTCPVCRISCID  100 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~--~~~CP~CR~~~~~  100 (104)
                      ..|.||++    .+...+.+ |+|.||.+|+..-+..  ...||+||..+..
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            78999998    33455566 9999999999998743  3359999987653

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.73  E-value=0.00076  Score=45.45  Aligned_cols=53  Identities=26%  Similarity=0.743  Sum_probs=36.9

Q ss_pred             CCCCccccccccccccCCCcE-EecCCC-----CCcccHHhHHHHHhcC--------CCCcccccccc
Q 045579           46 MTPSSNYCVICLENFVDGESC-RLFPVC-----YRIFHSVCIDQWLKEH--------LTCPVCRISCI   99 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~-~~lp~C-----~H~fh~~Ci~~wl~~~--------~~CP~CR~~~~   99 (104)
                      ..+.+..|-||+..=++...- -+-| |     .|..|.+|+..|+..+        .+||.|++++.
T Consensus        16 ~~e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   16 NQELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            345688999999875443322 2334 6     4789999999999322        25999998764

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

Probab=96.70  E-value=0.00075  Score=52.14  Aligned_cols=36  Identities=22%  Similarity=0.523  Sum_probs=29.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ++++.|.+|.-.+... ...+.| |||.||++||.+-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            5788999998887554 555677 99999999998764

>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=96.70  E-value=0.0019  Score=40.55  Aligned_cols=36  Identities=28%  Similarity=0.408  Sum_probs=22.0

Q ss_pred             ccccccccccccCCCcEEec---CC-----CC-CcccHHhHHHHH
Q 045579           50 SNYCVICLENFVDGESCRLF---PV-----CY-RIFHSVCIDQWL   85 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~l---p~-----C~-H~fh~~Ci~~wl   85 (104)
                      +..|+|||+--.+...+...   .+     |+ -.-|..|++++-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence            56899999876554322210   01     32 236889999875

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.

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

Probab=96.52  E-value=0.0019  Score=45.68  Aligned_cols=26  Identities=23%  Similarity=0.800  Sum_probs=20.2

Q ss_pred             CcccHHhHHHHHh-------------cCCCCcccccccc
Q 045579           74 RIFHSVCIDQWLK-------------EHLTCPVCRISCI   99 (104)
Q Consensus        74 H~fh~~Ci~~wl~-------------~~~~CP~CR~~~~   99 (104)
                      =..|.+|+.+||.             ++.+||+||+.+.
T Consensus       313 PmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  313 PMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             chHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            3578999999983             2347999999874

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

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

Probab=96.40  E-value=0.0011  Score=53.04  Aligned_cols=47  Identities=23%  Similarity=0.501  Sum_probs=39.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      ....|.||++.+..-..+..   |||.||..|+..|+..+..||+|+...
T Consensus      1152 ~~~~c~ic~dil~~~~~I~~---cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAG---CGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhcCCeee---echhHhhhHHHHHHHHhccCcchhhhh
Confidence            34589999999885444443   999999999999999999999998543

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

Probab=96.40  E-value=0.0029  Score=40.62  Aligned_cols=28  Identities=32%  Similarity=0.950  Sum_probs=22.8

Q ss_pred             CCCcccHHhHHHHHhc-----C------CCCcccccccc
Q 045579           72 CYRIFHSVCIDQWLKE-----H------LTCPVCRISCI   99 (104)
Q Consensus        72 C~H~fh~~Ci~~wl~~-----~------~~CP~CR~~~~   99 (104)
                      ||..||.-|+..||+.     +      ..||.|-.++.
T Consensus       190 CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  190 CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            9999999999999942     1      25999988764

>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=96.33  E-value=0.0037  Score=42.85  Aligned_cols=47  Identities=17%  Similarity=0.492  Sum_probs=33.5

Q ss_pred             cccccccc-ccCCCcEEecCCCCCcccHHhHHHHH-hcCCCCccccccc
Q 045579           52 YCVICLEN-FVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISC   98 (104)
Q Consensus        52 ~C~ICl~~-~~~~~~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~   98 (104)
                      .|++|... |-+++.......|+|..|.+|+..-+ .+...||-|-..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            48888875 33444333332399999999999988 5667899996544

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

Probab=96.13  E-value=0.0037  Score=48.03  Aligned_cols=40  Identities=28%  Similarity=0.619  Sum_probs=27.5

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPV   93 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~   93 (104)
                      .|.||--.+ .+...+... |+|+.|.+|...|+.....||.
T Consensus      1030 ~C~~C~l~V-~gss~~Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAV-RGSSNFCGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEe-eccchhhcc-ccccccHHHHHHHHhcCCcCCC
Confidence            355553332 222333444 9999999999999999999984

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

Probab=95.93  E-value=0.0035  Score=41.30  Aligned_cols=39  Identities=28%  Similarity=0.708  Sum_probs=29.8

Q ss_pred             cccccccccCCCcEEecCCCCC-cccHHhHHHHHhcCCCCcccccccc
Q 045579           53 CVICLENFVDGESCRLFPVCYR-IFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H-~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      |-+|-+   .+..|.++| |.| .+|..|-..    -..||+|+....
T Consensus       161 Cr~C~~---~~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGE---REATVLLLP-CRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCc---CCceEEeec-ccceEeccccccc----CccCCCCcChhh
Confidence            888854   456688899 998 589999875    335999987764

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

Probab=95.78  E-value=0.0022  Score=44.43  Aligned_cols=48  Identities=25%  Similarity=0.573  Sum_probs=31.8

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      .-.|--|=-.+  ..--+..| |+|+||.+|...  ..-+.||.|--.|..++
T Consensus        90 VHfCd~Cd~PI--~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~VqrIe  137 (389)
T KOG2932|consen   90 VHFCDRCDFPI--AIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQRIE  137 (389)
T ss_pred             eEeecccCCcc--eeeecccc-cchhhhhhhhhc--CccccCcCcccHHHHHH
Confidence            45676664332  22334567 999999999875  34567999987765443

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

Probab=95.78  E-value=0.0054  Score=42.53  Aligned_cols=46  Identities=22%  Similarity=0.455  Sum_probs=35.8

Q ss_pred             CCccccccccccccCCCcEEecCCC--CCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVC--YRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C--~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      ..-.+||||.+.+..+  +..   |  ||+-|..|-.+   ....||.||.++..+
T Consensus        46 ~~lleCPvC~~~l~~P--i~Q---C~nGHlaCssC~~~---~~~~CP~Cr~~~g~~   93 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP--IFQ---CDNGHLACSSCRTK---VSNKCPTCRLPIGNI   93 (299)
T ss_pred             hhhccCchhhccCccc--cee---cCCCcEehhhhhhh---hcccCCccccccccH
Confidence            4566899999998775  332   6  89999999874   567799999998754

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

Probab=95.77  E-value=0.0038  Score=44.71  Aligned_cols=37  Identities=19%  Similarity=0.482  Sum_probs=27.1

Q ss_pred             CccccccccccccCC-CcEEecCCCCCcccHHhHHHHHh
Q 045579           49 SSNYCVICLENFVDG-ESCRLFPVCYRIFHSVCIDQWLK   86 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~-~~~~~lp~C~H~fh~~Ci~~wl~   86 (104)
                      ...+|.||+.++... ....++. |+|.||.+|+.+.+.
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhh
Confidence            467899999444333 3444444 999999999999885

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.55  E-value=0.0075  Score=41.61  Aligned_cols=28  Identities=25%  Similarity=0.685  Sum_probs=22.2

Q ss_pred             CCCcccHHhHHHHHh-------------cCCCCcccccccc
Q 045579           72 CYRIFHSVCIDQWLK-------------EHLTCPVCRISCI   99 (104)
Q Consensus        72 C~H~fh~~Ci~~wl~-------------~~~~CP~CR~~~~   99 (104)
                      |.-..|.+|+.+|+.             ++-+||+||+.+.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            456789999999982             4558999999874

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

Probab=95.36  E-value=0.015  Score=41.45  Aligned_cols=49  Identities=18%  Similarity=0.405  Sum_probs=39.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC---CCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH---LTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~---~~CP~CR~~   97 (104)
                      .....|||=.+.-......+.|. |||+...+-+.+..++.   ..||+|=..
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             cceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            45778999888877778888888 99999999999977543   359999443

>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=95.30  E-value=0.0063  Score=40.89  Aligned_cols=48  Identities=21%  Similarity=0.585  Sum_probs=35.4

Q ss_pred             Ccccccccccccc-CCC-cEEecCCCCCcccHHhHHHHHh-cCCCCc--cccc
Q 045579           49 SSNYCVICLENFV-DGE-SCRLFPVCYRIFHSVCIDQWLK-EHLTCP--VCRI   96 (104)
Q Consensus        49 ~~~~C~ICl~~~~-~~~-~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP--~CR~   96 (104)
                      .+..||||..+.. +++ .+.+-|-|-|..|.+|+.+-|. ....||  -|-+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            4668999998643 333 4445566999999999999984 556799  6644

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

Probab=95.06  E-value=0.013  Score=40.38  Aligned_cols=49  Identities=27%  Similarity=0.741  Sum_probs=35.6

Q ss_pred             ccccccccccccCCCc-EEecCCCC-----CcccHHhHHHHHh--cCCCCcccccccc
Q 045579           50 SNYCVICLENFVDGES-CRLFPVCY-----RIFHSVCIDQWLK--EHLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~-~~~lp~C~-----H~fh~~Ci~~wl~--~~~~CP~CR~~~~   99 (104)
                      +..|-||+.+...... ....| |.     +..|..|+..|+.  ...+|.+|...+.
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            5789999997654321 34455 63     4589999999996  6667999987654

>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=94.96  E-value=0.021  Score=29.32  Aligned_cols=43  Identities=30%  Similarity=0.525  Sum_probs=22.6

Q ss_pred             cccccccccCC------CcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           53 CVICLENFVDG------ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        53 C~ICl~~~~~~------~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      |.-|+..|..+      .....-|.|++.||.+|=.--=..=..||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            55677776654      24566677999999999664223334699873

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.

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

Probab=94.84  E-value=0.022  Score=34.86  Aligned_cols=53  Identities=23%  Similarity=0.361  Sum_probs=37.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~~~~~  101 (104)
                      .-.+|-||.|...+...+.---.||-..|..|.....+   ...+||+|+.++...
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            57899999988554433221112899999999876543   456799999998643

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

Probab=94.64  E-value=0.017  Score=42.05  Aligned_cols=34  Identities=18%  Similarity=0.454  Sum_probs=28.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      +++..|+||-.-|.+   .++|| |+|..|..|...-+
T Consensus         2 eeelkc~vc~~f~~e---piil~-c~h~lc~~ca~~~~   35 (699)
T KOG4367|consen    2 EEELKCPVCGSFYRE---PIILP-CSHNLCQACARNIL   35 (699)
T ss_pred             cccccCceehhhccC---ceEee-cccHHHHHHHHhhc
Confidence            457789999988876   56778 99999999998765

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

Probab=94.63  E-value=0.037  Score=43.15  Aligned_cols=54  Identities=19%  Similarity=0.483  Sum_probs=38.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCC-----cccHHhHHHHHhc--CCCCccccccccCCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYR-----IFHSVCIDQWLKE--HLTCPVCRISCIDIEN  103 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H-----~fh~~Ci~~wl~~--~~~CP~CR~~~~~~~~  103 (104)
                      +++..|-||..+=..++.+.- | |+.     ..|.+|+.+|+.-  ...|-+|..++.-.+.
T Consensus        10 ~d~~~CRICr~e~~~d~pLfh-P-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I   70 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFH-P-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI   70 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcc-c-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence            567899999987655554432 3 543     4899999999954  4459999988754443

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

Probab=94.18  E-value=0.027  Score=43.72  Aligned_cols=53  Identities=9%  Similarity=0.112  Sum_probs=37.1

Q ss_pred             CCccccccccccccCC---CcEEecCCCCCcccHHhHHHHHh------cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDG---ESCRLFPVCYRIFHSVCIDQWLK------EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~---~~~~~lp~C~H~fh~~Ci~~wl~------~~~~CP~CR~~~~~  100 (104)
                      .+...|.||.-++..+   ..+-.+..|+|.||..||..|+.      ..-.|++|..-|..
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s  155 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS  155 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence            4566788888887762   22323335999999999999983      23358998776653

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

Probab=94.02  E-value=0.018  Score=43.66  Aligned_cols=41  Identities=24%  Similarity=0.459  Sum_probs=31.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCP   92 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP   92 (104)
                      -..|.||+..|......-+.+.|||+.|..|+....  +.+||
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp   51 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP   51 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC
Confidence            457999999887665554555699999999999864  44677

>TIGR00622 ssl1 transcription factor ssl1

Probab=93.81  E-value=0.11  Score=31.05  Aligned_cols=46  Identities=24%  Similarity=0.450  Sum_probs=35.0

Q ss_pred             ccccccccccccCC----------CcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           50 SNYCVICLENFVDG----------ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        50 ~~~C~ICl~~~~~~----------~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      ...|.-|+..|...          .....-++|++.||.+|=.-+-..=..||-|-
T Consensus        55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~  110 (112)
T TIGR00622        55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI  110 (112)
T ss_pred             CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence            45699999988643          12334566999999999988877777899985

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

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

Probab=93.14  E-value=0.063  Score=27.34  Aligned_cols=43  Identities=16%  Similarity=0.403  Sum_probs=19.7

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHh---c--CCCCcccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---E--HLTCPVCRIS   97 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~--~~~CP~CR~~   97 (104)
                      ..|+|-...+..+  ++... |.|.-|.+ +..||.   .  .-.||+|.++
T Consensus         3 L~CPls~~~i~~P--~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIP--VRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSE--EEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeC--ccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            4688888777663  44444 99986554 555652   2  2259999763

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

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

Probab=92.94  E-value=0.033  Score=41.87  Aligned_cols=44  Identities=27%  Similarity=0.740  Sum_probs=28.2

Q ss_pred             CCcccccccccc-----ccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           48 PSSNYCVICLEN-----FVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        48 ~~~~~C~ICl~~-----~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      .....|.||...     |+. +.+.....|+++||..|+..   .+.-||.|-
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~-~~~~rC~~C~avfH~~C~~r---~s~~CPrC~  557 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFET-RNTRRCSTCLAVFHKKCLRR---KSPCCPRCE  557 (580)
T ss_pred             cCeeeeeeccCCCccccccc-ccceeHHHHHHHHHHHHHhc---cCCCCCchH
Confidence            457788888432     222 22233223999999999886   444499993

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

Probab=92.75  E-value=0.06  Score=40.29  Aligned_cols=46  Identities=30%  Similarity=0.882  Sum_probs=37.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .....|.||+..+    ..++.+ |.   |..|+..|+..+.+||+|+..+...
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~  522 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKED  522 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcc
Confidence            5677899999988    344555 77   8999999999999999999887643

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

Probab=92.54  E-value=0.075  Score=38.82  Aligned_cols=36  Identities=22%  Similarity=0.435  Sum_probs=28.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK   86 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~   86 (104)
                      .....|-||.+.+..  .+..+. |||.|+..|+...+.
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~  103 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLG  103 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhh
Confidence            456789999988765  444555 999999999999984

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

Probab=92.43  E-value=0.03  Score=42.76  Aligned_cols=46  Identities=26%  Similarity=0.657  Sum_probs=35.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~~   98 (104)
                      -..+|+||+..+..+   ..+ +|.|.|+..|+..-|.   ....||+|+..+
T Consensus        20 k~lEc~ic~~~~~~p---~~~-kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~   68 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLL-KCDHIFLKFCLNKLFESKKGPKQCALCKSDI   68 (684)
T ss_pred             hhccCCceeEEeecc---chh-hhhHHHHhhhhhceeeccCccccchhhhhhh
Confidence            356899999998776   333 4999999999988763   345699998655

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

Probab=92.33  E-value=0.15  Score=39.42  Aligned_cols=41  Identities=20%  Similarity=0.346  Sum_probs=29.0

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPV   93 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~   93 (104)
                      ..|.+|-..+. +. ....+.|||.-|.+|+.+|+....-||.
T Consensus       780 ~~CtVC~~vi~-G~-~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIR-GV-DVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceee-ee-EeecccccccccHHHHHHHHhcCCCCcc
Confidence            36888865432 22 2234559999999999999987776665

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=92.17  E-value=0.12  Score=33.97  Aligned_cols=43  Identities=28%  Similarity=0.703  Sum_probs=30.3

Q ss_pred             CCcccccccccc-----ccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           48 PSSNYCVICLEN-----FVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        48 ~~~~~C~ICl~~-----~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      ..+..|-||-++     |+. +.+..-+.|+-+||..|..+     ..||-|-+
T Consensus       150 ~kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~~-----~~CpkC~R  197 (202)
T PF13901_consen  150 QKGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFRK-----KSCPKCAR  197 (202)
T ss_pred             hCCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcCC-----CCCCCcHh
Confidence            346788888753     333 24555566999999999883     56999953

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

Probab=91.93  E-value=0.091  Score=26.43  Aligned_cols=44  Identities=32%  Similarity=0.672  Sum_probs=29.4

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHh------cCCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK------EHLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~------~~~~CP~CR~   96 (104)
                      .|.||......+..+.-- .|+-.||..|+..-..      ..-.||.|+.
T Consensus         1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcCCCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            488998844444444444 4999999999976442      2346888864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

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

Probab=91.84  E-value=0.25  Score=25.73  Aligned_cols=43  Identities=21%  Similarity=0.521  Sum_probs=29.7

