Citrus Sinensis ID: 045853

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180----
Protein Sequence
MPFAATPSTCPNDEGLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTADDWSPD
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccEEccccccccccccccHHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHcccccccccccccccccccccccccccccccccHHHcccEEccccccccccccEEEEHccccccccEEEcccccccccHHHHHHHHHccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mpfaatpstcpndeglRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSteykvkedpraskfkkVSWTAFKRDIinnkshqnddavnkTSTCVICleefrdgdeckvrskcnhifhqtcmddwlddhstcplcrgrvrriawpsfttaddwspd
Flexible Loop (DISEMBL)
mpfaatpstcpndegLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINsteykvkedpraskfkkvswTAFKRDIinnkshqnddavnkTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGrvrriawpsfttaddwspd
Low Complexity Region (SEG)
MPFAATPSTCPNDEGLRLLVLTTPLVISSVVClilflfyisyylfTQLYSSRIQTQNQDIEQGLSSqqqqqqRVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTADDWSPD
Disordered region (IsUnstruct)
**************GLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRI**************************************FKKVSWTAFKRDIINNK*****DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTT*******
Disordered Region (DISOPRED)
*********************TTPLVISSVVCLILFLFYISYYLFTQLYSSRI***************************************KKVSWTAFKRDI*************KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV*****************
Disordered Region (DISEMBL)
*********CPNDEGLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQN***************RVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFT********
Disordered Region (DISPRO)
**************GLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQT*********************************ASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV*****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPFAATPSTCPNDEGLRLLVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTADDWSPD
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	184	2.2.26 [Sep-21-2011]
P0C041	310	Putative RING-H2 finger p	yes	no	0.755	0.448	0.331	6e-14
Q7XLY8	383	E3 ubiquitin-protein liga	yes	no	0.836	0.402	0.271	2e-12
Q8LFY8	413	RING-H2 finger protein AT	no	no	0.744	0.331	0.240	2e-11
Q9C919	178	Putative RING-H2 finger p	no	no	0.755	0.780	0.284	1e-10
Q9LF64	362	RING-H2 finger protein AT	no	no	0.396	0.201	0.369	1e-10
Q9LRB7	325	E3 ubiquitin-protein liga	no	no	0.233	0.132	0.534	3e-10
Q8RXX9	398	E3 ubiquitin-protein liga	no	no	0.679	0.314	0.260	3e-10
Q9ZV51	181	RING-H2 finger protein AT	no	no	0.385	0.392	0.380	4e-10
Q9SRQ8	356	RING-H2 finger protein AT	no	no	0.282	0.146	0.461	5e-10
Q5NCP0	784	E3 ubiquitin-protein liga	yes	no	0.358	0.084	0.463	5e-10

>sp|P0C041|ATL53_ARATH Putative RING-H2 finger protein ATL53 OS=Arabidopsis thaliana GN=ATL53 PE=3 SV=2

 Score = 77.0 bits (188), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 49/148 (33%), Positives = 67/148 (45%), Gaps = 9/148 (6%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+            +YY     Y +   T     E G S        + +NS E  
Sbjct: 59  SPLVIAIFGIFATAFLLAAYYTLVSKYCANDTTNEAASESGRS-----DIILDVNSPERG 113

Query: 83  VKEDPRA--SKFKKVSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRS 139
            ++DP A  S    +  T  K+      K HQN   +N T  C ICL EF + +  ++  
Sbjct: 114 DQDDPFALESSTAGLDDTLIKKIGFFKLKKHQNGFKINGTD-CSICLGEFNEDESLRLLP 172

Query: 140 KCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           KCNH FH  C+D WL  HS CPLCR ++
Sbjct: 173 KCNHTFHVVCIDRWLKSHSNCPLCRAKI 200

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XLY8|ATL41_ORYSJ E3 ubiquitin-protein ligase Os04g0590900 OS=Oryza sativa subsp. japonica GN=Os04g0590900 PE=2 SV=2

 Score = 72.0 bits (175), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 71/166 (42%), Gaps = 12/166 (7%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+ +  L      +SYY F   Y   + +    +    S                 
Sbjct: 56  SPLVIAIIGVLASAFLLVSYYTFISKYCGTVSSLRGRVFGSSSGGAAYGGGAGSGGRHGH 115

Query: 83  VKEDPRASKFKKVSWTAFKRDIINNK----SHQNDDAVNKTSTCVICLEEFRDGDECKVR 138
            +   R+ +   VS  +   + + NK     ++  D    T+ C +CL EF DG+  ++ 
Sbjct: 116 GQS--RSHESWNVSPPSGLDETLINKITVCKYRRGDGFVHTTDCSVCLGEFSDGESLRLL 173

Query: 139 SKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTADDWSPD 184
            +C+H FHQ C+D WL  HS CPLCR  +      +F T    SP+
Sbjct: 174 PRCSHAFHQQCIDTWLKSHSNCPLCRANI------TFVTVGLASPE 213

Possesses E3 ubiquitin-protein ligase in vitro.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8LFY8|ATL54_ARATH RING-H2 finger protein ATL54 OS=Arabidopsis thaliana GN=ATL54 PE=2 SV=2

 Score = 68.6 bits (166), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/154 (24%), Positives = 73/154 (47%), Gaps = 17/154 (11%)

Query: 25  LVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYKVK 84
           + I ++   +L +    ++L  + +S  +   NQ      + Q   +    +   E++ +
Sbjct: 83  ISIITITGAVLAILLTGFFLVAKFFSDSVNRVNQG-----TYQSDNEDNDTVMEEEFQDR 137

Query: 85  EDPRASKFKKVSW----TAFKRDIINNKS---HQNDDAVNKTSTCVICLEEFRDGDECKV 137
           E     +     W    T  ++ IIN+ +   ++  D + + + C +CL EF + +  ++
Sbjct: 138 E-----QVDHPIWLIRTTGLQQSIINSITICNYKRGDGLIERTDCPVCLNEFEEDESLRL 192

Query: 138 RSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA 171
             KCNH FH +C+D WL  H+ CPLCR  +  I+
Sbjct: 193 LPKCNHAFHISCIDTWLSSHTNCPLCRAGIAMIS 226

Arabidopsis thaliana (taxid: 3702)

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

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 45/158 (28%), Positives = 77/158 (48%), Gaps = 19/158 (12%)

Query: 18  LLVLTTPLVISSVVCLILFLFY---ISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRV 74
           L +L   L+ +S + L++++     +  +L T L        + D+E G+   QQ+ + V
Sbjct: 23  LCILLVVLIATSALILVIYVIIDCILRPFLGTCL--------DLDLEIGVQRGQQRARIV 74

Query: 75  I---INSTEYKVKEDPRASKFKK----VSWTAFKRDIINNKSHQNDDAVNKTS-TCVICL 126
               I ST  ++ +  R  K +     V  T   + ++   +H+ D+  +  S  C ICL
Sbjct: 75  TYHTIISTGLRLPDFEREGKKRGLKQSVIETLLPKLLVGQGNHEEDEEKSLESRECAICL 134

Query: 127 EEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
             +   +EC+V   C HI+H  C+D WL +H TCP CR
Sbjct: 135 SGYVVNEECRVFPVCRHIYHALCIDAWLKNHLTCPTCR 172

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LF64|ATL52_ARATH RING-H2 finger protein ATL52 OS=Arabidopsis thaliana GN=ATL52 PE=2 SV=1

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 40/73 (54%)

Query: 110 HQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
           +++ D     S C +CL EF + +  ++  KCNH FH  C+D WL  HS CPLCR  V  
Sbjct: 130 YKSGDGFVDGSDCSVCLSEFEENESLRLLPKCNHAFHLPCIDTWLKSHSNCPLCRAFVTG 189

Query: 170 IAWPSFTTADDWS 182
           +  P+ +   + S
Sbjct: 190 VNNPTASVGQNVS 202

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LRB7|EL5_ORYSJ E3 ubiquitin-protein ligase EL5 OS=Oryza sativa subsp. japonica GN=EL5.1 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 28/43 (65%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           C +CL E  DG+E +   +C H FH  C+D WL  HSTCPLCR
Sbjct: 134 CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 176

Functions as a E3 ubiquitin-protein ligase in cooperation with the E2 ubiquitin conjugating enzymes UBC5A and UBC5B. Involved in root development. Required for the maintenance of cell viability after the initiation of root primordial formation. May mediates the degradation of cytotoxic proteins produced in root cells after the actions of auxin, cytokinin and jasmonic acid. Mediates 'Lys-48'-linked polyubiquitination of MBP in vitro.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 63/142 (44%), Gaps = 17/142 (11%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +P +   VV LI  LF++ ++     + S +       + G+S     + R  +N+    
Sbjct: 46  SPAMAVIVVILIAALFFMGFFSIYFRHCSGVP------DAGVSPAGGARSRATVNAAARG 99

