Citrus Sinensis ID: 036506

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80------
Protein Sequence
ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDGLGFLSFFSFHSAETC
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEccccccccccccccHHHHHccccccccccccccccccccccccccccccccEEEccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEHccccccccEEEcccccccccHHHHHHHHHcccccccccccccccccccccccccccEEEEcccccccccc
Coil and Loop (DISEMBL)
etaakcpyycyctvcldgisdgqkfrrlpeckhcfhveCIDAwfqsrstcplcRIEVAIVIARQRrnhqdglgflsffsfhsaetc
Flexible Loop (DISEMBL)
etaakcpyycYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDGLGFLSffsfhsaetc
Low Complexity Region (SEG)
ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDglgflsffsfHSAETC
Disordered region (IsUnstruct)
****KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDGLGFLSFFSF******
Disordered Region (DISOPRED)
******P**CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRI*************************H*****
Disordered Region (DISEMBL)
ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDGLGFLSFFSFHSAETC
Disordered Region (DISPRO)
*******YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV**************************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDGLGFLSFFSFHSAETC
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	86	2.2.26 [Sep-21-2011]
P0C035	310	RING-H2 finger protein AT	yes	no	0.569	0.158	0.632	2e-13
Q9XF63	324	RING-H2 finger protein AT	no	no	0.5	0.132	0.627	1e-12
Q9LUL6	204	Putative RING-H2 finger p	no	no	0.674	0.284	0.551	2e-12
Q9FL07	376	RING-H2 finger protein AT	no	no	0.5	0.114	0.604	3e-11
Q7X843	349	RING-H2 finger protein AT	no	no	0.5	0.123	0.604	4e-11
Q8L9T5	304	RING-H2 finger protein AT	no	no	0.5	0.141	0.581	7e-11
Q9LSW9	375	RING-H2 finger protein AT	no	no	0.546	0.125	0.489	8e-11
Q9SL78	390	Putative RING-H2 finger p	no	no	0.558	0.123	0.5	1e-10
Q9ZV53	423	Putative RING-H2 finger p	no	no	0.5	0.101	0.604	1e-10
Q8GW38	369	RING-H2 finger protein AT	no	no	0.5	0.116	0.581	2e-10

>sp|P0C035|ATL60_ARATH RING-H2 finger protein ATL60 OS=Arabidopsis thaliana GN=ATL60 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/49 (63%), Positives = 33/49 (67%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV 60
           C VCL  + DG K R LP C H FHV+CID WFQS STCPLCR  V  V
Sbjct: 120 CAVCLSDLVDGDKARVLPRCNHGFHVDCIDMWFQSHSTCPLCRNTVGSV 168

Arabidopsis thaliana (taxid: 3702)

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

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 27/43 (62%), Positives = 32/43 (74%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C++CL  +  G K R LP+C H FHVECID WFQS STCP+CR
Sbjct: 127 CSICLSELVKGDKARLLPKCNHSFHVECIDMWFQSHSTCPICR 169

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUL6|ATL61_ARATH Putative RING-H2 finger protein ATL61 OS=Arabidopsis thaliana GN=ATL61 PE=3 SV=1

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 38/58 (65%)

Query: 8   YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQR 65
           Y   C VCL  ++DG K R LP C H FHVECID+W QS STCP+CR  V +  +R R
Sbjct: 84  YVLECVVCLSELADGDKARVLPSCDHWFHVECIDSWLQSNSTCPICRKRVCLKQSRTR 141

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FL07|ATL46_ARATH RING-H2 finger protein ATL46 OS=Arabidopsis thaliana GN=ATL46 PE=2 SV=1

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 26/43 (60%), Positives = 28/43 (65%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C VCL   S+  K R LP C H FH+ CID W QS STCPLCR
Sbjct: 143 CAVCLCEFSEKDKLRLLPMCSHAFHLNCIDTWLQSNSTCPLCR 185

Arabidopsis thaliana (taxid: 3702)

>sp|Q7X843|ATL48_ARATH RING-H2 finger protein ATL48 OS=Arabidopsis thaliana GN=ATL48 PE=2 SV=2

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 26/43 (60%), Positives = 28/43 (65%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C VCL+  SD  K R LP C H FH+ CID W  S STCPLCR
Sbjct: 207 CAVCLNEFSDTDKLRLLPVCSHAFHLHCIDTWLLSNSTCPLCR 249

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L9T5|ATL2_ARATH RING-H2 finger protein ATL2 OS=Arabidopsis thaliana GN=ATL2 PE=2 SV=2

 Score = 65.9 bits (159), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 25/43 (58%), Positives = 29/43 (67%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C VCL    + +  R LP C+H FHV+CID WF S STCPLCR
Sbjct: 119 CAVCLSEFEESETGRVLPNCQHTFHVDCIDMWFHSHSTCPLCR 161

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSW9|ATL16_ARATH RING-H2 finger protein ATL16 OS=Arabidopsis thaliana GN=ATL16 PE=2 SV=1

 Score = 65.5 bits (158), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
           C+VCL    D +K R +P C H FH++CID W Q+ + CPLCR  V+
Sbjct: 138 CSVCLSEFQDEEKLRIIPNCSHLFHIDCIDVWLQNNANCPLCRTRVS 184

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SL78|ATL12_ARATH Putative RING-H2 finger protein ATL12 OS=Arabidopsis thaliana GN=ATL12 PE=3 SV=1

 Score = 65.5 bits (158), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 24/48 (50%), Positives = 31/48 (64%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI 59
           C+VCL    D +  R LP+C+H FH+ CID W +  +TCPLCR  V I
Sbjct: 124 CSVCLSKFEDVEILRLLPKCRHAFHIGCIDQWLEQHATCPLCRNRVNI 171

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZV53|ATL49_ARATH Putative RING-H2 finger protein ATL49 OS=Arabidopsis thaliana GN=ATL49 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 26/43 (60%), Positives = 27/43 (62%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C VCL       K R LP+C H FHVECID W  S STCPLCR
Sbjct: 126 CPVCLCEFETEDKLRLLPKCSHAFHVECIDTWLLSHSTCPLCR 168

May be involved in female gametophyte development.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GW38|ATL47_ARATH RING-H2 finger protein ATL47 OS=Arabidopsis thaliana GN=ATL47 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 25/43 (58%), Positives = 28/43 (65%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C VCL   S+  K R LP C H FH++CID W  S STCPLCR
Sbjct: 144 CAVCLCEFSEDDKLRLLPNCSHAFHIDCIDTWLLSNSTCPLCR 186

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	86
224136534	144	predicted protein [Populus trichocarpa]	0.802	0.479	0.557	6e-14
147864033	357	hypothetical protein VITISV_018480 [Viti	0.627	0.151	0.629	5e-13
449492548	267	PREDICTED: RING-H2 finger protein ATL60-	0.697	0.224	0.55	6e-13
449448142	262	PREDICTED: RING-H2 finger protein ATL60-	0.697	0.229	0.55	8e-13
413943954	331	putative RING zinc finger domain superfa	0.546	0.141	0.617	1e-12
414875730	511	TPA: putative RING zinc finger domain su	0.534	0.090	0.630	1e-12
99866743	300	ring-H2 zinc finger protein [Zea mays]	0.627	0.18	0.574	2e-12
409108339	308	ring-H2 zinc finger protein [Coix lacrym	0.546	0.152	0.617	2e-12
338808454	326	ring-H2 zinc finger protein [Sorghum pro	0.546	0.144	0.617	2e-12
242092278	357	hypothetical protein SORBIDRAFT_10g00620	0.546	0.131	0.617	2e-12

>gi|224136534|ref|XP_002326884.1| predicted protein [Populus trichocarpa] gi|222835199|gb|EEE73634.1| predicted protein [Populus trichocarpa]

 Score = 81.6 bits (200), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 48/70 (68%), Gaps = 1/70 (1%)

Query: 11  YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQD 70
           YC VCL  + DG++ R+L +CKHCFHV CIDAWFQS STCPLCR +V +    Q +N + 
Sbjct: 70  YCVVCLHEVVDGERLRKLLKCKHCFHVACIDAWFQSHSTCPLCRNQVLLRHDHQHQNEKR 129

Query: 71  GLGFLSFFSF 80
            L F  F SF
Sbjct: 130 CL-FFHFLSF 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147864033|emb|CAN83231.1| hypothetical protein VITISV_018480 [Vitis vinifera]

 Score = 78.6 bits (192), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 42/54 (77%)

Query: 11  YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQ 64
           YC VCL    +G++ RRLP+CKHCFHV CIDAWFQ+ STCPLCR +V++   RQ
Sbjct: 62  YCVVCLCDAVEGERLRRLPDCKHCFHVGCIDAWFQAHSTCPLCRSQVSLPHRRQ 115

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449492548|ref|XP_004159030.1| PREDICTED: RING-H2 finger protein ATL60-like [Cucumis sativus]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 33/60 (55%), Positives = 40/60 (66%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDG 71
           C VCL  +S+G+K R LP C H FHV+CID WF+S STCPLCR  VAI      +N + G
Sbjct: 100 CAVCLSELSEGEKARLLPRCNHGFHVDCIDMWFKSNSTCPLCRNPVAITEPNSEQNPETG 159

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448142|ref|XP_004141825.1| PREDICTED: RING-H2 finger protein ATL60-like [Cucumis sativus]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/60 (55%), Positives = 40/60 (66%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQRRNHQDG 71
           C VCL  +S+G+K R LP C H FHV+CID WF+S STCPLCR  VAI      +N + G
Sbjct: 100 CAVCLSELSEGEKARLLPRCNHGFHVDCIDMWFKSNSTCPLCRNPVAITEPNSEQNPETG 159

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413943954|gb|AFW76603.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 33/47 (70%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
           C VCL  ++DG+K R LP+C H FHVECID WF S  TCPLCR  V 
Sbjct: 133 CAVCLSEVADGEKVRTLPKCGHAFHVECIDMWFHSHDTCPLCRAPVG 179

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414875730|tpg|DAA52861.1| TPA: putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
           C VCL  ++DG+K R LP C H FHV+CIDAW +SR+TCP+CR EV
Sbjct: 143 CAVCLSELADGEKVRALPGCSHVFHVDCIDAWLRSRTTCPVCRAEV 188

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|99866743|gb|ABF67955.1| ring-H2 zinc finger protein [Zea mays]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 31/54 (57%), Positives = 35/54 (64%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQR 65
           C VCL  + DG+K R LP+C H FHVECID WF S  TCPLCR  V  + A  R
Sbjct: 99  CAVCLSEVGDGEKVRTLPKCSHGFHVECIDMWFHSHDTCPLCRAPVGDLDALPR 152

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|409108339|gb|AFV13468.1| ring-H2 zinc finger protein [Coix lacryma-jobi]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 33/47 (70%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
           C VCL  ++DG+K R LP+C H FHVECID WF S  TCPLCR  V 
Sbjct: 102 CAVCLSEVADGEKVRTLPKCGHGFHVECIDMWFHSHDTCPLCRAPVG 148

Source: Coix lacryma-jobi

Species: Coix lacryma-jobi

Genus: Coix

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|338808454|gb|AEJ07954.1| ring-H2 zinc finger protein [Sorghum propinquum]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 33/47 (70%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
           C VCL  ++DG+K R LP+C H FHVECID WF S  TCPLCR  V 
Sbjct: 107 CAVCLSEVADGEKVRTLPKCGHGFHVECIDMWFHSHDTCPLCRAPVG 153

Source: Sorghum propinquum

Species: Sorghum propinquum

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242092278|ref|XP_002436629.1| hypothetical protein SORBIDRAFT_10g006200 [Sorghum bicolor] gi|241914852|gb|EER87996.1| hypothetical protein SORBIDRAFT_10g006200 [Sorghum bicolor]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 29/47 (61%), Positives = 33/47 (70%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
           C VCL  ++DG+K R LP+C H FHVECID WF S  TCPLCR  V 
Sbjct: 140 CAVCLSEVADGEKVRTLPKCGHGFHVECIDMWFHSHDTCPLCRAPVG 186

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	86
TAIR|locus:4010713708	145	AT2G44578 "AT2G44578" [Arabido	0.546	0.324	0.574	5.4e-15
TAIR|locus:4515102991	145	AT2G44581 "AT2G44581" [Arabido	0.546	0.324	0.553	1.1e-14
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.674	0.284	0.551	2.3e-14
UNIPROTKB|Q7XLY8	383	LOC_Os04g50100 "E3 ubiquitin-p	0.569	0.127	0.530	3.1e-13
TAIR|locus:2197026	310	AT1G53820 [Arabidopsis thalian	0.569	0.158	0.632	3.5e-13
TAIR|locus:2074678	158	AT3G11110 [Arabidopsis thalian	0.558	0.303	0.458	5.6e-13
TAIR|locus:2193992	324	ATL3 [Arabidopsis thaliana (ta	0.5	0.132	0.627	1.5e-12
TAIR|locus:1009023242	139	AT3G60966 "AT3G60966" [Arabido	0.546	0.338	0.510	2.4e-12
TAIR|locus:2062008	227	AT2G47560 [Arabidopsis thalian	0.534	0.202	0.586	3.9e-12
TAIR|locus:2207066	413	AT1G72220 [Arabidopsis thalian	0.569	0.118	0.448	4.4e-12

TAIR|locus:4010713708 AT2G44578 "AT2G44578" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 27/47 (57%), Positives = 36/47 (76%)

Query:    11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
             YCT+CL+  ++G+K RR+  C HCFHV+CID W   +STCPLCR E+
Sbjct:    69 YCTICLEDAAEGEKMRRITACSHCFHVDCIDPWLMKKSTCPLCRAEI 115

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:4515102991 AT2G44581 "AT2G44581" [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 26/47 (55%), Positives = 36/47 (76%)

Query:    11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
             YCT+CL+  ++G+K RR+  C HCFHV+CID W + +S CPLCR E+
Sbjct:    69 YCTICLENATEGEKMRRIAACSHCFHVDCIDPWLEKKSMCPLCRAEI 115

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 32/58 (55%), Positives = 38/58 (65%)

Query:     8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVIARQR 65
             Y   C VCL  ++DG K R LP C H FHVECID+W QS STCP+CR  V +  +R R
Sbjct:    84 YVLECVVCLSELADGDKARVLPSCDHWFHVECIDSWLQSNSTCPICRKRVCLKQSRTR 141

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

UNIPROTKB|Q7XLY8 LOC_Os04g50100 "E3 ubiquitin-protein ligase Os04g0590900" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 166 (63.5 bits), Expect = 3.1e-13, Sum P(2) = 3.1e-13
 Identities = 26/49 (53%), Positives = 31/49 (63%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV 60
             C+VCL   SDG+  R LP C H FH +CID W +S S CPLCR  +  V
Sbjct:   157 CSVCLGEFSDGESLRLLPRCSHAFHQQCIDTWLKSHSNCPLCRANITFV 205

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2197026 AT1G53820 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 3.5e-13, P = 3.5e-13
 Identities = 31/49 (63%), Positives = 33/49 (67%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV 60
             C VCL  + DG K R LP C H FHV+CID WFQS STCPLCR  V  V
Sbjct:   120 CAVCLSDLVDGDKARVLPRCNHGFHVDCIDMWFQSHSTCPLCRNTVGSV 168

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2074678 AT3G11110 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI 59
             C +CL G  +G+K + LP C HC+H EC+D W ++ S+CPLCR+ + +
Sbjct:   107 CCICLGGFEEGEKMKVLPPCSHCYHCECVDRWLKTESSCPLCRVSIRV 154

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2193992 ATL3 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 27/43 (62%), Positives = 32/43 (74%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
             C++CL  +  G K R LP+C H FHVECID WFQS STCP+CR
Sbjct:   127 CSICLSELVKGDKARLLPKCNHSFHVECIDMWFQSHSTCPICR 169

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:1009023242 AT3G60966 "AT3G60966" [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 24/47 (51%), Positives = 31/47 (65%)

Query:    11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
             +C VCL    +G+K RRL  C+HCFH +CID W    S CPLCR ++
Sbjct:    61 FCAVCLQEAEEGEKMRRLTICRHCFHADCIDTWLSEMSKCPLCRAQI 107

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2062008 AT2G47560 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 27/46 (58%), Positives = 33/46 (71%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
             C+VCL    +  + R LP+C H FHV+CID WF+SRSTCPLCR  V
Sbjct:   108 CSVCLSEFEEEDEGRLLPKCGHSFHVDCIDTWFRSRSTCPLCRAPV 153

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2207066 AT1G72220 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.4e-12, Sum P(2) = 4.4e-12
 Identities = 22/49 (44%), Positives = 31/49 (63%)

Query:    12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV 60
             C VCL+   + +  R LP+C H FH+ CID W  S + CPLCR  +A++
Sbjct:   177 CPVCLNEFEEDESLRLLPKCNHAFHISCIDTWLSSHTNCPLCRAGIAMI 225

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

---

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: grail3.0040011901 hypothetical protein (145 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	86
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-09
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	1e-09
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-09
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	4e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	5e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	9e-06
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	0.001
PHA02926	242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.001

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

 Score = 48.9 bits (117), Expect = 1e-09
 Identities = 22/43 (51%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
          C +CLD    G++   LP C H FH EC+D W +S +TCPLCR
Sbjct: 3  CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 5/54 (9%)

Query: 12   CTVC---LDGISDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVAIV 60
            C +C   LD +      +R   CK+ FH  C+  WF S  RS CPLCR E+  V
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITFV 1525

Length = 1525

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

 Score = 51.9 bits (124), Expect = 2e-09
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 10  CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEV 57
             C +C+       + R LP C H FHV C+D W     + CP+CR  +
Sbjct: 324 VECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 50.5 bits (121), Expect = 4e-09
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 12  CTVCLDGISD----GQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI 61
           C +C++ + D       F  L  C H F +ECID W + ++TCP+CR     VI
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVI 230

Length = 238

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

 Score = 50.7 bits (121), Expect = 5e-09
 Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 11/58 (18%)

Query: 11  YCTVCLDGI--SDGQ--------KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
            CT+C+D +   D +          +RLP C H  H+ C+  W + + TCP+CR  V 
Sbjct: 289 TCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI 345

Length = 491

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

 Score = 39.3 bits (92), Expect = 9e-06
 Identities = 15/27 (55%), Positives = 19/27 (70%)

Query: 28 LPECKHCFHVECIDAWFQSRSTCPLCR 54
            EC H FH+ CI  W ++R+TCPLCR
Sbjct: 47 WGECGHAFHLHCISRWLKTRNTCPLCR 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 = 38.2 bits (89), Expect = 2e-05
 Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEV 57
          C +CL+     ++   L  C H F   CID W +S   TCPLCR  +
Sbjct: 2  CPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

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 = 34.4 bits (79), Expect = 0.001
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 31 CKHCFHVECIDAWFQSRSTCPLCR 54
          C H FH  CI  W  ++  CPL R
Sbjct: 54 CNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)

Query: 10  CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR------STCPLCR 54
           CY  V    + + + F  L  C H F + CI+ W ++R        CP+CR
Sbjct: 176 CYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICR 226

Length = 242

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	86
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.73
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.65
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.57
PHA02929	238	N1R/p28-like protein; Provisional	99.56
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.51
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.43
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.39
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.38
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.36
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.35
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.33
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.32
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.3
PHA02926	242	zinc finger-like protein; Provisional	99.27
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.26
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.22
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.19
PF14634	44	zf-RING_5: zinc-RING finger domain	99.19
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.19
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.14
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.08
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.06
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.95
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.89
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.88
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.86
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.85
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.82
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.8
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.76
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.76
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.74
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.71
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.68
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.67
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.59
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.58
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.56
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.47
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.45
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.41
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.33
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.29
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.21
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.14
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.13
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.11
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.1
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.09
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.06
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.99
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.98
KOG2660	331	consensus Locus-specific chromosome binding protei	97.73
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
COG5152	259	Uncharacterized conserved protein, contains RING a	97.58
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.51
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.48
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.44
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.39
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.39
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.21
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.19
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.08
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.08
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.07
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.05
PHA02862	156	5L protein; Provisional	97.02
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.02
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	97.02
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.89
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.89
PHA03096	284	p28-like protein; Provisional	96.87
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.81
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.79
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.77
KOG3002	299	consensus Zn finger protein [General function pred	96.69
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.56
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.56
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	96.51
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.47
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.4
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.3
PF04641	260	Rtf2: Rtf2 RING-finger	96.28
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.15
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.08
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.99
KOG4739	233	consensus Uncharacterized protein involved in syna	95.92
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.9
KOG1940	276	consensus Zn-finger protein [General function pred	95.9
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.76
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.75
KOG1001	674	consensus Helicase-like transcription factor HLTF/	95.39
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	95.33
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.07
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.04
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.91
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.66
KOG3899	381	consensus Uncharacterized conserved protein [Funct	94.45
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.45
KOG4367	699	consensus Predicted Zn-finger protein [Function un	94.29
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.92
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	93.74
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.31
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	93.11
KOG3053	293	consensus Uncharacterized conserved protein [Funct	92.62
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	91.74
KOG0825	1134	consensus PHD Zn-finger protein [General function	91.67
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.4
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.2
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	90.64
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	90.46
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	89.64
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	89.13
PF10497	105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	88.68
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	88.64
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	87.62
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	87.31
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	86.97
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	86.93
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.88
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	86.82
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	86.55
KOG0269	839	consensus WD40 repeat-containing protein [Function	86.16
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	85.69
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	84.85
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	84.42
PLN02189	1040	cellulose synthase	83.98
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	82.99
PLN02436	1094	cellulose synthase A	82.99
KOG1829	580	consensus Uncharacterized conserved protein, conta	82.64
smart00064	68	FYVE Protein present in Fab1, YOTB, Vac1, and EEA1	82.29
PLN02400	1085	cellulose synthase	80.73
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	80.49

>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=99.73  E-value=1.5e-18  Score=87.35  Aligned_cols=43  Identities=44%  Similarity=1.239  Sum_probs=39.7

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR   54 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr   54 (86)
                      +|+||++.|..++.+..++ |||.||.+||.+|++++.+||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            6999999998888888998 999999999999999999999997

...

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

Probab=99.65  E-value=1.1e-16  Score=109.76  Aligned_cols=53  Identities=38%  Similarity=0.970  Sum_probs=47.4

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC-Cccccccccchhhhh
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEVAIVIAR   63 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~~~~   63 (86)
                      ..|+||+|+|..++.+++|| |+|.||..||++||.+.+ .||+|+..+......
T Consensus       230 ~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~  283 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGS  283 (348)
T ss_pred             ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCCCC
Confidence            49999999999999999999 999999999999999875 499999987665433

>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=99.57  E-value=2.7e-15  Score=82.95  Aligned_cols=45  Identities=38%  Similarity=0.943  Sum_probs=35.4

Q ss_pred             ccccccccccccCC----------CceeEcCCCCCcchHHhHHHHHhcCCCccccc
Q 036506            9 YCYCTVCLDGISDG----------QKFRRLPECKHCFHVECIDAWFQSRSTCPLCR   54 (86)
Q Consensus         9 ~~~C~ICl~~~~~~----------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr   54 (86)
                      +..|+||++.|.++          -.+...+ |||.||..||.+||+.+.+||+||
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            44599999999432          2344455 999999999999999999999997

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 ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.56  E-value=3.3e-15  Score=98.41  Aligned_cols=54  Identities=33%  Similarity=0.846  Sum_probs=43.8

Q ss_pred             CCCcccccccccccccCCC----ceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQ----KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~----~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      +...+.+|+||++.+..+.    .+.+++.|+|.||..||.+|++++.+||+||..+.
T Consensus       170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            3456789999999976543    12345459999999999999999999999999875

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

Probab=99.51  E-value=7.3e-15  Score=98.92  Aligned_cols=56  Identities=32%  Similarity=0.883  Sum_probs=49.2

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      +..+..+.+|+|||+.|...+.++++| |.|.||..|+++|+.. +..||+||.++++
T Consensus       317 ~~ea~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         317 AVEADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             HHhcCCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            344567799999999999889999999 9999999999999994 7789999998864

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.43  E-value=1.3e-13  Score=88.06  Aligned_cols=56  Identities=29%  Similarity=0.619  Sum_probs=44.7

Q ss_pred             CCCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----------------CCCccccccccchhh
Q 036506            2 TAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----------------RSTCPLCRIEVAIVI   61 (86)
Q Consensus         2 t~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----------------~~~CP~Cr~~~~~~~   61 (86)
                      |..+..++.+|+||++.+.++   ++++ |||.||..||..|+..                ...||+||..+....
T Consensus        11 ~~~~~~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         11 TLVDSGGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             eeccCCCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            344567889999999998876   4555 9999999999999852                247999999886543

>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=99.39  E-value=2.4e-13  Score=69.94  Aligned_cols=47  Identities=30%  Similarity=0.772  Sum_probs=38.8

Q ss_pred             cccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ++..|.||++...+   +..+| |||. ||..|+.+|+++...||+||+++.
T Consensus         1 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    1 EDEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             -HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             CcCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            46789999998654   36777 9999 999999999999999999999874

...