Q ss_pred             ccccccccccCCC-cEEecCCCCC--cccHHhHHHHHhcCCCCcccccccc
Q 045579           52 YCVICLENFVDGE-SCRLFPVCYR--IFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        52 ~C~ICl~~~~~~~-~~~~lp~C~H--~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .|-.|-.++.... ...+   |.+  +||.+|...-|  ...||.|-..++
T Consensus         7 nCE~C~~dLp~~s~~A~I---CSfECTFC~~C~e~~l--~~~CPNCgGelv   52 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI---CSFECTFCADCAETML--NGVCPNCGGELV   52 (57)
T ss_pred             CccccCCCCCCCCCcceE---EeEeCcccHHHHHHHh--cCcCcCCCCccc
Confidence            4556666665444 2222   654  79999999965  678999988775

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

>smart00249 PHD PHD zinc finger

Probab=91.78  E-value=0.12  Score=24.88  Aligned_cols=31  Identities=29%  Similarity=0.667  Sum_probs=21.0

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHH
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQ   83 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~   83 (104)
                      .|.+|.... .+..++.-..|+..||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            377887765 3334444334999999999865

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

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=91.27  E-value=0.18  Score=23.82  Aligned_cols=26  Identities=15%  Similarity=0.349  Sum_probs=15.7

Q ss_pred             ccccccccccCCCc-------EEecCCCCCccc
Q 045579           52 YCVICLENFVDGES-------CRLFPVCYRIFH   77 (104)
Q Consensus        52 ~C~ICl~~~~~~~~-------~~~lp~C~H~fh   77 (104)
                      .|+=|...|..++.       .+.-+.|+|+|+
T Consensus         4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~   36 (36)
T PF13717_consen    4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF   36 (36)
T ss_pred             ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence            57778877765542       122344888774

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

Probab=91.20  E-value=0.31  Score=33.78  Aligned_cols=41  Identities=20%  Similarity=0.317  Sum_probs=31.1

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH   88 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~   88 (104)
                      .....|.+|.|.+++...|..-..=.|.||.-|-.+-++.+
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q  306 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ  306 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence            34578999999998877665222238999999999988643

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=90.72  E-value=0.2  Score=23.82  Aligned_cols=26  Identities=23%  Similarity=0.459  Sum_probs=16.0

Q ss_pred             ccccccccccCCCc-------EEecCCCCCccc
Q 045579           52 YCVICLENFVDGES-------CRLFPVCYRIFH   77 (104)
Q Consensus        52 ~C~ICl~~~~~~~~-------~~~lp~C~H~fh   77 (104)
                      .|+-|...|..++.       .+.-+.|+|+|.
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            57778777765542       223445788774

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

Probab=90.67  E-value=0.29  Score=34.50  Aligned_cols=60  Identities=20%  Similarity=0.426  Sum_probs=39.1

Q ss_pred             CCccccCCCCCC--CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           36 MPCVNYSDQEMT--PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        36 ~~~~~~~~~~~~--~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      .|...+.+....  .....|-.|.++.......+.-. |.+.||.+|=.---..=..||.|-.
T Consensus       314 ~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~-Ck~~FCldCDv~iHesLh~CpgCeh  375 (378)
T KOG2807|consen  314 FPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCES-CKNVFCLDCDVFIHESLHNCPGCEH  375 (378)
T ss_pred             cCCcchhhccccccCCCcceeeeccccCCCCcEEchh-ccceeeccchHHHHhhhhcCCCcCC
Confidence            344444443333  35556999987776665555544 9999999997653344456999964

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

Probab=90.49  E-value=0.15  Score=22.35  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=12.6

Q ss_pred             ccccccccccCCCcEEecCCCCCcc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIF   76 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~f   76 (104)
                      .||-|-..+..  ....-|.|||.|
T Consensus         2 ~CP~C~~~V~~--~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPE--SAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchh--hcCcCCCCCCCC
Confidence            46667655432  233444577776

Several members are annotated as putative helicases.

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

Probab=90.34  E-value=0.13  Score=33.98  Aligned_cols=43  Identities=26%  Similarity=0.619  Sum_probs=33.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVC   94 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~C   94 (104)
                      .-..|-+|..-.-.+..  .-. |+-.+|..|+...+.....||.|
T Consensus       180 nlk~Cn~Ch~LvIqg~r--Cg~-c~i~~h~~c~qty~q~~~~cphc  222 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQGIR--CGS-CNIQYHRGCIQTYLQRRDICPHC  222 (235)
T ss_pred             HHHHHhHhHHHhheeec--cCc-ccchhhhHHHHHHhcccCcCCch
Confidence            35579999887655433  223 88889999999999998899999

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

Probab=89.97  E-value=0.17  Score=36.39  Aligned_cols=44  Identities=18%  Similarity=0.270  Sum_probs=31.3

Q ss_pred             CccccccccccccCCC--cEEecCCCCCcccHHhHHHHHhcCCCCcc
Q 045579           49 SSNYCVICLENFVDGE--SCRLFPVCYRIFHSVCIDQWLKEHLTCPV   93 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~--~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~   93 (104)
                      .-..|++|.-.++...  .-+... |||.||..|...|...+..|..
T Consensus       305 ~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~  350 (384)
T KOG1812|consen  305 RWRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYE  350 (384)
T ss_pred             hcCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccC
Confidence            3567888887665433  333444 8999999999999877776643

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.95  E-value=0.16  Score=27.23  Aligned_cols=37  Identities=24%  Similarity=0.416  Sum_probs=19.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ....|.+|...|..-..-..-..||++||..|.....
T Consensus         8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~   44 (69)
T PF01363_consen    8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI   44 (69)
T ss_dssp             G-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred             CCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence            4668999999997654444444599999999987544

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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.14  E-value=0.53  Score=32.10  Aligned_cols=52  Identities=12%  Similarity=0.201  Sum_probs=36.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .....|+|=--+|........+-.|||+|-..-+.+-  ...+|++|.+.+.+.
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~  160 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQED  160 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCccccc
Confidence            4466899876666555555555459999987766663  577899999887654

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

Probab=88.96  E-value=0.16  Score=39.49  Aligned_cols=45  Identities=20%  Similarity=0.481  Sum_probs=31.7

Q ss_pred             CccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCcccc
Q 045579           49 SSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR   95 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR   95 (104)
                      -+..|.-|++.....    ..++++. |||.||..|+.--+.++. |-.|-
T Consensus       783 ~e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~~  831 (846)
T KOG2066|consen  783 VEERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIES  831 (846)
T ss_pred             ehhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChhh
Confidence            455899998876422    4667776 999999999987764443 55443

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=88.69  E-value=0.7  Score=32.60  Aligned_cols=56  Identities=20%  Similarity=0.482  Sum_probs=37.5

Q ss_pred             CCcccccccccccc---------------CCC-cEEecCCCCCcccHHhHHHHHhc---------CCCCccccccccCCC
Q 045579           48 PSSNYCVICLENFV---------------DGE-SCRLFPVCYRIFHSVCIDQWLKE---------HLTCPVCRISCIDIE  102 (104)
Q Consensus        48 ~~~~~C~ICl~~~~---------------~~~-~~~~lp~C~H~fh~~Ci~~wl~~---------~~~CP~CR~~~~~~~  102 (104)
                      ..+..|++|+..-.               .+. .-...| |||+--..-+.-|.+.         +..||.|-..+....
T Consensus       339 ~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~  417 (429)
T KOG3842|consen  339 QRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQ  417 (429)
T ss_pred             cccCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhhccCC
Confidence            45778999986411               000 111345 9999888888889732         346999988887665


Q ss_pred             CC
Q 045579          103 NY  104 (104)
Q Consensus       103 ~~  104 (104)
                      +|
T Consensus       418 ~~  419 (429)
T KOG3842|consen  418 GY  419 (429)
T ss_pred             ce
Confidence            54

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=88.34  E-value=0.61  Score=32.83  Aligned_cols=51  Identities=24%  Similarity=0.364  Sum_probs=37.4

Q ss_pred             CCccccccccccccCCCcEE-ecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCR-LFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~-~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .-...|+||-+.....+... -.| |++..|..|+..-.....+||.||+...
T Consensus       247 ~v~~s~p~~~~~~~~~d~~~lP~~-~~~~~~l~~~~t~~~~~~~~~~~rk~~~  298 (327)
T KOG2068|consen  247 SVPPSCPICYEDLDLTDSNFLPCP-CGFRLCLFCHKTISDGDGRCPGCRKPYE  298 (327)
T ss_pred             ccCCCCCCCCCccccccccccccc-ccccchhhhhhcccccCCCCCccCCccc
Confidence            34568999999874444332 334 8888888888887788889999997654

>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;

Probab=88.12  E-value=0.4  Score=24.55  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=25.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ...|.+|-..|.....-.....||++|+.+|.....
T Consensus         2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~   37 (57)
T cd00065           2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRI   37 (57)
T ss_pred             cCcCcccCccccCCccccccCcCcCCcChHHcCCee
Confidence            346889988776644333333499999999998765

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

Probab=88.09  E-value=0.35  Score=22.29  Aligned_cols=37  Identities=22%  Similarity=0.446  Sum_probs=23.0

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      |..|-..+...+.....  =+..||.+|..        |..|...|.
T Consensus         2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf~--------C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRA--LGKVWHPECFK--------CSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEe--CCccccccCCC--------CcccCCcCc
Confidence            77787777665233222  35778877754        777776653

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

>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length

Probab=87.32  E-value=0.41  Score=25.79  Aligned_cols=11  Identities=27%  Similarity=1.105  Sum_probs=8.2

Q ss_pred             ccHHhHHHHHh
Q 045579           76 FHSVCIDQWLK   86 (104)
Q Consensus        76 fh~~Ci~~wl~   86 (104)
                      ||+.|+.+|+.
T Consensus        12 FCRNCLskWy~   22 (68)
T PF06844_consen   12 FCRNCLSKWYR   22 (68)
T ss_dssp             --HHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999984

The function of this family is unknown.; PDB: 2O35_A 3FYB_B.

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

Probab=86.52  E-value=1.3  Score=24.66  Aligned_cols=51  Identities=22%  Similarity=0.377  Sum_probs=21.2

Q ss_pred             CccccccccccccC---CCcEEecCCCCCcccHHhHHHHHh-cCCCCcccccccc
Q 045579           49 SSNYCVICLENFVD---GESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~---~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~   99 (104)
                      ....|-||=+++..   ++..+....|+--.|..|.+-=.+ ....||.|+..+.
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            46789999988753   333333233777899999876554 5567999998764

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

Probab=84.99  E-value=0.62  Score=31.95  Aligned_cols=49  Identities=22%  Similarity=0.471  Sum_probs=34.3

Q ss_pred             ccccccccccccCCCcEEe---cCCCCCcccHHhHHHHHh---------cCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRL---FPVCYRIFHSVCIDQWLK---------EHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~---lp~C~H~fh~~Ci~~wl~---------~~~~CP~CR~~~   98 (104)
                      ...|-+|..++.+.+..+.   -+.|+-++|..|+..-+.         ....||.|++.+
T Consensus       182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~  242 (276)
T KOG3005|consen  182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL  242 (276)
T ss_pred             chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence            3689999999954443332   233788899999998542         244699998754

>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1

Probab=84.84  E-value=0.97  Score=24.03  Aligned_cols=36  Identities=25%  Similarity=0.362  Sum_probs=26.1

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ...|.+|-..|..-..-.....||.+|+..|....+
T Consensus        10 ~~~C~~C~~~F~~~~rk~hCr~CG~i~C~~C~~~~~   45 (68)
T smart00064       10 VSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKA   45 (68)
T ss_pred             CCcCcccCccccCcccccccccCCCCcChHHcCCee
Confidence            467999988876543222233499999999998876

The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=83.23  E-value=1.1  Score=31.64  Aligned_cols=47  Identities=17%  Similarity=0.356  Sum_probs=34.8

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC---CCCcccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH---LTCPVCR   95 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~---~~CP~CR   95 (104)
                      ..-..||+=-+.-......+.|. |||+.-.+-+....++.   ..||.|=
T Consensus       334 Hs~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP  383 (396)
T COG5109         334 HSLFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCP  383 (396)
T ss_pred             cceeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence            45678998777666666777777 99999988888865432   3499993

>smart00647 IBR In Between Ring fingers

Probab=82.85  E-value=0.35  Score=25.15  Aligned_cols=21  Identities=24%  Similarity=0.341  Sum_probs=16.1

Q ss_pred             CcEEecCCCCCcccHHhHHHH
Q 045579           64 ESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        64 ~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      ...+..+.|+|.||..|...|
T Consensus        38 ~~~v~C~~C~~~fC~~C~~~~   58 (64)
T smart00647       38 CNRVTCPKCGFSFCFRCKVPW   58 (64)
T ss_pred             CCeeECCCCCCeECCCCCCcC
Confidence            344555459999999999888

the domains occurs between pairs og RING fingers

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

Probab=82.30  E-value=0.6  Score=23.81  Aligned_cols=38  Identities=21%  Similarity=0.438  Sum_probs=18.6

Q ss_pred             cccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        53 C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      |..|-..+.....++..  -+..||.+|..        |-.|+..|.+
T Consensus         1 C~~C~~~I~~~~~~~~~--~~~~~H~~Cf~--------C~~C~~~l~~   38 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKA--MGKFWHPECFK--------CSKCGKPLND   38 (58)
T ss_dssp             BTTTSSBESSSSEEEEE--TTEEEETTTSB--------ETTTTCBTTT
T ss_pred             CCCCCCCccCcEEEEEe--CCcEEEccccc--------cCCCCCccCC
Confidence            44555555544433211  45566655542        5556555543

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=82.18  E-value=0.95  Score=26.00  Aligned_cols=42  Identities=24%  Similarity=0.505  Sum_probs=31.8

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCCCC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIENY  104 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  104 (104)
                      ...|-||-..+..         =||.||..|..+    +..|.+|-..|.+.-.|
T Consensus        44 ~~~C~~CK~~v~q---------~g~~YCq~CAYk----kGiCamCGKki~dtk~y   85 (90)
T PF10235_consen   44 SSKCKICKTKVHQ---------PGAKYCQTCAYK----KGICAMCGKKILDTKNY   85 (90)
T ss_pred             Ccccccccccccc---------CCCccChhhhcc----cCcccccCCeecccccc
Confidence            5679999765322         477899999764    67899999999876654

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=81.55  E-value=0.084  Score=28.84  Aligned_cols=39  Identities=21%  Similarity=0.394  Sum_probs=18.9

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC   98 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~   98 (104)
                      ..||.|..++....        +|.+|..|-.. +.....||-|..++
T Consensus         2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~-~~~~a~CPdC~~~L   40 (70)
T PF07191_consen    2 NTCPKCQQELEWQG--------GHYHCEACQKD-YKKEAFCPDCGQPL   40 (70)
T ss_dssp             -B-SSS-SBEEEET--------TEEEETTT--E-EEEEEE-TTT-SB-
T ss_pred             CcCCCCCCccEEeC--------CEEECcccccc-ceecccCCCcccHH
Confidence            46888888765433        44555555554 34556688887765

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.97  E-value=3.3  Score=28.35  Aligned_cols=34  Identities=18%  Similarity=0.305  Sum_probs=27.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      .+...|+.||.++..+   ++.| =||+|+.+||.+++
T Consensus        41 K~FdcCsLtLqPc~dP---vit~-~GylfdrEaILe~i   74 (303)
T KOG3039|consen   41 KPFDCCSLTLQPCRDP---VITP-DGYLFDREAILEYI   74 (303)
T ss_pred             CCcceeeeecccccCC---ccCC-CCeeeeHHHHHHHH
Confidence            3567899999998773   3445 69999999999987

>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines

Probab=80.39  E-value=1.7  Score=19.36  Aligned_cols=29  Identities=17%  Similarity=0.221  Sum_probs=10.0

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhH
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCI   81 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci   81 (104)
                      .|.+|...... .....-+.|.-.+|..|+
T Consensus         2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca   30 (30)
T PF07649_consen    2 RCDACGKPIDG-GWFYRCSECDFDLHEECA   30 (30)
T ss_dssp             --TTTS----S---EEE-TTT-----HHHH
T ss_pred             cCCcCCCcCCC-CceEECccCCCccChhcC
Confidence            57788777655 233333348889999885

The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	104
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		1e-08
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		5e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-06
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		3e-04

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI 99
          C +CL    DGE  R  P C   FH+ C+D WL  H TCP+CR++ +
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 44 QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
          +E   S   C +C E++  GES R  P C  +FH  CI  WL++H +CPVCR S
Sbjct: 9  EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKS 61

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 53  CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE 102
           C ICL    +GE  R  P C  +FH VC+DQWL  +  CP+CR   +DIE
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR---VDIE 62

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 28 GDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE 87
          G       +P   ++          CV+C+ +F   +  R+ P C   FH+ C+D+WLK 
Sbjct: 1  GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59
Query: 88 HLTCPVCRI 96
          + TCP+CR 
Sbjct: 60 NRTCPICRA 68

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C IC   +V G+     P C+  FH  C+  WL++  TCPVCR
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	104
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-19
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	7e-17
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	8e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-15
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-15
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-14
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-13
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-12
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-09
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-09
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-08
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	2e-06
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-06
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	4e-06
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	4e-06
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	5e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-04
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-04

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

 Score = 73.5 bits (181), Expect = 4e-19
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 30 EALEQLMPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL 89
           +  QL P   ++          CV+C+ +F   +  R+ P C   FH+ C+D+WLK + 
Sbjct: 4  GSSGQL-PSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANR 61

Query: 90 TCPVCRIS 97
          TCP+CR  
Sbjct: 62 TCPICRAD 69

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

 Score = 67.2 bits (165), Expect = 7e-17
 Identities = 21/45 (46%), Positives = 27/45 (60%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
          C +CL    DGE  R  P C   FH+ C+D WL  H TCP+CR++
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLT 52

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

 Score = 68.1 bits (167), Expect = 8e-17
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 30 EALEQLMPCVNYSDQEMTPSSNY-CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH 88
          E+++ L P +  ++          C IC   +V G+     P C+  FH  C+  WL++ 
Sbjct: 20 ESIDAL-PEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKS 77