Query: 83  VKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCN 142
           +          +   T    D+   K  + +        C ICL EF D +  ++  KC+
Sbjct: 100 LD-----VSVVETFPTFLYSDVKTQKLGKGE------LECAICLNEFEDDETLRLLPKCD 148

Query: 143 HIFHQTCMDDWLDDHSTCPLCR 164
           H+FH  C+D WL+ H TCP+CR
Sbjct: 149 HVFHPHCIDAWLEAHVTCPVCR 170

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9ZV51|ATL56_ARATH RING-H2 finger protein ATL56 OS=Arabidopsis thaliana GN=ATL56 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 38/71 (53%)

Query: 98  TAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH 157
           + F + +   K  +        S CV+C + FR G  C+    C H+FH+ C+D WL   
Sbjct: 86  SRFVKKLPQFKFSEPSTYTRYESDCVVCFDGFRQGQWCRNLPGCGHVFHRKCVDTWLLKA 145

Query: 158 STCPLCRGRVR 168
           STCP+CR RVR
Sbjct: 146 STCPICRARVR 156

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SRQ8|ATL51_ARATH RING-H2 finger protein ATL51 OS=Arabidopsis thaliana GN=ATL51 PE=2 SV=2

 Score = 63.9 bits (154), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 33/52 (63%)

Query: 114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG 165
           D   ++S C +CL EF++ +  ++  KCNH FH  C+D WL  HS CPLCR 
Sbjct: 151 DGFVESSDCSVCLSEFQENESLRLLPKCNHAFHVPCIDTWLKSHSNCPLCRA 202

Arabidopsis thaliana (taxid: 3702)

>sp|Q5NCP0|RNF43_MOUSE E3 ubiquitin-protein ligase RNF43 OS=Mus musculus GN=Rnf43 PE=2 SV=1

 Score = 63.9 bits (154), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/69 (46%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPS 174
           + + T  C ICLEEF +G E +V S C H FH+TC+D WL  H TCPLC   +  +   S
Sbjct: 265 SCSSTPVCAICLEEFSEGQELRVIS-CLHEFHRTCVDPWLYQHRTCPLCMFNI--VEGDS 321

Query: 175 FTTADDWSP 183
           F+ A   SP
Sbjct: 322 FSQAPAASP 330

Probable E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

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	184
2894600	1208	putative protein [Arabidopsis thaliana]	0.744	0.113	0.333	1e-12
186511980	310	putative RING-H2 finger protein ATL53 [A	0.755	0.448	0.331	3e-12
242076978	398	hypothetical protein SORBIDRAFT_06g02698	0.804	0.371	0.278	4e-12
255584222	183	RING-H2 finger protein ATL5F, putative [	0.581	0.584	0.35	1e-11
357165731	387	PREDICTED: E3 ubiquitin-protein ligase O	0.766	0.364	0.295	3e-11
225464303	338	PREDICTED: RING-H2 finger protein ATL51	0.782	0.426	0.275	3e-11
147777624	1377	hypothetical protein VITISV_014334 [Viti	0.695	0.092	0.271	5e-11
414585686	406	TPA: putative RING zinc finger domain su	0.788	0.357	0.28	7e-11
356496378	364	PREDICTED: E3 ubiquitin-protein ligase O	0.722	0.365	0.267	8e-11
125549537	383	hypothetical protein OsI_17192 [Oryza sa	0.836	0.402	0.271	9e-11

>gi|2894600|emb|CAA17134.1| putative protein [Arabidopsis thaliana] gi|7268543|emb|CAB78793.1| putative protein [Arabidopsis thaliana]

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 50/150 (33%), Positives = 68/150 (45%), Gaps = 13/150 (8%)

Query: 23   TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVI--INSTE 80
            +PLVI+            +YY     Y +   T     E G S        +I  +NS E
Sbjct: 957  SPLVIAIFGIFATAFLLAAYYTLVSKYCANDTTNEAASESGRSD-------IILDVNSPE 1009

Query: 81   YKVKEDPRA--SKFKKVSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKV 137
               ++DP A  S    +  T  K+      K HQN   +N T  C ICL EF + +  ++
Sbjct: 1010 RGDQDDPFALESSTAGLDDTLIKKIGFFKLKKHQNGFKINGTD-CSICLGEFNEDESLRL 1068

Query: 138  RSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
              KCNH FH  C+D WL  HS CPLCR ++
Sbjct: 1069 LPKCNHTFHVVCIDRWLKSHSNCPLCRAKI 1098

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186511980|ref|NP_001119003.1| putative RING-H2 finger protein ATL53 [Arabidopsis thaliana] gi|302393676|sp|P0C041.2|ATL53_ARATH RecName: Full=Putative RING-H2 finger protein ATL53 gi|332658566|gb|AEE83966.1| putative RING-H2 finger protein ATL53 [Arabidopsis thaliana]

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 49/148 (33%), Positives = 67/148 (45%), Gaps = 9/148 (6%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+            +YY     Y +   T     E G S        + +NS E  
Sbjct: 59  SPLVIAIFGIFATAFLLAAYYTLVSKYCANDTTNEAASESGRS-----DIILDVNSPERG 113

Query: 83  VKEDPRA--SKFKKVSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRS 139
            ++DP A  S    +  T  K+      K HQN   +N T  C ICL EF + +  ++  
Sbjct: 114 DQDDPFALESSTAGLDDTLIKKIGFFKLKKHQNGFKINGTD-CSICLGEFNEDESLRLLP 172

Query: 140 KCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           KCNH FH  C+D WL  HS CPLCR ++
Sbjct: 173 KCNHTFHVVCIDRWLKSHSNCPLCRAKI 200

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242076978|ref|XP_002448425.1| hypothetical protein SORBIDRAFT_06g026980 [Sorghum bicolor] gi|241939608|gb|EES12753.1| hypothetical protein SORBIDRAFT_06g026980 [Sorghum bicolor]

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 42/151 (27%), Positives = 68/151 (45%), Gaps = 3/151 (1%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+ +  L +    +SYY F   Y     +    +    S    +++      +   
Sbjct: 63  SPLVIAIIGVLAIAFLLVSYYTFVSRYCGTFGSFRGRVFSSNSGGGARRRGNGGGGSSGG 122

Query: 83  VKEDPRASKFKKVSWTAFKRDIINNKS---HQNDDAVNKTSTCVICLEEFRDGDECKVRS 139
             +      +     T     +I+  +   ++  DA   T+ C +CL EFRDG+  ++  
Sbjct: 123 QGQSRSQESWNISPSTGLDETLISKITLCKYKRGDASVHTTDCSVCLGEFRDGESLRLLP 182

Query: 140 KCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI 170
           KC+H FHQ C+D WL  HS CPLCR  +  I
Sbjct: 183 KCSHAFHQQCIDKWLKSHSNCPLCRSNITFI 213

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255584222|ref|XP_002532849.1| RING-H2 finger protein ATL5F, putative [Ricinus communis] gi|223527386|gb|EEF29527.1| RING-H2 finger protein ATL5F, putative [Ricinus communis]

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 42/120 (35%), Positives = 60/120 (50%), Gaps = 13/120 (10%)

Query: 54  QTQNQ-DIEQGLSSQQQQQQRVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQN 112
           QTQN  D EQG    +  Q +        +     R ++ K +        +I  +  + 
Sbjct: 63  QTQNHNDTEQGRPRNRPPQPQPGNQPPRPQPLPPERMARAKVI--------VIAGRVFEY 114

Query: 113 DDAVNKTST----CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
              V K +     CVICLEEF+DG+EC++ +KCNH +H  C+D WL  H  CP+CR  VR
Sbjct: 115 KSEVQKPNVFCRECVICLEEFKDGEECRIFTKCNHFYHNGCIDKWLIKHRHCPICRESVR 174

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357165731|ref|XP_003580475.1| PREDICTED: E3 ubiquitin-protein ligase Os04g0590900-like [Brachypodium distachyon]

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 44/149 (29%), Positives = 62/149 (41%), Gaps = 8/149 (5%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+ +  L      +SYY F   Y     +    I     S      R         
Sbjct: 63  SPLVIAIIGVLASAFLLVSYYTFISKYCGTFSSLRGRI---FGSSSSSAARNAGGGGGSG 119