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

Probab=99.38  E-value=3.7e-13  Score=75.86  Aligned_cols=53  Identities=25%  Similarity=0.593  Sum_probs=40.4

Q ss_pred             CCcccccccccccccCC--------C-ceeEcCCCCCcchHHhHHHHHhc---CCCccccccccc
Q 036506            6 CPYYCYCTVCLDGISDG--------Q-KFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEVA   58 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~--------~-~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~   58 (86)
                      .+.+..|+||+..|...        + ...+...|+|.||..||.+|+++   +..||+||+.+.
T Consensus        18 ~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   18 VANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             cCCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            35688999999988621        1 11234469999999999999985   468999999874

>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=99.36  E-value=4.7e-13  Score=65.60  Aligned_cols=39  Identities=38%  Similarity=1.069  Sum_probs=32.0

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C   53 (86)
                      |+||++.+.++  ++.++ |||.||..|+.+|++.+..||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDP--VVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSE--EEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCc--CEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            89999998763  34555 99999999999999998899987

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

Probab=99.35  E-value=6.2e-13  Score=66.28  Aligned_cols=38  Identities=37%  Similarity=0.974  Sum_probs=29.3

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~C   53 (86)
                      |+||++.|.++   +.++ |||.|+..||.+|++..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999988   5676 99999999999999863    369987

>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=99.33  E-value=1.6e-12  Score=64.28  Aligned_cols=44  Identities=43%  Similarity=1.114  Sum_probs=35.8

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCcccccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEV   57 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~   57 (86)
                      +|+||++.+..  .+...+ |||.||..|+..|+++ +..||+||..+
T Consensus         1 ~C~iC~~~~~~--~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE--PVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC--ceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            58999999843  334444 9999999999999997 77899998753

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

Probab=99.32  E-value=1.4e-12  Score=90.08  Aligned_cols=51  Identities=35%  Similarity=0.913  Sum_probs=43.0

Q ss_pred             Cccccccccccc-ccCC---------CceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDG-ISDG---------QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~-~~~~---------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ..+..|.||+++ |..+         +..+.+| |||.+|.+|+..|++++.+||+||.++.
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            567899999999 4443         1236888 9999999999999999999999999843

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

Probab=99.30  E-value=1.8e-12  Score=86.74  Aligned_cols=50  Identities=32%  Similarity=0.747  Sum_probs=43.5

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      +....|.|||+..+++   ..+| |||+||..||..|...+..||+||..+.+.
T Consensus       237 ~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  237 EATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            4458899999998887   4666 999999999999999999999999987653

>PHA02926 zinc finger-like protein; Provisional

Probab=99.27  E-value=2e-12  Score=84.09  Aligned_cols=54  Identities=28%  Similarity=0.787  Sum_probs=41.0

Q ss_pred             CCCcccccccccccccCC-----CceeEcCCCCCcchHHhHHHHHhcC------CCccccccccc
Q 036506            5 KCPYYCYCTVCLDGISDG-----QKFRRLPECKHCFHVECIDAWFQSR------STCPLCRIEVA   58 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~-----~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~Cr~~~~   58 (86)
                      +.+.+.+|+|||+.+-.+     ....+++.|+|.||..||..|.+.+      ++||+||..+.
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            346689999999986321     1223566699999999999999752      46999999765

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

Probab=99.26  E-value=2.6e-12  Score=83.73  Aligned_cols=51  Identities=33%  Similarity=0.739  Sum_probs=41.2

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---CCCccccccccchhh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEVAIVI   61 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~~   61 (86)
                      ....+|.|||+.-+++   ++. .|||.||..||-+||..   ++.||+|+..+....
T Consensus        45 ~~~FdCNICLd~akdP---VvT-lCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDP---VVT-LCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CCceeeeeeccccCCC---EEe-ecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            4567999999997766   333 39999999999999985   456999999876554

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

Probab=99.22  E-value=6.7e-12  Score=79.06  Aligned_cols=51  Identities=27%  Similarity=0.666  Sum_probs=42.1

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      +-..|||||+.+.....  +..+|||+||..||...++....||+|+..+..+
T Consensus       130 ~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            34789999999876432  3345999999999999999999999999877654

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

Probab=99.19  E-value=7.7e-12  Score=90.59  Aligned_cols=53  Identities=36%  Similarity=0.893  Sum_probs=45.0

Q ss_pred             CcccccccccccccCCCc--eeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQK--FRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~--~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ..+..|+||++.+..+..  ...++ |+|+||..|+..|+++.++||+||..+...
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            458899999999987543  46887 999999999999999999999999954433

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.19  E-value=2.2e-11  Score=61.11  Aligned_cols=44  Identities=27%  Similarity=0.743  Sum_probs=36.1

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRI   55 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~   55 (86)
                      .|+||++.+.......+++ |||.||..|+.++......||+||+
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            4899999995444556665 9999999999998866778999984

>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=99.19  E-value=1.5e-11  Score=60.55  Aligned_cols=39  Identities=38%  Similarity=1.105  Sum_probs=32.7

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHh--cCCCcccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ--SRSTCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~C   53 (86)
                      |+||++.+..+.  ..++ |||.||..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999988662  3565 999999999999999  45679987

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 ....

>smart00504 Ubox Modified RING finger domain

Probab=99.14  E-value=6.3e-11  Score=63.12  Aligned_cols=46  Identities=22%  Similarity=0.461  Sum_probs=40.5

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..|+||++.+.++   ++++ |||.|++.||.+|++.+..||+|+..+..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            5799999999987   4566 99999999999999998899999987743

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

>smart00184 RING Ring finger

Probab=99.08  E-value=1.4e-10  Score=55.39  Aligned_cols=38  Identities=42%  Similarity=1.168  Sum_probs=31.1

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHh-cCCCcccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~C   53 (86)
                      |+||++....   ...++ |+|.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~~~~---~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD---PVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC---cEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998443   35666 999999999999998 56679987

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)

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.06  E-value=1.2e-10  Score=81.64  Aligned_cols=52  Identities=27%  Similarity=0.494  Sum_probs=44.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      +.......|+||++.|..+   ++++ |||.||..||..|+.....||+||..+..
T Consensus        21 ~~Le~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        21 YPLDTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            3456788999999999877   3555 99999999999999988899999998754

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

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

Probab=98.95  E-value=7e-10  Score=61.64  Aligned_cols=34  Identities=32%  Similarity=0.783  Sum_probs=29.5

Q ss_pred             EcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506           27 RLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus        27 ~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      .-..|.|.||..||.+||..+..||++|+.+...
T Consensus        50 ~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          50 VWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             EEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            3345999999999999999999999999987643

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

Probab=98.89  E-value=8.2e-10  Score=78.74  Aligned_cols=47  Identities=28%  Similarity=0.687  Sum_probs=39.2

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-----CCccccccccch
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-----STCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~   59 (86)
                      +..|||||+....+    ..+.|||+||..||.++|...     ..||+||..+..
T Consensus       186 ~~~CPICL~~~~~p----~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP----VRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCcc----cccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            78999999997766    333499999999999988753     479999998776

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

Probab=98.88  E-value=8.1e-10  Score=75.87  Aligned_cols=51  Identities=24%  Similarity=0.556  Sum_probs=44.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchhh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   61 (86)
                      ..-+.|.||.++|..+   .+.| |+|.||..||..+|..+..||.|+..+....
T Consensus        21 D~lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   21 DDLLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchhh
Confidence            3457899999999998   5666 9999999999999999999999999887654

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

Probab=98.86  E-value=2.6e-10  Score=62.85  Aligned_cols=50  Identities=28%  Similarity=0.653  Sum_probs=37.2

Q ss_pred             ccccccccccccC--------CC-ceeEcCCCCCcchHHhHHHHHhc---CCCccccccccc
Q 036506            9 YCYCTVCLDGISD--------GQ-KFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEVA   58 (86)
Q Consensus         9 ~~~C~ICl~~~~~--------~~-~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~   58 (86)
                      +..|.||...|..        ++ ...++..|.|.||..||.+|+..   ...||+||+.+.
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3489999888852        11 12233369999999999999985   457999999875

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

Probab=98.85  E-value=1.5e-09  Score=62.99  Aligned_cols=49  Identities=31%  Similarity=0.731  Sum_probs=37.3

Q ss_pred             cccccccccc-------------cCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506           10 CYCTVCLDGI-------------SDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus        10 ~~C~ICl~~~-------------~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ..|+||...+             ...+..+.-..|.|.||..||.+||+++..||++.+.+.
T Consensus        47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            4688887654             122333444469999999999999999999999988764

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

Probab=98.82  E-value=2.2e-09  Score=71.32  Aligned_cols=50  Identities=30%  Similarity=0.658  Sum_probs=40.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH-HHhcCCC-ccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA-WFQSRST-CPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~-wl~~~~~-CP~Cr~~~~~~   60 (86)
                      ..+..|+||++....+   ..++ |||+||..||.. |-.++.. ||+||+...+.
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            3577899999998877   4565 999999999999 7666554 99999987654

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

Probab=98.80  E-value=6.2e-09  Score=57.37  Aligned_cols=51  Identities=22%  Similarity=0.414  Sum_probs=40.5

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      .|+...|+|+.+.+.++   ++++ +||.|.+.+|.+|+++ +..||+++..+...
T Consensus         1 iP~~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    1 IPDEFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             SSGGGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             CCcccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            47889999999999988   5677 9999999999999998 88999999887653

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

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

Probab=98.76  E-value=1.1e-09  Score=60.04  Aligned_cols=51  Identities=27%  Similarity=0.656  Sum_probs=24.6

Q ss_pred             ccccccccccccCCCc--eeEcC--CCCCcchHHhHHHHHhc---C--------CCccccccccch
Q 036506            9 YCYCTVCLDGISDGQK--FRRLP--ECKHCFHVECIDAWFQS---R--------STCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~--~~~~~--~C~H~fh~~Ci~~wl~~---~--------~~CP~Cr~~~~~   59 (86)
                      +.+|+||++.+...+.  ..+.+  .|+..||..||.+||..   .        ..||.|+.++..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            5789999998663222  23332  69999999999999973   1        159999998754

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

Probab=98.76  E-value=6e-09  Score=52.04  Aligned_cols=34  Identities=26%  Similarity=0.702  Sum_probs=21.4

Q ss_pred             cccccccccCCCc-eeEcCCCCCcchHHhHHHHHhcC
Q 036506           12 CTVCLDGISDGQK-FRRLPECKHCFHVECIDAWFQSR   47 (86)
Q Consensus        12 C~ICl~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~   47 (86)
                      |+||++ |..++. .++|+ |||.|+.+||.+++.++
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcC
Confidence            899999 766443 36677 99999999999999853

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

Probab=98.74  E-value=3.6e-09  Score=70.74  Aligned_cols=56  Identities=32%  Similarity=0.670  Sum_probs=44.1

Q ss_pred             CCCcccccccccccccCCC-------ceeEcCCCCCcchHHhHHHHHh--cCCCccccccccchhh
Q 036506            5 KCPYYCYCTVCLDGISDGQ-------KFRRLPECKHCFHVECIDAWFQ--SRSTCPLCRIEVAIVI   61 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~-------~~~~~~~C~H~fh~~Ci~~wl~--~~~~CP~Cr~~~~~~~   61 (86)
                      ++-++..|+||-..+....       ++-.+. |+|+||..||..|-.  ++++||+|+..+....
T Consensus       220 khl~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            4467889999999876543       445675 999999999999954  5779999998876543

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

Probab=98.71  E-value=1.6e-08  Score=51.86  Aligned_cols=42  Identities=31%  Similarity=0.907  Sum_probs=31.6

Q ss_pred             ccccccccccCCCceeEcCCCC-----CcchHHhHHHHHhc--CCCccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECK-----HCFHVECIDAWFQS--RSTCPLCR   54 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~--~~~CP~Cr   54 (86)
                      .|-||++. ..++...+.| |.     |.+|..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            38899983 3334445677 74     89999999999975  44899985

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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.68  E-value=1.8e-08  Score=68.70  Aligned_cols=52  Identities=21%  Similarity=0.418  Sum_probs=38.0

Q ss_pred             ccccccccccc-ccCCC-ceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            8 YYCYCTVCLDG-ISDGQ-KFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~-~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      ++..||||... +.+++ ...+. .|||.||.+|+...+.. ...||.|+..+...
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~   56 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFVRGSGSCPECDTPLRKN   56 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence            35689999994 33443 33333 49999999999996654 56899999877654

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

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

Probab=98.67  E-value=9e-09  Score=67.47  Aligned_cols=46  Identities=28%  Similarity=0.696  Sum_probs=40.4

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR   54 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr   54 (86)
                      ...+...|+||++.|..+   .+++ |+|.||..|+..++.....||.||
T Consensus         9 ~~~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             hccccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            346789999999999988   5777 999999999999888556799999

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

Probab=98.59  E-value=2.5e-08  Score=67.52  Aligned_cols=49  Identities=27%  Similarity=0.518  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..-+.|-||-+.|..+   ... .|||.||..||...|..+..||+||.....
T Consensus        23 Ds~lrC~IC~~~i~ip---~~T-tCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          23 DSMLRCRICDCRISIP---CET-TCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             hhHHHhhhhhheeecc---eec-ccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            3456899999999988   344 499999999999999999999999987544

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

Probab=98.58  E-value=2.1e-08  Score=71.78  Aligned_cols=51  Identities=27%  Similarity=0.793  Sum_probs=38.8

Q ss_pred             CcccccccccccccCCC---c-----------eeEcCCCCCcchHHhHHHHHhc-CCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQ---K-----------FRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~---~-----------~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~   58 (86)
                      ..-.+|+|||.++.-..   .           -...| |.|+||..|+.+|+.. +-.||+||.+++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            34568999999864211   0           12446 9999999999999995 558999999875

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

Probab=98.56  E-value=1.5e-08  Score=76.98  Aligned_cols=53  Identities=36%  Similarity=0.787  Sum_probs=40.6

Q ss_pred             CCcccccccccccccCCC---ceeEcCCCCCcchHHhHHHHHhc--CCCccccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQ---KFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~---~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      -+.-.+|+||+..+..-+   +-...+.|.|.||..|+-+|++.  ++.||+||..++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            356689999999876211   11355579999999999999996  457999998764

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

Probab=98.47  E-value=8.5e-08  Score=66.93  Aligned_cols=51  Identities=31%  Similarity=1.011  Sum_probs=37.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---CCCcccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEV   57 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~   57 (86)
                      +....|.||.+-+-....+.....|||+||..|+.+|+..   ++.||+|+-.+
T Consensus         2 pi~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    2 PIMAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             CccceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            4567899995554444444444459999999999999985   35899999443

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

Probab=98.45  E-value=2.4e-08  Score=53.53  Aligned_cols=47  Identities=30%  Similarity=0.682  Sum_probs=24.0

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      +-..|++|.+.++.+   +.+..|.|+||..||..-+.  ..||+|+.+...
T Consensus         6 ~lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~   52 (65)
T PF14835_consen    6 ELLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWI   52 (65)
T ss_dssp             HTTS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-
T ss_pred             HhcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChHHH
Confidence            456899999999887   34456999999999977444  459999987543

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

Probab=98.41  E-value=2.7e-08  Score=68.55  Aligned_cols=51  Identities=27%  Similarity=0.599  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      ..+..|+|||+.++...   ..+.|.|.||.+||..-++. ++.||.||+.+...
T Consensus        41 ~~~v~c~icl~llk~tm---ttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKTM---TTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhhccHHHHHHHHhhc---ccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            46789999999998763   44469999999999998875 77899999987654

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

Probab=98.33  E-value=2.5e-07  Score=65.53  Aligned_cols=49  Identities=31%  Similarity=0.846  Sum_probs=38.7

Q ss_pred             CcccccccccccccCCC-ceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQ-KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .+--+|||||+.+.... .+.... |.|.||-.|+..|..  .+||+||....
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhccc--CcChhhhhhcC
Confidence            45678999999987654 344555 999999999999964  57999997654

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

Probab=98.29  E-value=2.1e-07  Score=48.36  Aligned_cols=47  Identities=28%  Similarity=0.593  Sum_probs=36.4

Q ss_pred             ccccccccccccCCCceeEcCCCCC-cchHHhHHHHHh-cCCCccccccccch
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKH-CFHVECIDAWFQ-SRSTCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~-~~~~CP~Cr~~~~~   59 (86)
                      +.+|.||++...+.    ++..||| -.|..|-.+.++ .+..||+||+++..
T Consensus         7 ~dECTICye~pvds----VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDS----VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchH----HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            47999999985554    3334999 578889888766 58899999997753

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

Probab=98.27  E-value=7.2e-07  Score=61.59  Aligned_cols=50  Identities=28%  Similarity=0.691  Sum_probs=41.9

Q ss_pred             CcccccccccccccCCCceeEcCCCCC-cchHHhHHHHHhcCCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKH-CFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ....+|.|||.+.++-   .++| |.| -.|.+|.+...-+++.||+||+++...
T Consensus       288 ~~gkeCVIClse~rdt---~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l  338 (349)
T KOG4265|consen  288 ESGKECVICLSESRDT---VVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEEL  338 (349)
T ss_pred             cCCCeeEEEecCCcce---EEec-chhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence            5578999999996654   6888 999 689999999877899999999987643

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

Probab=98.21  E-value=7.4e-07  Score=61.77  Aligned_cols=52  Identities=31%  Similarity=0.890  Sum_probs=40.2

Q ss_pred             CcccccccccccccCCC----ceeEcCCCCCcchHHhHHHHH--hc-----CCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQ----KFRRLPECKHCFHVECIDAWF--QS-----RSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~----~~~~~~~C~H~fh~~Ci~~wl--~~-----~~~CP~Cr~~~~   58 (86)
                      ..+..|.||++.+....    ...++|.|.|.||..||..|-  .+     .+.||.||....
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            45789999999875532    123556799999999999998  44     578999998643

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

Probab=98.14  E-value=6.5e-07  Score=66.50  Aligned_cols=48  Identities=25%  Similarity=0.688  Sum_probs=39.0

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      +-+.|++|-..+.+.    +++.|+|.||..|+.+.+.. .+.||.|...|..
T Consensus       642 ~~LkCs~Cn~R~Kd~----vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga  690 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDA----VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA  690 (698)
T ss_pred             hceeCCCccCchhhH----HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence            446899999776654    44459999999999998874 7789999998864

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

Probab=98.13  E-value=1.1e-06  Score=59.72  Aligned_cols=50  Identities=26%  Similarity=0.545  Sum_probs=40.6

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchhh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIVI   61 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~   61 (86)
                      -..+|+||+....-+   +.++ |+|.||.-||..-... ...|++||.++....
T Consensus         6 ~~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             cCCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            456899999987766   4565 9999999999887665 567999999987654

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

Probab=98.11  E-value=1.7e-06  Score=60.91  Aligned_cols=53  Identities=23%  Similarity=0.563  Sum_probs=44.2

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchhh
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   61 (86)
                      -++++.|+||...+.++..  .. .|||.||..|+..|+..+..||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl~~p~~--~~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQ--TT-TCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccCCCC--CC-CCCCcccccccchhhccCcCCcccccccchhh
Confidence            4678999999999988722  12 49999999999999999999999988766543

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

Probab=98.10  E-value=2.1e-06  Score=60.53  Aligned_cols=51  Identities=31%  Similarity=0.666  Sum_probs=44.5

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ....+.+|.||+..+..+   ++++ |||.||..||.+-+.+...||.||..+..
T Consensus        80 ~~~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   80 EIRSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cccchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            347889999999998877   4666 99999999999988888899999998874

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

Probab=98.09  E-value=7e-07  Score=67.06  Aligned_cols=52  Identities=29%  Similarity=0.516  Sum_probs=41.2

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ....|++|+..+.+.......+ |+|.||..||..|-+...+||+||..|...
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            3456788887776654444554 999999999999999999999999987643

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

Probab=98.06  E-value=3.3e-06  Score=59.46  Aligned_cols=51  Identities=27%  Similarity=0.707  Sum_probs=38.1

Q ss_pred             cccccccccccccCC-CceeEcCCCCCcchHHhHHHHHhc--CCCccccccccc
Q 036506            8 YYCYCTVCLDGISDG-QKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      ....||||++.+.-+ +...+.+.|||.|..+||++||.+  ...||.|...-.
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat   56 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT   56 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence            356899999987643 333344469999999999999964  347999976543

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

Probab=97.99  E-value=3.8e-06  Score=44.27  Aligned_cols=44  Identities=25%  Similarity=0.505  Sum_probs=28.6

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--CCCccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPL   52 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~   52 (86)
                      ..-+..|||.+..|.+|   +....|||.|-+..|.+|+++  ...||+
T Consensus         8 ~~~~~~CPiT~~~~~~P---V~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    8 GTISLKCPITLQPFEDP---VKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB--SB-TTTSSB-SSE---EEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cEeccCCCCcCChhhCC---cCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            45678999999999977   333359999999999999954  446998

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

Probab=97.98  E-value=2.3e-06  Score=58.29  Aligned_cols=52  Identities=27%  Similarity=0.756  Sum_probs=42.3

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-----------------------CCCccccccccchh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-----------------------RSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----------------------~~~CP~Cr~~~~~~   60 (86)
                      ....|.|||.-|.++..+.+.+ |.|.||..|+.++|..                       ...||+||..+...
T Consensus       114 p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            4578999999999988777776 9999999999988731                       22699999987654

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

Probab=97.73  E-value=6.6e-06  Score=56.43  Aligned_cols=51  Identities=25%  Similarity=0.569  Sum_probs=42.6

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .-....|.+|-.+|.++..   ...|-|.||++||...|.....||+|...+..
T Consensus        12 ~n~~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~   62 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIHK   62 (331)
T ss_pred             cccceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceeccC
Confidence            3556789999999987743   33599999999999999999999999877654

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

Probab=97.71  E-value=3.3e-05  Score=51.00  Aligned_cols=55  Identities=25%  Similarity=0.598  Sum_probs=46.0

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--------CCCccccccccchh
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--------RSTCPLCRIEVAIV   60 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~Cr~~~~~~   60 (86)
                      .|+.++..|.+|--.+..++.++..  |-|.||..|+..|..+        .-.||.|..++...
T Consensus        45 ~DsDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   45 QDSDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             hhcCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            4778899999999999999887654  9999999999999764        23799998886644

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

Probab=97.66  E-value=6.5e-05  Score=50.67  Aligned_cols=53  Identities=25%  Similarity=0.338  Sum_probs=41.2

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~   59 (86)
                      +...++.+|++|-+....|.  ... .|+|+||.-||..-+..  ...||.|..+..+
T Consensus       234 s~~t~~~~C~~Cg~~PtiP~--~~~-~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  234 STGTSDTECPVCGEPPTIPH--VIG-KCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             ccccCCceeeccCCCCCCCe--eec-cccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            34478899999999977663  344 49999999999886653  5689999887653

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

Probab=97.58  E-value=3.2e-05  Score=50.18  Aligned_cols=44  Identities=23%  Similarity=0.532  Sum_probs=37.6

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIE   56 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~   56 (86)
                      ...|.||-.+|..+    ++..|||.||..|..+-++....|-+|...
T Consensus       196 PF~C~iCKkdy~sp----vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         196 PFLCGICKKDYESP----VVTECGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             ceeehhchhhccch----hhhhcchhHHHHHHHHHhccCCcceecchh
Confidence            34799999999988    334599999999999999989999999664

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

Probab=97.51  E-value=9.9e-05  Score=37.51  Aligned_cols=45  Identities=22%  Similarity=0.564  Sum_probs=22.9

Q ss_pred             cccccccccCCC-ceeEcCCCCCcchHHhHHHHHh-cCCCcccccccc
Q 036506           12 CTVCLDGISDGQ-KFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEV   57 (86)
Q Consensus        12 C~ICl~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~   57 (86)
                      ||+|.+++...+ .+.-. .|+..++..|...-++ ....||-||.++
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999985433 33333 4899999999998886 478999999865

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

Probab=97.48  E-value=4.4e-05  Score=53.85  Aligned_cols=48  Identities=31%  Similarity=0.850  Sum_probs=38.3

Q ss_pred             cccccccccccccC-CCceeEcCCCCCcchHHhHHHHHhcC--CCccccccc
Q 036506            8 YYCYCTVCLDGISD-GQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIE   56 (86)
Q Consensus         8 ~~~~C~ICl~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~   56 (86)
                      -++.|..|-+.+-. ++....+| |.|+||..|+...|.++  ++||-||+.
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            45779999887643 34567888 99999999999999764  589999943

>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=97.44  E-value=6.6e-05  Score=45.77  Aligned_cols=36  Identities=19%  Similarity=0.522  Sum_probs=29.7

Q ss_pred             ccccccccccccCCCceeEcCCCC------CcchHHhHHHHHh
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECK------HCFHVECIDAWFQ   45 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~------H~fh~~Ci~~wl~   45 (86)
                      ..+|.||++.+.+.+.++.++ ||      |+||.+|+.+|-+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            789999999998856666666 63      7999999999943

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.