Query: 89 LTCPVCRIS 97
           TCPVCR  
Sbjct: 78 GTCPVCRCM 86

>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 = 65.1 bits (159), Expect = 1e-15
 Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 42 SDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
            +E   S   C +C E++  GES R  P C  +FH  CI  WL++H +CPVCR S
Sbjct: 7  GTEEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKS 61

>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 = 63.9 bits (156), Expect = 2e-15
 Identities = 21/45 (46%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
          C ICL    +GE  R  P C  +FH VC+DQWL  +  CP+CR+ 
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVD 60

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

 Score = 61.3 bits (149), Expect = 3e-14
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C +CLE+F   +   + P C   FH  C+ +WL+    CP+C 
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCN 59

>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 = 58.4 bits (142), Expect = 2e-13
 Identities = 14/45 (31%), Positives = 19/45 (42%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
          C ICLE+            C  + H  C ++ LKE   CP+C   
Sbjct: 8  CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGP 52

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

 Score = 56.1 bits (135), Expect = 3e-12
 Identities = 11/43 (25%), Positives = 22/43 (51%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C+ C       +   ++  C   FH+ C+  W+K++  CP+C+
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 48.9 bits (117), Expect = 2e-09
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 5/45 (11%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRIS 97
          C IC++   D     + P C   F   CID+W   H  CP+CR+ 
Sbjct: 18 CCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQ 57

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

 Score = 48.6 bits (116), Expect = 2e-09
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 46  MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI 101
           M   +  C ICLE+  +       P C   F  VCI +W++++ TCP+C++    +
Sbjct: 1   MATVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV 53

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

 Score = 47.2 bits (112), Expect = 7e-09
 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCR 95
          C IC++ + +        V   C  +F S C+   LK   TCP CR
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63

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

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCRISC 98
          C IC++ + +        V   C  +F S C+   LK   TCP CR   
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

>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 = 45.2 bits (107), Expect = 5e-08
 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCR 95
          C IC++ + +        V   C  +F S C+   LK   TCP CR
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 58

>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 = 44.0 bits (103), Expect = 1e-06
 Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 10/67 (14%)

Query: 44  QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISC---- 98
            EM  +   C IC EN  D    ++ P C  +  + C+  W   E   CP CR       
Sbjct: 326 CEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE 381

Query: 99  -IDIENY 104
            I ++ +
Sbjct: 382 PIVVDPF 388

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

 Score = 40.9 bits (96), Expect = 2e-06
 Identities = 12/46 (26%), Positives = 14/46 (30%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC 98
          C IC    +D         C   F   CI +       CP C I  
Sbjct: 18 CSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

>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 = 41.1 bits (96), Expect = 2e-06
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 5/45 (11%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCR 95
          C IC    + G+SC     C    H  C+ ++ + +    CP C 
Sbjct: 18 CNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCN 59

>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 = 41.4 bits (96), Expect = 4e-06
 Identities = 13/51 (25%), Positives = 18/51 (35%)

Query: 45 EMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
           +      C     +    E    + VC   FH  CI +WLK    CP+  
Sbjct: 46 HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 41.0 bits (96), Expect = 4e-06
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISC 98
          C IC+E   D   C   P C ++    CI +WL ++   CP CR   
Sbjct: 25 CFICMEKLRDARLC---PHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 40.6 bits (95), Expect = 4e-06
 Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 10/46 (21%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCR 95
          C IC + F +       PV   C   F   C  +  +    C +C 
Sbjct: 18 CFICRQAFQN-------PVVTKCRHYFCESCALEHFRATPRCYICD 56

>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 = 41.0 bits (95), Expect = 5e-06
 Identities = 13/51 (25%), Positives = 18/51 (35%)

Query: 45  EMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
            +      C     +    E    + VC   FH  CI +WLK    CP+  
Sbjct: 57  HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 39.7 bits (93), Expect = 1e-05
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC 98
          C IC E F       + P C   + S+CI ++L     CP C ++ 
Sbjct: 25 CGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 51  NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCRISC 98
             C IC    + G+SC     C    H  C+ ++ + +    CP C    
Sbjct: 181 KICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 227

>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 = 39.8 bits (92), Expect = 2e-05
 Identities = 13/75 (17%), Positives = 21/75 (28%), Gaps = 19/75 (25%)

Query: 40 NYSDQEMTPSSNYCVICLENFVDGESC--------------RLFPVCYRIFHSVCIDQWL 85
           Y+++        C+IC+E                           C   FH +C+    
Sbjct: 15 KYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMY 74

Query: 86 KE-----HLTCPVCR 95
                  L CP C+
Sbjct: 75 CNGNKDGSLQCPSCK 89

>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 = 39.0 bits (91), Expect = 2e-05
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISC 98
          CV+C   F+D         C   F   CI ++L+    CP+C +  
Sbjct: 18 CVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 39.5 bits (91), Expect = 5e-05
 Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 15/58 (25%)

Query: 53  CVICLENFVDGESCRLF----PVCYRIFHSVCIDQWLKE-----------HLTCPVCR 95
           C IC    +DG    L       C    H+VC+++W K               CP C+
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCK 368

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

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 4/92 (4%)

Query: 4   RNHNHNPDRDVNDSDLEVGERQGLGDEALEQLMPCVNYSDQEMTPSSNYCVICLENFVDG 63
            N +      +  +  +  E+     E ++     V     ++  +   C+IC E F++ 
Sbjct: 18  LNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEA 77

Query: 64  ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
            +      C   F S CI++W+K  + CP+CR
Sbjct: 78  VTL----NCAHSFCSYCINEWMKRKIECPICR 105

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

 Score = 36.0 bits (83), Expect = 2e-04
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 10/49 (20%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCRISC 98
          C ICL+  V        PV   C  +F  +C+         C +CR   
Sbjct: 18 CAICLQTCVH-------PVSLPCKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 36.7 bits (84), Expect = 3e-04
 Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 37  PCVNYSDQEMTPSSNYCVICLENFVD---GESCRLFPVCYRIFHSVCIDQWLKEHLTCPV 93
               Y    +   +  C IC++ + +        +   C  +F S C+   LK   TCP 
Sbjct: 59  NHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPT 118

Query: 94  CRISC 98
           CR   
Sbjct: 119 CRKKI 123

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

 Score = 35.9 bits (82), Expect = 5e-04
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 53 CVICLENFVDGESCRLFPV---CYRIFHSVCIDQWLKEHLTCPVCRISC 98
          C IC++ + +        V   C  +F S C+   LK   TCP CR   
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	104
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.89
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.85
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.82
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.82
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.81
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.8
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.76
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.76
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.75
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.75
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.74
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.73
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.73
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.71
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.71
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.7
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.7
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.69
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.69
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.69
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.68
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.67
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.66
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.66
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.65
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.63
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.62
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.62
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.62
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.61
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.6
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.59
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.59
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.59
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.58
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.58
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.58
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.56
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.56
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.56
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.55
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.55
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.54
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.52
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.51
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.51
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.51
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.48
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.47
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.45
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.44
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.44
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.44
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.44
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.42
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.39
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.39
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.38
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.33
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.32
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.29
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.28
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.28
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.26
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.23
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.21
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.21
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.07
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	99.06
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.0
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.92
3nw0_A	238	Non-structural maintenance of chromosomes element	98.4
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.42
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.39
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.64
1we9_A	64	PHD finger family protein; structural genomics, PH	96.49
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	95.89
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	95.77
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	95.59
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	95.44
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.27
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	95.15
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	94.91
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	94.27
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	94.19
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	94.02
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	93.84
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.83
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.83
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	93.76
1wew_A	78	DNA-binding family protein; structural genomics, P	93.58
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	93.45
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	93.42
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	93.32
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	93.26
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	93.05
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	93.02
1weu_A	91	Inhibitor of growth family, member 4; structural g	92.88
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	92.84
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	92.62
2yt5_A	66	Metal-response element-binding transcription facto	92.61
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	92.54
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	92.53
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	92.48
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	92.4
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	92.3
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	92.18
1z60_A	59	TFIIH basal transcription factor complex P44 subun	91.95
1wem_A	76	Death associated transcription factor 1; structura	91.88
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	91.83
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	91.82
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	91.4
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	91.32
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	91.27
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	91.18
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	90.9
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	90.65
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	90.65
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	90.41
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	90.2
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	89.94
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	89.82
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	89.79
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	89.45
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	89.33
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	88.91
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	88.8
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	88.79
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	87.89
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	87.58
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	87.47
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	87.41
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	87.29
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	86.98
1wee_A	72	PHD finger family protein; structural genomics, PH	86.85
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	86.32
2jvx_A	28	NF-kappa-B essential modulator; CCHC classical zin	86.25
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	86.0
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	84.37
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	84.31
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	84.15
3fyb_A	104	Protein of unknown function (DUF1244); hydrocar de	84.05
2o35_A	105	Hypothetical protein DUF1244; helix bundle, struct	83.9
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	83.74
3mpx_A	434	FYVE, rhogef and PH domain-containing protein 5; s	82.85
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	82.49
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	82.31
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	82.28
2co8_A	82	NEDD9 interacting protein with calponin homology a	80.89

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

Probab=99.89  E-value=5.4e-23  Score=117.99  Aligned_cols=84  Identities=24%  Similarity=0.587  Sum_probs=70.4

Q ss_pred             CCCcccccccCCCCHHHHHhhCCccccCCCC-CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcc
Q 045579           15 NDSDLEVGERQGLGDEALEQLMPCVNYSDQE-MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPV   93 (104)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~   93 (104)
                      .+.........|++++.+.. +|.+.+.... ....+..|+||++.|..++.+..+| |||.||..||..|+..+.+||+
T Consensus         5 ~~~~~~~~~~~~~s~~~i~~-lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~   82 (91)
T 2l0b_A            5 HHHHSHMVANPPASKESIDA-LPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPV   82 (91)
T ss_dssp             CCCSCCSSCCCCCCHHHHHT-SCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTT
T ss_pred             cccCCCCcCCCCCCHHHHHh-CCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcC
Confidence            34455566778999999988 6877776544 3356788999999999999899999 9999999999999999999999


Q ss_pred             ccccccC
Q 045579           94 CRISCID  100 (104)
Q Consensus        94 CR~~~~~  100 (104)
                      ||..+..
T Consensus        83 Cr~~~~~   89 (91)
T 2l0b_A           83 CRCMFPP   89 (91)
T ss_dssp             TCCBSSC
T ss_pred             cCccCCC
Confidence            9998864

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

Probab=99.85  E-value=4.7e-22  Score=110.18  Aligned_cols=66  Identities=30%  Similarity=0.820  Sum_probs=58.1

Q ss_pred             CCccccCCCCCCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           36 MPCVNYSDQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        36 ~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      +|...+.......+...|+||++.|..++.+..+| |+|.||..||.+|+..+.+||+||+.+....
T Consensus         9 lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            9 LPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPSS   74 (75)
T ss_dssp             CCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCCC
T ss_pred             CCcEEecCccccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCCC
Confidence            67777776666667889999999999998889999 9999999999999999999999999987653

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

Probab=99.82  E-value=2.1e-20  Score=103.19  Aligned_cols=55  Identities=27%  Similarity=0.826  Sum_probs=49.7

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ......|+||++.|..+..+.+++ |+|.||..||.+|+..+.+||+||+.+..+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            345778999999999988888898 9999999999999998899999999997654

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

Probab=99.82  E-value=3.2e-20  Score=101.13  Aligned_cols=55  Identities=38%  Similarity=0.946  Sum_probs=48.7

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .......|+||++.|..+..++.++ |||.||..||..|+..+.+||+||+.+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            3356778999999998888888998 999999999999999999999999998643

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

Probab=99.81  E-value=7.3e-21  Score=99.40  Aligned_cols=52  Identities=40%  Similarity=1.016  Sum_probs=46.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      +++..|+||++.|..++.+..++.|||.||..||.+|++.+.+||+||+.+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            3567899999999998888888779999999999999999999999999874

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

Probab=99.80  E-value=5.2e-20  Score=102.50  Aligned_cols=55  Identities=42%  Similarity=0.899  Sum_probs=49.2

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ......|+||++.|..+..+.+++ |+|.||..||.+|+..+.+||+||+.+...+
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            356779999999999888888898 9999999999999998899999999987543

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

Probab=99.76  E-value=4.8e-19  Score=92.36  Aligned_cols=50  Identities=32%  Similarity=0.747  Sum_probs=43.3

Q ss_pred             CccccccccccccCC-CcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDG-ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~-~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ....|+||++.|..+ ..+.+++ |||.||..||.+|+....+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            467899999998654 4566777 9999999999999998899999999875

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

Probab=99.76  E-value=1.4e-19  Score=101.68  Aligned_cols=52  Identities=25%  Similarity=0.762  Sum_probs=42.1

Q ss_pred             CccccccccccccC-----------CCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVD-----------GESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~-----------~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ++..|+||++.|..           ++.+++++.|+|.||.+||.+||..+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            46678888888854           34455555599999999999999999999999998753

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

Probab=99.75  E-value=6.3e-19  Score=96.31  Aligned_cols=54  Identities=26%  Similarity=0.532  Sum_probs=45.9

Q ss_pred             CCccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           48 PSSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      .++..|+||++.|..+    ..++.++ |||.||..||.+|+..+.+||+||+.+...+
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            4577899999998753    4556777 9999999999999999999999999987543

>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=99.75  E-value=8.6e-19  Score=103.90  Aligned_cols=52  Identities=27%  Similarity=0.635  Sum_probs=42.0

Q ss_pred             CccccccccccccCCC---------------cEEecCCCCCcccHHhHHHHH-----hcCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGE---------------SCRLFPVCYRIFHSVCIDQWL-----KEHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~fh~~Ci~~wl-----~~~~~CP~CR~~~~~~  101 (104)
                      .+..|+|||+.|..+.               .+.+++ |+|.||..||..|+     ..+.+||+||+.+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3568999999997653               344677 99999999999999     4567899999988643

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

Probab=99.74  E-value=1.3e-18  Score=94.49  Aligned_cols=52  Identities=27%  Similarity=0.563  Sum_probs=44.4

Q ss_pred             CCccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..+    ..+++++ |||.||..||..|+..+.+||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            5678899999998753    3456777 99999999999999999999999998753

>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=99.73  E-value=2.2e-18  Score=101.17  Aligned_cols=50  Identities=28%  Similarity=0.580  Sum_probs=42.8

Q ss_pred             CccccccccccccCCC---------------cEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGE---------------SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .+..|+||++.|....               .++.++ |+|.||..||.+||..+.+||+||+.+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            4678999999997651               356677 9999999999999999999999999853

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

Probab=99.73  E-value=1.6e-18  Score=92.83  Aligned_cols=52  Identities=27%  Similarity=0.533  Sum_probs=44.3

Q ss_pred             CccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      ++..|+||++.|..+    ..+..++ |||.||..||.+|+..+.+||+||+.+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            456899999998753    4556777 999999999999999999999999998754

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

Probab=99.71  E-value=1.6e-17  Score=91.08  Aligned_cols=54  Identities=22%  Similarity=0.494  Sum_probs=44.6

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      .......|+||++.|..  .+.+++ |||.||..||..|+..+.+||+||+.+...+
T Consensus        11 ~~~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           11 ELTPYILCSICKGYLID--ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCCGGGSCTTTSSCCSS--CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             hcCCCCCCCCCChHHHC--cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            33567899999999876  344446 9999999999999998999999999986543

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

Probab=99.71  E-value=3.2e-18  Score=93.35  Aligned_cols=51  Identities=31%  Similarity=0.874  Sum_probs=44.1

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ......|+||++.+..    +.++ |||.||..||..|+....+||+||+.+...+
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            3457789999999866    5677 9999999999999999999999999987554

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

Probab=99.70  E-value=2.6e-17  Score=88.85  Aligned_cols=53  Identities=17%  Similarity=0.382  Sum_probs=44.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH-hcCCCCccccccccCCCCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISCIDIENY  104 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~~~~~~~  104 (104)
                      .+...|+||++.+..+..   ++ |||.||..||..|+ ....+||+||+.+...+.|
T Consensus        13 ~~~~~C~IC~~~~~~p~~---~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~if   66 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSPKQ---TE-CGHRFCESCMAALLSSSSPKCTACQESIVKDKVF   66 (66)
T ss_dssp             CCCEECTTTCCEESSCCC---CS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTCC
T ss_pred             CcCCCCCCCChHhcCeeE---CC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhcC
Confidence            567899999999876533   56 99999999999999 4567899999999877765

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

Probab=99.70  E-value=1.7e-17  Score=92.83  Aligned_cols=52  Identities=29%  Similarity=0.674  Sum_probs=43.7

Q ss_pred             CCccccccccccccCCCcEEecCCCC-----CcccHHhHHHHHhcC--CCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCY-----RIFHSVCIDQWLKEH--LTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~-----H~fh~~Ci~~wl~~~--~~CP~CR~~~~~~  101 (104)
                      ..+..|.||+++|..++.+ ++| |+     |.||.+||.+||..+  .+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            4567899999999877766 588 96     999999999999755  5899999998643

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

Probab=99.69  E-value=4.2e-17  Score=92.32  Aligned_cols=54  Identities=22%  Similarity=0.522  Sum_probs=45.1

Q ss_pred             CCCCccccccccccccCCCc-EEecCCCCCcccHHhHHHHHhcC---CCCccccccccC
Q 045579           46 MTPSSNYCVICLENFVDGES-CRLFPVCYRIFHSVCIDQWLKEH---LTCPVCRISCID  100 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~-~~~lp~C~H~fh~~Ci~~wl~~~---~~CP~CR~~~~~  100 (104)
                      .......|+||++.|...+. .++++ |||.||..||..|+..+   .+||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             hccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            33567889999999987664 66777 99999999999999765   789999998753