Query: 83  VKEDPRASKFKKVSWTAFKRDIINN----KSHQNDDAVNKTSTCVICLEEFRDGDECKVR 138
             +      +     +     +IN     K  + D  VN T+ C +CL EF DG+  ++ 
Sbjct: 120 QGQSRSQESWNVSPSSGLDETLINKITVCKYRRGDGFVN-TTDCSVCLGEFHDGESLRLL 178

Query: 139 SKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
            KC+H FHQ C+D WL  HS CPLCR  +
Sbjct: 179 PKCSHAFHQQCIDTWLKSHSNCPLCRSNI 207

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225464303|ref|XP_002266511.1| PREDICTED: RING-H2 finger protein ATL51 [Vitis vinifera] gi|297744791|emb|CBI38059.3| unnamed protein product [Vitis vinifera]

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 73/167 (43%), Gaps = 23/167 (13%)

Query: 19  LVLTTPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINS 78
           L+L    +++S   L+++   IS Y   +                 S++    Q  ++N 
Sbjct: 53  LILAIIGILASAFLLVIYFTVISKYCRRRRGRR------------TSAEGNGNQDEMVND 100

Query: 79  TEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVR 138
              +V        F K S T +K        ++    V + + C +CL EF DG+  ++ 
Sbjct: 101 QPLQVASTGLEEGFIK-SITVYK--------YKKSGGVVEGTDCSVCLSEFEDGENLRLL 151

Query: 139 SKCNHIFHQTCMDDWLDDHSTCPLCRGRVR--RIAWPSFTTADDWSP 183
            KCNH FH  C+D WL  HS+CPLCR  +R  +I  P  + A    P
Sbjct: 152 PKCNHAFHLPCIDTWLKSHSSCPLCRFDIRSAKILPPELSEATQGVP 198

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777624|emb|CAN78205.1| hypothetical protein VITISV_014334 [Vitis vinifera]

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/151 (27%), Positives = 67/151 (44%), Gaps = 23/151 (15%)

Query: 23   TPLVISSVVCLILFLFYISYYLFTQLYS---SRIQTQNQDIEQGLSSQQQQQQRVIINST 79
            +PLVI+ +  L      +SYY     Y     R + +NQDI + L               
Sbjct: 1056 SPLVIAIIGILASAFLLVSYYTIISKYCGNMERERRENQDINEELEDNH----------- 1104

Query: 80   EYKVKEDPRASKFKKVSWTAFKRDIINNKS---HQNDDAVNKTSTCVICLEEFRDGDECK 136
                  +P   +   V+ T     +I + +   ++  D + + + C +CL EF + +  +
Sbjct: 1105 ------NPALHEPWHVATTGLDEALIKSITLCKYKKGDGLVEGTDCSVCLSEFEEDESLR 1158

Query: 137  VRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
            +  KC+H FH  C+D WL  HS CPLCR  +
Sbjct: 1159 LLPKCSHAFHVQCIDTWLKSHSNCPLCRANI 1189

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414585686|tpg|DAA36257.1| TPA: putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 42/150 (28%), Positives = 67/150 (44%), Gaps = 5/150 (3%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+ +  L +    +SYY F   Y    ++    +    S      +          
Sbjct: 63  SPLVIAIIGVLAIAFLLVSYYTFISRYCGTFRSFRGRVFSSSSGGGGGARGSGGGGGGGG 122

Query: 83  VKEDPRASKFKKVS-WTAFKRDIINN----KSHQNDDAVNKTSTCVICLEEFRDGDECKV 137
            +   R+ +   +S  T     +I+     K  + D +    + C +CL EFRDG+  ++
Sbjct: 123 GQGQSRSQESWNISPSTGLDETLISKIALCKYRRGDASSVHATDCPVCLGEFRDGESLRL 182

Query: 138 RSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
             KC+H FHQ C+D WL  HS CPLCR  +
Sbjct: 183 LPKCSHAFHQQCIDKWLKSHSNCPLCRSNI 212

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496378|ref|XP_003517045.1| PREDICTED: E3 ubiquitin-protein ligase Os04g0590900-like [Glycine max]

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 39/146 (26%), Positives = 71/146 (48%), Gaps = 13/146 (8%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLY-SSRIQTQNQDIEQGLSSQQQQQQRVIINSTEY 81
           +PLVI+ +  L+     +SYY     Y  SR  +Q+++ E+ +  ++     +       
Sbjct: 54  SPLVIAVIGVLVSAFLLVSYYTIISKYCGSRESSQSENHEENVELEEDHNPSLHEPWHAP 113

Query: 82  KVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKC 141
            +  D   +  K ++   +K+           D + + + C +CL EF+D +  ++  KC
Sbjct: 114 TIGLD--EALIKSITVCKYKKG----------DGLVEVTDCSVCLSEFQDDESVRLLPKC 161

Query: 142 NHIFHQTCMDDWLDDHSTCPLCRGRV 167
           +H FH  C+D WL  HS+CPLCR  +
Sbjct: 162 SHAFHLPCIDTWLKSHSSCPLCRASI 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125549537|gb|EAY95359.1| hypothetical protein OsI_17192 [Oryza sativa Indica Group]

 Score = 72.0 bits (175), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 71/166 (42%), Gaps = 12/166 (7%)

Query: 23  TPLVISSVVCLILFLFYISYYLFTQLYSSRIQTQNQDIEQGLSSQQQQQQRVIINSTEYK 82
           +PLVI+ +  L      +SYY F   Y   + +    +    S                 
Sbjct: 56  SPLVIAIIGVLASAFLLVSYYTFISKYCGTVSSLRGRVFGSSSGGAAYGGGAGSGGRHGH 115

Query: 83  VKEDPRASKFKKVSWTAFKRDIINNK----SHQNDDAVNKTSTCVICLEEFRDGDECKVR 138
            +   R+ +   VS  +   + + NK     ++  D    T+ C +CL EF DG+  ++ 
Sbjct: 116 GQS--RSHESWNVSPPSGLDETLINKITVCKYRRGDGFVHTTDCSVCLGEFSDGESLRLL 173

Query: 139 SKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTADDWSPD 184
            +C+H FHQ C+D WL  HS CPLCR  +      +F T    SP+
Sbjct: 174 PRCSHAFHQQCIDTWLKSHSNCPLCRANI------TFVTVGLASPE 213

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	184
TAIR|locus:4515103413	310	ATL4H [Arabidopsis thaliana (t	0.494	0.293	0.4	3.2e-14
TAIR|locus:2090980	204	AT3G14320 [Arabidopsis thalian	0.25	0.225	0.543	6.4e-12
UNIPROTKB|Q7XLY8	383	LOC_Os04g50100 "E3 ubiquitin-p	0.315	0.151	0.431	6.9e-12
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.489	0.409	0.372	1.3e-11
TAIR|locus:2207066	413	AT1G72220 [Arabidopsis thalian	0.402	0.179	0.350	1.4e-11
TAIR|locus:2053994	181	AT2G18670 [Arabidopsis thalian	0.266	0.270	0.510	1.7e-11
TAIR|locus:2118651	176	AT4G30370 [Arabidopsis thalian	0.260	0.272	0.5	2.8e-11
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.413	0.337	0.367	2.8e-11
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.483	0.505	0.364	3.5e-11
TAIR|locus:2057861	237	AT2G27940 [Arabidopsis thalian	0.271	0.210	0.48	4.5e-11

TAIR|locus:4515103413 ATL4H [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 3.2e-14, P = 3.2e-14
 Identities = 38/95 (40%), Positives = 51/95 (53%)

Query:    76 INSTEYKVKEDPRA--SKFKKVSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFRDG 132
             +NS E   ++DP A  S    +  T  K+      K HQN   +N T  C ICL EF + 
Sbjct:   107 VNSPERGDQDDPFALESSTAGLDDTLIKKIGFFKLKKHQNGFKINGTD-CSICLGEFNED 165

Query:   133 DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
             +  ++  KCNH FH  C+D WL  HS CPLCR ++
Sbjct:   166 ESLRLLPKCNHTFHVVCIDRWLKSHSNCPLCRAKI 200

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 25/46 (54%), Positives = 32/46 (69%)

Query:   122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
             CV+CL E  DGD+ +V   C+H FH  C+D WL  +STCP+CR RV
Sbjct:    88 CVVCLSELADGDKARVLPSCDHWFHVECIDSWLQSNSTCPICRKRV 133

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

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

 Score = 167 (63.8 bits), Expect = 6.9e-12, P = 6.9e-12
 Identities = 25/58 (43%), Positives = 36/58 (62%)

Query:   110 HQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
             ++  D    T+ C +CL EF DG+  ++  +C+H FHQ C+D WL  HS CPLCR  +
Sbjct:   145 YRRGDGFVHTTDCSVCLGEFSDGESLRLLPRCSHAFHQQCIDTWLKSHSNCPLCRANI 202