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

Probab=97.39  E-value=8.3e-05  Score=56.46  Aligned_cols=50  Identities=28%  Similarity=0.680  Sum_probs=41.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-------CCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-------STCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-------~~CP~Cr~~   56 (86)
                      ..-.+|.||++.+.....+.....|-|+||..||..|.++.       =.||.|+..
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            45679999999998887777666799999999999998751       159999843

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

Probab=97.39  E-value=7.8e-05  Score=52.83  Aligned_cols=45  Identities=33%  Similarity=0.885  Sum_probs=35.4

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--CCCccccccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      .-|.||-+.-   +.|++-| |||..|..|+..|-..  .+.||.||..+.
T Consensus       370 eLCKICaend---KdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  370 ELCKICAEND---KDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             HHHHHhhccC---CCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            3588887752   3456777 9999999999999754  678999998764

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

Probab=97.21  E-value=0.00012  Score=49.74  Aligned_cols=46  Identities=20%  Similarity=0.422  Sum_probs=38.5

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~   57 (86)
                      -+..|-||..+|..+    +...|+|.||..|...-++....|++|....
T Consensus       240 ~Pf~c~icr~~f~~p----Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  240 LPFKCFICRKYFYRP----VVTKCGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             CCccccccccccccc----hhhcCCceeehhhhccccccCCcceeccccc
Confidence            345699999999988    3445999999999999888889999997653

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.19  E-value=0.00037  Score=46.63  Aligned_cols=54  Identities=15%  Similarity=0.207  Sum_probs=47.9

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchhh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   61 (86)
                      ....||||.+.+.+.....+|..|||+|...|++++++....||+|-.++....
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            567899999999998888888789999999999999999999999988876544

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

Probab=97.08  E-value=0.0004  Score=47.94  Aligned_cols=57  Identities=21%  Similarity=0.352  Sum_probs=44.2

Q ss_pred             CCCCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            1 ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         1 ~t~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      |+.-..+....||||+....++.   ++..-|-+||..|+..++.+++.||+=..+....
T Consensus       292 e~e~l~~~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~  348 (357)
T KOG0826|consen  292 ESELLPPDREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVD  348 (357)
T ss_pred             ccccCCCccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHhcCCCCccCCcchHH
Confidence            34455677889999999988773   3333699999999999999999999866555443

>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=97.08  E-value=0.0002  Score=41.30  Aligned_cols=33  Identities=30%  Similarity=0.701  Sum_probs=27.5

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECID   41 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~   41 (86)
                      .++..|++|-..+.. ....+.| |||.||..|+.
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            567889999999877 4566777 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 [].

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

Probab=97.07  E-value=0.00038  Score=35.14  Aligned_cols=41  Identities=29%  Similarity=0.957  Sum_probs=25.6

Q ss_pred             cccccccccCCCceeEcC-CCCC---cchHHhHHHHHhc--CCCcccc
Q 036506           12 CTVCLDGISDGQKFRRLP-ECKH---CFHVECIDAWFQS--RSTCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~-~C~H---~fh~~Ci~~wl~~--~~~CP~C   53 (86)
                      |-||++.-..... .+.| .|.-   ..|..|+.+|+..  +..|++|
T Consensus         1 CrIC~~~~~~~~~-li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEP-LISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCc-eecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            6789998665442 2344 2444   7899999999984  5578876

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.05  E-value=0.00086  Score=42.02  Aligned_cols=52  Identities=23%  Similarity=0.532  Sum_probs=37.8

Q ss_pred             CCCcccccccccccccCCCceeEcC-CCCC---cchHHhHHHHHhc--CCCccccccccchh
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLP-ECKH---CFHVECIDAWFQS--RSTCPLCRIEVAIV   60 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~-~C~H---~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~   60 (86)
                      .+..+..|-||.+.-...    ..| .|..   ..|.+|+.+|+..  ...|++|+.++...
T Consensus         4 ~s~~~~~CRIC~~~~~~~----~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          4 VSLMDKCCWICKDEYDVV----TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             cCCCCCeeEecCCCCCCc----cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            456778999999984322    234 2544   6699999999986  45799999987654

>PHA02862 5L protein; Provisional

Probab=97.02  E-value=0.00072  Score=41.79  Aligned_cols=47  Identities=23%  Similarity=0.651  Sum_probs=34.3

Q ss_pred             ccccccccccccCCCceeEcC-CC---CCcchHHhHHHHHhc--CCCccccccccch
Q 036506            9 YCYCTVCLDGISDGQKFRRLP-EC---KHCFHVECIDAWFQS--RSTCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~-~C---~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~   59 (86)
                      +..|=||++.-.+.    .-| .|   -...|..|+.+|++.  +..|++|+.++..
T Consensus         2 ~diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            35689999984432    233 13   357899999999985  4579999998754

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

Probab=97.02  E-value=0.00053  Score=55.38  Aligned_cols=54  Identities=24%  Similarity=0.616  Sum_probs=41.0

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----------CCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----------STCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----------~~CP~Cr~~~~~   59 (86)
                      +...+..|-||+-+--.......+. |+|+||..|..+-|++.          -+||+|+.++..
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            4567889999998755555556776 99999999998776641          179999987643

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=97.02  E-value=0.00092  Score=34.74  Aligned_cols=35  Identities=31%  Similarity=0.714  Sum_probs=30.7

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      ....|++|-+.|.+++.+++.+.||-.+|+.|...
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            45679999999998888899999999999999654

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

Probab=96.89  E-value=0.00071  Score=43.36  Aligned_cols=54  Identities=26%  Similarity=0.669  Sum_probs=36.0

Q ss_pred             CCCcccccccccccccCC---Cce-eEcCCCCCcchHHhHHHHHhc---C--------CCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDG---QKF-RRLPECKHCFHVECIDAWFQS---R--------STCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~---~~~-~~~~~C~H~fh~~Ci~~wl~~---~--------~~CP~Cr~~~~~   59 (86)
                      ++.+-..|.||+.+-.++   +.+ -.. .||..||.-|+..||+.   .        ..||+|..++..
T Consensus       161 kdd~~~~cgicyayqldGTipDqtCdN~-qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  161 KDDELGACGICYAYQLDGTIPDQTCDNI-QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             cchhhhcccceeeeecCCcccccccccc-ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            345556778887753332   211 122 49999999999999974   1        159999887653

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

Probab=96.89  E-value=0.0004  Score=50.91  Aligned_cols=50  Identities=32%  Similarity=0.618  Sum_probs=38.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-----CCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-----RSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~~~CP~Cr~~~~~~   60 (86)
                      .++.+|.+|-++-++.    +...|.|.||+.|+..+...     +-+||+|...+..+
T Consensus       534 k~~~~C~lc~d~aed~----i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDY----IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhhh----HhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            4678999999986655    33349999999999888763     45799998876654

>PHA03096 p28-like protein; Provisional

Probab=96.87  E-value=0.00062  Score=46.38  Aligned_cols=46  Identities=33%  Similarity=0.665  Sum_probs=32.6

Q ss_pred             cccccccccccCC----CceeEcCCCCCcchHHhHHHHHhc---CCCcccccc
Q 036506           10 CYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRI   55 (86)
Q Consensus        10 ~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~   55 (86)
                      -.|.||++.....    ..-..++.|.|.||..|+..|...   ..+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5799999976532    122466779999999999999864   334555544

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

Probab=96.81  E-value=0.00071  Score=33.57  Aligned_cols=41  Identities=32%  Similarity=0.909  Sum_probs=22.5

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC--Ccccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS--TCPLC   53 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~--~CP~C   53 (86)
                      |.+|.+.+..+...... .|+-.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            56777776665322221 3888999999999998754  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.79  E-value=0.0011  Score=46.55  Aligned_cols=49  Identities=22%  Similarity=0.481  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||+..--..   +..| |+|.-|..||.+-+-+.+.|=.|+..+..
T Consensus       420 sEd~lCpICyA~pi~A---vf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGPINA---VFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecccchh---hccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            5778999999864433   4677 99999999999999999999999987653

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

Probab=96.77  E-value=0.00091  Score=47.45  Aligned_cols=47  Identities=26%  Similarity=0.648  Sum_probs=37.0

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--------CCCcccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--------RSTCPLCRI   55 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~Cr~   55 (86)
                      ....|.||++.......+..+| |+|+||+.|+..++..        .-.||-+.-
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            3468999999976667888998 9999999999999863        225876543

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

Probab=96.69  E-value=0.001  Score=45.66  Aligned_cols=45  Identities=24%  Similarity=0.591  Sum_probs=35.1

Q ss_pred             CcccccccccccccCCCceeEcCCC--CCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPEC--KHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C--~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+=++||||.+.+..+    +.. |  ||..|..|-.   +..+.||.||.++..
T Consensus        46 ~~lleCPvC~~~l~~P----i~Q-C~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP----IFQ-CDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             hhhccCchhhccCccc----cee-cCCCcEehhhhhh---hhcccCCcccccccc
Confidence            4457999999999987    332 5  7999988865   346789999998873

>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=96.56  E-value=0.0023  Score=40.09  Aligned_cols=37  Identities=19%  Similarity=0.515  Sum_probs=23.4

Q ss_pred             cccccccccccccCCCce---------eEcCCCCC-cchHHhHHHHHh
Q 036506            8 YYCYCTVCLDGISDGQKF---------RRLPECKH-CFHVECIDAWFQ   45 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~---------~~~~~C~H-~fh~~Ci~~wl~   45 (86)
                      ++..|||||+...+...+         +-.. |+- .-|..|++++-+
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpym-c~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYM-CDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccc-cCCccchhHHHHHHHH
Confidence            478999999987654211         1111 443 357789999864

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.

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

Probab=96.56  E-value=0.0017  Score=45.26  Aligned_cols=50  Identities=28%  Similarity=0.618  Sum_probs=36.1

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ....+-...|.||++...+.   ..+| |||.-+  |..- .+...+||+||..+..
T Consensus       299 ~~~~~~p~lcVVcl~e~~~~---~fvp-cGh~cc--ct~c-s~~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  299 FRELPQPDLCVVCLDEPKSA---VFVP-CGHVCC--CTLC-SKHLPQCPVCRQRIRL  348 (355)
T ss_pred             ccccCCCCceEEecCCccce---eeec-CCcEEE--chHH-HhhCCCCchhHHHHHH
Confidence            44557788999999987663   5777 999865  5443 2335569999987754

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

Probab=96.51  E-value=0.0019  Score=39.39  Aligned_cols=53  Identities=13%  Similarity=0.412  Sum_probs=39.4

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---CCCccccccccchh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~~   60 (86)
                      .-.+|.||.+...+..-+.--..||-..|..|-...|+.   +..||+|++++-..
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            456899999986554333222269999999999887764   67899999988643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.47  E-value=0.00099  Score=46.52  Aligned_cols=54  Identities=24%  Similarity=0.454  Sum_probs=39.6

Q ss_pred             CcccccccccccccCCCc-eeEcCCCCCcchHHhHHHHHhc-CCCccccccccchhh
Q 036506            7 PYYCYCTVCLDGISDGQK-FRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIVI   61 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~   61 (86)
                      .++..||+|++++...+. ..-.+ ||-..|.-|...--+. +..||-||+.+...+
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            455569999999876554 34455 9999999997664443 678999999876544

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

Probab=96.40  E-value=0.0022  Score=43.34  Aligned_cols=47  Identities=26%  Similarity=0.637  Sum_probs=37.4

Q ss_pred             cccccccccccCCC--ce-eEcCCCCCcchHHhHHHHHhcC-CCcccccccc
Q 036506           10 CYCTVCLDGISDGQ--KF-RRLPECKHCFHVECIDAWFQSR-STCPLCRIEV   57 (86)
Q Consensus        10 ~~C~ICl~~~~~~~--~~-~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~   57 (86)
                      ..|-||-++|+..+  .+ +.+ .|||.|+..|+...+... ..||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l-~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVL-KCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCccc-ccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998763  33 444 599999999999988764 4799999984

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

Probab=96.30  E-value=0.0012  Score=41.70  Aligned_cols=30  Identities=30%  Similarity=0.733  Sum_probs=27.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHV   37 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~   37 (86)
                      ....+|.|||+++..++.|..+| |--+||+
T Consensus       175 ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  175 DDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             ccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            45679999999999999999999 9988886

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.28  E-value=0.0062  Score=40.85  Aligned_cols=54  Identities=19%  Similarity=0.330  Sum_probs=42.8

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ......|||....|......+.+-.|||+|-..+|...- ....||+|-.+|...
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEE  163 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccC
Confidence            467789999999996655555555599999999999973 356799999988743

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

Probab=96.15  E-value=0.0038  Score=43.03  Aligned_cols=43  Identities=30%  Similarity=0.617  Sum_probs=35.5

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHh-cCCCcccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRI   55 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~   55 (86)
                      +.|+.|...+.++.   ..+.|+|.||..||...|. ....||.|..
T Consensus       275 LkCplc~~Llrnp~---kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPM---KTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcc---cCccccchHHHHHHhhhhhhccccCCCccc
Confidence            78999999988773   4467999999999998665 5678999954

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.08  E-value=0.0022  Score=33.41  Aligned_cols=31  Identities=26%  Similarity=0.703  Sum_probs=24.6

Q ss_pred             eEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506           26 RRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus        26 ~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+++ |+|..+..|+..  .+-+.||.|.+++..
T Consensus        21 ~~~p-CgH~I~~~~f~~--~rYngCPfC~~~~~~   51 (55)
T PF14447_consen   21 TVLP-CGHLICDNCFPG--ERYNGCPFCGTPFEF   51 (55)
T ss_pred             cccc-ccceeeccccCh--hhccCCCCCCCcccC
Confidence            5777 999999999765  456679999887754

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

Probab=95.99  E-value=0.0014  Score=44.90  Aligned_cols=43  Identities=26%  Similarity=0.623  Sum_probs=31.3

Q ss_pred             ccccccccccccCCCceeEcCCCCC-cchHHhHHHHHhcCCCccccccccch
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKH-CFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..-|.|||+...   ..+.|+ ||| +-|..|-.+    -+.||+||+.+..
T Consensus       300 ~~LC~ICmDaP~---DCvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLE-CGHMVTCTKCGKR----MNECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCc---ceEEee-cCcEEeehhhccc----cccCchHHHHHHH
Confidence            678999999744   335777 999 557777544    3489999987643

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

Probab=95.92  E-value=0.004  Score=41.29  Aligned_cols=45  Identities=33%  Similarity=0.740  Sum_probs=30.3

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .|.-|.---. ++...++ .|+|+||..|...  .....||+|+..+..
T Consensus         5 hCn~C~~~~~-~~~f~LT-aC~HvfC~~C~k~--~~~~~C~lCkk~ir~   49 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLT-ACRHVFCEPCLKA--SSPDVCPLCKKSIRI   49 (233)
T ss_pred             EeccccccCC-CCceeee-echhhhhhhhccc--CCccccccccceeee
Confidence            4666665433 5555555 4999999999754  223389999998543

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

Probab=95.90  E-value=0.0089  Score=42.02  Aligned_cols=49  Identities=27%  Similarity=0.598  Sum_probs=38.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHH--HhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW--FQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w--l~~~~~CP~Cr~~~~~   59 (86)
                      +++..|.||-+.+.-.   .++| |+|..|..|..+.  |-..+.||+||.....
T Consensus        59 Een~~C~ICA~~~TYs---~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~  109 (493)
T COG5236          59 EENMNCQICAGSTTYS---ARYP-CGHQICHACAVRLRALYMQKGCPLCRTETEA  109 (493)
T ss_pred             cccceeEEecCCceEE---Eecc-CCchHHHHHHHHHHHHHhccCCCccccccce
Confidence            5677899998876533   5777 9999999998764  4468899999987543

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

Probab=95.90  E-value=0.0055  Score=41.62  Aligned_cols=46  Identities=24%  Similarity=0.547  Sum_probs=36.0

Q ss_pred             ccccccccccccCCCce-eEcCCCCCcchHHhHHHHHhcCCCcccccc
Q 036506            9 YCYCTVCLDGISDGQKF-RRLPECKHCFHVECIDAWFQSRSTCPLCRI   55 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~-~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~   55 (86)
                      ...||||.+.+-..... ..++ |||..|..|+......+-.||+|..
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            34499999986554433 4555 9999999999998877788999987

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

Probab=95.76  E-value=0.0054  Score=47.06  Aligned_cols=43  Identities=23%  Similarity=0.663  Sum_probs=33.7

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV   57 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~   57 (86)
                      ...|..|-..+..|..  .- .|||.||.+|+.   .....||.|+..+
T Consensus       840 ~skCs~C~~~LdlP~V--hF-~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPFV--HF-LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcccccee--ee-ecccHHHHHhhc---cCcccCCccchhh
Confidence            3679999999887742  22 499999999998   4566899998843

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

Probab=95.75  E-value=0.0065  Score=42.68  Aligned_cols=29  Identities=38%  Similarity=1.133  Sum_probs=22.8

Q ss_pred             CCCcchHHhHHHHHhc-------------CCCccccccccch
Q 036506           31 CKHCFHVECIDAWFQS-------------RSTCPLCRIEVAI   59 (86)
Q Consensus        31 C~H~fh~~Ci~~wl~~-------------~~~CP~Cr~~~~~   59 (86)
                      |..+.|.+|+.+|+..             +..||+||+.+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCi  352 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCI  352 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCccccee
Confidence            5677899999999853             2269999998753

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

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

Probab=95.39  E-value=0.011  Score=44.70  Aligned_cols=47  Identities=34%  Similarity=0.757  Sum_probs=36.3

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--CCCccccccccchhh
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIEVAIVI   61 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~   61 (86)
                      ..|.||++ .   +.....+ |+|.||..|+...+..  ...||+||..+....
T Consensus       455 ~~c~ic~~-~---~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc-c---ccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            78999999 2   3334555 9999999999998775  336999998776544

>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=95.33  E-value=0.019  Score=39.18  Aligned_cols=50  Identities=22%  Similarity=0.474  Sum_probs=37.0

Q ss_pred             cccccccc-ccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506           11 YCTVCLDG-ISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus        11 ~C~ICl~~-~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      .||+|... |.+++.......|+|..|.+|+...+.. ...||.|...+...
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            48888873 5555554444459999999999998775 56899998776543

>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=95.07  E-value=0.0093  Score=30.18  Aligned_cols=29  Identities=21%  Similarity=0.763  Sum_probs=21.8

Q ss_pred             C-CCcchHHhHHHHHhcCCCccccccccch
Q 036506           31 C-KHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus        31 C-~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      | .|..|..|+...+..+..||+|..+++.
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            6 5999999999999999999999988764

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.