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

Probab=99.69  E-value=1.2e-17  Score=91.37  Aligned_cols=49  Identities=24%  Similarity=0.520  Sum_probs=42.4

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ......|+||++.|..   .+.++ |||.||..||..|+....+||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (71)
T 2d8t_A           12 SLTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIP   60 (71)
T ss_dssp             SSSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCC
T ss_pred             CCCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhC
Confidence            3467789999999865   35567 9999999999999998899999999875

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

Probab=99.69  E-value=1.1e-17  Score=90.66  Aligned_cols=49  Identities=33%  Similarity=0.892  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .+..|+||++.+..  .+..++ |||.||..||..|+..+.+||+||+.+..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            46789999999865  356778 99999999999999989999999998864

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

Probab=99.68  E-value=4.8e-17  Score=89.69  Aligned_cols=53  Identities=28%  Similarity=0.649  Sum_probs=43.1

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC--CCCccccccccCCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCRISCIDIE  102 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~--~~CP~CR~~~~~~~  102 (104)
                      ......|+||++.|..+   ++++.|||.||..||..|+..+  .+||+||+.+...+
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           12 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             SCGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            35678999999998763   3355599999999999999765  68999999876554

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

Probab=99.67  E-value=1.1e-16  Score=89.49  Aligned_cols=48  Identities=19%  Similarity=0.427  Sum_probs=41.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .....|+||++.|..   .++++ |||+||..||..|+....+||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            456789999999866   34577 9999999999999998999999999975

>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=99.66  E-value=6.6e-18  Score=100.57  Aligned_cols=50  Identities=28%  Similarity=0.580  Sum_probs=1.1

Q ss_pred             CccccccccccccCCC---------------cEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGE---------------SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .+..|+||++.|....               .+..++ |+|.||..||.+||..+.+||+||+++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            4678999999997531               233345 9999999999999999999999999864

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

Probab=99.66  E-value=4.7e-17  Score=99.51  Aligned_cols=48  Identities=33%  Similarity=0.902  Sum_probs=41.7

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .+..|+||++.|..   .+++| |||.||..||..|+..+.+||+||+++..
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            35679999999865   45677 99999999999999999999999998853

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

Probab=99.65  E-value=2.1e-16  Score=86.61  Aligned_cols=50  Identities=26%  Similarity=0.500  Sum_probs=41.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~~~~~  101 (104)
                      .....|+||++.|..   .+.++ |||.||..||..|+.   ...+||+||+.+...
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            567899999999875   45567 999999999999996   456899999998654

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

Probab=99.63  E-value=1.4e-16  Score=96.15  Aligned_cols=53  Identities=26%  Similarity=0.540  Sum_probs=45.0

Q ss_pred             CCccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .+...|+||++.|..+    ..++.++ |||+||..||.+|+..+.+||+||+.+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            3567899999998764    4456777 999999999999999999999999988643

>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=99.62  E-value=2e-16  Score=91.85  Aligned_cols=49  Identities=31%  Similarity=0.659  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC-CCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-LTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~-~~CP~CR~~~~~  100 (104)
                      +...|+||++.|..  .+..++ |||.||..||..|+... .+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~--p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           21 EVFRCFICMEKLRD--ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCccCCccccC--ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            46789999999865  343377 99999999999999877 699999999853

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

Probab=99.62  E-value=5.7e-16  Score=85.98  Aligned_cols=49  Identities=27%  Similarity=0.504  Sum_probs=41.8

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..   .++++ |||+||..||..|+.. ..+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            467899999999876   34467 9999999999999976 7889999998854

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

Probab=99.62  E-value=7.3e-16  Score=88.01  Aligned_cols=52  Identities=29%  Similarity=0.644  Sum_probs=41.7

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC--CCCccccccccCC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCRISCIDI  101 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~--~~CP~CR~~~~~~  101 (104)
                      ..+...|+||++.|..+   ++++.|||.||..||..|+...  .+||+||..+...
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   63 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   63 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCT
T ss_pred             CCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCc
Confidence            35678999999998763   3455499999999999999643  5899999997543

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

Probab=99.61  E-value=4.7e-16  Score=83.58  Aligned_cols=51  Identities=16%  Similarity=0.353  Sum_probs=41.0

Q ss_pred             Cccccccccc-cccCCCcE-EecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           49 SSNYCVICLE-NFVDGESC-RLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~-~~~~~~~~-~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      ++..|+||++ .|..+... .+++ |||+||..||.+|+.. ..+||+||+.+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            3568999999 77776543 3466 9999999999999754 5679999999864

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

Probab=99.60  E-value=1.6e-15  Score=85.09  Aligned_cols=49  Identities=29%  Similarity=0.527  Sum_probs=41.6

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc------CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE------HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~------~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..+   .+++ |||.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            4577899999998764   3577 9999999999999976      6789999998864

>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=99.59  E-value=8.9e-16  Score=92.17  Aligned_cols=49  Identities=20%  Similarity=0.466  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC-CCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~-~CP~CR~~~~~  100 (104)
                      .....|+||++.|..   .+.++ |||.||..||..|+.... +||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            346789999999875   44567 999999999999997544 89999999865

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

Probab=99.59  E-value=1.8e-15  Score=84.87  Aligned_cols=49  Identities=33%  Similarity=0.617  Sum_probs=41.6

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc------CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE------HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~------~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..+   ..++ |||.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            4678999999998763   3467 9999999999999976      7789999998864

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

Probab=99.59  E-value=8.2e-16  Score=88.98  Aligned_cols=49  Identities=27%  Similarity=0.615  Sum_probs=41.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ....|+||++.|..  .+.+++ |||.||..||..|+..+.+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFNI--AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhCC--cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            46789999999876  233346 99999999999999988999999998864

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

Probab=99.58  E-value=2.9e-16  Score=87.21  Aligned_cols=49  Identities=33%  Similarity=0.543  Sum_probs=41.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-------CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-------HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-------~~~CP~CR~~~~~  100 (104)
                      .+...|+||++.|..+   +.++ |||.||..||..|+..       ..+||+||..+..
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4678899999998764   3467 9999999999999976       5689999999864

>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=99.58  E-value=1.4e-15  Score=89.36  Aligned_cols=50  Identities=26%  Similarity=0.716  Sum_probs=42.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..  .+.+++ |||.||..||..|+..+.+||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             GGGTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             CCcCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCccccc
Confidence            357789999999865  344447 99999999999999988999999999864

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

Probab=99.58  E-value=2.5e-15  Score=80.21  Aligned_cols=44  Identities=27%  Similarity=0.561  Sum_probs=36.6

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCccc
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVC   94 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~C   94 (104)
                      ......|+||++.|..   .++++ |||.||..||.+|+.   ...+||+|
T Consensus        17 ~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3567899999999876   34467 999999999999997   45689998

>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=99.56  E-value=2.5e-15  Score=89.53  Aligned_cols=52  Identities=25%  Similarity=0.429  Sum_probs=42.9

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC-CCccccccccCC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCRISCIDI  101 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~-~CP~CR~~~~~~  101 (104)
                      ...+...|+||++.|..+   +.++ |||.||..||..|+.... +||+||..+...
T Consensus        14 ~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           14 PLESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            335678999999998763   4567 999999999999997655 999999998653

>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=99.56  E-value=1.7e-15  Score=94.93  Aligned_cols=51  Identities=27%  Similarity=0.566  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~~  101 (104)
                      .....|+||++.|..  .+.+++ |||.||..||..|+.. ..+||+||..+...
T Consensus        52 ~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           52 HSELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            346689999999876  344457 9999999999999986 77899999998543

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

Probab=99.56  E-value=3.4e-15  Score=78.27  Aligned_cols=43  Identities=30%  Similarity=0.857  Sum_probs=35.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH---hcCCCCccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL---KEHLTCPVC   94 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---~~~~~CP~C   94 (104)
                      .....|+||++.|..+   ++++ |||+||..||..|+   ....+||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4677899999999774   3467 99999999999995   456789998

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

Probab=99.55  E-value=2e-15  Score=90.99  Aligned_cols=53  Identities=26%  Similarity=0.540  Sum_probs=44.6

Q ss_pred             CCccccccccccccCC----CcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDG----ESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .....|+||++.|...    ..++.++ |||.||..||.+|+..+.+||+||..+...
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            4577899999998753    3446667 999999999999999999999999998653

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

Probab=99.55  E-value=4.2e-15  Score=81.75  Aligned_cols=50  Identities=24%  Similarity=0.614  Sum_probs=41.7

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC--CCCcccccccc
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCRISCI   99 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~--~~CP~CR~~~~   99 (104)
                      .+....|+||.+.|..+...  . .|+|.||..||.+||+.+  .+||+||+.+.
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C--~-~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSC--E-TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEEC--S-SSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             cCCCCcCcchhhHcccCCcc--C-CCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            35677899999999865433  2 499999999999999877  78999999875

>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=99.54  E-value=5.3e-15  Score=91.60  Aligned_cols=49  Identities=24%  Similarity=0.501  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC-CCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~-~CP~CR~~~~~~  101 (104)
                      ....|+||++.|..   .++++ |||.||..||..|+.... +||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45689999999866   44477 999999999999997654 899999998754

>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=99.52  E-value=4.9e-15  Score=87.22  Aligned_cols=48  Identities=27%  Similarity=0.573  Sum_probs=39.7

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC---CCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL---TCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~---~CP~CR~~~~~  100 (104)
                      ....|+||++.|..+   ..++ |||.||..||..|+..+.   +||+||..+..
T Consensus        20 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           20 KILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HHTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            356899999998764   3367 999999999999997654   89999998864

>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=99.51  E-value=1.7e-15  Score=89.83  Aligned_cols=48  Identities=29%  Similarity=0.645  Sum_probs=40.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~   99 (104)
                      ..+..|+||++.|..   .+.++ |||.||..||..|+.. ..+||+||..+.
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            457789999999875   34567 9999999999999965 678999999875

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

Probab=99.51  E-value=3.1e-14  Score=80.38  Aligned_cols=49  Identities=16%  Similarity=0.061  Sum_probs=43.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..   .++++ |||+|+..||..|+....+||+||..+..
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             chheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            467899999999977   55677 99999999999999988999999998754

>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=99.51  E-value=1e-14  Score=86.54  Aligned_cols=48  Identities=33%  Similarity=0.654  Sum_probs=40.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      ....|+||++.|..   .+.++ |||.||..||..|+.. ..+||+||..+..
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            46789999999865   34467 9999999999999976 7789999999864

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

Probab=99.48  E-value=5.5e-14  Score=78.18  Aligned_cols=52  Identities=19%  Similarity=0.378  Sum_probs=40.6

Q ss_pred             CCccccccccccccCCCc-EEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGES-CRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~-~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      .++..|+||++.+...+. +..++ |||.||..|+..|+. ....||+||+.+..
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~   62 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   62 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCC
Confidence            467789999999865433 22345 999999999999874 45689999998864

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=99.47  E-value=1.6e-14  Score=77.49  Aligned_cols=49  Identities=27%  Similarity=0.453  Sum_probs=40.0

Q ss_pred             CccccccccccccCCCcEE-ecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCR-LFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~-~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ++..|+||++.+.+.  +. .+| |||. ||.+|+..|...+..||+||+.+..
T Consensus         7 ~~~~C~IC~~~~~~~--~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKNG--CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSCE--EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCCE--EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            567899999986542  22 248 9999 8999999999888899999998853

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.45  E-value=8.9e-14  Score=80.72  Aligned_cols=49  Identities=18%  Similarity=0.087  Sum_probs=43.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|..   .++++ |||+|+..||..|+....+||+||..+..
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            567899999999977   45567 99999999999999988899999998864

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.44  E-value=1.9e-13  Score=79.01  Aligned_cols=49  Identities=16%  Similarity=0.023  Sum_probs=42.9

Q ss_pred             CCccccccccccccCCCcEEecCCCC-CcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCY-RIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~-H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|+||++.|.+   .++++ || |+|+..||..|+....+||+||..+..
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            467899999999977   45577 99 999999999999888899999998864

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

Probab=99.44  E-value=2.1e-13  Score=95.15  Aligned_cols=47  Identities=32%  Similarity=0.766  Sum_probs=40.8

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      ...|+||++.+..   ++.+| |||.||..|+..|+. ...+||+||+.+..
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            4689999998855   56678 999999999999998 78899999998864

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

Probab=99.44  E-value=3.6e-14  Score=87.03  Aligned_cols=48  Identities=17%  Similarity=0.343  Sum_probs=40.5

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC-CCccccccc
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCRISC   98 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~-~CP~CR~~~   98 (104)
                      ......|+||++.|..+   +.++ |||.||..||..|+.... +||+||.++
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~   76 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEG   76 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTT
T ss_pred             CCcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCcc
Confidence            35678999999998774   4466 999999999999997654 899999975

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.44  E-value=4.3e-14  Score=75.57  Aligned_cols=50  Identities=18%  Similarity=0.276  Sum_probs=39.9

Q ss_pred             CccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ....|+||++.+.+. .+..+| |||. ||..|+..|...+..||+||+++..
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             cCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            467899999876442 122347 9998 9999999999888899999998853

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

Probab=99.42  E-value=3.6e-14  Score=74.14  Aligned_cols=47  Identities=21%  Similarity=0.454  Sum_probs=38.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .+...|+||++.|..+   ++++ |||.||..||..|   ...||+||+.+...
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            3567899999999764   5577 9999999999884   66899999998643

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.39  E-value=6.5e-14  Score=77.08  Aligned_cols=44  Identities=20%  Similarity=0.560  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      +...|+||++.+..   .+.+| |||. ||..|+..|    ..||+||+.+..
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            45689999998755   55678 9999 999999998    789999998853

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

Probab=99.39  E-value=1.8e-13  Score=86.04  Aligned_cols=52  Identities=25%  Similarity=0.445  Sum_probs=42.7

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC-CCCccccccccCC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-LTCPVCRISCIDI  101 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~-~~CP~CR~~~~~~  101 (104)
                      ...+...|+||++.|..+   +.++ |||+||..||.+|+..+ .+||+||..+...
T Consensus        14 ~~~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           14 PLESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            335678999999998764   4467 99999999999999654 4899999988653

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.38  E-value=4.6e-14  Score=83.89  Aligned_cols=45  Identities=24%  Similarity=0.532  Sum_probs=38.4

Q ss_pred             CccccccccccccCCCcEEec-CCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLF-PVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ....|+||++.|..+   +++ + |||.||..||..|+.  ..||+||..+.
T Consensus        21 ~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           21 KLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            467899999998764   344 6 999999999999987  78999999984

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

Probab=99.33  E-value=3.7e-13  Score=92.37  Aligned_cols=52  Identities=27%  Similarity=0.622  Sum_probs=40.1

Q ss_pred             CCccccccccccccCCCcEE----ecCCCCCcccHHhHHHHHhcC-----------CCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCR----LFPVCYRIFHSVCIDQWLKEH-----------LTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~----~lp~C~H~fh~~Ci~~wl~~~-----------~~CP~CR~~~~   99 (104)
                      ....+|+||++.+..+..+.    ..++|+|.||..||.+||+..           ++||+||+++.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            46778999999987733222    223599999999999999642           46999999875

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.32  E-value=1.1e-12  Score=75.22  Aligned_cols=47  Identities=21%  Similarity=0.372  Sum_probs=37.8

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC------CCCcc--cccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH------LTCPV--CRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~------~~CP~--CR~~   97 (104)
                      .....|+||++.|..+  | +++.|||+|+..||..|+...      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~dP--V-~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP--V-KNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSSE--E-EESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcCC--E-EcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            4578899999999763  3 443399999999999999653      58999  9865

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.29  E-value=2.8e-12  Score=85.54  Aligned_cols=50  Identities=18%  Similarity=0.153  Sum_probs=41.8

Q ss_pred             CCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           47 TPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        47 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      ......|+||++.|..   .+++| |||+||..||..|+.. ..+||+||.++..
T Consensus       205 ~~~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          205 IPDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CCSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCcccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            3568899999999877   45677 9999999999999975 4459999998853

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=1.1e-12  Score=72.28  Aligned_cols=44  Identities=20%  Similarity=0.565  Sum_probs=36.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ....|+||++.+..   ++.+| |||. ||..|+..    ...||+||..+..
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            35679999998755   55678 9999 99999964    3789999999865

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=99.28  E-value=3.9e-12  Score=67.24  Aligned_cols=48  Identities=23%  Similarity=0.597  Sum_probs=37.1

Q ss_pred             CCccccccccccccCCCcEEecCCCC--C---cccHHhHHHHHh--cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCY--R---IFHSVCIDQWLK--EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~--H---~fh~~Ci~~wl~--~~~~CP~CR~~~~   99 (104)
                      ++...|.||+++..  +.+ ++| |.  |   .||.+||.+|+.  .+.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            35678999999743  333 577 65  4   899999999995  3678999999875

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=99.26  E-value=3e-12  Score=73.29  Aligned_cols=48  Identities=25%  Similarity=0.681  Sum_probs=39.6

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc--------CCCCcc--cccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE--------HLTCPV--CRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~--------~~~CP~--CR~~   97 (104)
                      ...+|+||++.+..++.+..++ |||.||.+|+..++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4678999999998776666667 9999999999999842        236999  9987

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=9.2e-12  Score=67.38  Aligned_cols=45  Identities=29%  Similarity=0.712  Sum_probs=37.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .....|.||++.+..   ++.+| |||. ||..|+..    ...||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            456789999987644   67788 9999 99999984    4689999998864

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.21  E-value=1.1e-11  Score=78.49  Aligned_cols=51  Identities=18%  Similarity=0.124  Sum_probs=42.3

Q ss_pred             CCCCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC-CCCccccccccC
Q 045579           46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-LTCPVCRISCID  100 (104)
Q Consensus        46 ~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~-~~CP~CR~~~~~  100 (104)
                      .......||||++.|..   .+++| |||+|+..||..|+... .+||+||.++..
T Consensus       102 ~ip~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          102 EIPDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCCGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCcHhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            33678899999999976   45567 99999999999999753 479999998753