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 35/94 (37%), Positives = 46/94 (48%)

Query:    73 RVIINSTEYKVKEDPRASKFKK-VSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFR 130
             R  + S    +   PR S   K +   A K   ++N     N   V +   CVICL +F 
Sbjct:    81 RSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPEINLPGVGEE--CVICLSDFV 138

Query:   131 DGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
              G++ +V  KCNH FH  C+D WL  H TCP CR
Sbjct:   139 AGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCR 172

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

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

 Score = 165 (63.1 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 27/77 (35%), Positives = 46/77 (59%)

Query:    98 TAFKRDIINNKS---HQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL 154
             T  ++ IIN+ +   ++  D + + + C +CL EF + +  ++  KCNH FH +C+D WL
Sbjct:   150 TGLQQSIINSITICNYKRGDGLIERTDCPVCLNEFEEDESLRLLPKCNHAFHISCIDTWL 209

Query:   155 DDHSTCPLCRGRVRRIA 171
               H+ CPLCR  +  I+
Sbjct:   210 SSHTNCPLCRAGIAMIS 226

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

TAIR|locus:2053994 AT2G18670 [Arabidopsis thaliana (taxid:3702)]

 Score = 157 (60.3 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 25/49 (51%), Positives = 32/49 (65%)

Query:   120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
             S CV+C + FR G  C+    C H+FH+ C+D WL   STCP+CR RVR
Sbjct:   108 SDCVVCFDGFRQGQWCRNLPGCGHVFHRKCVDTWLLKASTCPICRARVR 156

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2118651 AT4G30370 [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 24/48 (50%), Positives = 33/48 (68%)

Query:   122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
             CV+C++ FR G  C+   +C H+FH+ C+D WL   STCP+CR RV R
Sbjct:   115 CVVCIDGFRQGQWCRKLPRCGHVFHRKCVDLWLIKVSTCPICRDRVYR 162

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP

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

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 29/79 (36%), Positives = 43/79 (54%)

Query:    87 PRASKFKKVSWTAFKR-DIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIF 145
             PR+S  K +   A +   +++     N   + +   CVICL +F  G++ ++  KCNH F
Sbjct:   101 PRSSSNKGIKKKALRMFPVVSYSREMNLPGIGEE--CVICLSDFVSGEQLRLLPKCNHGF 158

Query:   146 HQTCMDDWLDDHSTCPLCR 164
             H  C+D WL  H TCP CR
Sbjct:   159 HVRCIDKWLQHHLTCPKCR 177

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 154 (59.3 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 35/96 (36%), Positives = 52/96 (54%)

Query:    73 RVIINSTE-YKVKEDP---RASKFKKVSWTAFKRDIINNKSHQNDDAVNKTSTCVICLEE 128
             R ++  T  +   EDP    A+  K +   A K  +I   S+ + +   K + C+ICL +
Sbjct:    63 RCVLRCTRRFTPNEDPVDTNANVAKGIKKRALK--VIPVDSY-SPELKMKATECLICLGD 119

Query:   129 FRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
             F +G+  +V  KCNH FH  C+D WL  HS+CP CR
Sbjct:   120 FVEGETVRVLPKCNHGFHVKCIDTWLLSHSSCPTCR 155

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

TAIR|locus:2057861 AT2G27940 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query:   115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
             A  +   CVICL +F +G+  KV   C H+FH  C+D WL  + TCPLCR
Sbjct:   133 AKQRNEDCVICLSDFEEGETVKVIPHCGHVFHVDCVDTWLSSYVTCPLCR 182

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: ATL4H ATL4H; protein binding / zinc ion binding; Putative RING-H2 finger protein ATL4H. (310 aa) (Arabidopsis thaliana)

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	184
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	6e-14
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-11
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	5e-10
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	8e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	5e-08
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	9e-08
smart00184	40	smart00184, RING, Ring finger	6e-07
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	6e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	3e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	7e-04

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

 Score = 62.4 bits (152), Expect = 6e-14
 Identities = 23/44 (52%), Positives = 29/44 (65%), Gaps = 1/44 (2%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C ICL+EF  G+E  V   C H+FH+ C+D WL   +TCPLCR
Sbjct: 2   ECPICLDEFEPGEEV-VVLPCGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 57.4 bits (139), Expect = 1e-11
 Identities = 21/53 (39%), Positives = 25/53 (47%), Gaps = 9/53 (16%)

Query: 121 TCVICLEEFRD--------GDECKV-RSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C IC   F          GD+C V   +C H FH  C+  WL   +TCPLCR
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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 = 52.4 bits (126), Expect = 5e-10
 Identities = 22/48 (45%), Positives = 29/48 (60%), Gaps = 4/48 (8%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRV 167
            C ICLEEFR+     V   C H+F ++C+D WL    +TCPLCR  +
Sbjct: 1   ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 53.5 bits (128), Expect = 8e-09
 Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 2/44 (4%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCR 164
           C IC+  F   D  +V   C+H FH  C+D WL  +S  CP+CR
Sbjct: 326 CAICMSNFIKNDRLRV-LPCDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 3/44 (6%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C ICL+  RD     V + C H+F + C+  +L   S CP+CR
Sbjct: 4   ECPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 47.5 bits (113), Expect = 9e-08
 Identities = 21/45 (46%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 121 TCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDHSTCPLCR 164
           TC  C      GDEC V    CNH FH  C+  WLD    CPL R
Sbjct: 33  TCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 44.0 bits (104), Expect = 6e-07
 Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLC 163
           C ICLEE+    +  V   C H F ++C+  WL+  + TCP+C
Sbjct: 1   CPICLEEY---LKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 47.7 bits (113), Expect = 1e-06
 Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 117 NKTSTCVICLEEF---------RDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           N   TC IC++E          R  D    R  C HI H  C+ +WL+   TCP+CR
Sbjct: 285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICR 341

Length = 491

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

 Score = 44.8 bits (106), Expect = 6e-06
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 118 KTSTCVICLEEFRDGDECK-----VRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           K   C IC+E+  D  E K     + S CNH+F   C+D W  + +TCP+CR
Sbjct: 173 KDKECAICMEKVYD-KEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLC 163
           C ICLEE +D         C H+F   C+  WL+  + TCPLC
Sbjct: 1   CPICLEEPKD---PVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)

Query: 132 GDECK-VRSKCNHIFHQTCMDDWLDDHST---CPLCR 164
           GD+C  V  KC H FH  C+  WL   ++   CP+CR
Sbjct: 42  GDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 78

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.85
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.73
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.58
PHA02929	238	N1R/p28-like protein; Provisional	99.55
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.51
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.49
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.42
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.4
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.36
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.34
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.33
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.32
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.31
PHA02926	242	zinc finger-like protein; Provisional	99.28
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.25
PF14634	44	zf-RING_5: zinc-RING finger domain	99.2
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.19
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.18
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.14
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.09
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.07
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.06
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.05
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.03
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.99
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.91
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.91
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.85
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.83
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.82
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.78
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.77
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.71
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.7
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.68
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.67
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.66
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.61
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.58
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.55
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.29
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.27
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.25
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.24
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.21
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.15
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.13
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.04
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.99
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.8
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.77
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.77
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.74
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.69
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.68
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.67
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.65
PHA02862	156	5L protein; Provisional	97.62
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.51
COG5152	259	Uncharacterized conserved protein, contains RING a	97.3
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.3
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.26
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.21
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	97.17
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.15
KOG2660	331	consensus Locus-specific chromosome binding protei	97.13
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.11
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.1
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.09
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.08
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.07
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.04
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG1940	276	consensus Zn-finger protein [General function pred	96.92
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.9
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
PHA03096	284	p28-like protein; Provisional	96.85
PF04641	260	Rtf2: Rtf2 RING-finger	96.81
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.75
KOG4739	233	consensus Uncharacterized protein involved in syna	96.75
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.68
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.66
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.51
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.45
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.36
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.3
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.2
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.06
KOG1001	674	consensus Helicase-like transcription factor HLTF/	95.86
KOG3002	299	consensus Zn finger protein [General function pred	95.55
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.54
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	95.52
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	95.48
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	95.46
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.34
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.32
KOG3053	293	consensus Uncharacterized conserved protein [Funct	95.28
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.17
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	95.01
KOG1609	323	consensus Protein involved in mRNA turnover and st	94.77
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	94.4
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.38
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	94.22
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.76
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	93.58
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.57
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.81
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	92.62
KOG0825	1134	consensus PHD Zn-finger protein [General function	92.42
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	90.77
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	90.4
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	90.18
PF15050	133	SCIMP: SCIMP protein	89.5
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	89.34
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.73
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	88.63
COG5415	251	Predicted integral membrane metal-binding protein	88.39
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	88.28
KOG2068	327	consensus MOT2 transcription factor [Transcription	88.09
KOG1829	580	consensus Uncharacterized conserved protein, conta	88.08
KOG3005	276	consensus GIY-YIG type nuclease [General function	87.85
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	87.73
KOG0269	839	consensus WD40 repeat-containing protein [Function	87.43
KOG3113	293	consensus Uncharacterized conserved protein [Funct	87.37
PF13974	80	YebO: YebO-like protein	86.97
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	86.68
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	86.61
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	86.28
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	85.96
PF06716	54	DUF1201: Protein of unknown function (DUF1201); In	85.43
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	85.28
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	85.01
KOG4367	699	consensus Predicted Zn-finger protein [Function un	84.2
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	83.96
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	83.6
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	83.03
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	82.98
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	80.8
PTZ00370	296	STEVOR; Provisional	80.7
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	80.51