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

Probab=95.04  E-value=0.0074  Score=48.08  Aligned_cols=47  Identities=26%  Similarity=0.624  Sum_probs=38.4

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~   57 (86)
                      ....|.||++.+.+-..+  . .|||.++..|+..|+..+..||+|+...
T Consensus      1152 ~~~~c~ic~dil~~~~~I--~-~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGI--A-GCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhcCCe--e-eechhHhhhHHHHHHHHhccCcchhhhh
Confidence            344799999998854433  3 3999999999999999999999998543

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

Probab=94.91  E-value=0.0014  Score=46.35  Aligned_cols=51  Identities=20%  Similarity=0.570  Sum_probs=41.1

Q ss_pred             ccccccccccccCC-CceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            9 YCYCTVCLDGISDG-QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         9 ~~~C~ICl~~~~~~-~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ...++||...+... +.+..+. |||.+|.++|.+||.....||.|+..+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            35688988887654 4455554 999999999999999988999999987654

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

Probab=94.66  E-value=0.031  Score=39.63  Aligned_cols=46  Identities=26%  Similarity=0.516  Sum_probs=35.6

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC---Cccccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS---TCPLCRIE   56 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~---~CP~Cr~~   56 (86)
                      ..|||=.+.-.+......+. |||+..++-+.+..+++.   .||+|-..
T Consensus       335 F~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  335 FICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             eecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            46888777655555566776 999999999999887644   69999554

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.45  E-value=0.026  Score=38.86  Aligned_cols=29  Identities=28%  Similarity=0.780  Sum_probs=23.4

Q ss_pred             CCCcchHHhHHHHHh-------------cCCCccccccccch
Q 036506           31 CKHCFHVECIDAWFQ-------------SRSTCPLCRIEVAI   59 (86)
Q Consensus        31 C~H~fh~~Ci~~wl~-------------~~~~CP~Cr~~~~~   59 (86)
                      |....|.+|+.+|+.             ++.+||+||+.+..
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            678899999999974             24489999998754

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

Probab=94.45  E-value=0.023  Score=43.91  Aligned_cols=36  Identities=28%  Similarity=0.585  Sum_probs=27.8

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWF   44 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl   44 (86)
                      ..+..|.+|...+... ...+-+ |||.||.+|+.+-.
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            4567899999987664 334555 99999999998754

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

Probab=94.29  E-value=0.032  Score=40.46  Aligned_cols=36  Identities=22%  Similarity=0.361  Sum_probs=31.2

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS   46 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~   46 (86)
                      ++++.|+||..-|.++   .+++ |+|..|..|...-+.+
T Consensus         2 eeelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREP---IILP-CSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhccCc---eEee-cccHHHHHHHHhhccc
Confidence            4788999999999988   5787 9999999999876654

>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=93.92  E-value=0.026  Score=37.92  Aligned_cols=51  Identities=27%  Similarity=0.520  Sum_probs=37.1

Q ss_pred             ccccccccccc-ccCCC-ceeEcCCCCCcchHHhHHHHHhc-CCCcc--ccccccc
Q 036506            8 YYCYCTVCLDG-ISDGQ-KFRRLPECKHCFHVECIDAWFQS-RSTCP--LCRIEVA   58 (86)
Q Consensus         8 ~~~~C~ICl~~-~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP--~Cr~~~~   58 (86)
                      .+..||||..+ +-+|+ .+.+-|.|-|.+|.+|+.+-+.. ...||  -|...+.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR   64 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR   64 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence            45689999985 44444 44555579999999999998876 45799  5765443

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

Probab=93.74  E-value=0.029  Score=38.91  Aligned_cols=30  Identities=47%  Similarity=1.033  Sum_probs=22.9

Q ss_pred             eEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506           26 RRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus        26 ~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      +.++ |+|+||.+|...  ..-+.||.|-..+.
T Consensus       105 RmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen  105 RMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             cccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            5777 999999999754  34568999966553

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

Probab=93.31  E-value=0.04  Score=39.10  Aligned_cols=38  Identities=21%  Similarity=0.484  Sum_probs=27.3

Q ss_pred             ccccccccccc-ccCCCceeEcCCCCCcchHHhHHHHHhc
Q 036506            8 YYCYCTVCLDG-ISDGQKFRRLPECKHCFHVECIDAWFQS   46 (86)
Q Consensus         8 ~~~~C~ICl~~-~~~~~~~~~~~~C~H~fh~~Ci~~wl~~   46 (86)
                      ...+|.||+.. ....+...+. .|+|.||.+|+.+.+..
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhh
Confidence            46789999944 3333333434 59999999999988763

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

Probab=93.11  E-value=0.065  Score=41.21  Aligned_cols=39  Identities=26%  Similarity=0.692  Sum_probs=28.0

Q ss_pred             cccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPL   52 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~   52 (86)
                      |.||--.+... ..... .|+|..|.+|...|++..-.||.
T Consensus      1031 C~~C~l~V~gs-s~~Cg-~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVRGS-SNFCG-TCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeEeeEeecc-chhhc-cccccccHHHHHHHHhcCCcCCC
Confidence            55554443322 22334 49999999999999999989985

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.62  E-value=0.06  Score=36.39  Aligned_cols=53  Identities=26%  Similarity=0.679  Sum_probs=36.4

Q ss_pred             CcccccccccccccCCCce-eEcCCC-----CCcchHHhHHHHHhcCC--------Cccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKF-RRLPEC-----KHCFHVECIDAWFQSRS--------TCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~-~~~~~C-----~H~fh~~Ci~~wl~~~~--------~CP~Cr~~~~~~   60 (86)
                      ..+-.|-||+..=++...- .+-| |     .|-.|.+|+.+|+..+.        +||.|++++...
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv   84 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIV   84 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheee
Confidence            4567799999874433211 2334 4     47899999999996421        699999986543

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

Probab=91.74  E-value=0.33  Score=27.05  Aligned_cols=56  Identities=20%  Similarity=0.368  Sum_probs=22.4

Q ss_pred             CcccccccccccccC---CCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccchhhh
Q 036506            7 PYYCYCTVCLDGISD---GQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAIVIA   62 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~---~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~   62 (86)
                      -....|.||-+.+-.   ++..+....|+-..|+.|.+-=.+ .++.||.|++.+....+
T Consensus         7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg   66 (80)
T PF14569_consen    7 LNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG   66 (80)
T ss_dssp             -SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----TT
T ss_pred             cCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccccC
Confidence            345679999998642   333344445888899999876444 36789999988765443

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

Probab=91.67  E-value=0.14  Score=39.74  Aligned_cols=56  Identities=13%  Similarity=0.105  Sum_probs=39.1

Q ss_pred             CCCCCcccccccccccccCCC---ceeEcCCCCCcchHHhHHHHHhc------CCCccccccccc
Q 036506            3 AAKCPYYCYCTVCLDGISDGQ---KFRRLPECKHCFHVECIDAWFQS------RSTCPLCRIEVA   58 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~---~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~   58 (86)
                      .++..+...|.+|.-++.+++   .+-.+..|+|.||..||..|+.+      +-.|+.|.+-|.
T Consensus        90 DeK~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   90 DEKTAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             CcccccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            445577788899988887732   22222359999999999999875      225777766553

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

Probab=91.40  E-value=0.13  Score=34.76  Aligned_cols=51  Identities=25%  Similarity=0.677  Sum_probs=34.6

Q ss_pred             cccccccccccCCCc-eeEcC-CCC---CcchHHhHHHHHh--cCCCccccccccchh
Q 036506           10 CYCTVCLDGISDGQK-FRRLP-ECK---HCFHVECIDAWFQ--SRSTCPLCRIEVAIV   60 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~-~~~~~-~C~---H~fh~~Ci~~wl~--~~~~CP~Cr~~~~~~   60 (86)
                      ..|-||.+....... ....| .|.   ...|+.|+..|+.  .+..|.+|...+...
T Consensus        79 ~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   79 PICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            789999997543321 12333 132   5679999999998  456799998865443

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

Probab=91.20  E-value=0.06  Score=40.73  Aligned_cols=48  Identities=27%  Similarity=0.732  Sum_probs=37.3

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---CCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~~~~   59 (86)
                      ..++|+||+..+..+   ..+ .|.|.|+..|+..-+..   ...||+|+..+..
T Consensus        20 k~lEc~ic~~~~~~p---~~~-kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLL-KCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hhccCCceeEEeecc---chh-hhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            467999999998887   244 59999999999886654   3469999865543

>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=90.64  E-value=0.35  Score=24.50  Aligned_cols=42  Identities=24%  Similarity=0.600  Sum_probs=19.8

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---C--CCcccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---R--STCPLCRI   55 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~--~~CP~Cr~   55 (86)
                      +.|||-...+..+  ++.. .|.|.-|.+ +..|+..   .  -.||+|.+
T Consensus         3 L~CPls~~~i~~P--~Rg~-~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~   49 (50)
T PF02891_consen    3 LRCPLSFQRIRIP--VRGK-NCKHLQCFD-LESFLESNQRTPKWKCPICNK   49 (50)
T ss_dssp             SB-TTTSSB-SSE--EEET-T--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred             eeCCCCCCEEEeC--ccCC-cCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence            5789988887765  3444 499985432 3445542   2  26999975

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.

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

Probab=90.46  E-value=0.083  Score=39.95  Aligned_cols=45  Identities=20%  Similarity=0.494  Sum_probs=32.2

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCP   51 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP   51 (86)
                      ++.+-+.|+||+..|-......+...|||..|+.|+....+  .+||
T Consensus         7 ~w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen    7 KWVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             hhHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            44556789999998866543334445999999999987554  4566

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

Probab=89.64  E-value=0.27  Score=35.46  Aligned_cols=37  Identities=19%  Similarity=0.500  Sum_probs=29.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS   46 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~   46 (86)
                      ....+|.||.+.+..  .+..+. |+|.|+..|...++.+
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            456899999998765  334554 9999999999998864

>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=89.13  E-value=0.22  Score=21.94  Aligned_cols=23  Identities=22%  Similarity=0.524  Sum_probs=11.7

Q ss_pred             ccccccccccCCCceeEcCCCCCcc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCF   35 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~f   35 (86)
                      .||-|...+...  ....|.|||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            366666654322  23444566665

Several members are annotated as putative helicases.

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression

Probab=88.68  E-value=0.64  Score=27.23  Aligned_cols=51  Identities=20%  Similarity=0.313  Sum_probs=32.7

Q ss_pred             CCCcccccccccccccCCCceeE-----cCCC---CCcchHHhHHHHHhc---------CCCccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRR-----LPEC---KHCFHVECIDAWFQS---------RSTCPLCRIE   56 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~-----~~~C---~H~fh~~Ci~~wl~~---------~~~CP~Cr~~   56 (86)
                      |+.....|..|...-.+.. +.-     .+.|   .-.||..||..++..         .-.||.||..
T Consensus         3 d~~~g~~CHqCrqKt~~~~-~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi   70 (105)
T PF10497_consen    3 DSVNGKTCHQCRQKTLDFK-TICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI   70 (105)
T ss_pred             cCCCCCCchhhcCCCCCCc-eEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence            5667778888888532211 111     1236   678999999888753         2269998864

This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].

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

Probab=88.64  E-value=0.28  Score=32.33  Aligned_cols=45  Identities=29%  Similarity=0.626  Sum_probs=34.2

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV   57 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~   57 (86)
                      -.|.+|...+-.+   +....|+=.+|..|+..++++...||.|.--+
T Consensus       182 k~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~d~w  226 (235)
T KOG4718|consen  182 KNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCGDLW  226 (235)
T ss_pred             HHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchhccc
Confidence            4688888875544   23334888899999999999988999995444

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

Probab=87.62  E-value=0.37  Score=26.02  Aligned_cols=13  Identities=23%  Similarity=0.974  Sum_probs=9.3

Q ss_pred             cchHHhHHHHHhc
Q 036506           34 CFHVECIDAWFQS   46 (86)
Q Consensus        34 ~fh~~Ci~~wl~~   46 (86)
                      -||+.|+.+|+..
T Consensus        11 gFCRNCLskWy~~   23 (68)
T PF06844_consen   11 GFCRNCLSKWYRE   23 (68)
T ss_dssp             S--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3999999999863

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

>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=87.31  E-value=0.59  Score=23.95  Aligned_cols=43  Identities=30%  Similarity=0.693  Sum_probs=20.9

Q ss_pred             cccccccccCC------CceeEcCCCCCcchHHhHHHHHhcCCCccccc
Q 036506           12 CTVCLDGISDG------QKFRRLPECKHCFHVECIDAWFQSRSTCPLCR   54 (86)
Q Consensus        12 C~ICl~~~~~~------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr   54 (86)
                      |--|+..|..+      ......+.|++.||.+|=.=-=+.-..||-|.
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            45566666654      23456678999999999432112345688773

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.

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

Probab=86.97  E-value=0.38  Score=23.89  Aligned_cols=43  Identities=30%  Similarity=0.709  Sum_probs=28.0

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhc------CCCccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS------RSTCPLCR   54 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr   54 (86)
                      .|.||...... ..++.-..|+..||..|+..-...      .-.||.|+
T Consensus         1 ~C~vC~~~~~~-~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQSDDD-GDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTSSCTT-SSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCCcCCC-CCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            37899984333 344445569999999998664331      23577775

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 ....

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

Probab=86.93  E-value=0.31  Score=31.85  Aligned_cols=38  Identities=32%  Similarity=0.822  Sum_probs=26.6

Q ss_pred             cccccccccCCCceeEcCCCCC-cchHHhHHHHHhcCCCcccccccc
Q 036506           12 CTVCLDGISDGQKFRRLPECKH-CFHVECIDAWFQSRSTCPLCRIEV   57 (86)
Q Consensus        12 C~ICl~~~~~~~~~~~~~~C~H-~fh~~Ci~~wl~~~~~CP~Cr~~~   57 (86)
                      |-+|.+.   +..+..+| |.| .+|..|-..    -..||+|+...
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChh
Confidence            5555544   45577888 997 778888543    45699998754

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

Probab=86.88  E-value=0.35  Score=34.38  Aligned_cols=44  Identities=23%  Similarity=0.471  Sum_probs=32.2

Q ss_pred             ccccccccccccCCC--ceeEcCCCCCcchHHhHHHHHhcCCCcccc
Q 036506            9 YCYCTVCLDGISDGQ--KFRRLPECKHCFHVECIDAWFQSRSTCPLC   53 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~--~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C   53 (86)
                      -..|++|.-.+....  ...+.. |||.||..|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence            357888887654333  345665 99999999999998877766543

>smart00249 PHD PHD zinc finger

Probab=86.82  E-value=0.64  Score=22.00  Aligned_cols=31  Identities=23%  Similarity=0.659  Sum_probs=20.6

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .|.+|...... ..++.-..|+..||..|+..
T Consensus         1 ~C~~C~~~~~~-~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDG-GELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCC-CCEEECCCCCchhhhhhCCC
Confidence            36788776533 33334445999999999744

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

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

Probab=86.55  E-value=0.88  Score=35.65  Aligned_cols=51  Identities=22%  Similarity=0.588  Sum_probs=36.5

Q ss_pred             CcccccccccccccCCCceeEcC-CCC---CcchHHhHHHHHhc--CCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLP-ECK---HCFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~-~C~---H~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      .+...|-||..+-..++.. --| +|.   ...|.+|+.+|+.-  ...|-+|..++.
T Consensus        10 ~d~~~CRICr~e~~~d~pL-fhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPL-FHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             ccchhceeecCCCCCCCcC-cccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            5668999999885554443 223 232   46899999999985  346999988764

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

Probab=86.16  E-value=0.9  Score=35.10  Aligned_cols=42  Identities=29%  Similarity=0.402  Sum_probs=30.7

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPL   52 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~   52 (86)
                      ...|.+|-..+.. . ....+.|||.-|.+++.+|+..+.-||.
T Consensus       779 ~~~CtVC~~vi~G-~-~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIRG-V-DVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hcCceeecceeee-e-EeecccccccccHHHHHHHHhcCCCCcc
Confidence            3467777776542 1 2344469999999999999998877765

>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=85.69  E-value=0.44  Score=25.28  Aligned_cols=39  Identities=13%  Similarity=0.198  Sum_probs=19.8

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHH
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW   43 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w   43 (86)
                      +..+...|.+|...|..-..--....||++||..|....
T Consensus         5 ~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~   43 (69)
T PF01363_consen    5 PDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR   43 (69)
T ss_dssp             SGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred             CCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence            345567899999999654333344469999999887543

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 ....

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=84.85  E-value=0.74  Score=21.78  Aligned_cols=26  Identities=27%  Similarity=0.553  Sum_probs=15.3

Q ss_pred             cccccccccccCCCc-------eeEcCCCCCcc
Q 036506           10 CYCTVCLDGISDGQK-------FRRLPECKHCF   35 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~-------~~~~~~C~H~f   35 (86)
                      ..||-|...|..++.       .+..+.|+|.|
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            467777777765442       23444566665

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit

Probab=84.42  E-value=1.4  Score=35.32  Aligned_cols=54  Identities=20%  Similarity=0.415  Sum_probs=37.7

Q ss_pred             ccccccccccccc---CCCceeEcCCCCCcchHHhHHHHH-hcCCCccccccccchhh
Q 036506            8 YYCYCTVCLDGIS---DGQKFRRLPECKHCFHVECIDAWF-QSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         8 ~~~~C~ICl~~~~---~~~~~~~~~~C~H~fh~~Ci~~wl-~~~~~CP~Cr~~~~~~~   61 (86)
                      ....|.||-+++.   +++..+....|+--.|+.|.+==. +.++.||.|++.+....
T Consensus        16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr~k   73 (1079)
T PLN02638         16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKRHK   73 (1079)
T ss_pred             CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhhhc
Confidence            4458999999864   344445555688889999994312 23678999999876433

>PLN02189 cellulose synthase

Probab=83.98  E-value=1.5  Score=35.05  Aligned_cols=54  Identities=24%  Similarity=0.447  Sum_probs=37.9

Q ss_pred             ccccccccccccc---CCCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccchhh
Q 036506            8 YYCYCTVCLDGIS---DGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAIVI   61 (86)
Q Consensus         8 ~~~~C~ICl~~~~---~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~   61 (86)
                      ....|.||-+++.   +++..+....|+-..|+.|.+-=.+ .++.||.|++.+....
T Consensus        33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~k   90 (1040)
T PLN02189         33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLK   90 (1040)
T ss_pred             cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence            3458999999875   3344455556888899999944222 3678999999886433

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

Probab=82.99  E-value=0.42  Score=26.10  Aligned_cols=43  Identities=16%  Similarity=0.436  Sum_probs=21.9

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      +..||.|..++....        ++.+|..|-.. +.....||.|..++..-
T Consensus         1 e~~CP~C~~~L~~~~--------~~~~C~~C~~~-~~~~a~CPdC~~~Le~L   43 (70)
T PF07191_consen    1 ENTCPKCQQELEWQG--------GHYHCEACQKD-YKKEAFCPDCGQPLEVL   43 (70)
T ss_dssp             --B-SSS-SBEEEET--------TEEEETTT--E-EEEEEE-TTT-SB-EEE
T ss_pred             CCcCCCCCCccEEeC--------CEEECcccccc-ceecccCCCcccHHHHH
Confidence            367999999876442        45555555443 24466799998887543

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

>PLN02436 cellulose synthase A

Probab=82.99  E-value=1.7  Score=34.87  Aligned_cols=54  Identities=24%  Similarity=0.477  Sum_probs=38.2

Q ss_pred             ccccccccccccc---CCCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccchhh
Q 036506            8 YYCYCTVCLDGIS---DGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAIVI   61 (86)
Q Consensus         8 ~~~~C~ICl~~~~---~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~   61 (86)
                      ....|.||-+++.   +++..+....|+-..|+.|.+-=.+ .++.||.|++.+....
T Consensus        35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~k   92 (1094)
T PLN02436         35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIK   92 (1094)
T ss_pred             CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhcc
Confidence            3458999999863   3444455556888899999944222 3678999999876433

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

Probab=82.64  E-value=0.54  Score=35.22  Aligned_cols=27  Identities=33%  Similarity=0.850  Sum_probs=19.2

Q ss_pred             eEcCCCCCcchHHhHHHHHhcCCCcccccc
Q 036506           26 RRLPECKHCFHVECIDAWFQSRSTCPLCRI   55 (86)
Q Consensus        26 ~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~   55 (86)
                      .....|+++||..|+.+   .+.-||.|-.
T Consensus       532 ~rC~~C~avfH~~C~~r---~s~~CPrC~R  558 (580)
T KOG1829|consen  532 RRCSTCLAVFHKKCLRR---KSPCCPRCER  558 (580)
T ss_pred             eeHHHHHHHHHHHHHhc---cCCCCCchHH
Confidence            34445999999999654   3444999943

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

Probab=82.29  E-value=1.7  Score=22.90  Aligned_cols=39  Identities=13%  Similarity=0.223  Sum_probs=26.5

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ   45 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~   45 (86)
                      .+...|..|...|..-..-.....||.+|+..|......
T Consensus         8 ~~~~~C~~C~~~F~~~~rk~hCr~CG~i~C~~C~~~~~~   46 (68)
T smart00064        8 EEVSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKAP   46 (68)
T ss_pred             CCCCcCcccCccccCcccccccccCCCCcChHHcCCeee
Confidence            345689999888764322223335999999999876543

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

>PLN02400 cellulose synthase

Probab=80.73  E-value=1.4  Score=35.29  Aligned_cols=53  Identities=21%  Similarity=0.423  Sum_probs=36.7

Q ss_pred             ccccccccccccc---CCCceeEcCCCCCcchHHhHHHHH-hcCCCccccccccchh
Q 036506            8 YYCYCTVCLDGIS---DGQKFRRLPECKHCFHVECIDAWF-QSRSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~---~~~~~~~~~~C~H~fh~~Ci~~wl-~~~~~CP~Cr~~~~~~   60 (86)
                      ....|.||-+++.   +++..+....|+--.|+.|.+==. ..++.||.|++.+...
T Consensus        35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR~   91 (1085)
T PLN02400         35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRH   91 (1085)
T ss_pred             CCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccccc
Confidence            3458999999864   334445555688889999984311 2367899999987633

>TIGR00622 ssl1 transcription factor ssl1

Probab=80.49  E-value=2.4  Score=25.21  Aligned_cols=46  Identities=24%  Similarity=0.426  Sum_probs=32.5

Q ss_pred             ccccccccccccCC----------CceeEcCCCCCcchHHhHHHHHhcCCCccccc
Q 036506            9 YCYCTVCLDGISDG----------QKFRRLPECKHCFHVECIDAWFQSRSTCPLCR   54 (86)
Q Consensus         9 ~~~C~ICl~~~~~~----------~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr   54 (86)
                      ...|--|+..|..+          ......+.|++.||.+|-.=+-+.-..||-|.
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            34699999887643          11234567999999999766666666799885

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	86
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		5e-11
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-05
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-04
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		9e-04

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 32/48 (66%)
Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI 59
          C VCL  + DG++ R LP C H FH EC+D W  S STCPLCR+ V +
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          CT+CL  + +G+  RRLP C H FH  C+D W  +   CP+CR+++
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
          C VC+      Q  R LP C H FH +C+D W ++  TCP+CR +  
Sbjct: 26 CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSG 71

>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 = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
          C VC +  + G+  R+LP C H FH  CI  W +   +CP+CR
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCR 59

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

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
           C VCL+      +    P CKH FH +C+  W + R  CPLC + V
Sbjct: 17 LCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	86
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-19
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	6e-18
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	6e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	9e-17
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-16
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	9e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	9e-14
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-12
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	7e-12
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	9e-11
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	7e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	8e-09
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-08
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-08
3nw0_A	238	Non-structural maintenance of chromosomes element	9e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	9e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-06
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	7e-06
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-05
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	4e-05
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	8e-05
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	9e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-04
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-04

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

 Score = 72.6 bits (179), Expect = 3e-19
 Identities = 26/48 (54%), Positives = 32/48 (66%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI 59
          C VCL  + DG++ R LP C H FH EC+D W  S STCPLCR+ V +
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

 Score = 70.1 bits (172), Expect = 6e-18
 Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C      G     LP C H FH  C+  W Q   TCP+CR   
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 67.4 bits (165), Expect = 6e-17
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
          C VC+      Q  R LP C H FH +C+D W ++  TCP+CR +  
Sbjct: 26 CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSG 71

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

 Score = 67.1 bits (164), Expect = 9e-17
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C VC +  + G+  R+LP C H FH  CI  W +   +CP+CR  +
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

 Score = 66.6 bits (163), Expect = 1e-16
 Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          CT+CL  + +G+  RRLP C H FH  C+D W  +   CP+CR+++
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

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

 Score = 61.7 bits (150), Expect = 9e-15
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C VCL+      +    P CKH FH +C+  W + R  CPLC + V
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 = 58.8 bits (143), Expect = 9e-14
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA 58
          C +CL+ I   +    +  C H  H  C +   +    CPLC    +
Sbjct: 8  CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS 54

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

 Score = 56.4 bits (136), Expect = 1e-12
 Identities = 13/45 (28%), Positives = 18/45 (40%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIE 56
          C  C              EC H FH  C+  W +  + CPLC+ +
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73

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

 Score = 54.3 bits (131), Expect = 7e-12
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 5/46 (10%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C+DG +D      LP C H F  +CID W      CP+CR+++
Sbjct: 18 CCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQM 58

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

 Score = 51.6 bits (124), Expect = 9e-11
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI 61
          C +CL+  S+         C H F   CI  W +   TCPLC++ V  V+
Sbjct: 8  CPICLEDPSNY---SMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVV 54

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

 Score = 48.4 bits (115), Expect = 2e-09
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 12 CTVCLDGISDGQKFRRLP---ECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C+DG S+  +  RL    EC H F  +C+    ++ +TCP CR ++
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 47.5 bits (112), Expect = 7e-09
 Identities = 12/48 (25%), Positives = 16/48 (33%)