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=99.21  E-value=2.8e-12  Score=71.36  Aligned_cols=43  Identities=28%  Similarity=0.704  Sum_probs=36.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      ....|+||++.+..   ++.+| |||. ||..|+..|    ..||+||..+.
T Consensus        17 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            35689999988654   66778 9999 999999987    38999999875

>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=99.07  E-value=6.2e-11  Score=78.80  Aligned_cols=49  Identities=18%  Similarity=0.319  Sum_probs=40.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC--CCCcc--cccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH--LTCPV--CRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~--~~CP~--CR~~~~   99 (104)
                      .....||||++.|..+  |..+. |||+|+..||..|+...  .+||+  ||..+.
T Consensus       179 ~~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~  231 (267)
T 3htk_C          179 KIELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS  231 (267)
T ss_dssp             BCCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEEC
T ss_pred             ceeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCc
Confidence            4577899999999764  54445 99999999999999654  47999  998764

>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=99.06  E-value=2.8e-11  Score=83.60  Aligned_cols=44  Identities=23%  Similarity=0.625  Sum_probs=37.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCc-ccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRI-FHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ++..|+||++.+..   ++.+| |||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            45789999998765   56678 9999 999999998    689999998853

>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=99.00  E-value=1.8e-10  Score=61.03  Aligned_cols=48  Identities=17%  Similarity=0.119  Sum_probs=40.1

Q ss_pred             ccccccccccccCCCcEEec-CCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           50 SNYCVICLENFVDGESCRLF-PVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~l-p~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      ...|+|+++.|.++   +++ + +||+|...||.+||..+.+||+.+.++...
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCC---EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            35799999999863   445 5 999999999999998888899999988643

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.92  E-value=5.9e-10  Score=63.78  Aligned_cols=48  Identities=27%  Similarity=0.477  Sum_probs=38.5

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccCCC
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCIDIE  102 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~~~  102 (104)
                      .|.+|--++..  ..+..| |+|+||.+|+..|.+ ...+||+|+.++..+|
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            47788655433  566778 999999999999984 5678999999997665

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

Probab=98.40  E-value=1.2e-07  Score=62.57  Aligned_cols=48  Identities=21%  Similarity=0.540  Sum_probs=38.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCC--CCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL--TCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~--~CP~CR~~~~   99 (104)
                      ....|.||.+-+..+  ... +.|+|.||..|+..|++...  .||.|+....
T Consensus       179 ~i~~C~iC~~iv~~g--~~C-~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~  228 (238)
T 3nw0_A          179 AVKICNICHSLLIQG--QSC-ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP  228 (238)
T ss_dssp             TCCBCTTTCSBCSSC--EEC-SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCC
T ss_pred             CCCcCcchhhHHhCC--ccc-CccChHHHHHHHHHHHHhCCCCCCCCCCCCCC
Confidence            467899999987765  333 34999999999999997654  8999998865

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=97.39  E-value=0.00012  Score=41.67  Aligned_cols=34  Identities=12%  Similarity=0.340  Sum_probs=25.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ   83 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~   83 (104)
                      ++..|.||++.+........+. |+|.||..|+..
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~   35 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKA   35 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHH
Confidence            3568999998653333344476 999999999998

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=96.64  E-value=0.0017  Score=34.34  Aligned_cols=48  Identities=19%  Similarity=0.336  Sum_probs=34.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC----CCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH----LTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~----~~CP~CR~~~~   99 (104)
                      .....|.||.+.   ++ ++.-..|...||..|+...|...    =.||.|.....
T Consensus        10 ~~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C           10 APGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CTTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            456679999753   33 44444599999999998877432    36999987553

>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=96.49  E-value=0.00084  Score=35.16  Aligned_cols=52  Identities=25%  Similarity=0.453  Sum_probs=36.3

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-----cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-----EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-----~~~~CP~CR~~~~   99 (104)
                      .+...|+||...+..+...+.-..|...||..|+.--..     ....||.|+..-.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~~   60 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG   60 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTTC
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCcCC
Confidence            456789999988765555555445999999999964321     3456999986543

>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=95.89  E-value=0.008  Score=31.63  Aligned_cols=35  Identities=26%  Similarity=0.579  Sum_probs=26.4

Q ss_pred             CCccccccccccccCCCcEEecC-CCCCcccHHhHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFP-VCYRIFHSVCID   82 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp-~C~H~fh~~Ci~   82 (104)
                      .+...|++|...+......+.-. .|.-.||..|+.
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            45778999999987776666655 599999999984

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=95.77  E-value=0.0036  Score=39.60  Aligned_cols=49  Identities=27%  Similarity=0.484  Sum_probs=35.7

Q ss_pred             ccccccccccccCCCc---EEecCCCCCcccHHhHHHH------Hh-----cCCCCccccccc
Q 045579           50 SNYCVICLENFVDGES---CRLFPVCYRIFHSVCIDQW------LK-----EHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~---~~~lp~C~H~fh~~Ci~~w------l~-----~~~~CP~CR~~~   98 (104)
                      +..|+||...|..++.   .+....|...||..|+.--      +.     ..-.||.|+..-
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            3569999999887763   5555559999999998421      11     156899998764

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=95.59  E-value=0.0087  Score=31.00  Aligned_cols=46  Identities=30%  Similarity=0.801  Sum_probs=32.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh----cCCCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----EHLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~~~~CP~CR~~   97 (104)
                      ..+..|.||...   + .++.-..|...||..|+..-+.    ..-.||.|+..
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            356789999863   3 3444445888999999987542    22359999764

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=95.44  E-value=0.0038  Score=33.63  Aligned_cols=51  Identities=18%  Similarity=0.240  Sum_probs=35.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh----cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~~~~CP~CR~~~~   99 (104)
                      .....|.||..... ++.++.-..|.-.||..|+..-+.    ..-.||.|+..+.
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            45667999987653 444555445899999999975442    2346999987764

>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=95.27  E-value=0.022  Score=31.42  Aligned_cols=35  Identities=23%  Similarity=0.583  Sum_probs=23.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      ..+..|.||- .+...+... ...|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceec-cccccccccHhhcccc
Confidence            4678899994 343333222 1228999999999995

>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=95.15  E-value=0.024  Score=28.29  Aligned_cols=44  Identities=23%  Similarity=0.357  Sum_probs=30.5

Q ss_pred             ccccccccccCCCcEEecC-CCCCcccHHhHHHHH----hcCCCCcccc
Q 045579           52 YCVICLENFVDGESCRLFP-VCYRIFHSVCIDQWL----KEHLTCPVCR   95 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp-~C~H~fh~~Ci~~wl----~~~~~CP~CR   95 (104)
                      .|.||...+..+...+.-. .|.-.||..|+.--.    ..+..||.|+
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            5788988886555555544 488899999985321    3556799885

>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=94.91  E-value=0.029  Score=30.45  Aligned_cols=49  Identities=20%  Similarity=0.478  Sum_probs=32.7

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH-----hcCCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-----KEHLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-----~~~~~CP~CR~~~   98 (104)
                      ....| ||...+......+.-..|...||..|+.--.     .....||.|+...
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            34556 9988775444444444599999999995322     1345699998754

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.27  E-value=0.018  Score=28.53  Aligned_cols=44  Identities=30%  Similarity=0.643  Sum_probs=28.5

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~   96 (104)
                      .|.||...-..+ .++.-..|...||..|+..=+..    .-.||.|+.
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            488897653333 34444459999999999753322    225999965

>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=94.19  E-value=0.033  Score=31.99  Aligned_cols=49  Identities=20%  Similarity=0.401  Sum_probs=34.5

Q ss_pred             ccccccccccccCCCcEEecC-CCCCcccHHhHHHHH----------hcCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFP-VCYRIFHSVCIDQWL----------KEHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp-~C~H~fh~~Ci~~wl----------~~~~~CP~CR~~~   98 (104)
                      ...|+||...+......+.-- .|.-.||..|+.--.          ...-.||.|+...
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            567999999886655555543 589999999985221          0345699998754

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=94.02  E-value=0.0035  Score=32.34  Aligned_cols=48  Identities=27%  Similarity=0.757  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~~~  100 (104)
                      .+..|.||...   ++.+ .-..|.-.||..|+..-+..    .-.||.|......
T Consensus         4 ~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~   55 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLK   55 (60)
T ss_dssp             CCSSCTTTCCC---SSCE-ECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEE-EcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhc
Confidence            46679999863   3334 44458999999999864422    2359999876543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=93.84  E-value=0.11  Score=29.91  Aligned_cols=34  Identities=21%  Similarity=0.325  Sum_probs=23.7

Q ss_pred             Cccccccccccc-----cCCCcEEecCCCCCcccHHhHH
Q 045579           49 SSNYCVICLENF-----VDGESCRLFPVCYRIFHSVCID   82 (104)
Q Consensus        49 ~~~~C~ICl~~~-----~~~~~~~~lp~C~H~fh~~Ci~   82 (104)
                      +...|.+|+..=     ..++.++.-..|+..||..|+.
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            466899998752     1233444444599999999995

>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=93.83  E-value=0.011  Score=30.65  Aligned_cols=48  Identities=25%  Similarity=0.648  Sum_probs=31.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~~   99 (104)
                      ..+..|.||.+.   ++ ++.-..|...||..|+..-|..    .-.||.|+....
T Consensus         7 ~~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   58 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CCCCcCCCCCCC---CC-EEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchh
Confidence            346779999752   33 3333448889999999864422    225999987543

>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=93.83  E-value=0.014  Score=33.64  Aligned_cols=37  Identities=19%  Similarity=0.332  Sum_probs=26.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ..+..|.||.+.-...+.+.-. .|+..||..|+...+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~-~C~~~~H~~Cl~~~~   41 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCT-TCGQHYHGMCLDIAV   41 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECS-SSCCEECTTTTTCCC
T ss_pred             CCCCCCcCCCCCCCCcCCeECC-CCCCCcChHHhCCcc
Confidence            3577899998763333334443 499999999998765

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=93.76  E-value=0.031  Score=31.05  Aligned_cols=52  Identities=17%  Similarity=0.346  Sum_probs=34.5

Q ss_pred             CCccccccccccc-cCCCcEEecCCCCCcccHHhHHHHHh--cCCCCcccccccc
Q 045579           48 PSSNYCVICLENF-VDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~-~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~~~   99 (104)
                      ..+..|.||...- ...+.++.-..|.-.||..|+..-+.  ..-.||.|.....
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~   77 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRA   77 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTT
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccc
Confidence            4577899998653 23335555555888999999975321  2235999976553

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=93.58  E-value=0.042  Score=29.74  Aligned_cols=52  Identities=19%  Similarity=0.340  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCcEEec-CCCCCcccHHhHHHHH---------hcCCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLF-PVCYRIFHSVCIDQWL---------KEHLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~fh~~Ci~~wl---------~~~~~CP~CR~~~~~~  101 (104)
                      ....| ||-.....+..|..- +.|...||..|+.---         .....||.|+......
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~~~   76 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGPS   76 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSCC
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcccCCC
Confidence            45667 898764444333322 0499999999996321         1245699998765543

>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=93.45  E-value=0.026  Score=34.97  Aligned_cols=48  Identities=21%  Similarity=0.513  Sum_probs=33.2

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH-----hcCCCCcccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-----KEHLTCPVCRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-----~~~~~CP~CR~~   97 (104)
                      ....| ||......+...+....|...||..|+.--.     ...-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            46678 9988765455555555599999999995321     234469999863

>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=93.42  E-value=0.12  Score=28.32  Aligned_cols=40  Identities=23%  Similarity=0.305  Sum_probs=31.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE   87 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~   87 (104)
                      .....|.+|.+.++....|..-..=.|.||..|-...++.
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            4567899999999888777633223899999999998853

>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=93.32  E-value=0.022  Score=35.73  Aligned_cols=46  Identities=26%  Similarity=0.640  Sum_probs=32.1

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      .+..|.||...   ++ +.....|.-.||..|+..-+..    .-.||.|+..-
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            35679999744   44 4444458999999999765532    23699998754

>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=93.26  E-value=0.024  Score=36.20  Aligned_cols=46  Identities=24%  Similarity=0.591  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      .+..|.+|...   + .+.....|...||..|+.+-+..    .-.||.|+..-
T Consensus         6 ~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            6 NEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            46679999743   2 35555568999999999775532    23699998754

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=93.05  E-value=0.019  Score=33.31  Aligned_cols=46  Identities=26%  Similarity=0.540  Sum_probs=30.3

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRI   96 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~   96 (104)
                      ..|.||...-...+.++.-..|...||..|+..-|..    .=.||.|+.
T Consensus        62 ~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           62 KTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            3688887643233345444459999999999764422    236999975

>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=93.02  E-value=0.12  Score=27.47  Aligned_cols=47  Identities=26%  Similarity=0.564  Sum_probs=29.8

Q ss_pred             CCccccccccccccCCCcEEecCC--CC-CcccHHhHHHHHh----cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPV--CY-RIFHSVCIDQWLK----EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~--C~-H~fh~~Ci~~wl~----~~~~CP~CR~~~~   99 (104)
                      .+...| ||..... + .++.-..  |. ..||..|+.  |.    .+-.||.|+....
T Consensus        14 ~~~~~C-~C~~~~~-g-~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           14 NEPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             TSCCCS-TTCCCSC-S-SEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCCEE-ECCCCCC-C-CEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            345667 8987542 3 3444344  55 689999997  42    2336999987643

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=92.88  E-value=0.08  Score=29.64  Aligned_cols=47  Identities=28%  Similarity=0.588  Sum_probs=29.7

Q ss_pred             CCccccccccccccCCCcEEecCC--CC-CcccHHhHHHHHh----cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPV--CY-RIFHSVCIDQWLK----EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~--C~-H~fh~~Ci~~wl~----~~~~CP~CR~~~~   99 (104)
                      .+...| ||..... +. ++.-..  |. ..||..|+.  |.    .+-.||.|+....
T Consensus        34 ~e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           34 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            345667 9987643 33 333333  54 689999997  32    2346999987643

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.84  E-value=0.054  Score=30.17  Aligned_cols=47  Identities=23%  Similarity=0.552  Sum_probs=32.4

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      ..+..|.||...   ++ +..-..|.-.||..|+.+=|..    .-.||.|+...
T Consensus        23 ~n~~~C~vC~~~---g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           23 DSATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            456789999854   33 4444458889999999775532    22599998654

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=92.62  E-value=0.018  Score=30.64  Aligned_cols=45  Identities=31%  Similarity=0.604  Sum_probs=28.4

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHh----c-CCCCcccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----E-HLTCPVCRIS   97 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~-~~~CP~CR~~   97 (104)
                      .|.||...- .+..++.-..|...||..|+..=|.    . .=.||.|+.+
T Consensus        20 ~C~~C~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcC-CCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            566776432 2334555455899999999985432    1 2369998753

>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=92.61  E-value=0.071  Score=27.69  Aligned_cols=52  Identities=23%  Similarity=0.533  Sum_probs=34.8

Q ss_pred             CCcccccccccccc-CCCcEEecCCCCCcccHHhHHHHHh-------cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFV-DGESCRLFPVCYRIFHSVCIDQWLK-------EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~-~~~~~~~lp~C~H~fh~~Ci~~wl~-------~~~~CP~CR~~~~   99 (104)
                      ..+..|.||..... ....++.-..|.-.||..|+..-+.       ..-.||.|.....
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            35678999987643 2344555555999999999885331       2235999976543

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.54  E-value=0.019  Score=31.16  Aligned_cols=44  Identities=25%  Similarity=0.542  Sum_probs=28.8

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHh----c-CCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----E-HLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~-~~~CP~CR~   96 (104)
                      .|.||...-. +..++.-..|...||..|+..=|.    . .=.||.|..
T Consensus        28 ~C~vC~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHE-PNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCC-STTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCC-CCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            7889975432 334444445899999999985332    1 236998864

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.53  E-value=0.013  Score=32.91  Aligned_cols=49  Identities=24%  Similarity=0.479  Sum_probs=32.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~   97 (104)
                      .....|.||...-.. ..++.-..|...||..|+..=|..    .=.||.|+..
T Consensus        14 ~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           14 IDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             cCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            456689999876432 334444459999999999743321    2259999764

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=92.48  E-value=0.15  Score=39.61  Aligned_cols=49  Identities=16%  Similarity=0.097  Sum_probs=41.4

Q ss_pred             CCccccccccccccCCCcEEecCCCC-CcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCY-RIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~-H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .+...|||=++-|.+   .+++| -| ++|-+..|.+||....+||+=|.++..
T Consensus       889 P~~F~cPIs~~lM~D---PVilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          889 PDEFLDPLMYTIMKD---PVILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             cHHhCCcchhhHHhC---CeEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            567889999998877   55677 76 699999999999889999999888753

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.40  E-value=0.015  Score=29.54  Aligned_cols=45  Identities=29%  Similarity=0.775  Sum_probs=30.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRI   96 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~   96 (104)
                      ..+..|.||...   ++ ++.-..|...||..|+..-|..    .-.||.|..
T Consensus         7 ~~~~~C~vC~~~---g~-ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SC-CEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---Ce-EEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            356789999864   33 3443458999999999864422    224888864