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

Probab=99.85  E-value=2.4e-21  Score=151.43  Aligned_cols=59  Identities=37%  Similarity=0.940  Sum_probs=50.5

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCc-ccccccccccccCCCCCCCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHST-CPLCRGRVRRIAWPSFTTAD  179 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~i~~~~~~~~~~~~  179 (184)
                      ..|+||+|+|..+|++|+|| |+|.||..||+.||..+++ ||+||+++....-......|
T Consensus       230 ~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~~~~~~e~  289 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSGSEPVSED  289 (348)
T ss_pred             ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCCCCCCccCC
Confidence            58999999999999999985 9999999999999987765 99999999766644444443

>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=1.1e-18  Score=98.62  Aligned_cols=43  Identities=47%  Similarity=1.293  Sum_probs=39.6

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR  164 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  164 (184)
                      +|+||+++|..++.+..++ |||.||.+||..|++.+.+||+||
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            6999999999988888885 999999999999999999999998

...

>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=99.58  E-value=1.4e-15  Score=94.85  Aligned_cols=46  Identities=43%  Similarity=1.024  Sum_probs=35.8

Q ss_pred             CcccccCcccccCC---------ccceeecCCCccccHhhHHHHhcCCCcccccc
Q 045853          119 TSTCVICLEEFRDG---------DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR  164 (184)
Q Consensus       119 ~~~C~ICl~~~~~~---------~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  164 (184)
                      ++.|+||++.+.+.         +-...+.+|||.||..||.+|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            44699999999422         22234457999999999999999999999998

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=99.55  E-value=3.8e-15  Score=112.06  Aligned_cols=55  Identities=35%  Similarity=0.848  Sum_probs=45.5

Q ss_pred             CCCcccccCcccccCCc----cceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGD----ECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~----~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..+.+|+||++.+.+.+    .+.++++|+|.||.+||.+|+..+.+||+||.++....
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~v~  230 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVI  230 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeEEe
Confidence            45678999999987643    23466789999999999999999999999999886443

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

Probab=99.51  E-value=9.5e-14  Score=108.29  Aligned_cols=52  Identities=42%  Similarity=1.027  Sum_probs=42.6

Q ss_pred             CCCCcccccCccc-ccCC--------ccceeecCCCccccHhhHHHHhcCCCccccccccc
Q 045853          116 VNKTSTCVICLEE-FRDG--------DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV  167 (184)
Q Consensus       116 ~~~~~~C~ICl~~-~~~~--------~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i  167 (184)
                      ..++..|.||+++ |..+        ++.+..++|||+||.+|++.|++++++||+||.++
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence            4566789999999 4443        23444557999999999999999999999999995

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

Probab=99.49  E-value=1.3e-14  Score=110.25  Aligned_cols=52  Identities=37%  Similarity=0.913  Sum_probs=46.0

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRR  169 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~  169 (184)
                      ..+.+|+|||++|..+|.++++| |+|.||..|++.|+. -+..||+||..+.+
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            34478999999999999999985 999999999999998 56779999998853

>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=99.42  E-value=1.1e-13  Score=80.15  Aligned_cols=47  Identities=34%  Similarity=0.845  Sum_probs=39.4

Q ss_pred             CcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      +..|.||++...+    .++.+|||. |+..|+..|++.+..||+||+++..
T Consensus         2 ~~~C~iC~~~~~~----~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPRD----VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBSS----EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCCc----eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            3579999999777    555579999 9999999999999999999999864

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.40  E-value=1.8e-13  Score=99.04  Aligned_cols=55  Identities=29%  Similarity=0.744  Sum_probs=43.3

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----------------CCcccccccccccccCCC
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----------------HSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----------------~~~CP~CR~~i~~~~~~~  174 (184)
                      ..++.+|+||++.+.+    .+.++|||.||..||..|+..                ..+||+||.++....+..
T Consensus        15 ~~~~~~CpICld~~~d----PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP   85 (193)
T PLN03208         15 SGGDFDCNICLDQVRD----PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP   85 (193)
T ss_pred             CCCccCCccCCCcCCC----cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence            3455789999999877    555679999999999999852                357999999997655433

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

Probab=99.36  E-value=4.2e-13  Score=84.36  Aligned_cols=50  Identities=40%  Similarity=0.996  Sum_probs=39.8

Q ss_pred             CcccccCccccc--------CCccce-eecCCCccccHhhHHHHhcC---CCcccccccccc
Q 045853          119 TSTCVICLEEFR--------DGDECK-VRSKCNHIFHQTCMDDWLDD---HSTCPLCRGRVR  168 (184)
Q Consensus       119 ~~~C~ICl~~~~--------~~~~~~-~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~i~  168 (184)
                      ++.|.||...|+        .+|..+ +...|+|.||..||.+|+..   +..||+||++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            668999999998        334433 33479999999999999984   568999999764

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

Probab=99.34  E-value=6.2e-13  Score=100.81  Aligned_cols=52  Identities=31%  Similarity=0.794  Sum_probs=45.4

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCC
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~  173 (184)
                      ....|.+||+...+    +...||||+||..||..|...+..||+||....+..+.
T Consensus       238 a~~kC~LCLe~~~~----pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi  289 (293)
T KOG0317|consen  238 ATRKCSLCLENRSN----PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI  289 (293)
T ss_pred             CCCceEEEecCCCC----CCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence            34689999999988    66678999999999999999999999999998766543

>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=99.33  E-value=1e-12  Score=72.01  Aligned_cols=38  Identities=42%  Similarity=1.177  Sum_probs=32.5

Q ss_pred             cccCcccccCCccce-eecCCCccccHhhHHHHhcCCCccccc
Q 045853          122 CVICLEEFRDGDECK-VRSKCNHIFHQTCMDDWLDDHSTCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~-~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  163 (184)
                      |+||++.+.+    + +..+|||.|+.+|+.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~----~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD----PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS----EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC----cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999988    4 456799999999999999999999998

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

Probab=99.32  E-value=8.2e-13  Score=97.36  Aligned_cols=61  Identities=26%  Similarity=0.609  Sum_probs=50.1

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCcccccccccccccCCCCCCCCC
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLCRGRVRRIAWPSFTTADD  180 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i~~~~~~~~~~~~~  180 (184)
                      .....+|.|||+.-++    .++..|||.||..||.+||+   ....||+||..+....+.+.+.++.
T Consensus        44 ~~~~FdCNICLd~akd----PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~  107 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD----PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGS  107 (230)
T ss_pred             CCCceeeeeeccccCC----CEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCC
Confidence            4455689999999888    66666999999999999998   4556999999998888777666554

>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=99.31  E-value=1.3e-12  Score=73.46  Aligned_cols=44  Identities=50%  Similarity=1.207  Sum_probs=36.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRV  167 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i  167 (184)
                      +|+||++.+.  +. ..+++|||.||..|++.|+.. +..||+||..+
T Consensus         1 ~C~iC~~~~~--~~-~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EP-VVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--Cc-eEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999982  23 444469999999999999986 77899999864

>PHA02926 zinc finger-like protein; Provisional

Probab=99.28  E-value=2.3e-12  Score=94.42  Aligned_cols=60  Identities=38%  Similarity=0.813  Sum_probs=43.9

Q ss_pred             CCCCcccccCcccccCC----c-cceeecCCCccccHhhHHHHhcCC------CcccccccccccccCCCC
Q 045853          116 VNKTSTCVICLEEFRDG----D-ECKVRSKCNHIFHQTCMDDWLDDH------STCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~----~-~~~~l~~C~H~FH~~Ci~~Wl~~~------~~CP~CR~~i~~~~~~~~  175 (184)
                      .+.+.+|+||++..-+.    + .-.++++|+|.||..||..|.+.+      .+||+||..+.......|
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf  237 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKF  237 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeeccccc
Confidence            34456899999986331    1 234677899999999999999742      459999998875554433