Query: 7  PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
               C       +  +       C H FH  CI  W ++R  CPL  
Sbjct: 49 DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 46.4 bits (110), Expect = 8e-09
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 12 CTVCLDGISDGQKFRRLP---ECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C+DG S+  +  RL    EC H F  +C+    ++ +TCP CR ++
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

>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 = 47.2 bits (111), Expect = 1e-08
 Identities = 12/48 (25%), Positives = 16/48 (33%)

Query: 7   PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
                C       +  +       C H FH  CI  W ++R  CPL  
Sbjct: 60  DLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 44.8 bits (106), Expect = 3e-08
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 12 CTVCLDGISDGQKFRRLP---ECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C+DG S+  +  RL    EC H F  +C+    ++ +TCP CR ++
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 46.3 bits (109), Expect = 9e-08
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 5/49 (10%)

Query: 10  CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIE 56
             C +C   +  GQ       C    H+ C+  +FQS     CP C   
Sbjct: 181 KICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

>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 = 44.1 bits (104), Expect = 9e-08
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIE 56
          C +C   +  GQ       C    H+ C+  +FQS     CP C   
Sbjct: 18 CNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

>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 = 44.8 bits (105), Expect = 4e-07
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEV 57
           C +C +   D     ++  C H     C+ +W +S    CP CR E+
Sbjct: 335 CKICAENDKDV----KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 43.3 bits (101), Expect = 1e-06
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 15/66 (22%)

Query: 12  CTVCLDGISDGQKFRRL----PECKHCFHVECIDAWFQSRS-----------TCPLCRIE 56
           C +C     DG +   +     +C    H  C++ WF++              CP C+ +
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 57  VAIVIA 62
           ++   A
Sbjct: 371 LSTSFA 376

>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 = 2e-06
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEV 57
          C +C++ + D    R  P C       CI  W    R+ CP CR  +
Sbjct: 25 CFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 39.0 bits (91), Expect = 7e-06
 Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C++C   + D      + EC H F   CI   F   + CP C I V
Sbjct: 18 CSICKGYLIDAT---TITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

>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 = 38.3 bits (89), Expect = 3e-05
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C     D      + EC H F   CI  + ++   CP+C ++V
Sbjct: 18 CVLCGGYFIDA---TTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

>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 = 37.9 bits (87), Expect = 4e-05
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 19/72 (26%)

Query: 12 CTVCLDGISDG--------------QKFRRLPECKHCFHVECIDAWFQSRS-----TCPL 52
          C +C++ ++                    RL +C H FH+ C+ A + + +      CP 
Sbjct: 28 CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 53 CRIEVAIVIARQ 64
          C+         Q
Sbjct: 88 CKTIYGEKTGTQ 99

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

 Score = 36.4 bits (84), Expect = 8e-05
 Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 4/43 (9%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
          C +C     +      + +C+H F   C    F++   C +C 
Sbjct: 18 CFICRQAFQNPV----VTKCRHYFCESCALEHFRATPRCYICD 56

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

 Score = 36.0 bits (83), Expect = 9e-05
 Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +CL           LP CKH F   C+         C LCR E+
Sbjct: 18 CAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 36.3 bits (84), Expect = 1e-04
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C +C +  +       +P+C H +   CI  +   ++ CP C + V
Sbjct: 25 CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 36.2 bits (83), Expect = 3e-04
 Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 4/43 (9%)

Query: 12  CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCR 54
           C +C +   +         C H F   CI+ W + +  CP+CR
Sbjct: 67  CIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICR 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	86
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.77
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.75
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.74
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.74
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.74
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.73
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.71
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.7
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.67
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.67
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.67
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.66
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.66
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.63
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.63
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.63
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.62
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.62
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.61
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.61
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.6
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.59
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.58
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.57
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.56
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.56
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.56
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.56
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.55
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.55
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.54
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.53
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.52
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.52
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.51
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.51
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.49
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.48
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.47
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.47
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.45
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.45
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.45
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.44
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.43
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.43
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.43
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.42
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.42
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.38
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.33
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.31
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.29
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.29
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.28
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.27
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.26
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.24
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.23
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.17
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.16
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.15
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.08
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.07
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.02
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.02
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.82
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.79
3nw0_A	238	Non-structural maintenance of chromosomes element	98.57
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.53
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.03
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.74
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.63
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.62
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	95.12
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.85
1we9_A	64	PHD finger family protein; structural genomics, PH	94.68
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	94.51
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.21
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	93.54
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	93.47
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.1
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	92.77
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	92.73
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	92.7
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	92.08
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.87
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	91.84
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	91.8
2yt5_A	66	Metal-response element-binding transcription facto	91.4
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	90.84
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	90.05
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	89.7
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	89.6
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	89.56
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	89.09
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	88.52
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	88.43
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	88.21
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	88.02
1wem_A	76	Death associated transcription factor 1; structura	88.0
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	87.58
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	87.46
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	87.35
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	86.09
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	85.74
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	85.73
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	85.17
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	84.98
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	84.48
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	84.01
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	84.0
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	83.93
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	83.74
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	83.54
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	83.47
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	83.37
2o35_A	105	Hypothetical protein DUF1244; helix bundle, struct	83.32
1weu_A	91	Inhibitor of growth family, member 4; structural g	83.29
3fyb_A	104	Protein of unknown function (DUF1244); hydrocar de	83.14
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	82.96
1wew_A	78	DNA-binding family protein; structural genomics, P	82.87
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	82.04
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	81.75
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	81.39
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	81.0
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	80.68

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

Probab=99.77  E-value=3.5e-19  Score=98.17  Aligned_cols=58  Identities=31%  Similarity=0.737  Sum_probs=50.7

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchhh
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   61 (86)
                      .+....+..|+||++.|..+..+..++ |+|.||..||.+|++.+..||+||..+....
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A            9 EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             CTTSSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             cccCCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            345567889999999999888777887 9999999999999999999999999987643

>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=99.75  E-value=1.1e-18  Score=94.16  Aligned_cols=57  Identities=35%  Similarity=0.920  Sum_probs=49.4

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      .++...+..|+||++.|..+..++.++ |||.||..||.+|+..+..||+||..+...
T Consensus         8 ~~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A            8 GTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CCSTTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCcCCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            344567789999999998877778888 999999999999999999999999987643

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

Probab=99.74  E-value=8.2e-19  Score=90.79  Aligned_cols=52  Identities=50%  Similarity=1.063  Sum_probs=46.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .++.+|+||++.+..++.+..++.|||.||..||.+|++++.+||+||..+.
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            5678999999999987777777669999999999999999999999998764

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

Probab=99.74  E-value=7.1e-19  Score=96.41  Aligned_cols=53  Identities=36%  Similarity=0.903  Sum_probs=48.1

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..++..|+||++.|..++.++.++ |+|.||..||.+|++.+..||+||+.+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            456789999999999988888898 99999999999999999999999998764

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

Probab=99.74  E-value=1.4e-18  Score=94.80  Aligned_cols=55  Identities=33%  Similarity=0.821  Sum_probs=49.2

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+...+..|+||++.|..+..+..++ |+|.||..||.+|++.+..||+||..+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           10 KELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCCCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             ccCCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            45567889999999999888888888 99999999999999999999999998764

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

Probab=99.73  E-value=2.2e-18  Score=97.84  Aligned_cols=54  Identities=31%  Similarity=0.783  Sum_probs=48.1

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ....+..|+||++.|..++.+..++ |||.||..||.+|++.+.+||+||..+..
T Consensus        36 ~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           36 AVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             ccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            3456788999999999888888898 99999999999999999999999998754

>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=99.71  E-value=1e-17  Score=98.08  Aligned_cols=60  Identities=22%  Similarity=0.444  Sum_probs=46.5

Q ss_pred             CcccccccccccccCCC---------------ceeEcCCCCCcchHHhHHHHHh-----cCCCccccccccchhhhhhhc
Q 036506            7 PYYCYCTVCLDGISDGQ---------------KFRRLPECKHCFHVECIDAWFQ-----SRSTCPLCRIEVAIVIARQRR   66 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~~~~~~~~~~~~   66 (86)
                      +.+.+|+||++.|..+.               .+..++ |+|.||..||.+|+.     .+.+||+||..+....+.++.
T Consensus        23 ~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~  101 (114)
T 1v87_A           23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPW  101 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTT
T ss_pred             CCCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCC
Confidence            45679999999997643               233565 999999999999994     467899999998776555544


Q ss_pred             c
Q 036506           67 N   67 (86)
Q Consensus        67 ~   67 (86)
                      +
T Consensus       102 g  102 (114)
T 1v87_A          102 G  102 (114)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.70  E-value=1.1e-17  Score=93.25  Aligned_cols=53  Identities=26%  Similarity=0.664  Sum_probs=43.3

Q ss_pred             CcccccccccccccC-----------CCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISD-----------GQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~-----------~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.|..           ++.++.++.|+|.||..||.+|+.++++||+||+.+..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            467789999999864           23344555599999999999999999999999998754

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

Probab=99.67  E-value=2.4e-17  Score=88.47  Aligned_cols=55  Identities=25%  Similarity=0.632  Sum_probs=45.7

Q ss_pred             CCCCCcccccccccccccCC----CceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            3 AAKCPYYCYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .+...+...|+||++.+.++    ..+..++ |||.||..||.+|+..+..||+||..+.
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   67 (69)
T 2ea6_A            9 GLRPSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKIN   67 (69)
T ss_dssp             CCCTTCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             ccCCCCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccC
Confidence            34557788999999998764    2335666 9999999999999999999999999875

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

Probab=99.67  E-value=2.1e-17  Score=89.27  Aligned_cols=55  Identities=25%  Similarity=0.615  Sum_probs=45.7

Q ss_pred             CCCCcccccccccccccCC----CceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ....++..|+||++.+.++    ..+..++ |||.||..||.+|++++..||+||..+..
T Consensus         5 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (71)
T 3ng2_A            5 LRPSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   63 (71)
T ss_dssp             -CCTTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCC
T ss_pred             CCCCCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccCh
Confidence            3456788999999998764    3445666 99999999999999999999999998764

>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=99.67  E-value=3.8e-17  Score=84.34  Aligned_cols=51  Identities=27%  Similarity=0.647  Sum_probs=43.1

Q ss_pred             CcccccccccccccCCC-ceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQ-KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~-~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ..+.+|+||++.+.+++ .+..++ |+|.||..||.+|++.+..||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45788999999986543 455666 9999999999999999999999998764

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

Probab=99.66  E-value=1e-16  Score=87.10  Aligned_cols=55  Identities=29%  Similarity=0.625  Sum_probs=46.0

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      .++..++..|+||++.+.++   +.+..|||.||..||.+|++.+..||+||..+...
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A            9 LSELTPYILCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CCCCCGGGSCTTTSSCCSSC---EECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             HhhcCCCCCCCCCChHHHCc---CEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            45567889999999999876   34423999999999999999999999999988643

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

Probab=99.66  E-value=5.7e-17  Score=87.93  Aligned_cols=53  Identities=28%  Similarity=0.525  Sum_probs=45.3

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchhh
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI   61 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   61 (86)
                      ...++..|+||++.+.++   +.++ |||.||..||.+|+..+..||+||..+....
T Consensus        11 ~~~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHHH
T ss_pred             cCCCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHhh
Confidence            346678999999998765   5666 9999999999999999999999999887543

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

Probab=99.63  E-value=2.4e-16  Score=86.18  Aligned_cols=55  Identities=25%  Similarity=0.541  Sum_probs=45.3

Q ss_pred             CCCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC--CCccccccccch
Q 036506            2 TAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIEVAI   59 (86)
Q Consensus         2 t~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~   59 (86)
                      ..++.+++..|+||++.|.++   +.++.|||.||..||.+|+..+  ..||+||..+..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            8 EDDPIPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CCCCSCGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             ccccCCCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            345667889999999999877   4454599999999999999865  689999997543

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

Probab=99.63  E-value=8.7e-17  Score=85.08  Aligned_cols=51  Identities=27%  Similarity=0.694  Sum_probs=43.3

Q ss_pred             cccccccccccccCC----CceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ++.+|+||++.+.++    +.+..++ |||.||..|+.+|++++..||+||..+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   56 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   56 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCc
Confidence            467899999998754    3345666 99999999999999999999999998764

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

Probab=99.63  E-value=1.5e-16  Score=85.30  Aligned_cols=50  Identities=36%  Similarity=0.829  Sum_probs=43.1

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.+.++  +..++ |||.||..|+.+|++++..||+||..+..
T Consensus         3 ~~~~~C~IC~~~~~~~--~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccCC--cEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            4567899999998754  35676 99999999999999999999999998864

>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=99.62  E-value=3.7e-16  Score=91.13  Aligned_cols=50  Identities=32%  Similarity=0.676  Sum_probs=42.3

Q ss_pred             cccccccccccccCCC---------------ceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            8 YYCYCTVCLDGISDGQ---------------KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ++..|+||++.|..+.               .++.++ |+|.||..||.+||..+.+||+||+.+.
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            5678999999987541               245566 9999999999999999999999999864

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

Probab=99.62  E-value=1.1e-16  Score=86.33  Aligned_cols=52  Identities=35%  Similarity=0.861  Sum_probs=45.0

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..++..|+||++.+.+    +.++ |||.||..||.+|+.++..||+||..+..
T Consensus         9 ~~~~~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   60 (70)
T 2ecn_A            9 VKQLTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTG   60 (70)
T ss_dssp             CCCCCCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTC
T ss_pred             hhcCCCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccC
Confidence            3455778999999999876    4677 99999999999999999999999998764

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

Probab=99.61  E-value=7.4e-16  Score=86.13  Aligned_cols=57  Identities=21%  Similarity=0.522  Sum_probs=46.8

Q ss_pred             CCCCCcccccccccccccCCCc-eeEcCCCCCcchHHhHHHHHhcC---CCccccccccchh
Q 036506            3 AAKCPYYCYCTVCLDGISDGQK-FRRLPECKHCFHVECIDAWFQSR---STCPLCRIEVAIV   60 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~-~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~~   60 (86)
                      .++..+...|+||++.|.+.+. .+.++ |||.||..||.+|+..+   ..||+||..+...
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A            9 LDALREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCCCCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             hhhccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            3455778899999999987543 45666 99999999999999875   6899999987643

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

Probab=99.61  E-value=5.2e-16  Score=85.96  Aligned_cols=51  Identities=18%  Similarity=0.458  Sum_probs=43.8

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ++......|+||++.+.++   ++++ |||.||..||.+|+.....||+||..+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3446678999999999775   4566 9999999999999999999999999875

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

Probab=99.60  E-value=9.8e-16  Score=81.87  Aligned_cols=52  Identities=19%  Similarity=0.438  Sum_probs=43.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~   59 (86)
                      +...++..|+||++.+.++   +.++ |||.||..||.+|+. ....||+||..+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           10 KTVEDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             CSCCCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             hcCCcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            3457789999999999877   3455 999999999999995 56789999998764

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

Probab=99.59  E-value=9.6e-16  Score=83.12  Aligned_cols=52  Identities=29%  Similarity=0.595  Sum_probs=43.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh---cCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ---SRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~Cr~~~~~   59 (86)
                      ++..++..|+||++.+.++   +.++ |||.||..||..|+.   ....||+||..+..
T Consensus        15 ~~~~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   69 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRK   69 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSE---EECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCC
T ss_pred             HhCccCCEeccCCcccCCe---EEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCc
Confidence            4457788999999998865   4566 999999999999997   35689999998754

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

Probab=99.58  E-value=5.8e-16  Score=93.59  Aligned_cols=48  Identities=27%  Similarity=0.781  Sum_probs=42.4

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ++..|+||++.|.++   ++++ |||.||..||..|+..+..||+||..+..
T Consensus        52 ~~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            456899999999866   5677 99999999999999999999999998754

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

Probab=99.57  E-value=1.5e-15  Score=83.41  Aligned_cols=52  Identities=19%  Similarity=0.478  Sum_probs=45.3

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      .+.+++..|+||++.|.++   ++++ |||.||..||.+|+.. +..||+||..+..
T Consensus         3 ~~~~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            3 PEFPEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CCCSSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cCCcccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            4568899999999999876   4566 9999999999999987 7789999998754

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

Probab=99.56  E-value=1.4e-15  Score=84.61  Aligned_cols=53  Identities=26%  Similarity=0.642  Sum_probs=43.8

Q ss_pred             CCcccccccccccccCCCceeEcCCCC-----CcchHHhHHHHHhcC--CCccccccccchh
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECK-----HCFHVECIDAWFQSR--STCPLCRIEVAIV   60 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~-----H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~   60 (86)
                      ..++..|.||++++..++.+ ++| |+     |.||..||.+|+..+  .+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            35677999999998766654 577 86     999999999999875  4899999988654

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

Probab=99.56  E-value=3.9e-15  Score=82.42  Aligned_cols=52  Identities=25%  Similarity=0.662  Sum_probs=44.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc------CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS------RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~   59 (86)
                      ++..++..|+||++.+.++   ..++ |||.||..||..|+..      ...||+||..+..
T Consensus        14 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           14 EMIKEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CCCCTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             HhCccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            4456788999999999877   4666 9999999999999987      6689999998764

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

Probab=99.56  E-value=9.5e-16  Score=84.22  Aligned_cols=52  Identities=25%  Similarity=0.627  Sum_probs=44.5

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-------CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-------RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~~~~~   59 (86)
                      ++..++..|+||++.|.++   +.++ |||.||..||.+|+..       ...||+||..+..
T Consensus         7 ~~~~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            7 GNVQEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             hhcccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4567889999999999876   3566 9999999999999986       5689999998865

>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=99.56  E-value=1.7e-15  Score=87.12  Aligned_cols=50  Identities=24%  Similarity=0.707  Sum_probs=42.8

Q ss_pred             CcccccccccccccCCCceeE-cCCCCCcchHHhHHHHHhcC-CCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRR-LPECKHCFHVECIDAWFQSR-STCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~-~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~   60 (86)
                      .++..|+||++.|.++   +. ++ |||.||..||.+|+..+ ..||+||..+...
T Consensus        20 ~~~~~C~IC~~~~~~p---~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           20 AEVFRCFICMEKLRDA---RLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCccCCccccCc---cccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            4678999999999865   34 55 99999999999999987 6999999988643

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

Probab=99.55  E-value=5.9e-15  Score=78.09  Aligned_cols=46  Identities=30%  Similarity=0.650  Sum_probs=38.9

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh---cCCCcccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ---SRSTCPLC   53 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C   53 (86)
                      ++..++..|+||++.+.++   +.++ |||.||..||.+|++   ....||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3457789999999999876   4566 999999999999998   35589987

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

Probab=99.55  E-value=2.1e-15  Score=89.49  Aligned_cols=54  Identities=26%  Similarity=0.614  Sum_probs=45.5

Q ss_pred             CCcccccccccccccCC----CceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            6 CPYYCYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ++++..|+||++.|.++    +.++.++ |||.||..||.+|++.+.+||+||..+...
T Consensus         4 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            4 GSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             -CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            46788999999998764    3446676 999999999999999999999999988654

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

Probab=99.54  E-value=6.4e-15  Score=83.16  Aligned_cols=52  Identities=27%  Similarity=0.583  Sum_probs=43.4

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC--CCcccccccc
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIEV   57 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~   57 (86)
                      .++.+++..|+||++.|.++   +.++.|||.||..||..|+..+  ..||+||..+
T Consensus         7 ~~~~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A            7 DDPIPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CCCCCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             cccCCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            34557889999999999877   4554499999999999999753  5899999986

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

Probab=99.53  E-value=6e-15  Score=81.67  Aligned_cols=52  Identities=29%  Similarity=0.659  Sum_probs=44.3

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc------CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS------RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~------~~~CP~Cr~~~~~   59 (86)
                      ++..+...|+||++.+.++   ..++ |||.||..|+..|+..      ...||+||..+..
T Consensus        14 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           14 VNVKEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             HHccCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            3457789999999999876   3556 9999999999999987      6789999998864

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

Probab=99.52  E-value=7e-15  Score=84.12  Aligned_cols=50  Identities=22%  Similarity=0.638  Sum_probs=42.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.|.++   +.++.|||.||..||..|+..+..||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           20 DDLLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHHTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCCcccCChhhCCc---CEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            4568999999999875   3442399999999999999999999999998864

>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=99.52  E-value=1.1e-15  Score=90.52  Aligned_cols=50  Identities=32%  Similarity=0.676  Sum_probs=1.0

Q ss_pred             cccccccccccccCCC---------------ceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            8 YYCYCTVCLDGISDGQ---------------KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .+..|+||++.|..+.               .+..++ |+|.||..||.+||..+.+||+||+.+.
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            4578999999997531               122344 9999999999999999999999999864

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

Probab=99.51  E-value=1e-14  Score=75.73  Aligned_cols=46  Identities=28%  Similarity=0.787  Sum_probs=38.3

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh---cCCCcccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ---SRSTCPLC   53 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---~~~~CP~C   53 (86)
                      ++..++..|+||++.+.++   +.++ |||.||..||.+|+.   ....||+|
T Consensus        10 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           10 ENLQVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCSCCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             hccccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4456788999999999887   3566 999999999999954   46689987

>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=99.51  E-value=9.2e-15  Score=84.86  Aligned_cols=50  Identities=24%  Similarity=0.604  Sum_probs=43.6

Q ss_pred             CCcccccccccccccCCCceeEc-CCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRL-PECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~-~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..++..|+||++.+.++   +.+ + |||.||..||..|+..+..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDA---TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHK   62 (108)
T ss_dssp             HGGGTBCTTTSSBCSSE---EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCS
T ss_pred             cCCcCCCccCChHHhCc---CEeCC-CCChhhHHHHHHHHHhCCcCcCCCccccc
Confidence            46788999999999865   344 6 99999999999999999999999998764

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

Probab=99.51  E-value=1.1e-14  Score=77.55  Aligned_cols=51  Identities=20%  Similarity=0.358  Sum_probs=41.2

Q ss_pred             cccccccccc-cccCCCce-eEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            8 YYCYCTVCLD-GISDGQKF-RRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~-~~~~~~~~-~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      ++..|+||++ .+.++... ..++ |||.||..||.+|+.+ ...||+||..+..
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            4678999999 88776543 3455 9999999999999765 4679999998754

>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=99.49  E-value=1.4e-14  Score=85.96  Aligned_cols=49  Identities=22%  Similarity=0.559  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-CCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-STCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.|.++   +.++ |||.||..||..|+..+ ..||+||..+..
T Consensus        50 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            4567899999999876   4566 99999999999999854 489999998864

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

Probab=99.48  E-value=4.4e-14  Score=79.19  Aligned_cols=53  Identities=17%  Similarity=0.101  Sum_probs=47.1

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..+.+++..|+||++.|.++   ++++ |||.|++.||.+|+..+.+||+||..+..
T Consensus         8 ~~~~p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A            8 YSDAPDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTCCTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             hhcCchheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            35568899999999999988   5676 99999999999999988999999998764

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

Probab=99.47  E-value=2.9e-14  Score=84.01  Aligned_cols=53  Identities=21%  Similarity=0.424  Sum_probs=45.0

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC-Cccccccccchh
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEVAIV   60 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~   60 (86)
                      +..+++..|+||++.+.++   +.++ |||.||..||..|+..+. .||+||..+...
T Consensus        13 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           13 PPLESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             SCCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             cCCCCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            4567789999999999876   4566 999999999999998755 999999988653

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

Probab=99.47  E-value=4.1e-14  Score=77.63  Aligned_cols=51  Identities=25%  Similarity=0.547  Sum_probs=42.1

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC--CCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~   60 (86)
                      ....+|+||++.+..++   ..+.|+|.||..||.+||+++  .+||+||..+...
T Consensus        13 ~~i~~C~IC~~~i~~g~---~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSCBCSSSCCBCSSSE---ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCCcCcchhhHcccCC---ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            44578999999998663   333599999999999999976  7899999988644