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=92.30  E-value=0.048  Score=30.85  Aligned_cols=47  Identities=21%  Similarity=0.334  Sum_probs=30.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh---cCCCCcccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK---EHLTCPVCRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~---~~~~CP~CR~~   97 (104)
                      +...| ||-.....+..| .-..|.-.||..|+..=+.   ..-.||.|+..
T Consensus        27 d~vrC-iC~~~~~~~~mi-~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDGYMI-CCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CBCCC-TTSCCSCSSCEE-EBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CCEEe-ECCCccCCCcEE-EcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            34557 897765554444 4445999999999975322   23469999754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=92.18  E-value=0.018  Score=30.21  Aligned_cols=47  Identities=28%  Similarity=0.624  Sum_probs=31.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      ..+..|.||...   ++ ++.-..|.-.||..|+..-|..    .-.||.|...-
T Consensus         6 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~~   56 (66)
T 1xwh_A            6 KNEDECAVCRDG---GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQAT   56 (66)
T ss_dssp             SCCCSBSSSSCC---SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHTC
T ss_pred             CCCCCCccCCCC---CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccCcc
Confidence            357789999863   33 4444458889999999864422    22599997643

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=91.95  E-value=0.094  Score=26.99  Aligned_cols=43  Identities=23%  Similarity=0.515  Sum_probs=30.4

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVC   94 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~C   94 (104)
                      ..|..|+..|... .+..-++|++.||.+|=.---..=..||-|
T Consensus        16 ~~C~~C~~~~~~~-~~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCC-ccEECCccCcCcccchhHHHHhhccCCcCC
Confidence            4599999988532 235566799999999976532344569987

>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=91.88  E-value=0.1  Score=27.93  Aligned_cols=48  Identities=27%  Similarity=0.500  Sum_probs=31.4

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH---------hcCCCCcccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL---------KEHLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---------~~~~~CP~CR~~~~   99 (104)
                      ...| ||...+... ..+.-..|...||..|+.--.         .....||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            4456 898876533 344434499999999994211         24667999986543

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=91.83  E-value=0.032  Score=29.53  Aligned_cols=48  Identities=25%  Similarity=0.486  Sum_probs=31.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH---hcCCCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL---KEHLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---~~~~~CP~CR~~   97 (104)
                      .+...| ||..... +...+.-..|...||..|+.--.   .....||.|+..
T Consensus        17 ~~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~s   67 (68)
T 3o70_A           17 QGLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDS   67 (68)
T ss_dssp             TTCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHTC
T ss_pred             CCceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCCC
Confidence            356678 9987664 44444444599999999996422   133469998753

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=91.82  E-value=0.27  Score=26.09  Aligned_cols=50  Identities=18%  Similarity=0.380  Sum_probs=33.5

Q ss_pred             CCccccccccccc-cCCCcEEecCCCCCcccHHhHHHHHh--cCCCCcccccc
Q 045579           48 PSSNYCVICLENF-VDGESCRLFPVCYRIFHSVCIDQWLK--EHLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~-~~~~~~~~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~   97 (104)
                      ..+..|.||...- ...+.++.-..|.-.||..|+..-..  ..=.||.|+..
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            4577899998653 23445555556999999999975321  22258888754

>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=91.40  E-value=0.64  Score=25.86  Aligned_cols=51  Identities=18%  Similarity=0.347  Sum_probs=36.3

Q ss_pred             CccccccccccccC---CCcEEecCCCCCcccHHhHHHHH-hcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVD---GESCRLFPVCYRIFHSVCIDQWL-KEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~---~~~~~~lp~C~H~fh~~Ci~~wl-~~~~~CP~CR~~~~   99 (104)
                      ....|-||=+++..   ++..+....|+--.|..|++.=. ..+..||.|+..+.
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            46789999988643   33333222377789999998655 45667999999885

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=91.32  E-value=0.21  Score=27.66  Aligned_cols=37  Identities=19%  Similarity=0.427  Sum_probs=26.7

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ....|.+|...|..-..-.....||++||..|...++
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~   55 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKC   55 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEE
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCee
Confidence            3557999999987544333334599999999987653

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=91.27  E-value=0.022  Score=30.02  Aligned_cols=48  Identities=23%  Similarity=0.413  Sum_probs=28.5

Q ss_pred             CccccccccccccCCCcEEec-CCCCCcccHHhHHHHH---h-----cCCCCcccccc
Q 045579           49 SSNYCVICLENFVDGESCRLF-PVCYRIFHSVCIDQWL---K-----EHLTCPVCRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~fh~~Ci~~wl---~-----~~~~CP~CR~~   97 (104)
                      ....| ||-.....+..|..- +.|.-.||..|+.---   .     .+..||.||..
T Consensus         9 ~~v~C-~C~~~~~~g~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~~   65 (68)
T 2rsd_A            9 AKVRC-ICSSTMVNDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRLS   65 (68)
T ss_dssp             CEECC-TTCCCSCCSCEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHHH
T ss_pred             CCEEe-ECCCCcCCCCEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccCc
Confidence            34456 796655544433322 1388899999984210   0     13469999864

>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=91.18  E-value=0.26  Score=29.34  Aligned_cols=45  Identities=22%  Similarity=0.424  Sum_probs=30.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH------hc-----CCCCcccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL------KE-----HLTCPVCRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl------~~-----~~~CP~CR~~   97 (104)
                      .+..|.||-+.    ..++.-..|-..||..||.+-+      ..     .=.|++|+-.
T Consensus        56 ~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           56 MDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             CBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            45679999754    3344444589999999999752      11     1259999654

>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=90.90  E-value=0.078  Score=30.74  Aligned_cols=34  Identities=26%  Similarity=0.413  Sum_probs=22.7

Q ss_pred             ccccccccccc------CCCcEEecCCCCCcccHHhHHHH
Q 045579           51 NYCVICLENFV------DGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        51 ~~C~ICl~~~~------~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      ..|.||+..-.      .++.++.-..|+..||..|+..+
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            46999987541      12334443449999999999754

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=90.65  E-value=0.45  Score=28.73  Aligned_cols=46  Identities=24%  Similarity=0.474  Sum_probs=31.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-----------cCCCCcccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-----------EHLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-----------~~~~CP~CR~~   97 (104)
                      ..+..|.||.+.   ++ ++....|...||..||.+-+.           ..=.||+|+..
T Consensus        61 g~~d~C~vC~~G---G~-LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           61 GMDEQCRWCAEG---GN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             SCBCSCSSSCCC---SS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCeecccCCC---Cc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            346789999754   33 444445899999999997652           12259999753

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=90.65  E-value=0.2  Score=26.61  Aligned_cols=35  Identities=20%  Similarity=0.293  Sum_probs=24.7

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      +..|.+|...|..-..-.--..||.+||..|....
T Consensus        11 ~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~~   45 (73)
T 1vfy_A           11 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   45 (73)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CCcccCCCCccCCccccccCCCCCEEEcccccCCe
Confidence            35799999998754322333349999999997643

>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=90.41  E-value=0.018  Score=33.54  Aligned_cols=49  Identities=20%  Similarity=0.442  Sum_probs=31.8

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccccCC
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISCIDI  101 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~~~~  101 (104)
                      .|.||...-..+ .++.-..|...||..|+..=|..    .-.||.|+..+.++
T Consensus        60 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~~~~~k  112 (114)
T 2kwj_A           60 SCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKEK  112 (114)
T ss_dssp             CCTTTTCCTTTT-TEEECSSSCCEEETTTSSSCCSSCCSSCCCCHHHHHHHHHT
T ss_pred             ccCcccccCCCC-ceEEcCCCCccccccccCCCccCCCCCCeECccccchhhcc
Confidence            588887653333 44444459999999999853322    22599998766544

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=90.20  E-value=0.19  Score=29.61  Aligned_cols=36  Identities=19%  Similarity=0.341  Sum_probs=25.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      ....|.+|...|.....-.-...||++||..|....
T Consensus        68 ~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           68 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            355799999998754332333349999999997654

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=89.94  E-value=0.25  Score=26.83  Aligned_cols=36  Identities=19%  Similarity=0.354  Sum_probs=25.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      +...|.+|...|.....----..||.+||..|....
T Consensus        18 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   53 (82)
T 2yw8_A           18 EATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNE   53 (82)
T ss_dssp             CCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEE
T ss_pred             cCCcccCcCCcccCccccccCCCCCCEEChHHhCCe
Confidence            455799999998754332333349999999998753

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=89.82  E-value=0.37  Score=26.60  Aligned_cols=37  Identities=19%  Similarity=0.194  Sum_probs=26.1

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      .....|.+|...|..-..----..||.+||..|....
T Consensus         7 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~   43 (88)
T 1wfk_A            7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFS   43 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEE
T ss_pred             CcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCc
Confidence            3456899999998765433333349999999997653

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=89.79  E-value=0.29  Score=26.70  Aligned_cols=37  Identities=14%  Similarity=0.156  Sum_probs=26.7

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      .....|.+|...|..-..----..||++||..|....
T Consensus        19 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           19 EDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             TTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCCCcCcCCccccchhcccccCCCcEEChHHhCCe
Confidence            3466899999998765433333349999999998764

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=89.45  E-value=0.23  Score=29.67  Aligned_cols=36  Identities=19%  Similarity=0.385  Sum_probs=25.8

Q ss_pred             CCcccccccccccc-CCCcEEecCCCCCcccHHhHHH
Q 045579           48 PSSNYCVICLENFV-DGESCRLFPVCYRIFHSVCIDQ   83 (104)
Q Consensus        48 ~~~~~C~ICl~~~~-~~~~~~~lp~C~H~fh~~Ci~~   83 (104)
                      .....|.+|...|. ....-..-..|.|.+|..|-..
T Consensus        53 ~~~~~C~~C~~~~g~l~~~g~~C~~C~~~VC~~C~~~   89 (134)
T 1zbd_B           53 DGVNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGVE   89 (134)
T ss_dssp             CSSSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEEE
T ss_pred             CCCccccccCCCcccccCCCCCCCCCCcccccccCCc
Confidence            46788999999984 3333334445999999998764

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=89.33  E-value=0.045  Score=32.22  Aligned_cols=48  Identities=19%  Similarity=0.331  Sum_probs=29.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      ....|..|...|..-..---...||.+||..|.........+|-.|-.
T Consensus        18 ~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~   65 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   65 (120)
T ss_dssp             --CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             ccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHH
Confidence            345799999988654322233349999999998776555556766644

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=88.91  E-value=0.12  Score=26.50  Aligned_cols=43  Identities=28%  Similarity=0.642  Sum_probs=27.1

Q ss_pred             CccccccccccccCCCcEEecCC--CC-CcccHHhHHHHHh----cCCCCccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPV--CY-RIFHSVCIDQWLK----EHLTCPVCRI   96 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~--C~-H~fh~~Ci~~wl~----~~~~CP~CR~   96 (104)
                      +...| ||.... .+ .++.-..  |. ..||..|+.  |.    ..-.||.|+.
T Consensus         9 e~~~C-~C~~~~-~g-~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            9 EPTYC-LCHQVS-YG-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CCEET-TTTEEC-CS-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCEE-ECCCcC-CC-CEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            34556 898763 23 3444344  44 689999998  42    2335999865

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=88.80  E-value=0.13  Score=26.25  Aligned_cols=43  Identities=30%  Similarity=0.654  Sum_probs=27.7

Q ss_pred             CccccccccccccCCCcEEecCC--CC-CcccHHhHHHHHh----cCCCCccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPV--CY-RIFHSVCIDQWLK----EHLTCPVCRI   96 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~--C~-H~fh~~Ci~~wl~----~~~~CP~CR~   96 (104)
                      +...| ||.... .+ .++.-..  |. ..||..|+.  |.    .+-.||.|+.
T Consensus         8 e~~yC-~C~~~~-~g-~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            8 EPTYC-LCHQVS-YG-EMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CCEET-TTTEEC-CS-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCcEE-ECCCCC-CC-CeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            35566 898764 23 3444444  55 699999998  32    2336999975

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=88.79  E-value=0.089  Score=34.27  Aligned_cols=46  Identities=28%  Similarity=0.511  Sum_probs=26.0

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHHh----c-CCCCcccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----E-HLTCPVCRIS   97 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~-~~~CP~CR~~   97 (104)
                      ..|.+|...-..+ .+.....|...||..|+.+=|.    . .=.||.|+..
T Consensus       175 c~C~vC~~~~~~~-~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          175 CACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             TSCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCCcCCCCCCCCC-CeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            3688887542223 3444445999999999985442    1 2269999753

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=87.89  E-value=0.37  Score=26.28  Aligned_cols=35  Identities=23%  Similarity=0.306  Sum_probs=24.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ   83 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~   83 (104)
                      ....|.+|...|..-..----..||.+||..|...
T Consensus        13 ~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           13 NFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            45679999999865432222234999999999764

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=87.58  E-value=0.29  Score=31.66  Aligned_cols=37  Identities=19%  Similarity=0.341  Sum_probs=27.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      .++..|.+|...|..-..-.-...||++||..|....
T Consensus       162 ~~~~~C~~C~~~F~~~~RrhHCR~CG~v~C~~Cs~~~  198 (226)
T 3zyq_A          162 VDAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSKY  198 (226)
T ss_dssp             CCCSBCTTTCCBCBTTBCCEECTTTCCEECTTTCCEE
T ss_pred             ccCCCCcCcCCCCCccccccccCCCcCEeChhhcCCc
Confidence            3466899999998765433334459999999998754

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=87.47  E-value=0.052  Score=29.42  Aligned_cols=44  Identities=30%  Similarity=0.588  Sum_probs=27.4

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----C-CCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----H-LTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~-~~CP~CR~   96 (104)
                      .|.||...- .+..++.-..|...||..|+..-|..    . =.||.|+.
T Consensus        28 ~C~vC~~~~-d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCC-CCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            466665443 22345554458999999999865421    1 36999875

>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1

Probab=87.41  E-value=0.51  Score=30.25  Aligned_cols=37  Identities=16%  Similarity=0.326  Sum_probs=26.6

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      .++..|.+|...|..-..-.-...||++||..|....
T Consensus       159 ~~~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~~  195 (220)
T 1dvp_A          159 ADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ  195 (220)
T ss_dssp             CCCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCCCccCCCCCccCCcccccccCCcCCEEChHHhCCe
Confidence            3467999999998754333333349999999997654

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=87.29  E-value=0.092  Score=33.13  Aligned_cols=45  Identities=24%  Similarity=0.572  Sum_probs=29.9

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHh----cCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----EHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~~~~CP~CR~~~   98 (104)
                      +..|.+|...   ++ +.....|.-.||..|+..=+.    ..-.||.|+...
T Consensus         2 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SS-CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---Cc-eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            4579999754   33 333344888999999976442    222599998653

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}

Probab=86.98  E-value=0.19  Score=22.89  Aligned_cols=16  Identities=13%  Similarity=0.488  Sum_probs=11.3

Q ss_pred             CccccccccccccCCC
Q 045579           49 SSNYCVICLENFVDGE   64 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~   64 (104)
                      +...||||+..+...+
T Consensus         4 EGFiCP~C~~~l~s~~   19 (34)
T 3mjh_B            4 EGFICPQCMKSLGSAD   19 (34)
T ss_dssp             EEEECTTTCCEESSHH
T ss_pred             cccCCcHHHHHcCCHH
Confidence            4578888888776543

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=86.85  E-value=0.4  Score=25.29  Aligned_cols=51  Identities=22%  Similarity=0.191  Sum_probs=33.8

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH----hcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL----KEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl----~~~~~CP~CR~~~~   99 (104)
                      .....| ||......+...+.-..|...||..|+.--.    .....||.|+..-.
T Consensus        14 ~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~~   68 (72)
T 1wee_A           14 NWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSG   68 (72)
T ss_dssp             SSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCS
T ss_pred             CcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCCC
Confidence            345678 7987765555455544589999999986431    23446999986543

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=86.32  E-value=0.11  Score=29.85  Aligned_cols=26  Identities=23%  Similarity=0.520  Sum_probs=18.0

Q ss_pred             CCCcccHHhHHHHHhcCCCCccccccccCCC
Q 045579           72 CYRIFHSVCIDQWLKEHLTCPVCRISCIDIE  102 (104)
Q Consensus        72 C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~  102 (104)
                      ||+.|.     .-+.....||.|+..-++.-
T Consensus        73 CG~~F~-----~~~~kPsrCP~CkSe~Ie~P   98 (105)
T 2gmg_A           73 CGFVFK-----AEINIPSRCPKCKSEWIEEP   98 (105)
T ss_dssp             TCCBCC-----CCSSCCSSCSSSCCCCBCCC
T ss_pred             CcCeec-----ccCCCCCCCcCCCCCccCCc
Confidence            999991     11245567999999876554

>2jvx_A NF-kappa-B essential modulator; CCHC classical zinc finger, NEMO zinc finger, beta-BETA- alpha fold, coiled coil, cytoplasm, disease mutation; NMR {Synthetic} PDB: 2jvy_A

Probab=86.25  E-value=0.09  Score=22.91  Aligned_cols=14  Identities=29%  Similarity=0.878  Sum_probs=9.5

Q ss_pred             CCCCccccccccCC
Q 045579           88 HLTCPVCRISCIDI  101 (104)
Q Consensus        88 ~~~CP~CR~~~~~~  101 (104)
                      +.+||+|+..+++.
T Consensus         3 k~~CpvCk~q~Pd~   16 (28)
T 2jvx_A            3 DFCCPKCQYQAPDM   16 (28)
T ss_dssp             CEECTTSSCEESSH
T ss_pred             cccCccccccCcCh
Confidence            34688888777654

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=86.00  E-value=0.68  Score=26.57  Aligned_cols=45  Identities=22%  Similarity=0.634  Sum_probs=28.9

Q ss_pred             CCccccccccccccCCCcEEecC--CCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFP--VCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp--~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      ..+..|.+|.+.   + .++.-.  .|...||..|+.  |..    .-.||.|+-.+
T Consensus        13 ~~~~~C~~C~~~---G-~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~   63 (107)
T 4gne_A           13 MHEDYCFQCGDG---G-ELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDE   63 (107)
T ss_dssp             SSCSSCTTTCCC---S-EEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTT
T ss_pred             CCCCCCCcCCCC---C-cEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCc
Confidence            456789999832   3 344433  388899999997  432    22488776544