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

Probab=99.25  E-value=3.3e-12  Score=90.41  Aligned_cols=52  Identities=33%  Similarity=0.797  Sum_probs=43.3

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ....|+|||+.+....  .+-.+|||+||+.||+.-++....||+||+.|....
T Consensus       130 ~~~~CPiCl~~~sek~--~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKV--PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccCCCceecchhhcc--ccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            3357999999998733  344579999999999999999999999999886544

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.20  E-value=1.2e-11  Score=69.44  Aligned_cols=44  Identities=30%  Similarity=0.859  Sum_probs=36.4

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      +|.||++.|.++.. ..++.|||+|+..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~-~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERR-PRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCC-eEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            49999999944444 455579999999999999866788999985

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

Probab=99.19  E-value=3.6e-11  Score=101.79  Aligned_cols=56  Identities=36%  Similarity=0.846  Sum_probs=45.8

Q ss_pred             CCCcccccCcccccCCcc--ceeecCCCccccHhhHHHHhcCCCcccccccccccccCC
Q 045853          117 NKTSTCVICLEEFRDGDE--CKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~--~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~  173 (184)
                      ..+..|+||++++..+..  ...+ +|||+||..|+..|+++..+||+||..+......
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL-~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~~  346 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRL-PCGHIFHDSCLRSWFERQQTCPTCRTVLYDYVLW  346 (543)
T ss_pred             hcCCeeeeechhhcccccccccee-ecccchHHHHHHHHHHHhCcCCcchhhhhccccc
Confidence            345689999999998754  4455 5999999999999999999999999966555443

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

Probab=99.18  E-value=1.7e-11  Score=68.01  Aligned_cols=38  Identities=37%  Similarity=0.982  Sum_probs=30.1

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhcCC----Cccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH----STCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~C  163 (184)
                      |+||++.|.+    ++.++|||.|+..||.+|++..    ..||.|
T Consensus         1 CpiC~~~~~~----Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD----PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS----EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC----ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999999    8878899999999999999843    369987

>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=99.14  E-value=3.8e-11  Score=66.45  Aligned_cols=39  Identities=44%  Similarity=1.113  Sum_probs=33.4

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhc--CCCccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~C  163 (184)
                      |+||++.+....   .+.+|||.|+..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV---ILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE---EETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC---EEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999998832   2567999999999999998  67789998

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 ....

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

Probab=99.09  E-value=4e-10  Score=84.73  Aligned_cols=61  Identities=25%  Similarity=0.548  Sum_probs=46.9

Q ss_pred             CcccCCCCcccccCcccccCCc-------cceeecCCCccccHhhHHHHhc--CCCcccccccccccccCC
Q 045853          112 NDDAVNKTSTCVICLEEFRDGD-------ECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       112 ~~~~~~~~~~C~ICl~~~~~~~-------~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~~~~~  173 (184)
                      ......++..|+||-..+..+.       .+-.+ .|+|+||+.||.-|..  .+++||.||+.+.-...+
T Consensus       217 lPtkhl~d~vCaVCg~~~~~s~~eegvienty~L-sCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmf  286 (328)
T KOG1734|consen  217 LPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKL-SCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMF  286 (328)
T ss_pred             CCCCCCCcchhHhhcchheeecchhhhhhhheee-ecccchHHHhhhhheeecCCCCCchHHHHhhHhhhc
Confidence            3344556678999998887554       44556 5999999999999975  788999999988755533

>smart00184 RING Ring finger

Probab=99.07  E-value=1e-10  Score=63.44  Aligned_cols=38  Identities=47%  Similarity=1.214  Sum_probs=30.9

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~C  163 (184)
                      |+||++....   ...+ +|||.||..|++.|+. .+..||+|
T Consensus         1 C~iC~~~~~~---~~~~-~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD---PVVL-PCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC---cEEe-cCCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998433   3444 6999999999999998 67779987

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)

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

Probab=99.06  E-value=1.1e-10  Score=71.54  Aligned_cols=47  Identities=43%  Similarity=0.897  Sum_probs=34.9

Q ss_pred             cccCcccccCCccceee-cCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          122 CVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      |+=|...+..+++..+. ..|+|.||.+||.+||..+..||++|+...
T Consensus        34 C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             CcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            33333444456655542 259999999999999999999999999764

>smart00504 Ubox Modified RING finger domain

Probab=99.05  E-value=1.3e-10  Score=70.38  Aligned_cols=47  Identities=23%  Similarity=0.459  Sum_probs=41.0

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      .|+||.+.+.+    ++..+|||+|+..||..|++.+.+||+|+..+...+
T Consensus         3 ~Cpi~~~~~~~----Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        3 LCPISLEVMKD----PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             CCcCCCCcCCC----CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            59999999988    555679999999999999998889999999885443

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

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

Probab=99.03  E-value=3.9e-11  Score=72.87  Aligned_cols=51  Identities=37%  Similarity=0.948  Sum_probs=39.4

Q ss_pred             CCcccccCccccc--------CCccceee-cCCCccccHhhHHHHhc---CCCcccccccccc
Q 045853          118 KTSTCVICLEEFR--------DGDECKVR-SKCNHIFHQTCMDDWLD---DHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~--------~~~~~~~l-~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i~  168 (184)
                      .++.|.||.-.|.        .+|..+++ -.|.|.||..||.+|+.   .+..||+||+...
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3448999999997        45555542 26999999999999997   3456999999753

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.99  E-value=2.7e-10  Score=91.83  Aligned_cols=52  Identities=29%  Similarity=0.713  Sum_probs=43.8

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ......|+||++.|..    .++.+|||.||..||..|+.....||+||..+....
T Consensus        23 Le~~l~C~IC~d~~~~----PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~   74 (397)
T TIGR00599        23 LDTSLRCHICKDFFDV----PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESK   74 (397)
T ss_pred             cccccCCCcCchhhhC----ccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccccc
Confidence            4455689999999977    555679999999999999998889999999886543

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

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

Probab=98.91  E-value=8.2e-10  Score=61.22  Aligned_cols=39  Identities=28%  Similarity=0.757  Sum_probs=23.8

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCP  161 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP  161 (184)
                      |+||.+ |.+++..++.++|||+|+.+|+++++..    ..+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 8777777766679999999999999983    33576

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

Probab=98.91  E-value=5.2e-10  Score=87.54  Aligned_cols=84  Identities=24%  Similarity=0.452  Sum_probs=55.7

Q ss_pred             cccCcchhhhcccchHHHHHHhhhhcCCCCcc--cCCCCcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCc
Q 045853           83 VKEDPRASKFKKVSWTAFKRDIINNKSHQNDD--AVNKTSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHST  159 (184)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~  159 (184)
                      .+..+++...+...+.......+..+..+..+  ..+...+|.||+.+-.+    .+++||+|. .|..|.+..--++++
T Consensus       252 ~~~~kQ~~~v~g~~y~LqEiyGien~~v~~~~~~~~~~gkeCVIClse~rd----t~vLPCRHLCLCs~Ca~~Lr~q~n~  327 (349)
T KOG4265|consen  252 IKVLKQILWVDGTRYLLQEIYGIENSTVEGTDADESESGKECVICLSESRD----TVVLPCRHLCLCSGCAKSLRYQTNN  327 (349)
T ss_pred             eeeeeeEEEEeCceeeeehhhccccCCCCCCccccccCCCeeEEEecCCcc----eEEecchhhehhHhHHHHHHHhhcC
Confidence            33344444444444444443333333332222  33557899999999988    555579997 999999998778889


Q ss_pred             ccccccccccc
Q 045853          160 CPLCRGRVRRI  170 (184)
Q Consensus       160 CP~CR~~i~~~  170 (184)
                      ||+||+++..-
T Consensus       328 CPICRqpi~~l  338 (349)
T KOG4265|consen  328 CPICRQPIEEL  338 (349)
T ss_pred             CCccccchHhh
Confidence            99999998643

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

Probab=98.85  E-value=5.6e-10  Score=68.88  Aligned_cols=49  Identities=29%  Similarity=0.712  Sum_probs=24.4

Q ss_pred             cccccCcccccCCccc--eee--cCCCccccHhhHHHHhcC---C--------Ccccccccccc
Q 045853          120 STCVICLEEFRDGDEC--KVR--SKCNHIFHQTCMDDWLDD---H--------STCPLCRGRVR  168 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~--~~l--~~C~H~FH~~Ci~~Wl~~---~--------~~CP~CR~~i~  168 (184)
                      .+|.||+....+++++  .+.  ..|++.||..|+.+||..   .        .+||.|+++|.
T Consensus         3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            4799999997744433  223  268899999999999971   1        24999999884