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

Probab=99.45  E-value=4.8e-14  Score=83.58  Aligned_cols=54  Identities=26%  Similarity=0.614  Sum_probs=44.9

Q ss_pred             CCcccccccccccccCC----CceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            6 CPYYCYCTVCLDGISDG----QKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~----~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      .++...|+||++.+..+    ...+.++ |||.||..||.+|+..+++||+||..+...
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            35678999999998753    2335666 999999999999999999999999988654

>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=99.45  E-value=3.4e-14  Score=87.87  Aligned_cols=50  Identities=28%  Similarity=0.642  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.|.++  +..++ |||.||..||..|+.. +..||+||..+..
T Consensus        52 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            4567999999999865  33336 9999999999999997 7789999998753

>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=99.45  E-value=1.6e-14  Score=84.56  Aligned_cols=52  Identities=25%  Similarity=0.669  Sum_probs=44.1

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      ....++..|+||++.+.++   +.++ |||.||..||.+|+.. ...||+||..+..
T Consensus        10 ~~~~~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           10 IPSLSECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCCHHHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             cCCCCCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3446678999999999877   4666 9999999999999986 6689999998864

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

Probab=99.44  E-value=1e-13  Score=76.65  Aligned_cols=56  Identities=14%  Similarity=0.209  Sum_probs=43.1

Q ss_pred             CCCCcccccccccccccCCCce-eEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            4 AKCPYYCYCTVCLDGISDGQKF-RRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~-~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      ....++.+|+||++.+...+.. ..++ |||.||..|+.+++.. ...||+||..+...
T Consensus         6 ~~~~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSC
T ss_pred             cccccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCC
Confidence            3457789999999998644322 2233 9999999999998864 56899999988654

>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=99.43  E-value=6.5e-14  Score=82.11  Aligned_cols=50  Identities=28%  Similarity=0.493  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      .++..|+||++.+.++   +.++ |||.||..||.+|+.. +..||+||..+...
T Consensus        21 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           21 VKSISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HHHTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCCCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            4567899999999876   4566 9999999999999997 77899999988653

>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=99.43  E-value=1.1e-13  Score=79.77  Aligned_cols=52  Identities=17%  Similarity=0.122  Sum_probs=46.5

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+.+++..||||++.|.+|   ++++ |||.|++.||.+|+..+.+||+||.++..
T Consensus        24 ~~~p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           24 SDAPDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             SSCSTTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             ccCcHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            4568899999999999988   5677 99999999999999988899999998764

>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=99.43  E-value=5e-14  Score=81.80  Aligned_cols=49  Identities=24%  Similarity=0.632  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC---Cccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS---TCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~---~CP~Cr~~~~~   59 (86)
                      .+...|+||++.+.++   +.++ |||.||..||..|+..+.   .||+||..+..
T Consensus        19 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           19 QKILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HHHTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            3567899999999876   3456 999999999999998653   89999998764

>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=99.42  E-value=1.5e-13  Score=78.91  Aligned_cols=52  Identities=17%  Similarity=0.098  Sum_probs=46.2

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCC-CcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECK-HCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+.+++..||||++.|.+|   ++++ || |.|++.||.+||..+.+||+||..+..
T Consensus        17 ~~~p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           17 ADACDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CSCCTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             hcCcHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            4568899999999999988   5666 99 999999999999988899999998764

>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=99.42  E-value=6.4e-14  Score=85.87  Aligned_cols=50  Identities=20%  Similarity=0.527  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC-Cccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~~~   60 (86)
                      ++...|+||++.|.++   ++++ |||.||..||..|+.... .||+||..+...
T Consensus        76 ~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           76 EQSFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             ccCCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            3567899999999876   4566 999999999999999754 899999988653

>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=99.38  E-value=1.3e-13  Score=83.77  Aligned_cols=50  Identities=20%  Similarity=0.424  Sum_probs=42.6

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC-Cccccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEVA   58 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~-~CP~Cr~~~~   58 (86)
                      ..+++..|+||++.+.++   +.++ |||.||..||.+|+.... .||+||..+.
T Consensus        27 ~l~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             cCCcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            457788999999999877   4565 999999999999998765 8999999753

>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=99.33  E-value=4.5e-13  Score=71.37  Aligned_cols=49  Identities=18%  Similarity=0.413  Sum_probs=41.1

Q ss_pred             CCcccccccccccccCCCceeEc--CCCCCc-chHHhHHHHHhcCCCccccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRL--PECKHC-FHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~--~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      ..++.+|+||++.+.+.   ..+  | |||. ||..|+.+|++.+..||+||..+.
T Consensus         5 ~~~~~~C~IC~~~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            5 LNAIEPCVICQGRPKNG---CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             CGGGSCCTTTSSSCSCE---EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCCcCCCCcCCCCCCCE---EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            35677899999986654   333  7 9999 899999999998899999999874

>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=99.31  E-value=1.2e-12  Score=81.17  Aligned_cols=53  Identities=21%  Similarity=0.420  Sum_probs=44.7

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-CCccccccccchh
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-STCPLCRIEVAIV   60 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~~   60 (86)
                      ++.++...|+||++.+.++   +.++ |||.||..||.+|+..+ ..||+||..+...
T Consensus        13 ~~~~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           13 PPLESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             SCCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             cCCCCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            4567889999999999877   4566 99999999999999864 4999999988653

>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=99.29  E-value=3e-13  Score=79.48  Aligned_cols=46  Identities=22%  Similarity=0.568  Sum_probs=40.1

Q ss_pred             CcccccccccccccCCCceeEc-CCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRL-PECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~-~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .+...|+||++.|.++   +.+ + |||.||..||..|+.  ..||+||..+.
T Consensus        20 ~~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           20 EKLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HHTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hhCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            4678999999999877   355 5 999999999999998  78999999874

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

Probab=99.29  E-value=3e-13  Score=70.22  Aligned_cols=46  Identities=26%  Similarity=0.644  Sum_probs=38.8

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+...|+||++.|.++   +.++ |||.||..|+..   ....||+||..+..
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~---~~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEA---SGMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSS---SSSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHcc---CCCCCCcCCcEeec
Confidence            5678899999999887   4676 999999999977   36689999998754

>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=99.28  E-value=1.4e-12  Score=69.26  Aligned_cols=50  Identities=20%  Similarity=0.466  Sum_probs=40.2

Q ss_pred             CcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      .....|+||++...+.. +..+| |||. ||..|+.+|.+++..||+||..+.
T Consensus         5 ~~~~~C~IC~~~~~~~~-~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGN-IIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSCEE-EEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCCeE-EEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            45678999999866531 12237 9998 999999999988889999999874

>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=99.27  E-value=2.1e-12  Score=73.43  Aligned_cols=49  Identities=18%  Similarity=0.396  Sum_probs=40.9

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC------CCccc--cccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR------STCPL--CRIE   56 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~------~~CP~--Cr~~   56 (86)
                      +.+.+..||||++.|.+|   ++++.|||.|++.||.+||..+      ..||+  |+..
T Consensus         3 ~~~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            3 SGSSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCSSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CCCcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            457889999999999987   4553499999999999999864      48999  9865

>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=99.26  E-value=2.8e-12  Score=88.67  Aligned_cols=48  Identities=27%  Similarity=0.778  Sum_probs=41.3

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~   59 (86)
                      ....|+||++.+.++   +.++ |||.||..|+..|+. .+..||+||..+..
T Consensus       331 ~~~~C~ICle~~~~p---v~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          331 TFQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSSBCTTTSSSBCCE---EEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCCccCcCCCCe---EEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            347999999998665   5677 999999999999999 68899999998764

>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=99.24  E-value=5.7e-12  Score=82.46  Aligned_cols=51  Identities=14%  Similarity=0.201  Sum_probs=44.1

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-CCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-STCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~   59 (86)
                      +.+....|+||++.|.+|   ++++ |||.|++.||.+|+..+ .+||+||.++..
T Consensus       204 ~~~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCCcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            457889999999999988   5676 99999999999999864 459999998864

>4ic3_A E3 ubiquitin-protein ligase XIAP; ring domain, zinc-finger, E3 ligase; 1.78A {Homo sapiens} PDB: 4ic2_A

Probab=99.23  E-value=1.6e-12  Score=70.90  Aligned_cols=45  Identities=24%  Similarity=0.579  Sum_probs=38.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.+.++   +.++ |||. ||..|+..|    ..||+||..+..
T Consensus        22 ~~~~~C~iC~~~~~~~---~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           22 QEEKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHTBCTTTSSSBCCE---EEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             ccCCCCCCCCCCCCCE---EEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            4567899999998765   5677 9999 999999988    789999998753

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

Probab=99.17  E-value=6.7e-12  Score=85.67  Aligned_cols=57  Identities=21%  Similarity=0.603  Sum_probs=43.0

Q ss_pred             CCCcccccccccccccCCCcee----EcCCCCCcchHHhHHHHHhcC-----------CCccccccccchhh
Q 036506            5 KCPYYCYCTVCLDGISDGQKFR----RLPECKHCFHVECIDAWFQSR-----------STCPLCRIEVAIVI   61 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~----~~~~C~H~fh~~Ci~~wl~~~-----------~~CP~Cr~~~~~~~   61 (86)
                      +.....+|+||++.+.+...+.    ..+.|+|.||..||.+|+++.           +.||+||.++....
T Consensus       304 ~ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf  375 (381)
T 3k1l_B          304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSF  375 (381)
T ss_dssp             CCCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGG
T ss_pred             cccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccH
Confidence            3457789999999988733221    122599999999999999752           46999999887554

>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=99.16  E-value=2e-11  Score=69.17  Aligned_cols=53  Identities=19%  Similarity=0.397  Sum_probs=42.2

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc--------CCCccc--cccc--cchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS--------RSTCPL--CRIE--VAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~--------~~~CP~--Cr~~--~~~~   60 (86)
                      .+..+|+||++.+..++.+...+ |||.||..|+.+++..        ...||.  |+..  +...
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~   67 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN   67 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHH
T ss_pred             CCCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHH
Confidence            46789999999998776555556 9999999999999863        137999  9988  5543

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.15  E-value=3.5e-11  Score=75.66  Aligned_cols=52  Identities=13%  Similarity=0.189  Sum_probs=45.0

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC-CCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR-STCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~-~~CP~Cr~~~~~   59 (86)
                      .+.|+...||||++.|.+|   ++++ |||.|++.||..|+..+ .+||+|+.++..
T Consensus       101 ~~ip~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          101 REIPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCCcHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            4568999999999999987   5666 99999999999999864 479999998764

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.08  E-value=2.5e-11  Score=66.22  Aligned_cols=45  Identities=24%  Similarity=0.583  Sum_probs=36.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.+.++   +.++ |||. ||..|+.+    ...||+||..+..
T Consensus        23 ~~~~~C~IC~~~~~~~---~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHHSCSSSCSSCCCB---CCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCCcCCCCCCCE---EEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            3467899999998765   4567 9999 99999964    4789999998753

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.07  E-value=1.1e-10  Score=62.76  Aligned_cols=47  Identities=30%  Similarity=0.601  Sum_probs=38.4

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ...++..|.||++...+.   +.+| |||. ||..|+..    ...||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~---v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           11 SEENSKDCVVCQNGTVNW---VLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             SCCCSSCCSSSSSSCCCC---EETT-TTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             cCCCCCCCCCcCcCCCCE---EEEC-CCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            345678999999987654   6777 9999 99999984    5789999998754

>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=99.04  E-value=2.6e-11  Score=67.00  Aligned_cols=46  Identities=28%  Similarity=0.611  Sum_probs=37.7

Q ss_pred             CcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccchh
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      .++..|+||++.+.+.   +.+| |||. ||..|+..|    ..||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~~---v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           16 KEAMLCMVCCEEEINS---TFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHHTBCTTTSSSBCCE---EEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCCEeEEeCcccCcE---EEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            4567899999987654   5777 9999 999999876    4899999987653

>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=99.02  E-value=1.4e-10  Score=76.55  Aligned_cols=52  Identities=19%  Similarity=0.389  Sum_probs=42.3

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC--CCccc--cccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPL--CRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~--Cr~~~~~   59 (86)
                      ....+..||||++.|.+|   ++...|||.|++.||..|+..+  ..||+  |+..+..
T Consensus       177 ~~~~el~CPIcl~~f~DP---Vts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          177 GGKIELTCPITCKPYEAP---LISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             SSBCCSBCTTTSSBCSSE---EEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             CCceeeECcCccCcccCC---eeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            347788999999999877   3332499999999999999864  47999  9987754

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=99.02  E-value=2.3e-10  Score=60.21  Aligned_cols=51  Identities=16%  Similarity=0.496  Sum_probs=38.3

Q ss_pred             CCCcccccccccccccCCCceeEcC-CCCC---cchHHhHHHHHhc--CCCccccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLP-ECKH---CFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~-~C~H---~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      +..+...|.||++...++  . ++| .|.+   .||..||.+|+..  +.+||+|+..+.
T Consensus         2 e~~~~~~CrIC~~~~~~~--l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            2 EDEDVPVCWICNEELGNE--R-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TTCSCCEETTTTEECSCC--C-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCEeEEeecCCCCc--e-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            345677899999984332  2 466 2444   9999999999975  578999998874

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.82  E-value=5.5e-10  Score=76.29  Aligned_cols=45  Identities=29%  Similarity=0.572  Sum_probs=38.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCc-chHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHC-FHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~-fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .++..|+||++.+.++   +.++ |||. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~~~---v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEVSV---VFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBCCE---EEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCCce---EEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            3567899999998765   5677 9999 999999987    789999998753

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.79  E-value=2.3e-09  Score=56.43  Aligned_cols=49  Identities=10%  Similarity=0.203  Sum_probs=41.1

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ...|+|+++.+.++   ++++.+||.|.+.+|.+|+..+.+||+.+.++...
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCC---EEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            35799999999977   45524999999999999999888899999988654

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

Probab=98.57  E-value=4e-08  Score=64.08  Aligned_cols=49  Identities=24%  Similarity=0.581  Sum_probs=40.6

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC--CCccccccccchh
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR--STCPLCRIEVAIV   60 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~--~~CP~Cr~~~~~~   60 (86)
                      -..|.||.+.+..+   ...+.|+|.||..|+..|++.+  ..||.|+..+...
T Consensus       180 i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            56799999998876   3454599999999999999864  4899999988654

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.53  E-value=7.8e-08  Score=55.01  Aligned_cols=47  Identities=30%  Similarity=0.562  Sum_probs=37.3

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      .|++|--++..  ..+.+| |+|+||.+|+..|..+ .+.||.|+.++...
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            36777777653  346888 9999999999999865 68999999987654

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=97.03  E-value=0.00046  Score=38.78  Aligned_cols=35  Identities=17%  Similarity=0.364  Sum_probs=25.1

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHH
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW   43 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w   43 (86)
                      ++..|+||++.+..+....-+. |+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            5688999997643322222255 9999999999984

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=96.74  E-value=0.0011  Score=34.99  Aligned_cols=49  Identities=29%  Similarity=0.465  Sum_probs=35.3

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC----Cccccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS----TCPLCRIE   56 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~----~CP~Cr~~   56 (86)
                      .....+..|.||.+.    ..+.....|...||..|+.+.+....    .||.|...
T Consensus         7 ~~~~~~~~C~vC~~~----~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C            7 QNLAPGARCGVCGDG----TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             TCCCTTCCCTTTSCC----TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             cCCCCCCCcCCCCCC----CeEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            344556789999753    33445556999999999988776532    69999764

>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=95.62  E-value=0.013  Score=32.36  Aligned_cols=39  Identities=21%  Similarity=0.347  Sum_probs=27.0

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHH
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW   43 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w   43 (86)
                      .+..+.+..|.||-.. ...+.. -...|+-+||..|+.+.
T Consensus         9 ~e~~~~D~~C~VC~~~-t~~~l~-pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A            9 REPVVNDEMCDVCEVW-TAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCCSCCCTTTCCC-CSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             ccCCCCCcccCccccc-ccccee-ccccccccccHhhcccc
Confidence            4566788999999754 222221 11248999999999996

>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=95.12  E-value=0.021  Score=29.86  Aligned_cols=37  Identities=22%  Similarity=0.478  Sum_probs=25.5

Q ss_pred             CCCCcccccccccccccCCCceeEcC-CCCCcchHHhH
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLP-ECKHCFHVECI   40 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~-~C~H~fh~~Ci   40 (86)
                      ++++....|++|...+.+....+... .|..-||..|+
T Consensus         3 ~~~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cv   40 (65)
T 2vpb_A            3 SSSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICT   40 (65)
T ss_dssp             ------CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHH
T ss_pred             CCCCCcCcCccCCCccCCCCCeEecccCccccCchhcc
Confidence            34677788999999987665555555 69999999998

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=94.85  E-value=0.023  Score=29.21  Aligned_cols=48  Identities=25%  Similarity=0.647  Sum_probs=33.7

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----CCCcccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----RSTCPLCRI   55 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~   55 (86)
                      .+...+..|.||...    ..+.....|...||..|+..-+..    .=.||.|+.
T Consensus         6 ~~~~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            6 YETDHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CSSCCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             ccCCCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            345667889999874    334444468899999999875443    226999965

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=94.68  E-value=0.02  Score=29.54  Aligned_cols=51  Identities=18%  Similarity=0.379  Sum_probs=35.6

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-----cCCCcccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-----SRSTCPLCRI   55 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~   55 (86)
                      ++.++..|+||...+.+....+....|..-||..|+.--..     ..-.||.|+.
T Consensus         2 s~~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            2 SSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             CCSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            45678889999998764444444446899999999854221     2346999965

>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=94.51  E-value=0.05  Score=41.65  Aligned_cols=52  Identities=21%  Similarity=0.218  Sum_probs=45.7

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCC-CcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECK-HCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~-H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+.|++..|||=++.+.+|   ++++ -| +.|=+..|.+|+.++.+||.=|.++..
T Consensus       886 ~~iP~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          886 GDVPDEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             CCSCGGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             cCCcHHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            5679999999999999988   5676 66 689999999999999999999988764

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.21  E-value=0.013  Score=31.27  Aligned_cols=52  Identities=17%  Similarity=0.401  Sum_probs=35.1

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----CCCcccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----RSTCPLCRIEV   57 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~   57 (86)
                      +..+...|.||..... +..++....|...||..|+..-...    .-.||.|+..+
T Consensus        14 ~~~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~   69 (75)
T 2k16_A           14 WGNQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKI   69 (75)
T ss_dssp             SSCEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHH
T ss_pred             cCCCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCch
Confidence            3456667999988753 3334444468999999999764432    33699997654

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.54  E-value=0.0081  Score=30.38  Aligned_cols=48  Identities=23%  Similarity=0.683  Sum_probs=33.1

Q ss_pred             CCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCccccc
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCR   54 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr   54 (86)
                      ..+...+..|.||...   + .+.....|...||..|+.+-+...    -.||.|.
T Consensus         3 ~g~~~~~~~C~vC~~~---g-~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~   54 (56)
T 2yql_A            3 SGSSGHEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQ   54 (56)
T ss_dssp             CCCCSSCCSCSSSCCS---S-CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHH
T ss_pred             CCcCCCCCCCccCCCC---C-eEEEcCCCCcceECccCCCCcCCCCCCceEChhhh
Confidence            4566778889999875   2 334444689999999998644432    1577774

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=93.47  E-value=0.035  Score=27.29  Aligned_cols=44  Identities=30%  Similarity=0.634  Sum_probs=29.1

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRI   55 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~   55 (86)
                      .|.||...-.. ..+.....|...||..|+.+=+...    =.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCC-CCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            58888876333 3344445699999999997644432    25888864

>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=93.10  E-value=0.014  Score=30.03  Aligned_cols=49  Identities=22%  Similarity=0.583  Sum_probs=33.0

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCccccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRIE   56 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~   56 (86)
                      ++...+..|.||.+.    ..+.....|...||..|+.+-+...    =.||.|+..
T Consensus         4 ~~d~~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            4 GSDHHMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSCSSCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             cccCCCCcCCCCCCC----CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            345667889999863    2233334588999999998644432    269999764

>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=92.77  E-value=0.11  Score=27.89  Aligned_cols=50  Identities=20%  Similarity=0.418  Sum_probs=32.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-----cCCCcccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-----SRSTCPLCRIEV   57 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~~~   57 (86)
                      .+...| ||...+......+....|..-||..|+.--..     ..-.||.|+...
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            455666 89888753333444446999999999842211     244799998754

>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=92.73  E-value=0.34  Score=26.96  Aligned_cols=53  Identities=23%  Similarity=0.437  Sum_probs=38.0

Q ss_pred             cccccccccccccC---CCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccchh
Q 036506            8 YYCYCTVCLDGISD---GQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~---~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~   60 (86)
                      ....|.||-+.+-.   ++..+....|+-..|+.|.+-=.+ .++.||.|++.+...
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr~   71 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccccc
Confidence            45689999998642   333344445888899999976444 477899999988643

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=92.70  E-value=0.038  Score=31.07  Aligned_cols=48  Identities=21%  Similarity=0.364  Sum_probs=31.8

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc---CCCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS---RSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~---~~~CP~Cr~~   56 (86)
                      .+...| ||......+.. +....|.-.||..|+..-+..   .-.||.|+..
T Consensus        26 ~d~vrC-iC~~~~~~~~m-i~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           26 TDVTRC-ICGFTHDDGYM-ICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CCBCCC-TTSCCSCSSCE-EEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CCCEEe-ECCCccCCCcE-EEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            344667 89877555443 444569999999998653332   2379999743

>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=92.08  E-value=0.027  Score=34.82  Aligned_cols=47  Identities=28%  Similarity=0.648  Sum_probs=33.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRIEV   57 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~   57 (86)
                      +.+..|.+|.+.   ++ +.....|...||..|+.+-+...    =.||.|+..-
T Consensus         2 ~~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            2 PNEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             CSCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            566789999854   23 44555689999999997766542    2699998653

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.87  E-value=0.037  Score=31.71  Aligned_cols=46  Identities=26%  Similarity=0.563  Sum_probs=30.4

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRI   55 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~   55 (86)
                      ..|.||...-.+++.+.....|...||..|+.+-|...    =.||.|+.
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            36778876533334444555699999999997655432    26888864

>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=91.84  E-value=0.031  Score=35.28  Aligned_cols=48  Identities=27%  Similarity=0.559  Sum_probs=34.5

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRIE   56 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~   56 (86)
                      +.+.+..|.+|...    ..+.....|...||..|+.+-+...    =.||.|+..
T Consensus         3 ~d~~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            3 DDPNEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             CCSSCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            44566779999854    2344555689999999998766542    269999864

>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=91.80  E-value=0.4  Score=26.25  Aligned_cols=42  Identities=17%  Similarity=0.262  Sum_probs=31.1

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS   46 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~   46 (86)
                      .....+.|.+|.+.+++..-+..-..=.|.||..|-...+++
T Consensus        11 ~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           11 ANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            345678999999999876544322233799999999998874

>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=91.40  E-value=0.11  Score=26.76  Aligned_cols=51  Identities=18%  Similarity=0.414  Sum_probs=35.1

Q ss_pred             CCCccccccccccccc-CCCceeEcCCCCCcchHHhHHHHHh-------cCCCcccccc
Q 036506            5 KCPYYCYCTVCLDGIS-DGQKFRRLPECKHCFHVECIDAWFQ-------SRSTCPLCRI   55 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~-~~~~~~~~~~C~H~fh~~Ci~~wl~-------~~~~CP~Cr~   55 (86)
                      +..++..|.||..... ++..+.....|.-.||..|+.+-+.       ..=.||.|..
T Consensus         2 ~~~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~   60 (66)
T 2yt5_A            2 SSGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVF   60 (66)
T ss_dssp             CCCCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcC
Confidence            5667889999998643 2344555557999999999876332       1236888865