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=84.37  E-value=0.12  Score=29.65  Aligned_cols=47  Identities=23%  Similarity=0.541  Sum_probs=29.9

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHh----cCCCCcccccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK----EHLTCPVCRISCI   99 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~----~~~~CP~CR~~~~   99 (104)
                      .|.||...-.. ..+..-..|...||..|+..=|.    ..-.||.|+....
T Consensus        56 ~C~~C~~~~~~-~~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c~~  106 (111)
T 2ysm_A           56 VCQNCKQSGED-SKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIS  106 (111)
T ss_dssp             CCTTTCCCSCC-TTEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCCSC
T ss_pred             cccccCccCCC-CCeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCcCC
Confidence            56777654332 34555455999999999986442    2235998876543

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=84.31  E-value=0.12  Score=25.61  Aligned_cols=41  Identities=24%  Similarity=0.506  Sum_probs=26.0

Q ss_pred             cccccccCCCcEEecCCCCCcccHHhHHHHH---hcCCCCccccc
Q 045579           55 ICLENFVDGESCRLFPVCYRIFHSVCIDQWL---KEHLTCPVCRI   96 (104)
Q Consensus        55 ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---~~~~~CP~CR~   96 (104)
                      ||..... +...+.-..|...||..|+.--.   .....||.|+.
T Consensus         8 ~C~~~~~-~~~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~~   51 (52)
T 3o7a_A            8 FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   51 (52)
T ss_dssp             TTCCBCT-TCCEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHHT
T ss_pred             EeCCcCC-CCCEEEcCCCCccccccccCCCcccCCCcEECcCCCC
Confidence            6766544 33444444489999999996322   23446999875

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=84.15  E-value=0.47  Score=26.13  Aligned_cols=51  Identities=20%  Similarity=0.381  Sum_probs=34.5

Q ss_pred             CccccccccccccC-CCcEEecCCCCCcccHHhHHHHHh--------cCCCCcccccccc
Q 045579           49 SSNYCVICLENFVD-GESCRLFPVCYRIFHSVCIDQWLK--------EHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl~--------~~~~CP~CR~~~~   99 (104)
                      .+..|.||...-.. ...++.-..|...||..|+..-|.        ..=.|+.|+....
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~   74 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhh
Confidence            35689999876332 244555555999999999986442        1236999976554

>3fyb_A Protein of unknown function (DUF1244); hydrocar degrading, structural genomics, PSI-2; HET: PEG; 1.80A {Alcanivorax borkumensis SK2}

Probab=84.05  E-value=0.48  Score=26.81  Aligned_cols=11  Identities=36%  Similarity=1.078  Sum_probs=10.3

Q ss_pred             ccHHhHHHHHh
Q 045579           76 FHSVCIDQWLK   86 (104)
Q Consensus        76 fh~~Ci~~wl~   86 (104)
                      ||..|+.+|+.
T Consensus        42 FCRNCLskWy~   52 (104)
T 3fyb_A           42 FCRNCLAKWLM   52 (104)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999984

>2o35_A Hypothetical protein DUF1244; helix bundle, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.12A {Sinorhizobium meliloti} SCOP: a.293.1.1

Probab=83.90  E-value=0.49  Score=26.82  Aligned_cols=11  Identities=27%  Similarity=1.081  Sum_probs=10.2

Q ss_pred             ccHHhHHHHHh
Q 045579           76 FHSVCIDQWLK   86 (104)
Q Consensus        76 fh~~Ci~~wl~   86 (104)
                      ||+.|+.+|+.
T Consensus        43 FCRNCLskWy~   53 (105)
T 2o35_A           43 FCRNCLSNWYR   53 (105)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999984

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=83.74  E-value=0.24  Score=25.54  Aligned_cols=46  Identities=28%  Similarity=0.560  Sum_probs=27.8

Q ss_pred             CccccccccccccCCCcEEecCC--CC-CcccHHhHHHHH--hcCCCCcccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPV--CY-RIFHSVCIDQWL--KEHLTCPVCRIS   97 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~--C~-H~fh~~Ci~~wl--~~~~~CP~CR~~   97 (104)
                      +...| ||.... .+ ..+.-..  |. ..||..|+.---  ..+-.||.|+..
T Consensus        10 e~~yC-~C~~~~-~g-~MI~CD~c~C~~~WfH~~Cvgl~~~p~~~w~Cp~C~~~   60 (62)
T 2g6q_A           10 EPTYC-LCNQVS-YG-EMIGCDNEQCPIEWFHFSCVSLTYKPKGKWYCPKCRGD   60 (62)
T ss_dssp             CCEET-TTTEEC-CS-EEEECSCTTCSSCEEETGGGTCSSCCSSCCCCHHHHTC
T ss_pred             CCcEE-ECCCCC-CC-CeeeeeCCCCCcccEecccCCcCcCCCCCEECcCcccC
Confidence            34566 898753 33 3444344  44 799999997210  123469999753

>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural genomics consortium, DH domain, SGC, L binding protein; 2.80A {Homo sapiens}

Probab=82.85  E-value=0.24  Score=34.57  Aligned_cols=50  Identities=16%  Similarity=0.184  Sum_probs=0.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-------cCCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-------EHLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-------~~~~CP~CR~~~   98 (104)
                      ....|.+|...|.....-.....||++||..|...++.       ...+|-.|-..+
T Consensus       374 ~~~~c~~c~~~f~~~~r~h~Cr~Cg~~~C~~Cs~~~~~~~~~~~~~~rvC~~C~~~l  430 (434)
T 3mpx_A          374 HVMMCMNCGCDFSLTLRRHHCHACGKIVCRNCSRNKYPLKYLKDRMAKVCDGCFGEL  430 (434)
T ss_dssp             ---------------------------------------------------------
T ss_pred             cCCcCCCcCCCCCCcchhhhcccCcCEeehhhCCCeeeCCCCCCCcCEecHHHHHHH
Confidence            35679999998864322222224999999999987651       234577775544

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.49  E-value=0.77  Score=24.02  Aligned_cols=41  Identities=17%  Similarity=0.377  Sum_probs=28.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ....|+.|-..+..++.+..   -+..||.+|.        +|-.|+..|..
T Consensus         8 ~~~~C~~C~~~I~~~~~v~a---~~~~~H~~CF--------~C~~C~~~L~~   48 (76)
T 2cu8_A            8 MASKCPKCDKTVYFAEKVSS---LGKDWHKFCL--------KCERCSKTLTP   48 (76)
T ss_dssp             CCCBCTTTCCBCCTTTEEEE---TTEEEETTTC--------BCSSSCCBCCT
T ss_pred             CCCCCcCCCCEeECCeEEEE---CCeEeeCCCC--------CCCCCCCccCC
Confidence            35678899888876666554   4677887775        37777777654

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=82.31  E-value=1.6  Score=30.38  Aligned_cols=46  Identities=22%  Similarity=0.425  Sum_probs=29.1

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH---hc--CCCCcccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL---KE--HLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---~~--~~~CP~CR~~~~   99 (104)
                      ...|||=+..|..+  ++... |.|.=|.+ +..||   ..  .-.||+|.+.+.
T Consensus       215 SL~CPlS~~ri~~P--~Rg~~-C~HlqCFD-l~sfL~~~~~~~~W~CPiC~k~~~  265 (360)
T 4fo9_A          215 SLMCPLGKMRLTIP--CRAVT-CTHLQCFD-AALYLQMNEKKPTWICPVCDKKAA  265 (360)
T ss_dssp             ESBCTTTCSBCSSE--EEETT-CCCCCCEE-HHHHHHHHHHSCCCBCTTTCSBCC
T ss_pred             eeeCCCccceeccC--CcCCC-CCCCccCC-HHHHHHHHhhCCCeECCCCCcccC
Confidence            44688877776553  55555 99984433 33344   22  336999998774

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=82.28  E-value=1.5  Score=30.57  Aligned_cols=46  Identities=22%  Similarity=0.332  Sum_probs=29.2

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHH---h--cCCCCcccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL---K--EHLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl---~--~~~~CP~CR~~~~   99 (104)
                      ...|||=+..|..+  ++-.. |.|+-|.+ +..||   .  ..-.||+|.+.+.
T Consensus       249 SL~CPlS~~ri~~P--vRg~~-C~HlQCFD-l~sfL~~~~~~~~W~CPIC~k~~~  299 (371)
T 3i2d_A          249 SLQCPISYTRMKYP--SKSIN-CKHLQCFD-ALWFLHSQLQIPTWQCPVCQIDIA  299 (371)
T ss_dssp             ESBCTTTSSBCSSE--EEETT-CCSSCCEE-HHHHHHHHHHSCCCBCTTTCCBCC
T ss_pred             eecCCCcccccccc--CcCCc-CCCcceEC-HHHHHHHhhcCCceeCCCCCcccC
Confidence            45788877776553  55555 99984444 33344   2  2346999988763

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.89  E-value=1  Score=24.09  Aligned_cols=41  Identities=22%  Similarity=0.520  Sum_probs=27.8

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ....|..|-..+...+.+..   =+..||.+|..        |-.|+..|..
T Consensus        14 ~~~~C~~C~~~I~~~e~v~a---~~~~wH~~CF~--------C~~C~~~L~~   54 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLCV---NGHFFHRSCFR--------CHTCEATLWP   54 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCCB---TTBCCBTTTCB--------CSSSCCBCCT
T ss_pred             CCCCCcccCCCcccceEEEE---CCCeeCCCcCE--------EcCCCCCcCC
Confidence            45679999888766655543   46678887753        6677666543

---

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	104
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	5e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-08
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-08
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-06
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-05
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-04
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	4e-04
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	6e-04
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.001
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	0.003

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 56.4 bits (136), Expect = 5e-13
 Identities = 21/47 (44%), Positives = 28/47 (59%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI 99
          C +CL    DGE  R  P C   FH+ C+D WL  H TCP+CR++ +
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 44.9 bits (106), Expect = 2e-08
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 46 MTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          M   +  C ICLE+  +         C   F  VCI +W++++ TCP+C+
Sbjct: 1  MATVAERCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCK 47

>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 = 44.0 bits (103), Expect = 7e-08
 Identities = 13/52 (25%), Positives = 18/52 (34%)

Query: 44 QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
            +      C     +    E    + VC   FH  CI +WLK    CP+  
Sbjct: 29 NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>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 = 38.8 bits (90), Expect = 6e-06
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 44 QEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHL-TCPVCR 95
           EM  +   C IC EN  D    ++ P C  +  + C+  W +     CP CR
Sbjct: 17 CEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCR 65

>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 = 37.5 bits (86), Expect = 2e-05
 Identities = 10/45 (22%), Positives = 12/45 (26%), Gaps = 2/45 (4%)

Query: 53 CVICLENFVDGESCRLFPV-CYRIFHSVCIDQWLKE-HLTCPVCR 95
          C  C        S +L    C       C+D         CP C 
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECG 50

>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 = 36.2 bits (82), Expect = 1e-04
 Identities = 13/75 (17%), Positives = 21/75 (28%), Gaps = 19/75 (25%)

Query: 40 NYSDQEMTPSSNYCVICLENFVD--------------GESCRLFPVCYRIFHSVCIDQWL 85
           Y+++        C+IC+E                           C   FH +C+    
Sbjct: 15 KYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMY 74

Query: 86 KE-----HLTCPVCR 95
                  L CP C+
Sbjct: 75 CNGNKDGSLQCPSCK 89

>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 = 33.5 bits (76), Expect = 4e-04
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 1/46 (2%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRIS 97
          C +C+E     +       C       C  +    E+  CP CR  
Sbjct: 3  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 48

>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 = 32.9 bits (75), Expect = 6e-04
 Identities = 8/43 (18%), Positives = 14/43 (32%), Gaps = 7/43 (16%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCR 95
          C  C       +       C     S C++      + CP+C+
Sbjct: 9  CQQCQAEAKCPKLLP----CLHTLCSGCLEAS---GMQCPICQ 44

>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 = 33.0 bits (75), Expect = 0.001
 Identities = 15/47 (31%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 53 CVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH-LTCPVCRISC 98
          C IC     D         C  +F  +CI + LK     CP CR  C
Sbjct: 26 CQICEHILADPVETS----CKHLFCRICILRCLKVMGSYCPSCRYPC 68

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 31.4 bits (70), Expect = 0.003
 Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 3/46 (6%)

Query: 53 CVICLENFVDG-ESCRLFPVCYRIFHSVCIDQWLKEH--LTCPVCR 95
          C IC E   +               H  C+  WL       C +C 
Sbjct: 9  CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICG 54

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	104
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.89
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.79
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.76
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.76
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.75
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.74
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.66
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.63
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.61
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.58
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.58
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.48
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.48
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.45
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.37
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.17
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.85
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.59
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	96.22
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	95.29
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	94.78
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	94.73
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	94.57
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	94.51
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	94.39
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	94.17
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	93.73
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	92.62
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	92.04
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	91.62
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	91.06
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	90.3
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	89.97
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	88.76
d2co8a2	36	Nedd9 interacting protein with calponin homology,	88.24
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	86.56
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	86.51
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	86.23
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	85.05
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	84.35
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	82.68
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	81.88
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	81.12

>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=99.89  E-value=2.9e-24  Score=111.31  Aligned_cols=52  Identities=40%  Similarity=1.016  Sum_probs=47.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      +++.+|+|||++|..++.+..++.|+|.||..||.+||+.+.+||+||++|+
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            3566799999999999988888679999999999999999999999999875

>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=99.79  E-value=2.9e-20  Score=99.99  Aligned_cols=49  Identities=33%  Similarity=0.892  Sum_probs=42.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ..+.|+||++.|..  .++.++ |||.||..||.+|++.+.+||+||+++..
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            45679999999865  466778 99999999999999999999999998753

>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=99.76  E-value=2.8e-19  Score=100.53  Aligned_cols=50  Identities=28%  Similarity=0.580  Sum_probs=41.9

Q ss_pred             CccccccccccccCCC---------------cEEecCCCCCcccHHhHHHHHhcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGE---------------SCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~   99 (104)
                      .+..|+||++.+....               .+..++ |||.||.+||.+||..+.+||+||+++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            4567999998886533               356677 9999999999999999999999999875

>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=99.76  E-value=9.1e-20  Score=93.16  Aligned_cols=48  Identities=19%  Similarity=0.409  Sum_probs=40.1

Q ss_pred             ccccccccccCCCcE-EecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           52 YCVICLENFVDGESC-RLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~-~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      +|+||+++|..++.+ ..++ |||.||.+||.+|+.. +.+||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            699999999876554 4456 9999999999999975 5579999998864

>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=99.75  E-value=6.1e-19  Score=93.91  Aligned_cols=51  Identities=16%  Similarity=0.322  Sum_probs=40.3

Q ss_pred             CccccccccccccCC-C-cEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           49 SSNYCVICLENFVDG-E-SCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~-~-~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      ++..|+||++.+..+ + .+.+++ |||.||.+||.+|+.. +.+||+||+.+..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            467899999986433 3 345566 9999999999999954 5679999998854

>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=99.74  E-value=1.1e-18  Score=96.20  Aligned_cols=49  Identities=33%  Similarity=0.755  Sum_probs=41.3

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccCCC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCIDIE  102 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~~~  102 (104)
                      ...|+||++.+..   ++++| |||.||..||..||. ++.+||+||..|...+
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            3579999998765   67788 999999999999997 4568999999997644

>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=99.74  E-value=1.5e-18  Score=101.65  Aligned_cols=52  Identities=27%  Similarity=0.604  Sum_probs=40.7

Q ss_pred             CccccccccccccCC---------------CcEEecCCCCCcccHHhHHHHHhcC-----CCCccccccccCC
Q 045579           49 SSNYCVICLENFVDG---------------ESCRLFPVCYRIFHSVCIDQWLKEH-----LTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~---------------~~~~~lp~C~H~fh~~Ci~~wl~~~-----~~CP~CR~~~~~~  101 (104)
                      .+..|+||++.|...               ..+.+++ |||+||..||..||..+     .+||+||+.+...
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            456899999998642               2455667 99999999999999643     4799999987543

>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=99.66  E-value=1.2e-17  Score=86.30  Aligned_cols=47  Identities=19%  Similarity=0.174  Sum_probs=39.8

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCC
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDI  101 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~  101 (104)
                      .|+||++.|.+   .++++.|||+||.+||.+||+.+.+||+||+++...
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            69999999865   334445999999999999999999999999988653

>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=99.63  E-value=8.7e-17  Score=89.60  Aligned_cols=49  Identities=33%  Similarity=0.636  Sum_probs=40.5

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCIDI  101 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~~  101 (104)
                      ....|+||++.|..   .++++ |||+||..||.+|++. ..+||+||.++...
T Consensus        22 ~~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            34579999999866   56677 9999999999999964 45799999987643

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.4e-17  Score=84.47  Aligned_cols=48  Identities=21%  Similarity=0.476  Sum_probs=39.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccCCCC
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCIDIEN  103 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  103 (104)
                      +...|+||++.|..   .+++| |||+||..||.+|   +.+||+||+++....+
T Consensus         5 ~~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             CCCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCC
Confidence            34689999999876   34677 9999999999876   6689999999975544

>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=99.58  E-value=4.2e-16  Score=89.58  Aligned_cols=47  Identities=28%  Similarity=0.585  Sum_probs=38.9

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcC---CCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEH---LTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~---~~CP~CR~~~~~  100 (104)
                      ...|+||++.|..+   +.++ |||+||..||..|+...   ..||+||..+..
T Consensus        21 ~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            45799999998764   3467 99999999999999654   379999998853

>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=99.58  E-value=4.5e-16  Score=81.36  Aligned_cols=52  Identities=19%  Similarity=0.428  Sum_probs=38.1