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

Probab=98.83  E-value=1.5e-09  Score=88.44  Aligned_cols=56  Identities=29%  Similarity=0.649  Sum_probs=44.5

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhc-----CCCcccccccccccccCCCCCCC
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----DHSTCPLCRGRVRRIAWPSFTTA  178 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~i~~~~~~~~~~~  178 (184)
                      +..|+|||++...    ..++.|||+||..||-++|.     ....||+||..|...++..-...
T Consensus       186 ~~~CPICL~~~~~----p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e  246 (513)
T KOG2164|consen  186 DMQCPICLEPPSV----PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIE  246 (513)
T ss_pred             CCcCCcccCCCCc----ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeec
Confidence            5689999999877    55567999999999998886     34679999999987665444333

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

Probab=98.82  E-value=1.5e-09  Score=81.70  Aligned_cols=52  Identities=31%  Similarity=0.680  Sum_probs=43.6

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHH-HhcCCCc-ccccccccccccC
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDD-WLDDHST-CPLCRGRVRRIAW  172 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~-Wl~~~~~-CP~CR~~i~~~~~  172 (184)
                      ..+..|+||++....    ....+|||+||..||-. |=.++.. ||+||+...+.+.
T Consensus       213 ~~d~kC~lC~e~~~~----ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEV----PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCC----cccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            345689999999888    66668999999999999 8776666 9999999876654

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

Probab=98.78  E-value=8.3e-10  Score=85.60  Aligned_cols=55  Identities=25%  Similarity=0.543  Sum_probs=47.9

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCCCCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTA  178 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~~~~  178 (184)
                      ..|.||.+.|..    +++.+|+|.||.-||..+|..+..||.|+..+.+..+..-++-
T Consensus        24 LRC~IC~eyf~i----p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il   78 (442)
T KOG0287|consen   24 LRCGICFEYFNI----PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRIL   78 (442)
T ss_pred             HHHhHHHHHhcC----ceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHH
Confidence            379999999998    7777899999999999999999999999999987776655443

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

Probab=98.77  E-value=5.9e-09  Score=59.66  Aligned_cols=42  Identities=33%  Similarity=0.952  Sum_probs=31.4

Q ss_pred             ccccCcccccCCccceeecCCC-----ccccHhhHHHHhc--CCCcccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLD--DHSTCPLCR  164 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~--~~~~CP~CR  164 (184)
                      .|.||++. .+++...+. ||.     |.+|..|+.+|+.  .+.+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~-PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVS-PCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEe-ccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            38999993 333443455 485     9999999999995  456899995

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

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

Probab=98.71  E-value=3.5e-09  Score=60.20  Aligned_cols=46  Identities=30%  Similarity=0.695  Sum_probs=38.2

Q ss_pred             cccccCcccccCCccceeecCCCcc-ccHhhHHHHhc-CCCccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLD-DHSTCPLCRGRVRR  169 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~-~~~~CP~CR~~i~~  169 (184)
                      ++|.||++.-.+    .++..|||. ++.+|--+.++ .+..||+||++|..
T Consensus         8 dECTICye~pvd----sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    8 DECTICYEHPVD----SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             cceeeeccCcch----HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            689999999887    555669997 99999766665 78899999999853

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

Probab=98.70  E-value=5.8e-09  Score=84.54  Aligned_cols=53  Identities=34%  Similarity=0.827  Sum_probs=40.0

Q ss_pred             CCCCcccccCcccccCC----------ccc---eeecCCCccccHhhHHHHhc-CCCcccccccccc
Q 045853          116 VNKTSTCVICLEEFRDG----------DEC---KVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVR  168 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~----------~~~---~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~  168 (184)
                      .+....|+||+.+..--          +.+   ..+.||.|+||..|+.+|.. .+-.||+||.++.
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            34556799999887621          111   13447999999999999999 5668999999884

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.70  E-value=1.6e-08  Score=78.72  Aligned_cols=57  Identities=19%  Similarity=0.504  Sum_probs=41.5

Q ss_pred             CcccccCccc-ccCCccceeecCCCccccHhhHHHHh-cCCCcccccccccccccCCCC
Q 045853          119 TSTCVICLEE-FRDGDECKVRSKCNHIFHQTCMDDWL-DDHSTCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       119 ~~~C~ICl~~-~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~i~~~~~~~~  175 (184)
                      +..|++|..+ |...+......+|||.||..|++..+ .....||.|+..+....+...
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q   61 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQ   61 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcccc
Confidence            3579999996 44444322222699999999999966 456689999999987765543

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).

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

Probab=98.68  E-value=5.7e-09  Score=79.47  Aligned_cols=53  Identities=23%  Similarity=0.510  Sum_probs=47.2

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCCCC
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTT  177 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~~~  177 (184)
                      .|-||-+.+..    +.+.+|||.||.-||...|..+..||+||.+.....+++...
T Consensus        27 rC~IC~~~i~i----p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~   79 (391)
T COG5432          27 RCRICDCRISI----PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSG   79 (391)
T ss_pred             Hhhhhhheeec----ceecccccchhHHHHHHHhcCCCCCccccccHHhhhcccchh
Confidence            69999999988    887889999999999999999999999999987777666543

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

Probab=98.67  E-value=1.2e-08  Score=82.01  Aligned_cols=53  Identities=34%  Similarity=0.805  Sum_probs=42.0

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      ....+-.+|++||+.+.++..-.+...|.|.||..|+..|..  .+||+||.-..
T Consensus       170 ~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  170 TGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             CCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence            334566789999999998764333335999999999999954  78999998665

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

Probab=98.66  E-value=9.8e-09  Score=66.16  Aligned_cols=29  Identities=38%  Similarity=0.898  Sum_probs=26.6

Q ss_pred             CCCccccHhhHHHHhcCCCcccccccccc
Q 045853          140 KCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       140 ~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      .|+|.||..||.+||+.+..||+|.++-.
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            69999999999999999999999988653

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

Probab=98.61  E-value=3.8e-08  Score=61.32  Aligned_cols=48  Identities=25%  Similarity=0.459  Sum_probs=38.3

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      ..|+|+.+-|.+    ++..++||+|-..||..|+.. +.+||+|++++....
T Consensus         5 f~CpIt~~lM~d----PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    5 FLCPITGELMRD----PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GB-TTTSSB-SS----EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             cCCcCcCcHhhC----ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            479999999999    777789999999999999998 899999999987654

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 ....

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

Probab=98.58  E-value=2.1e-08  Score=79.21  Aligned_cols=48  Identities=31%  Similarity=0.926  Sum_probs=35.8

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i  167 (184)
                      ..|.||.+-+....++--.-.|||+||..|+.+|+.   .+++||+||-.+
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            379999555555445544435999999999999998   347899999443

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

Probab=98.55  E-value=1.8e-08  Score=87.38  Aligned_cols=55  Identities=27%  Similarity=0.751  Sum_probs=40.7

Q ss_pred             cccCCCCcccccCcccccC-Cccce--eecCCCccccHhhHHHHhc--CCCccccccccc
Q 045853          113 DDAVNKTSTCVICLEEFRD-GDECK--VRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRV  167 (184)
Q Consensus       113 ~~~~~~~~~C~ICl~~~~~-~~~~~--~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i  167 (184)
                      ....+...+|+||+.-... +-.++  .++.|+|.||..|+.+|++  .+.+||+||..+
T Consensus      1463 ~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219        1463 DEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred             hhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence            3445677899999987662 11111  2335889999999999998  577899999776

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

Probab=98.29  E-value=2.9e-07  Score=72.30  Aligned_cols=46  Identities=37%  Similarity=0.832  Sum_probs=38.6

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      ..+...|+||++.|...    .+.+|||.|+..|+..++.....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP----VLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC----ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            34556899999999995    44579999999999999986668999993

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

Probab=98.27  E-value=2.1e-07  Score=79.44  Aligned_cols=49  Identities=24%  Similarity=0.697  Sum_probs=42.3

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCcccccccccccccC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~  172 (184)
                      ..|+.|-+...+    .+.+.|||+||.+|+..-+. +++.||.|...+...++
T Consensus       644 LkCs~Cn~R~Kd----~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  644 LKCSVCNTRWKD----AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             eeCCCccCchhh----HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            369999988888    77778999999999999996 78899999998865554

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

Probab=98.26  E-value=4.9e-07  Score=71.87  Aligned_cols=59  Identities=27%  Similarity=0.699  Sum_probs=44.2