>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=90.84  E-value=0.24  Score=24.39  Aligned_cols=44  Identities=18%  Similarity=0.375  Sum_probs=28.0

Q ss_pred             ccccccccccCCCceeEcC-CCCCcchHHhHHHH----HhcCCCccccc
Q 036506           11 YCTVCLDGISDGQKFRRLP-ECKHCFHVECIDAW----FQSRSTCPLCR   54 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~-~C~H~fh~~Ci~~w----l~~~~~CP~Cr   54 (86)
                      .|.||...+.++...+... .|..-||..|+.--    ....-.||.|+
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            5788988876544444444 48889999997421    12345687774

>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=90.05  E-value=0.075  Score=30.22  Aligned_cols=40  Identities=20%  Similarity=0.307  Sum_probs=28.1

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ   45 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~   45 (86)
                      ....+..|.||.+.-...+.+ ....|+..||..|+...+.
T Consensus         3 ~~~~~~~C~~C~~~g~~~~ll-~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            3 SGSSGANCAVCDSPGDLLDQF-FCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCCCSCBTTTCCCCCTTTSE-ECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCCCcCCCCCCCCcCCe-ECCCCCCCcChHHhCCccc
Confidence            346778899998874332223 3345999999999987654

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=89.70  E-value=0.67  Score=27.79  Aligned_cols=48  Identities=21%  Similarity=0.384  Sum_probs=33.6

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh---------c--CCCccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ---------S--RSTCPLCRIE   56 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~---------~--~~~CP~Cr~~   56 (86)
                      +...+..|.+|.+.    ..+.....|...||..||.+-+.         .  .=.||+|+..
T Consensus        59 ~Dg~~d~C~vC~~G----G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           59 SDGMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TTSCBCSCSSSCCC----SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCCeecccCCC----CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            34567889999875    23334445899999999997653         1  2269999753

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=89.60  E-value=0.041  Score=28.65  Aligned_cols=46  Identities=26%  Similarity=0.560  Sum_probs=31.9

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRI   55 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~   55 (86)
                      ...+..|.||.+.   + .+.....|...||..|+.+-+...    =.||.|..
T Consensus         5 ~~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            5 QKNEDECAVCRDG---G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             CSCCCSBSSSSCC---S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCccCCCC---C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccC
Confidence            3567789999864   2 334444688999999998644432    25999964

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=89.56  E-value=0.037  Score=28.20  Aligned_cols=46  Identities=24%  Similarity=0.708  Sum_probs=31.6

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCcccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~~   57 (86)
                      .+..|.||...   + .+.....|...||..|+.+-+...    -.||.|....
T Consensus         4 ~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   53 (60)
T 2puy_A            4 HEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM   53 (60)
T ss_dssp             CCSSCTTTCCC---S-SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHH
T ss_pred             CCCCCcCCCCC---C-cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChh
Confidence            46789999874   2 334444699999999998644432    2699996543

>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=89.09  E-value=0.36  Score=25.44  Aligned_cols=36  Identities=17%  Similarity=0.168  Sum_probs=24.9

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      ..+..|.+|...|..-..--....||.+||..|...
T Consensus         9 ~~~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A            9 IDSDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             CCCSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             ccCCcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            345689999998875322223346999999999643

>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=88.52  E-value=0.045  Score=30.44  Aligned_cols=51  Identities=24%  Similarity=0.479  Sum_probs=34.3

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC----CCccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR----STCPLCRIE   56 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~----~~CP~Cr~~   56 (86)
                      +..++..|.||...-.. ..+.....|...||..|+.+=+...    =.||.|+..
T Consensus        12 ~~~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           12 QFIDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             hccCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            34556689999886432 3344555699999999997544432    259999653

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=88.43  E-value=0.69  Score=24.35  Aligned_cols=52  Identities=19%  Similarity=0.418  Sum_probs=35.3

Q ss_pred             CCCCcccccccccccc-cCCCceeEcCCCCCcchHHhHHHHHhc--CCCcccccc
Q 036506            4 AKCPYYCYCTVCLDGI-SDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRI   55 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~-~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~   55 (86)
                      .....+..|.||.+.- .+++.+.....|.-.||..|+..-..-  .=.||.|+.
T Consensus        11 ~~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           11 SLIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CCCCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             cCCCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            4557788999998763 234455555579999999999753211  226888864

>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=88.21  E-value=0.26  Score=27.91  Aligned_cols=48  Identities=25%  Similarity=0.499  Sum_probs=32.6

Q ss_pred             cccccccccccCCCceeEcC-CCCCcchHHhHHHH------Hh----cCCCcccccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLP-ECKHCFHVECIDAW------FQ----SRSTCPLCRIEV   57 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~-~C~H~fh~~Ci~~w------l~----~~~~CP~Cr~~~   57 (86)
                      ..|+||...+.+....+..- .|..-||..|+.--      +.    ..-.||.|+...
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            46999999986654444443 58999999998321      10    234799997643

>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=88.02  E-value=0.015  Score=34.06  Aligned_cols=48  Identities=19%  Similarity=0.365  Sum_probs=31.2

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIE   56 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~   56 (86)
                      ...|..|...|..-..--....||.+||..|........+.|-.|...
T Consensus        19 ~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~   66 (120)
T 1y02_A           19 EPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRF   66 (120)
T ss_dssp             -CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHH
T ss_pred             cCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHH
Confidence            357999999886432223444699999999977665556778888553

>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=88.00  E-value=0.61  Score=24.58  Aligned_cols=48  Identities=25%  Similarity=0.615  Sum_probs=31.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHH------H---hcCCCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW------F---QSRSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w------l---~~~~~CP~Cr~~   56 (86)
                      +....| ||.........| ....|..-||..|+.--      +   ...-.||.|+..
T Consensus        14 ~~~~~C-~C~~~~~~~~MI-~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           14 PNALYC-ICRQPHNNRFMI-CCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TTCCCS-TTCCCCCSSCEE-ECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCCCEE-ECCCccCCCCEE-EeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            445677 898876543344 34459999999998321      1   235679999754

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=87.58  E-value=0.18  Score=27.93  Aligned_cols=47  Identities=28%  Similarity=0.681  Sum_probs=33.0

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC----Cccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS----TCPLCRIE   56 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~----~CP~Cr~~   56 (86)
                      ...+..|.+|...   + .+.....|.-.||..|+.+=+....    .||.|+..
T Consensus        22 d~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           22 DDSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            3566789999865   2 3344446889999999987655422    69999753

>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=87.46  E-value=0.39  Score=25.31  Aligned_cols=46  Identities=26%  Similarity=0.644  Sum_probs=28.3

Q ss_pred             CCcccccccccccccCCCceeEcCC--CC-CcchHHhHHHHHhc----CCCccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPE--CK-HCFHVECIDAWFQS----RSTCPLCRIE   56 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~~   56 (86)
                      ..+...| ||..... +. ++..-.  |. ..||..|+.  |..    .-.||.|+..
T Consensus        13 ~~~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~   65 (71)
T 1wen_A           13 PNEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   65 (71)
T ss_dssp             TTSCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcc
Confidence            3456677 8988643 33 222223  44 589999997  333    2369999764

>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=87.35  E-value=1.3  Score=26.10  Aligned_cols=49  Identities=20%  Similarity=0.391  Sum_probs=33.1

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHH-----hc------CCCccccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWF-----QS------RSTCPLCRIE   56 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl-----~~------~~~CP~Cr~~   56 (86)
                      ++...+..|.||.+.    ..+.....|-..||..||.+-+     ..      .=.|++|+..
T Consensus        52 d~Dg~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           52 DSDGMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             CTTSCBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCCCCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            345567789999875    2333444588999999999752     11      2279999653

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=86.09  E-value=0.79  Score=24.72  Aligned_cols=36  Identities=11%  Similarity=0.136  Sum_probs=25.5

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .+...|.+|...|..-..--....||.+||..|...
T Consensus        19 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   54 (84)
T 1z2q_A           19 EDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRH   54 (84)
T ss_dssp             TTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCC
T ss_pred             CCCCCCcCcCCccccchhcccccCCCcEEChHHhCC
Confidence            455689999999875432223346999999999755

>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=85.74  E-value=0.74  Score=25.18  Aligned_cols=53  Identities=15%  Similarity=0.243  Sum_probs=34.3

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-------cCCCccccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-------SRSTCPLCRIEVA   58 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-------~~~~CP~Cr~~~~   58 (86)
                      +.+...|.+|...|..-..--....||.+||..|....+.       ..+.|-.|...+.
T Consensus         6 ~~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~   65 (88)
T 1wfk_A            6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILT   65 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHH
T ss_pred             CCcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHH
Confidence            4455689999999875432223446999999999765321       1345777765443

>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=85.73  E-value=0.55  Score=29.23  Aligned_cols=50  Identities=18%  Similarity=0.419  Sum_probs=35.5

Q ss_pred             ccccccccccccCCCc---eeEcCCCCCcchHHhHHH------HHh-----cCCCccccccccc
Q 036506            9 YCYCTVCLDGISDGQK---FRRLPECKHCFHVECIDA------WFQ-----SRSTCPLCRIEVA   58 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~---~~~~~~C~H~fh~~Ci~~------wl~-----~~~~CP~Cr~~~~   58 (86)
                      +..|+||...+.+++.   .+....|..-||..|+.-      -+.     ..-.||.|+..-.
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            4579999999887652   445556999999999832      111     1458999987644

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=85.17  E-value=0.66  Score=24.93  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=25.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .+...|.+|...|..-..--....||.+||..|...
T Consensus        17 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   52 (82)
T 2yw8_A           17 DEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSN   52 (82)
T ss_dssp             CCCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCE
T ss_pred             ccCCcccCcCCcccCccccccCCCCCCEEChHHhCC
Confidence            344579999999875432223446999999999754

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=84.98  E-value=2.1  Score=24.18  Aligned_cols=34  Identities=18%  Similarity=0.456  Sum_probs=23.1

Q ss_pred             cccccccccccc-----cCCCceeEcCCCCCcchHHhHH
Q 036506            8 YYCYCTVCLDGI-----SDGQKFRRLPECKHCFHVECID   41 (86)
Q Consensus         8 ~~~~C~ICl~~~-----~~~~~~~~~~~C~H~fh~~Ci~   41 (86)
                      ....|.+|+..-     ..++.+..-..|+..||..|+.
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            346789998752     1223344555699999999995

>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=84.48  E-value=0.7  Score=26.91  Aligned_cols=35  Identities=23%  Similarity=0.422  Sum_probs=24.3

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      +-..|.+|...|..-..--....||++||..|...
T Consensus        68 ~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~  102 (125)
T 1joc_A           68 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAK  102 (125)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCE
T ss_pred             CCCCCcCcCCccccccccccCCCCCeEEChHHhCC
Confidence            34579999999875332223446999999999644

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=84.01  E-value=0.86  Score=24.97  Aligned_cols=50  Identities=14%  Similarity=0.291  Sum_probs=32.0

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHh------cCCCcccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ------SRSTCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~------~~~~CP~Cr~~~   57 (86)
                      +...|.+|...|..-..--....||.+||..|...+..      ..+.|-.|...+
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l   74 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETI   74 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEEEETTTTEEEEECHHHHHHH
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCeeecCCCCCCCeECHHHHHHH
Confidence            34579999998865332224446999999999765432      123566665544

>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=84.00  E-value=0.36  Score=24.53  Aligned_cols=45  Identities=24%  Similarity=0.628  Sum_probs=26.2

Q ss_pred             CCcccccccccccccCCCceeEcCC--CC-CcchHHhHHHHHhc----CCCcccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPE--CK-HCFHVECIDAWFQS----RSTCPLCRI   55 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~   55 (86)
                      ..+...| ||..... + .++....  |. ..||..|+.  |..    .-.||.|+.
T Consensus         7 ~~e~~~C-~C~~~~~-g-~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            7 PNEPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             --CCEET-TTTEECC-S-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCCCEE-ECCCcCC-C-CEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            3455666 8988632 3 2333334  44 579999997  333    226888854

>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=83.93  E-value=0.92  Score=25.84  Aligned_cols=49  Identities=22%  Similarity=0.559  Sum_probs=30.6

Q ss_pred             CCCCCcccccccccccccCCCceeEcC--CCCCcchHHhHHHHHhcCC----Ccccccccc
Q 036506            3 AAKCPYYCYCTVCLDGISDGQKFRRLP--ECKHCFHVECIDAWFQSRS----TCPLCRIEV   57 (86)
Q Consensus         3 ~~~~~~~~~C~ICl~~~~~~~~~~~~~--~C~H~fh~~Ci~~wl~~~~----~CP~Cr~~~   57 (86)
                      ..+...+..|.+|.+.    ..+....  .|...||..|+.  |....    .||.|+-.+
T Consensus         9 ~~~~~~~~~C~~C~~~----G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~   63 (107)
T 4gne_A            9 EPKQMHEDYCFQCGDG----GELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDE   63 (107)
T ss_dssp             -CCCSSCSSCTTTCCC----SEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTT
T ss_pred             CCcCCCCCCCCcCCCC----CcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCc
Confidence            3455677889999843    2333333  377899999997  44322    588765433

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=83.74  E-value=0.17  Score=27.28  Aligned_cols=44  Identities=34%  Similarity=0.642  Sum_probs=27.0

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----C-CCcccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----R-STCPLCRI   55 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~-~~CP~Cr~   55 (86)
                      .|.||...- ++..+.....|...||..|+.+-|..    . =.||.|+.
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            455555442 22344455568999999999875543    1 26888864

>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=83.54  E-value=0.8  Score=28.90  Aligned_cols=36  Identities=14%  Similarity=0.257  Sum_probs=25.1

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .++..|.+|...|..-..--....||++||..|...
T Consensus       159 ~~~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~  194 (220)
T 1dvp_A          159 ADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAK  194 (220)
T ss_dssp             CCCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCE
T ss_pred             CCCCccCCCCCccCCcccccccCCcCCEEChHHhCC
Confidence            346799999998864332223446999999988643

>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=83.47  E-value=0.41  Score=24.29  Aligned_cols=45  Identities=27%  Similarity=0.665  Sum_probs=26.9

Q ss_pred             CCcccccccccccccCCCceeEcCC--CC-CcchHHhHHHHHhc----CCCcccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPE--CK-HCFHVECIDAWFQS----RSTCPLCRI   55 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~   55 (86)
                      ..+...| ||.... .+. ++....  |. .-||..|+.  +..    .-.||.|+.
T Consensus         6 ~~e~~yC-~C~~~~-~g~-mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            6 SNEPTYC-LCHQVS-YGE-MIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             --CCEET-TTTEEC-CSE-EEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCCcEE-ECCCCC-CCC-eeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            3456667 898864 232 333334  55 689999997  333    226888864

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.37  E-value=0.89  Score=24.50  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=24.4

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .+-..|.+|...|..-..--....||.+||..|...
T Consensus        12 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           12 NNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            445689999998864322223336999999999543

>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=83.32  E-value=0.46  Score=26.91  Aligned_cols=12  Identities=25%  Similarity=1.113  Sum_probs=10.9

Q ss_pred             chHHhHHHHHhc
Q 036506           35 FHVECIDAWFQS   46 (86)
Q Consensus        35 fh~~Ci~~wl~~   46 (86)
                      ||+.|+.+|+..
T Consensus        43 FCRNCLskWy~~   54 (105)
T 2o35_A           43 FCRNCLSNWYRE   54 (105)
T ss_dssp             CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999974

>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=83.29  E-value=0.48  Score=26.28  Aligned_cols=45  Identities=27%  Similarity=0.659  Sum_probs=27.6

Q ss_pred             CcccccccccccccCCCceeEcCC--CC-CcchHHhHHHHHhc----CCCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPE--CK-HCFHVECIDAWFQS----RSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~--C~-H~fh~~Ci~~wl~~----~~~CP~Cr~~   56 (86)
                      .+...| ||..... +.. +....  |. ..||..|+.  |..    .-.||.|+..
T Consensus        34 ~e~~yC-iC~~~~~-g~M-I~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~   85 (91)
T 1weu_A           34 NEPTYC-LCHQVSY-GEM-IGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   85 (91)
T ss_dssp             CCCBCS-TTCCBCC-SCC-CCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCC
T ss_pred             CCCcEE-ECCCCCC-CCE-eEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCc
Confidence            455667 9988643 322 22223  44 579999997  332    2369999764

>3fyb_A Protein of unknown function (DUF1244); hydrocar degrading, structural genomics, PSI-2; HET: PEG; 1.80A {Alcanivorax borkumensis SK2}

Probab=83.14  E-value=0.47  Score=26.82  Aligned_cols=12  Identities=25%  Similarity=0.933  Sum_probs=10.9

Q ss_pred             chHHhHHHHHhc
Q 036506           35 FHVECIDAWFQS   46 (86)
Q Consensus        35 fh~~Ci~~wl~~   46 (86)
                      ||+.|+..|+..
T Consensus        42 FCRNCLskWy~~   53 (104)
T 3fyb_A           42 FCRNCLAKWLME   53 (104)
T ss_dssp             CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999973

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=82.96  E-value=1.1  Score=24.52  Aligned_cols=50  Identities=20%  Similarity=0.450  Sum_probs=33.7

Q ss_pred             Ccccccccccccc-cCCCceeEcCCCCCcchHHhHHHHHhc--CCCccccccc
Q 036506            7 PYYCYCTVCLDGI-SDGQKFRRLPECKHCFHVECIDAWFQS--RSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~-~~~~~~~~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~   56 (86)
                      ..+..|.||...- .+.+.+.....|.-.||..|+..-+.-  .=.||.|...
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~   75 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCc
Confidence            5678899999763 233345555568899999999753221  2269999654

>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=82.87  E-value=1.6  Score=23.16  Aligned_cols=48  Identities=21%  Similarity=0.466  Sum_probs=30.6

Q ss_pred             CcccccccccccccCCCceeEcC--CCCCcchHHhHHHHHh---------cCCCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLP--ECKHCFHVECIDAWFQ---------SRSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~--~C~H~fh~~Ci~~wl~---------~~~~CP~Cr~~   56 (86)
                      .+...| ||......+..| ..-  .|..-||..|+.---.         ..-.||.|+..
T Consensus        14 ~~~~~C-iC~~~~~~g~MI-~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           14 EIKVRC-VCGNSLETDSMI-QCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCC-SSCCCCCCSCEE-ECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCEEe-ECCCcCCCCCEE-EECCccCCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            456677 898874444333 333  4889999999853211         24479999754

>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=82.04  E-value=0.46  Score=21.62  Aligned_cols=16  Identities=13%  Similarity=0.453  Sum_probs=9.9

Q ss_pred             CcccccccccccccCC
Q 036506            7 PYYCYCTVCLDGISDG   22 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~   22 (86)
                      .+...||||+..+...
T Consensus         3 ~EGFiCP~C~~~l~s~   18 (34)
T 3mjh_B            3 SEGFICPQCMKSLGSA   18 (34)
T ss_dssp             SEEEECTTTCCEESSH
T ss_pred             CcccCCcHHHHHcCCH
Confidence            4456677777766544

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.75  E-value=1  Score=23.18  Aligned_cols=46  Identities=20%  Similarity=0.442  Sum_probs=31.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+......|+-|...+...+.+...  -+..||..|+        .|-.|+..+..
T Consensus         6 ~~~~~~~~C~~C~~~I~~~~~~~~a--~~~~~H~~CF--------~C~~C~~~L~~   51 (77)
T 1g47_A            6 ANALASATCERCKGGFAPAEKIVNS--NGELYHEQCF--------VCAQCFQQFPE   51 (77)
T ss_dssp             CSCCCCCBCSSSCCBCCSTTTCEEE--TTEEECTTTC--------CCTTTCCCCGG
T ss_pred             ccCCCCCCchhcCCccCCCceEEEe--CccEeccccC--------eECCCCCCCCC
Confidence            4456677899999998754443222  5678888775        67788777653

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=81.39  E-value=1.1  Score=28.45  Aligned_cols=36  Identities=14%  Similarity=0.180  Sum_probs=25.3

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      ..+..|.+|...|..-..--....||.+||..|...
T Consensus       162 ~~~~~C~~C~~~F~~~~RrhHCR~CG~v~C~~Cs~~  197 (226)
T 3zyq_A          162 VDAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSK  197 (226)
T ss_dssp             CCCSBCTTTCCBCBTTBCCEECTTTCCEECTTTCCE
T ss_pred             ccCCCCcCcCCCCCccccccccCCCcCEeChhhcCC
Confidence            345689999998875332234446999999999654

>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=81.00  E-value=1.2  Score=25.31  Aligned_cols=34  Identities=24%  Similarity=0.613  Sum_probs=22.8

Q ss_pred             ccccccccccc------CCCceeEcCCCCCcchHHhHHHH
Q 036506           10 CYCTVCLDGIS------DGQKFRRLPECKHCFHVECIDAW   43 (86)
Q Consensus        10 ~~C~ICl~~~~------~~~~~~~~~~C~H~fh~~Ci~~w   43 (86)
                      ..|.||+..-.      .+..+.....|+..||..|+...
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            46899987541      12233444469999999998653

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=80.68  E-value=0.25  Score=30.71  Aligned_cols=44  Identities=30%  Similarity=0.764  Sum_probs=29.8

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----CCCccccccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----RSTCPLCRIE   56 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~   56 (86)
                      +..|.+|...   ++ +.....|...||..|+.+=+..    .-.||.|+..
T Consensus         2 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~   49 (189)
T 2ro1_A            2 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   49 (189)
T ss_dssp             CCCBTTTCCC---SS-CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCS
T ss_pred             CCcCccCCCC---Cc-eeECCCCCchhccccCCCCcccCCCCCCCCcCccCC
Confidence            4578999854   22 2333458899999999764443    2269999865

---

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	86
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	7e-14
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-08
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-07
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	5e-07
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	7e-06
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-04
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-04
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	0.001
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.002

>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 = 58.0 bits (140), Expect = 7e-14
 Identities = 26/48 (54%), Positives = 32/48 (66%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI 59
          C VCL  + DG++ R LP C H FH EC+D W  S STCPLCR+ V +
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>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 = 1e-08
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIVI 61
          C +CL+  S+         C H F   CI  W +   TCPLC++ V  V+
Sbjct: 8  CPICLEDPSNY---SMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVV 54

>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 = 43.5 bits (101), Expect = 1e-07
 Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 5/64 (7%)

Query: 6  CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-----TCPLCRIEVAIV 60
               Y  +            RL +C H FH+ C+ A + + +      CP C+      
Sbjct: 36 AVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK 95

Query: 61 IARQ 64
             Q
Sbjct: 96 TGTQ 99

>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 = 41.3 bits (96), Expect = 5e-07
 Identities = 13/47 (27%), Positives = 17/47 (36%)

Query: 10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIE 56
            C       +  +       C H FH  CI  W ++R  CPL   E
Sbjct: 36 IECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82

>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 = 38.1 bits (88), Expect = 7e-06
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 5/47 (10%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS-TCPLCRIEV 57
          C +C +   D     ++  C H     C+ +W +S    CP CR E+
Sbjct: 26 CKICAENDKDV----KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 34.0 bits (77), Expect = 2e-04
 Identities = 10/48 (20%), Positives = 15/48 (31%), Gaps = 2/48 (4%)