Q ss_pred             CCccccccccccccCCCcEE-ecCCCCCcccHHhHHHHHh--cCCCCcccccccc
Q 045579           48 PSSNYCVICLENFVDGESCR-LFPVCYRIFHSVCIDQWLK--EHLTCPVCRISCI   99 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~-~lp~C~H~fh~~Ci~~wl~--~~~~CP~CR~~~~   99 (104)
                      ++...|.||++++....... ...+|+|.||..||.+|+.  .+.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            45678999999886543221 1112469999999999994  5568999999874

>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=99.48  E-value=1.7e-14  Score=79.28  Aligned_cols=49  Identities=18%  Similarity=0.154  Sum_probs=41.2

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      .++..|+||++.|..+   ++++ |||+|+..||..|+. .+.+||+||.++..
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            4678899999999773   4577 999999999999996 45679999998754

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=2.5e-15  Score=85.44  Aligned_cols=46  Identities=26%  Similarity=0.478  Sum_probs=37.5

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      ...|+||++.|..+  +.+.+ |||+||..||.+|+.  ..||+||..+..
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             cCCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCch
Confidence            55899999999765  33345 999999999999984  469999988754

>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=99.45  E-value=3.9e-14  Score=77.39  Aligned_cols=49  Identities=27%  Similarity=0.514  Sum_probs=41.5

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-CCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-HLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-~~~CP~CR~~~~~  100 (104)
                      .++..|+||++.|.++   ++++ |||+|+..||..|+.. ..+||.|+..+..
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            4678999999999774   4567 9999999999999965 4679999998864

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=6.1e-13  Score=75.51  Aligned_cols=50  Identities=16%  Similarity=0.017  Sum_probs=42.4

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~~~~~  100 (104)
                      .++..|+||++.|.+   .++++.|+|.|+..||..||..+.+||+||.++..
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            467899999999977   45677355689999999999999999999998864

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.17  E-value=5.1e-12  Score=70.94  Aligned_cols=47  Identities=23%  Similarity=0.628  Sum_probs=37.0

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc-----C---CCCcccc
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE-----H---LTCPVCR   95 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~-----~---~~CP~CR   95 (104)
                      .+...|+||++++...+.+..++ |+|.||.+||..|+..     .   .+||.|.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            35678999999997766666666 9999999999999942     1   2599864

>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=96.85  E-value=0.00014  Score=36.94  Aligned_cols=51  Identities=25%  Similarity=0.461  Sum_probs=36.6

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH-----hcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL-----KEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl-----~~~~~CP~CR~~~~   99 (104)
                      ....|.||......+..++.-..|+..||..|+..-.     ...-.||.|+..-.
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~~   60 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG   60 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTTC
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcCC
Confidence            4668999998876766656555699999999996321     12346999987543

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.59  E-value=0.00035  Score=33.80  Aligned_cols=44  Identities=30%  Similarity=0.643  Sum_probs=30.2

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~   96 (104)
                      .|.||...-..+ .++.-..|...||..|+..-+..    .-.||.||.
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            588887654433 34444459999999999886532    225999975

>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=96.22  E-value=0.0026  Score=33.61  Aligned_cols=40  Identities=25%  Similarity=0.569  Sum_probs=27.4

Q ss_pred             CCCCCCCccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           43 DQEMTPSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        43 ~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      +.+....+..|.|| +.|...+.+ -...|+-+||..|+.+-
T Consensus         8 ~re~v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_           8 PREPVVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             SCCCCCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             cccCCCcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            33344568899999 666554433 22238999999999985

>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=95.29  E-value=0.034  Score=28.84  Aligned_cols=49  Identities=16%  Similarity=0.356  Sum_probs=33.1

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHH--H-Hh--cCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQ--W-LK--EHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~--w-l~--~~~~CP~CR~~~   98 (104)
                      ...+.||...+......+.-..|.-.||..|+.-  . +.  ....||.|+...
T Consensus        11 ~pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          11 VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            3445599887665555555556999999999952  1 12  235799998754

>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=94.78  E-value=0.0079  Score=29.71  Aligned_cols=45  Identities=22%  Similarity=0.517  Sum_probs=32.3

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVC   94 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~C   94 (104)
                      ....|.-|+..+.. ..+..-++|++.||.+|=.---..-..||-|
T Consensus        14 ~~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            45679999988854 3456667799999999966432344569887

>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=94.73  E-value=0.0026  Score=31.70  Aligned_cols=46  Identities=26%  Similarity=0.664  Sum_probs=30.9

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      .+..|.||.+.   ++ ++.-..|.-.||..|+...+..    .-.||.|+...
T Consensus         8 ~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            34579999743   33 4443448999999999765532    33699998654

>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=94.57  E-value=0.005  Score=31.50  Aligned_cols=45  Identities=22%  Similarity=0.566  Sum_probs=30.2

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHHHhc----CCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKE----HLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~----~~~CP~CR~~~   98 (104)
                      ...|.||..   .++ ++.-..|...||..|+...+..    .-.||.|+...
T Consensus         7 c~~C~~C~~---~~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQK---PGD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCS---SSC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCC---cCE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            446777753   344 4444459999999999987632    22599997654

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.51  E-value=0.0023  Score=34.16  Aligned_cols=50  Identities=20%  Similarity=0.439  Sum_probs=32.5

Q ss_pred             ccccccccccccC-CCcEEecCCCCCcccHHhHHHHH-----hc---CCCCcccccccc
Q 045579           50 SNYCVICLENFVD-GESCRLFPVCYRIFHSVCIDQWL-----KE---HLTCPVCRISCI   99 (104)
Q Consensus        50 ~~~C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl-----~~---~~~CP~CR~~~~   99 (104)
                      ...|.||...... ...++.-..|...||..|+...+     ..   .-.||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            4579999865432 23455445599999999986432     21   336999976543

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.39  E-value=0.0017  Score=31.45  Aligned_cols=45  Identities=20%  Similarity=0.374  Sum_probs=29.5

Q ss_pred             ccccccccccCCCcEEecCCCCCcccHHhHHHHHhcCCCCccccc
Q 045579           52 YCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLKEHLTCPVCRI   96 (104)
Q Consensus        52 ~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~~~~~CP~CR~   96 (104)
                      .|.+|...|.....-..-..||.+|+..|..........|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            588888888654433333349999999998765555567888754

>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=94.17  E-value=0.017  Score=29.48  Aligned_cols=38  Identities=24%  Similarity=0.317  Sum_probs=30.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHHh
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWLK   86 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl~   86 (104)
                      ....|.+|.+.++....|..-..=+|.||..|-...++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHH
Confidence            34689999999988877663332389999999999885

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.73  E-value=0.051  Score=28.01  Aligned_cols=50  Identities=20%  Similarity=0.396  Sum_probs=31.8

Q ss_pred             CccccccccccccCCCcEEec-CCCCCcccHHhHHH----HH-----hcCCCCcccccccc
Q 045579           49 SSNYCVICLENFVDGESCRLF-PVCYRIFHSVCIDQ----WL-----KEHLTCPVCRISCI   99 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~fh~~Ci~~----wl-----~~~~~CP~CR~~~~   99 (104)
                      +...| ||......+..+... ..|...||..|+.-    +.     .....||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             CccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            34567 898877655444443 13999999999842    10     01357999986543

>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=92.62  E-value=0.086  Score=26.78  Aligned_cols=47  Identities=30%  Similarity=0.610  Sum_probs=29.8

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHH----HH--H---hcCCCCccccccc
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCID----QW--L---KEHLTCPVCRISC   98 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~----~w--l---~~~~~CP~CR~~~   98 (104)
                      ...| ||......+ .++.-..|.-.||..|+.    ..  +   ...-.||.|+...
T Consensus        16 ~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          16 ALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             cCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            3457 897665443 344444589999999982    11  1   2346799997554

>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=92.04  E-value=0.36  Score=25.30  Aligned_cols=53  Identities=17%  Similarity=0.327  Sum_probs=37.6

Q ss_pred             CCccccccccccccC---CCcEEecCCCCCcccHHhHHHHHh-cCCCCccccccccC
Q 045579           48 PSSNYCVICLENFVD---GESCRLFPVCYRIFHSVCIDQWLK-EHLTCPVCRISCID  100 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~---~~~~~~lp~C~H~fh~~Ci~~wl~-~~~~CP~CR~~~~~  100 (104)
                      .....|-||-+.+..   ++..+....|+--.|..|.+-=.+ .+..||.|+..+..
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            456789999988753   333333333788899999986554 56679999988754

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=91.62  E-value=0.09  Score=26.73  Aligned_cols=36  Identities=17%  Similarity=0.332  Sum_probs=26.4

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      ++..|.+|...|..-..-..-..||++||..|....
T Consensus        12 ~~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~~   47 (72)
T d1dvpa2          12 DGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ   47 (72)
T ss_dssp             CCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             cCCccccCCCcccCccccccccccCCeeChhhhCCc
Confidence            456799999998765443344459999999998654

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.06  E-value=0.084  Score=26.42  Aligned_cols=35  Identities=20%  Similarity=0.293  Sum_probs=25.0

Q ss_pred             ccccccccccccCCCcEEecCCCCCcccHHhHHHH
Q 045579           50 SNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQW   84 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~w   84 (104)
                      +..|.+|...|..-..-.--..||.+||..|...+
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCCc
Confidence            35799999988654433333349999999997654

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.30  E-value=0.056  Score=27.52  Aligned_cols=44  Identities=32%  Similarity=0.654  Sum_probs=26.0

Q ss_pred             ccccccccccccCCCcEEec-CCCC-CcccHHhHHHHHh----cCCCCcccccc
Q 045579           50 SNYCVICLENFVDGESCRLF-PVCY-RIFHSVCIDQWLK----EHLTCPVCRIS   97 (104)
Q Consensus        50 ~~~C~ICl~~~~~~~~~~~l-p~C~-H~fh~~Ci~~wl~----~~~~CP~CR~~   97 (104)
                      ...| ||.... .++.+... ..|. ..||..|+.  |.    ..-.||.|+..
T Consensus        16 ~~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          16 PTYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            3445 998754 33334332 2254 579999984  32    23369999864

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.97  E-value=0.11  Score=25.68  Aligned_cols=37  Identities=19%  Similarity=0.321  Sum_probs=26.1

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      +...|.+|...|..-..----..||++||..|....+
T Consensus         7 ~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~~   43 (64)
T d1joca1           7 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNA   43 (64)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEE
T ss_pred             cCCcCcCcCCcccCCccccchhhhCCeecccccCCce
Confidence            3457999999887644333333499999999976543

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.76  E-value=0.13  Score=28.74  Aligned_cols=50  Identities=18%  Similarity=0.361  Sum_probs=30.9

Q ss_pred             CCccccccccccccC-CCcEEecCCCCCcccHHhHHHHHh----cCCCCcccccc
Q 045579           48 PSSNYCVICLENFVD-GESCRLFPVCYRIFHSVCIDQWLK----EHLTCPVCRIS   97 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~-~~~~~~lp~C~H~fh~~Ci~~wl~----~~~~CP~CR~~   97 (104)
                      .....|.+|...|.. ...-..-..||+.||..|-..-..    ..-.|.+|...
T Consensus        46 ~~~~~C~~C~~~f~~~~~~~~~C~~C~~~~C~~C~~~~~~~~~~~~w~C~~C~k~  100 (124)
T d1zbdb_          46 DGVNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQ  100 (124)
T ss_dssp             CSSSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEEECCCSSSSCCEEEHHHHHH
T ss_pred             cCCCcCcccCCcccCCCCCCCcCccCCcccccCCCCCccCCCCCCCEECccCcch
Confidence            345679999998864 223333445999999999533111    11247777653

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.24  E-value=0.18  Score=22.15  Aligned_cols=30  Identities=23%  Similarity=0.474  Sum_probs=21.9

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHh
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVC   80 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~C   80 (104)
                      .....|.+|-.....-+.+..   =|++||..|
T Consensus         6 g~~~~C~~C~K~VY~~Erl~a---~g~~yHk~C   35 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLCV---NGHFFHRSC   35 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCB---TTBCCBTTT
T ss_pred             CCCCcccccCCEEeeeeEEEe---cCcEecccc
Confidence            356789999877666555542   478999988

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.56  E-value=0.16  Score=21.48  Aligned_cols=28  Identities=18%  Similarity=0.335  Sum_probs=23.0

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHh
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVC   80 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~C   80 (104)
                      ..|+-|...+...+.|+..  =+++||..|
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~C   30 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKC   30 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGG
T ss_pred             cccccccCcCChhHhheec--ccceeeecc
Confidence            4699999999888888764  368999988

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.51  E-value=0.24  Score=24.81  Aligned_cols=48  Identities=23%  Similarity=0.232  Sum_probs=32.3

Q ss_pred             cccccccccccCCCcEEecCCCCCcccHHhHHHHH----hcCCCCcccccccc
Q 045579           51 NYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL----KEHLTCPVCRISCI   99 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl----~~~~~CP~CR~~~~   99 (104)
                      ..| ||......+..++.-..|.-.||..|+..-.    .....||.|+..-.
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~~   68 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELSG   68 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCS
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcCC
Confidence            457 7877666666556555599999999985422    13346999976543

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=86.23  E-value=0.15  Score=26.21  Aligned_cols=11  Identities=27%  Similarity=1.081  Sum_probs=10.2

Q ss_pred             ccHHhHHHHHh
Q 045579           76 FHSVCIDQWLK   86 (104)
Q Consensus        76 fh~~Ci~~wl~   86 (104)
                      ||+.|+.+|+.
T Consensus        40 FCRNCLskWy~   50 (79)
T d2o35a1          40 FCRNCLSNWYR   50 (79)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999983

>d1wfka_ g.50.1.1 (A:) Zinc finger FYVE domain containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Zinc finger FYVE domain containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.05  E-value=0.5  Score=24.77  Aligned_cols=38  Identities=18%  Similarity=0.178  Sum_probs=28.4

Q ss_pred             CCccccccccccccCCCcEEecCCCCCcccHHhHHHHH
Q 045579           48 PSSNYCVICLENFVDGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        48 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      ..+..|.+|...|..-..-.--..||-+||..|...++
T Consensus         7 ~~~s~C~~C~~~Fs~~~rrhhCr~CG~vfC~~Cs~~~~   44 (88)
T d1wfka_           7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSA   44 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEE
T ss_pred             cccCcCcccCchhccccccccccccChhhChHHhCCcc
Confidence            34667999999997655444444599999999987654

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=84.35  E-value=0.17  Score=23.77  Aligned_cols=42  Identities=33%  Similarity=0.747  Sum_probs=23.6

Q ss_pred             cccccccccccCCCcEEec-CCC-CCcccHHhHHHHHhc----CCCCccccc
Q 045579           51 NYCVICLENFVDGESCRLF-PVC-YRIFHSVCIDQWLKE----HLTCPVCRI   96 (104)
Q Consensus        51 ~~C~ICl~~~~~~~~~~~l-p~C-~H~fh~~Ci~~wl~~----~~~CP~CR~   96 (104)
                      .-| ||.... .++.+..- ..| .-.||..|+.  |..    .-.||.|++
T Consensus         3 ~yC-~C~~~~-~~~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~   50 (51)
T d2pnxa1           3 TYC-LCHQVS-YGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   50 (51)
T ss_dssp             EET-TTTEEC-CSEEEECSCTTCSSCEEEGGGGT--CSSCCSSCCCCHHHHC
T ss_pred             cEE-EcCCCC-CCCEEEEecCCCCCCCEeCCccC--CCcCCCCcEECcCCCC
Confidence            357 787654 33333321 113 3479999996  321    235998875

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.68  E-value=0.4  Score=20.81  Aligned_cols=29  Identities=24%  Similarity=0.458  Sum_probs=22.0

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHh
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVC   80 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~C   80 (104)
                      ....|.+|--....-+.+..   =|++||..|
T Consensus         6 ~~~kC~~C~K~VY~~E~~~a---~g~~~Hk~C   34 (35)
T d2d8ya1           6 ARETCVECQKTVYPMERLLA---NQQVFHISC   34 (35)
T ss_dssp             SSCBCTTTCCBCCTTSEEEC---SSSEEETTT
T ss_pred             CCcccccCCCEEeeeeeEec---CCeehhhcc
Confidence            46689999887777666653   478999988

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=81.88  E-value=0.31  Score=22.17  Aligned_cols=29  Identities=21%  Similarity=0.350  Sum_probs=23.2

Q ss_pred             CccccccccccccCCCcEEecCCCCCcccHHh
Q 045579           49 SSNYCVICLENFVDGESCRLFPVCYRIFHSVC   80 (104)
Q Consensus        49 ~~~~C~ICl~~~~~~~~~~~lp~C~H~fh~~C   80 (104)
                      ....|+.|--....-+.+..   =|+.||..|
T Consensus        14 ~~~kC~~C~k~VY~~E~~~~---~g~~~Hk~C   42 (43)
T d1b8ta3          14 GSDGCPRCGQAVYAAEKVIG---AGKSWHKSC   42 (43)
T ss_dssp             CCEECTTTSCEECSSSCEEE---TTEEECTTT
T ss_pred             CCCcCccCCCEeeHHHHhhc---CCCccccCC
Confidence            45789999888777777765   578999988

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.12  E-value=0.15  Score=25.78  Aligned_cols=37  Identities=24%  Similarity=0.533  Sum_probs=25.0

Q ss_pred             Ccccccccccccc--CCCcEEecCCCCCcccHHhHHHHH
Q 045579           49 SSNYCVICLENFV--DGESCRLFPVCYRIFHSVCIDQWL   85 (104)
Q Consensus        49 ~~~~C~ICl~~~~--~~~~~~~lp~C~H~fh~~Ci~~wl   85 (104)
                      .-.-||-|-..+.  .+...++-+.||+.||..|-..|-
T Consensus        17 ~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~   55 (73)
T d2ct7a1          17 KFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWE   55 (73)
T ss_dssp             CEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCC
T ss_pred             CCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchh
Confidence            3456777765443  233444556699999999999883