Query: 12 CTVCLDGISDGQKFRRLP-ECKHCFHVECIDAWFQSRS-TCPLCRIEV 57
          C  C          + +   C H     C+D  F   +  CP C   +
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (74), Expect = 6e-04
 Identities = 8/47 (17%), Positives = 14/47 (29%), Gaps = 1/47 (2%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRST-CPLCRIEV 57
          C +C++ +           C +     C        +  CP CR   
Sbjct: 3  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>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 = 32.2 bits (73), Expect = 0.001
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 7/46 (15%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEV 57
          C  C           +L  C H     C++A       CP+C+   
Sbjct: 9  CQQCQAEAKCP----KLLPCLHTLCSGCLEAS---GMQCPICQAPW 47

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.3 bits (73), Expect = 0.002
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 12 CTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS---TCPLCRIEV 57
          C +CL+ I +        +C H F   C+      +     CPLC+ ++
Sbjct: 24 CPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	86
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.83
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.72
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.7
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.67
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.66
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.63
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.61
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.61
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.53
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.48
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.46
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.44
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.41
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.38
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.37
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.96
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	96.72
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.27
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.81
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	94.25
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.35
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	93.27
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.96
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	92.83
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	92.63
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	92.56
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	92.05
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	90.88
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.51
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	89.82
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	89.7
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	87.35
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	85.35
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	84.67
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	84.54
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	84.44
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	84.06
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	84.04
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	83.61
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	80.44

>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=99.83  E-value=1.1e-21  Score=101.31  Aligned_cols=52  Identities=50%  Similarity=1.063  Sum_probs=46.9

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVA   58 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~   58 (86)
                      +++.+|+||+++|..++.+..++.|+|.||..||.+|++++++||+||+++.
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            4667899999999998888777679999999999999999999999999764

>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=99.72  E-value=1.5e-18  Score=92.72  Aligned_cols=49  Identities=37%  Similarity=0.845  Sum_probs=41.8

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ...+|+||++.+.++  ++.++ |||.||..||.+|++++++||+||.++..
T Consensus         4 ~~d~C~IC~~~~~~~--~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccCC--cEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            456799999998754  45566 99999999999999999999999998753

>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=99.70  E-value=2e-18  Score=87.90  Aligned_cols=50  Identities=16%  Similarity=0.276  Sum_probs=40.2

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      .+|+||+++|..++....+..|||.||..|+.+|++. +..||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            4799999999776544333249999999999999986 5579999998753

>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=99.67  E-value=2.2e-17  Score=95.58  Aligned_cols=60  Identities=22%  Similarity=0.433  Sum_probs=45.3

Q ss_pred             CcccccccccccccCC---------------CceeEcCCCCCcchHHhHHHHHhcC-----CCccccccccchhhhhhhc
Q 036506            7 PYYCYCTVCLDGISDG---------------QKFRRLPECKHCFHVECIDAWFQSR-----STCPLCRIEVAIVIARQRR   66 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~---------------~~~~~~~~C~H~fh~~Ci~~wl~~~-----~~CP~Cr~~~~~~~~~~~~   66 (86)
                      ..+.+|+||++.|..+               ..+..++ |+|.||..||..|++..     .+||+||+.+....+.++.
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~~~qP~  101 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPW  101 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTT
T ss_pred             cccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccCcCCCCC
Confidence            4567899999987542               1234555 99999999999999753     3799999998776655544


Q ss_pred             c
Q 036506           67 N   67 (86)
Q Consensus        67 ~   67 (86)
                      .
T Consensus       102 ~  102 (114)
T d1v87a_         102 G  102 (114)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.66  E-value=3.8e-17  Score=91.04  Aligned_cols=51  Identities=31%  Similarity=0.669  Sum_probs=41.7

Q ss_pred             cccccccccccccCCC---------------ceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQ---------------KFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+.+|+||++.+..+.               .+..++ |||.||..||.+||+.+++||+||+++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            4557999999876532               245566 99999999999999999999999998753

>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=99.63  E-value=8.5e-17  Score=85.08  Aligned_cols=51  Identities=20%  Similarity=0.356  Sum_probs=39.7

Q ss_pred             cccccccccccccC-CCc-eeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            8 YYCYCTVCLDGISD-GQK-FRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~-~~~-~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      ++..||||++.+.. ++. +.+.+ |||.||..||.+|+.. ++.||+||..+..
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            46899999997643 333 34455 9999999999999965 5679999998753

>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=99.61  E-value=1.9e-16  Score=86.61  Aligned_cols=47  Identities=30%  Similarity=0.822  Sum_probs=39.7

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      ...|+||++.+.++   ++++ |||.||..||.+|+.. ++.||+||..+..
T Consensus        23 ~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~   70 (79)
T d1fbva4          23 FQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKG   70 (79)
T ss_dssp             TTBCTTTSSSBCCE---ECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCC
T ss_pred             CCCCccCCCcCCCe---EEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccC
Confidence            35699999998764   5676 9999999999999975 5789999998854

>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=99.61  E-value=1e-16  Score=82.54  Aligned_cols=48  Identities=10%  Similarity=0.223  Sum_probs=41.8

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      +.|+||++.+.++   +.++.|||.|++.||.+|+++++.||+||.++...
T Consensus         1 l~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           1 MLCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            3699999999876   45556999999999999999999999999988654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=1.6e-16  Score=88.26  Aligned_cols=49  Identities=29%  Similarity=0.516  Sum_probs=41.4

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccchh
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAIV   60 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~~   60 (86)
                      +...|+||++.+.++   ++++ |||.||..||.+|++. ++.||+||.++...
T Consensus        22 ~~l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          22 KSISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HHTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCcCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            456899999999876   5666 9999999999999974 56899999987644

>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=99.53  E-value=1.3e-15  Score=86.76  Aligned_cols=49  Identities=27%  Similarity=0.646  Sum_probs=41.1

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcC---CCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSR---STCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~---~~CP~Cr~~~~~   59 (86)
                      .+.+.|+||++.|.++   +.++ |||.||..||..|+.+.   ..||+||..+..
T Consensus        19 ~~~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          19 QKILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHHTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             ccCcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            3567899999999887   4566 99999999999999764   379999998754

>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=1.3e-14  Score=79.23  Aligned_cols=52  Identities=13%  Similarity=0.200  Sum_probs=45.4

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      .+.|++..|+||++.|.++   ++++ |||.|++.||.+|+.+ +..||.||..+..
T Consensus         2 ~eiP~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           2 RDIPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CCCCSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCCCccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            4679999999999999987   4666 9999999999999975 5579999998764

>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=99.46  E-value=1.6e-15  Score=77.99  Aligned_cols=45  Identities=24%  Similarity=0.645  Sum_probs=37.7

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      ..++|+||++.+.++   ++++ |||.||..||.+|   +..||+||..+..
T Consensus         5 ~~l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T d1bora_           5 QFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             CCCCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccC
Confidence            347999999999877   4677 9999999999764   6689999998864

>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=99.44  E-value=3.6e-14  Score=76.97  Aligned_cols=51  Identities=20%  Similarity=0.485  Sum_probs=44.6

Q ss_pred             CCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-CCCccccccccch
Q 036506            5 KCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-RSTCPLCRIEVAI   59 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-~~~CP~Cr~~~~~   59 (86)
                      +.|++..|+||++.|.++   ++++ |||.|++.||.+|++. ...||.|+.++..
T Consensus         4 eiP~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CCCccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            578999999999999987   4666 9999999999999986 4579999998754

>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=99.41  E-value=7.1e-14  Score=72.41  Aligned_cols=54  Identities=13%  Similarity=0.378  Sum_probs=39.2

Q ss_pred             CCCcccccccccccccCCCcee-EcCCCCCcchHHhHHHHHhc--CCCccccccccc
Q 036506            5 KCPYYCYCTVCLDGISDGQKFR-RLPECKHCFHVECIDAWFQS--RSTCPLCRIEVA   58 (86)
Q Consensus         5 ~~~~~~~C~ICl~~~~~~~~~~-~~~~C~H~fh~~Ci~~wl~~--~~~CP~Cr~~~~   58 (86)
                      +.++...|+||++.+..+.... ....|+|.||..||.+|+..  +.+||+||+.+.
T Consensus         2 eded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           2 EDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TTCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            3456778999999887552211 11124699999999999964  568999999874

>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=99.38  E-value=2.1e-13  Score=76.95  Aligned_cols=56  Identities=18%  Similarity=0.093  Sum_probs=47.8

Q ss_pred             CCCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            2 TAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         2 t~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      ...+.|++..||||++.|.++   ++++.|+|.|++.||.+||.++..||+|+.++...
T Consensus        15 ~~~~~P~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          15 TYADACDEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             CCCSCCTTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             hhcCCcHHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            456789999999999999988   56764556899999999999999999999987643

>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=99.37  E-value=2.6e-14  Score=80.44  Aligned_cols=48  Identities=23%  Similarity=0.566  Sum_probs=39.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccch
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAI   59 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~   59 (86)
                      .+...|+||++.|.++   +.++.|||.||..||.+|+.  ..||+||..+..
T Consensus        20 ~~~l~C~IC~~~~~~p---v~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          20 EKLLRCSRCTNILREP---VCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             HHTTSCSSSCSCCSSC---BCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hhcCCCccCCchhhcC---ceeCCCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            4567999999999877   33434999999999999985  459999987653

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=1.2e-10  Score=64.51  Aligned_cols=47  Identities=19%  Similarity=0.386  Sum_probs=36.6

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-----C---CCccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-----R---STCPLCR   54 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-----~---~~CP~Cr   54 (86)
                      ....+|+||++++...+.+..++ |+|.||..|+..|++.     .   -.||.|+
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            45678999999987655555555 9999999999999963     1   1599854

>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=96.72  E-value=0.00063  Score=36.15  Aligned_cols=41  Identities=20%  Similarity=0.384  Sum_probs=30.8

Q ss_pred             CCCCCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHH
Q 036506            1 ETAAKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAW   43 (86)
Q Consensus         1 ~t~~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~w   43 (86)
                      |+.+....+..|.|| +.+....... ...|+-+||..|+.+.
T Consensus         7 ~~re~v~~D~mC~vC-~v~t~~~l~p-CRvCtRv~H~~CL~r~   47 (89)
T d1wila_           7 GPREPVVNDEMCDVC-EVWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCCCCSCCCTTT-CCCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CcccCCCcCcccccc-Ccccccceec-ceeecchhhHHHHHHh
Confidence            456778899999999 6666554332 2258999999999986

>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=96.27  E-value=0.00039  Score=34.99  Aligned_cols=51  Identities=18%  Similarity=0.386  Sum_probs=36.3

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHh-----cCCCccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ-----SRSTCPLCRIE   56 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~-----~~~~CP~Cr~~   56 (86)
                      +.....|.||.......+..+....|+..||..|+..-..     ..-.||.|+..
T Consensus         3 ~~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            4567799999988766655555567999999999853211     13479999753

>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=95.81  E-value=0.0017  Score=31.01  Aligned_cols=44  Identities=30%  Similarity=0.662  Sum_probs=30.9

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC----Ccccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS----TCPLCRI   55 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~----~CP~Cr~   55 (86)
                      .|.||...-.. +.+..-..|...||..|+..-+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            58889776433 34445557999999999988655422    5888875

>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=94.25  E-value=0.076  Score=27.21  Aligned_cols=49  Identities=20%  Similarity=0.431  Sum_probs=32.7

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHH--H-Hhc--CCCcccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA--W-FQS--RSTCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~--w-l~~--~~~CP~Cr~~~   57 (86)
                      ..+.| ||...+......+....|.--||..|+.-  . ...  +-.||.|+...
T Consensus        11 ~pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            44566 89887655544455567999999999942  1 122  34799998644

>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=93.35  E-value=0.01  Score=30.05  Aligned_cols=46  Identities=28%  Similarity=0.714  Sum_probs=30.9

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCC----Ccccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRS----TCPLCRIEV   57 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~----~CP~Cr~~~   57 (86)
                      ....|.||.+.   ++ +.....|...||..|+.+.+....    .||.|+...
T Consensus         6 ~c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           6 SATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            34566677543   33 445556999999999988765432    599997543

>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=93.27  E-value=0.05  Score=27.49  Aligned_cols=48  Identities=25%  Similarity=0.627  Sum_probs=30.8

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHH----H--HH---hcCCCccccccc
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECID----A--WF---QSRSTCPLCRIE   56 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~----~--wl---~~~~~CP~Cr~~   56 (86)
                      +....| ||......+ .++....|.-.||..|+.    .  .+   ...-.||.|+..
T Consensus        14 ~~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          14 PNALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TTCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            455567 898765443 344555699999999982    1  11   124589999653

>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=92.96  E-value=0.007  Score=29.89  Aligned_cols=48  Identities=25%  Similarity=0.667  Sum_probs=31.4

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc----CCCcccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS----RSTCPLCRIEV   57 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~----~~~CP~Cr~~~   57 (86)
                      ...+..|.+|.+.   ++ ++....|.-.||..|+...+..    .-.||.|+...
T Consensus         6 d~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           6 DHHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            3445578899753   22 3344468999999998765443    22699997543

>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=92.83  E-value=0.059  Score=27.57  Aligned_cols=51  Identities=22%  Similarity=0.452  Sum_probs=32.2

Q ss_pred             CCcccccccccccccCCCceeEc-CCCCCcchHHhHHH----HHh-----cCCCcccccccc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRL-PECKHCFHVECIDA----WFQ-----SRSTCPLCRIEV   57 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~-~~C~H~fh~~Ci~~----wl~-----~~~~CP~Cr~~~   57 (86)
                      ..+...| ||......+..+... ..|..-||..|+.-    +..     ..-.||.|+..-
T Consensus        13 ~~~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          13 PEIKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCCccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            4455678 899877655444332 14999999999831    111     124799997643

>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=92.63  E-value=0.15  Score=26.79  Aligned_cols=56  Identities=21%  Similarity=0.389  Sum_probs=39.6

Q ss_pred             CcccccccccccccC---CCceeEcCCCCCcchHHhHHHHHh-cCCCccccccccchhhh
Q 036506            7 PYYCYCTVCLDGISD---GQKFRRLPECKHCFHVECIDAWFQ-SRSTCPLCRIEVAIVIA   62 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~---~~~~~~~~~C~H~fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~   62 (86)
                      -....|.||-+.+-.   ++..+....|+--.|+.|..==.+ .++.||.|+..+.....
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~kg   73 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLRG   73 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCTT
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhhcC
Confidence            456789999998643   333344445888999999875444 47789999998865443

>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=92.56  E-value=0.0066  Score=29.17  Aligned_cols=45  Identities=20%  Similarity=0.461  Sum_probs=28.8

Q ss_pred             ccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccccc
Q 036506           11 YCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRI   55 (86)
Q Consensus        11 ~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~   55 (86)
                      .|.+|...|..-..--.-..||.+|+..|........+.|..|..
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            477888887654332344469999999997655445667887753

>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=92.05  E-value=0.014  Score=30.64  Aligned_cols=48  Identities=21%  Similarity=0.479  Sum_probs=31.8

Q ss_pred             ccccccccccccC-CCceeEcCCCCCcchHHhHHHHH-----hc---CCCccccccc
Q 036506            9 YCYCTVCLDGISD-GQKFRRLPECKHCFHVECIDAWF-----QS---RSTCPLCRIE   56 (86)
Q Consensus         9 ~~~C~ICl~~~~~-~~~~~~~~~C~H~fh~~Ci~~wl-----~~---~~~CP~Cr~~   56 (86)
                      ...|.||...... ...++....|...||..|+.+.+     ..   .-.||.|...
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~   72 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCch
Confidence            4669999875443 23444455699999999976432     21   2369999654

>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=90.88  E-value=0.093  Score=26.53  Aligned_cols=36  Identities=14%  Similarity=0.257  Sum_probs=26.0

Q ss_pred             CcccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            7 PYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         7 ~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      .++..|.+|...|..-..-.....||++||..|...
T Consensus        11 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~   46 (72)
T d1dvpa2          11 ADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAK   46 (72)
T ss_dssp             CCCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCE
T ss_pred             CcCCccccCCCcccCccccccccccCCeeChhhhCC
Confidence            356789999999875433334446999999999643

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.51  E-value=0.3  Score=24.76  Aligned_cols=41  Identities=17%  Similarity=0.271  Sum_probs=30.5

Q ss_pred             CCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc
Q 036506            6 CPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS   46 (86)
Q Consensus         6 ~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~   46 (86)
                      .+..+.|.+|.+.+++..-+..-..=+|.||..|-...+++
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            35568999999999876544322233799999999998874

>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=89.82  E-value=0.13  Score=25.16  Aligned_cols=45  Identities=24%  Similarity=0.492  Sum_probs=30.6

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCcccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLC   53 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~C   53 (86)
                      ....|--|+..+.+. .+...+.|++.||.+|=.=-=..-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            456788899887643 445567899999999953222234568876

>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=89.70  E-value=0.059  Score=27.29  Aligned_cols=45  Identities=27%  Similarity=0.643  Sum_probs=25.9

Q ss_pred             cccccccccccccCCCceeEc-CCCC-CcchHHhHHHHHhc----CCCccccccc
Q 036506            8 YYCYCTVCLDGISDGQKFRRL-PECK-HCFHVECIDAWFQS----RSTCPLCRIE   56 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~-~~C~-H~fh~~Ci~~wl~~----~~~CP~Cr~~   56 (86)
                      ++..| ||..... ++.+... ..|. .-||..|+.  |..    .-.||.|+..
T Consensus        15 e~~~C-iC~~~~~-~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          15 EPTYC-LCNQVSY-GEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             SCCCS-TTCCCCC-SSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCEE-EeCCCCC-CCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            44566 9997643 3332221 1243 469999984  232    2369999764

>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=87.35  E-value=0.26  Score=24.36  Aligned_cols=34  Identities=18%  Similarity=0.230  Sum_probs=23.9

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      +..|.+|...|..-..--....||.+||..|...
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~   38 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   38 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCC
Confidence            3469999998865433234446999999999644

>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=85.35  E-value=0.16  Score=26.12  Aligned_cols=13  Identities=23%  Similarity=0.976  Sum_probs=11.2

Q ss_pred             cchHHhHHHHHhc
Q 036506           34 CFHVECIDAWFQS   46 (86)
Q Consensus        34 ~fh~~Ci~~wl~~   46 (86)
                      -||+.|+.+|+..
T Consensus        39 GFCRNCLskWy~~   51 (79)
T d2o35a1          39 GFCRNCLSNWYRE   51 (79)
T ss_dssp             SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3999999999863

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=84.67  E-value=0.16  Score=25.74  Aligned_cols=43  Identities=16%  Similarity=0.478  Sum_probs=27.0

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhHHHHHhcCCCccccccccchh
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQSRSTCPLCRIEVAIV   60 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~~~~CP~Cr~~~~~~   60 (86)
                      +..||.|..++...........|...|         +....||.|..++..-
T Consensus         2 ~~~CP~C~~eL~~~~~~~~C~~C~~~~---------~~~a~CPdC~~~Le~L   44 (71)
T d2jnea1           2 ELHCPQCQHVLDQDNGHARCRSCGEFI---------EMKALCPDCHQPLQVL   44 (71)
T ss_dssp             CCBCSSSCSBEEEETTEEEETTTCCEE---------EEEEECTTTCSBCEEE
T ss_pred             CCcCCCccCcccccCCCEehhhhhhhh---------eeEEeCCccccHHHHH
Confidence            467999999876543333333344443         3355799999887643

>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=84.54  E-value=0.16  Score=21.60  Aligned_cols=29  Identities=21%  Similarity=0.548  Sum_probs=22.9

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhH
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECI   40 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci   40 (86)
                      ..|+-|...+...+.++..  =+++||..|+
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            4688899999888877665  4789999884

>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=84.44  E-value=0.44  Score=24.84  Aligned_cols=54  Identities=15%  Similarity=0.231  Sum_probs=37.8

Q ss_pred             CCCCcccccccccccccCCCceeEcCCCCCcchHHhHHHHHhc-------CCCcccccccc
Q 036506            4 AKCPYYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQS-------RSTCPLCRIEV   57 (86)
Q Consensus         4 ~~~~~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~~-------~~~CP~Cr~~~   57 (86)
                      +.+..+..|.+|...|..-..-.....||-+||..|....+..       .+.|..|...+
T Consensus         4 ~~~~~~s~C~~C~~~Fs~~~rrhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l   64 (88)
T d1wfka_           4 GSSGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTIL   64 (88)
T ss_dssp             CCCCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHH
T ss_pred             CCCcccCcCcccCchhccccccccccccChhhChHHhCCccccCCCCCCCCeECHHHHHHH
Confidence            4567788999999998765444455579999999998654321       23587785444

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.06  E-value=0.051  Score=23.90  Aligned_cols=28  Identities=25%  Similarity=0.502  Sum_probs=20.6

Q ss_pred             ccccccccccccCCCceeEcCCCCCcchHHhH
Q 036506            9 YCYCTVCLDGISDGQKFRRLPECKHCFHVECI   40 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci   40 (86)
                      -..|.+|...+.+.    ++..-|..||..|+
T Consensus         8 lEkC~~C~~~I~dr----iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDR----ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSC----CEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHHH----HHHHhCCCCCCCCC
Confidence            45799999998765    33348888998773

>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=84.04  E-value=0.41  Score=23.37  Aligned_cols=35  Identities=23%  Similarity=0.422  Sum_probs=24.1

Q ss_pred             cccccccccccccCCCceeEcCCCCCcchHHhHHH
Q 036506            8 YYCYCTVCLDGISDGQKFRRLPECKHCFHVECIDA   42 (86)
Q Consensus         8 ~~~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~   42 (86)
                      +-..|.+|...|..-..--....||.+||..|...
T Consensus         7 ~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~   41 (64)
T d1joca1           7 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAK   41 (64)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCE
T ss_pred             cCCcCcCcCCcccCCccccchhhhCCeecccccCC
Confidence            34569999998875432234446999999999643

>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=83.61  E-value=0.29  Score=24.26  Aligned_cols=46  Identities=24%  Similarity=0.383  Sum_probs=30.7

Q ss_pred             cccccccccccCCCceeEcCCCCCcchHHhHHHHHh----cCCCccccccc
Q 036506           10 CYCTVCLDGISDGQKFRRLPECKHCFHVECIDAWFQ----SRSTCPLCRIE   56 (86)
Q Consensus        10 ~~C~ICl~~~~~~~~~~~~~~C~H~fh~~Ci~~wl~----~~~~CP~Cr~~   56 (86)
                      ..| ||.......+.++....|...||..|+..-..    ..-.||.|+..
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            557 78876655555555667999999999754222    13369998653

>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=80.44  E-value=0.33  Score=22.64  Aligned_cols=42  Identities=26%  Similarity=0.723  Sum_probs=23.5

Q ss_pred             ccccccccccccCCCceeEcC--CC-CCcchHHhHHHHHhc----CCCcccccc
Q 036506            9 YCYCTVCLDGISDGQKFRRLP--EC-KHCFHVECIDAWFQS----RSTCPLCRI   55 (86)
Q Consensus         9 ~~~C~ICl~~~~~~~~~~~~~--~C-~H~fh~~Ci~~wl~~----~~~CP~Cr~   55 (86)
                      ...| ||.... +++.+ ...  .| .--||..|+.  +..    .-.||.|+.
T Consensus         2 ~~yC-~C~~~~-~~~mi-~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~   50 (51)
T d2pnxa1           2 PTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   50 (51)
T ss_dssp             CEET-TTTEEC-CSEEE-ECSCTTCSSCEEEGGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CcEE-EcCCCC-CCCEE-EEecCCCCCCCEeCCccC--CCcCCCCcEECcCCCC
Confidence            4567 788764 33332 222  13 3469999985  232    225888864