Q ss_pred             CCCcccccCcccccCCc----cceeecCCCccccHhhHHHHhc--C-----CCcccccccccccccCCCC
Q 045853          117 NKTSTCVICLEEFRDGD----ECKVRSKCNHIFHQTCMDDWLD--D-----HSTCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~----~~~~l~~C~H~FH~~Ci~~Wl~--~-----~~~CP~CR~~i~~~~~~~~  175 (184)
                      ..+.+|.||++...+..    ...++|+|.|.|+..||..|-.  +     .+.||.||..........+
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~  228 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSF  228 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccce
Confidence            55778999999876532    1235688999999999999984  3     4679999998765544433

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

Probab=98.25  E-value=2.8e-07  Score=70.62  Aligned_cols=54  Identities=31%  Similarity=0.821  Sum_probs=44.2

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-----------------------CCCcccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----------------------DHSTCPLCRGRVR  168 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----------------------~~~~CP~CR~~i~  168 (184)
                      +..-....|.|||.-|.+++...+. .|.|.||..|+.++|.                       ....||+||..|.
T Consensus       110 ~nn~p~gqCvICLygfa~~~~ft~T-~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~  186 (368)
T KOG4445|consen  110 ENNHPNGQCVICLYGFASSPAFTVT-ACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIK  186 (368)
T ss_pred             cCCCCCCceEEEEEeecCCCceeee-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcc
Confidence            3445667899999999999987777 4999999999988876                       1234999999885

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

Probab=98.24  E-value=6.6e-07  Score=71.32  Aligned_cols=50  Identities=34%  Similarity=0.959  Sum_probs=38.9

Q ss_pred             CCcccccCcccccCC-ccceeecCCCccccHhhHHHHhcC--CCccccccccc
Q 045853          118 KTSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLDD--HSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~i  167 (184)
                      .+..|+||++.+.-. +...+.+.|||.|-.+||+.|+.+  ...||.|..+-
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            346899999999854 444456689999999999999962  34599998653

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

Probab=98.21  E-value=2.9e-07  Score=78.63  Aligned_cols=57  Identities=26%  Similarity=0.503  Sum_probs=44.2

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCCCCC
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTTA  178 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~~~~  178 (184)
                      .|++|+..+.+....-.. +|+|.||..||..|-+.-.+||+||..+....+..++..
T Consensus       125 ~CP~Ci~s~~DqL~~~~k-~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~eS~~~  181 (1134)
T KOG0825|consen  125 QCPNCLKSCNDQLEESEK-HTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVLESTGI  181 (1134)
T ss_pred             hhhHHHHHHHHHhhcccc-ccccccHHHHhhhhhhhcccCchhhhhhheeeeeccccc
Confidence            466666666654443334 599999999999999999999999999887776666554

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

Probab=98.15  E-value=8.4e-07  Score=68.18  Aligned_cols=49  Identities=24%  Similarity=0.533  Sum_probs=39.6

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      ..+|+||+....-    ++-++|+|.|+..||+--..+ +.+|++||.+|...-
T Consensus         7 ~~eC~IC~nt~n~----Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    7 KKECLICYNTGNC----PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             CCcceeeeccCCc----CccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            3589999999877    555679999999999887664 556999999996543

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

Probab=98.13  E-value=5e-07  Score=53.66  Aligned_cols=44  Identities=32%  Similarity=0.852  Sum_probs=23.3

Q ss_pred             ccccCcccccCCcccee-ecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          121 TCVICLEEFRDGDECKV-RSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~-l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      .|++|.+-+.+    ++ +..|.|+|++.||..-+.  ..||+|+.+--..
T Consensus         9 rCs~C~~~l~~----pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~q   53 (65)
T PF14835_consen    9 RCSICFDILKE----PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQ   53 (65)
T ss_dssp             S-SSS-S--SS-----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-S
T ss_pred             CCcHHHHHhcC----CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHH
Confidence            69999999988    54 458999999999988654  4599999876433

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

Probab=98.04  E-value=7.7e-07  Score=69.77  Aligned_cols=52  Identities=25%  Similarity=0.565  Sum_probs=42.2

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      ..+..|+|||+-+...   +..+.|.|.||.+||..-++ .+++||.||+.+....
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr   93 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR   93 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence            3345799999998873   44557999999999988886 6788999999987654

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

Probab=97.99  E-value=2.8e-06  Score=67.51  Aligned_cols=49  Identities=31%  Similarity=0.653  Sum_probs=38.6

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcC--CCcccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD--HSTCPLCRGRVR  168 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~i~  168 (184)
                      ..|..|-+.+-..++-...+||.|+||..|+...|.+  .++||.||+-..
T Consensus       366 L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrS  416 (518)
T KOG1941|consen  366 LYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRS  416 (518)
T ss_pred             hhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence            4699999998866554444579999999999999975  467999995443

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

Probab=97.80  E-value=1.5e-05  Score=58.98  Aligned_cols=51  Identities=24%  Similarity=0.686  Sum_probs=43.3

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC--------CCccccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD--------HSTCPLCRGRVRRIA  171 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~i~~~~  171 (184)
                      +..|..|-..+..+|.+|+.  |-|+||..|+++|--+        ...||-|.++|.+..
T Consensus        50 ~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             CCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            34799999999999999975  9999999999999762        345999999997654

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

Probab=97.77  E-value=1.5e-05  Score=64.78  Aligned_cols=49  Identities=31%  Similarity=0.748  Sum_probs=43.4

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..+.+|.||+..+..    ++..+|||.|+..||++-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~----pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP----PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC----CccccccccccHHHHHHHhccCCCCccccccccc
Confidence            566789999999888    6666899999999999988888899999998875

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

Probab=97.77  E-value=1.3e-05  Score=72.93  Aligned_cols=56  Identities=27%  Similarity=0.725  Sum_probs=43.1

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----------CCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----------HSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----------~~~CP~CR~~i~~~~  171 (184)
                      ....++.|.||+.+--.......+ .|+|+||.+|..+-|.+          -..||+|+.+|....
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL-~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~~ 3547 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQL-DCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIV 3547 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceec-CCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhHH
Confidence            345567899999997776665666 69999999999887763          235999999886543

>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=97.74  E-value=1.9e-05  Score=54.11  Aligned_cols=45  Identities=22%  Similarity=0.559  Sum_probs=33.5

Q ss_pred             CcccccCcccccCCccceeecCCC------ccccHhhHHHHhcCCCcccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCN------HIFHQTCMDDWLDDHSTCPLCR  164 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~------H~FH~~Ci~~Wl~~~~~CP~CR  164 (184)
                      ..+|+||++...+++.+...+ ||      |.||.+|+.+|-+.+++=|.=|
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~~~~rDPfnR   76 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRRERNRDPFNR   76 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHhhccCCCccc
Confidence            358999999999966666665 76      9999999999954333334333

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.

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

Probab=97.69  E-value=1.1e-05  Score=61.90  Aligned_cols=43  Identities=33%  Similarity=0.768  Sum_probs=35.2

Q ss_pred             CcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..-|+||++.-.+    .++++|||. -|.+|-...    +.||+||+.|..
T Consensus       300 ~~LC~ICmDaP~D----CvfLeCGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD----CVFLECGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc----eEEeecCcEEeehhhcccc----ccCchHHHHHHH
Confidence            5679999999988    666689994 888887554    479999998864

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

Probab=97.68  E-value=2e-05  Score=64.44  Aligned_cols=52  Identities=31%  Similarity=0.816  Sum_probs=44.2

Q ss_pred             CCCCcccccCcccccCCccceee-cCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..++..|++|...+.+    ++. ..|||.|+..|+..|+..+..||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl~~----p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRD----PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccC----CCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            4555689999999998    555 379999999999999999999999998876544

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

Probab=97.67  E-value=1.9e-05  Score=63.04  Aligned_cols=47  Identities=34%  Similarity=0.950  Sum_probs=37.7

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhc--CCCccccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~~~  171 (184)
                      -|-||-+.=.+   +.+. +|||..|..|+..|-.  ..++||.||..|....
T Consensus       371 LCKICaendKd---vkIE-PCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte  419 (563)
T KOG1785|consen  371 LCKICAENDKD---VKIE-PCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTE  419 (563)
T ss_pred             HHHHhhccCCC---cccc-cccchHHHHHHHhhcccCCCCCCCceeeEecccc
Confidence            59999886444   5666 5999999999999974  3678999999986443

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

Probab=97.65  E-value=3.3e-05  Score=43.67  Aligned_cols=40  Identities=28%  Similarity=0.913  Sum_probs=27.8

Q ss_pred             cccCcccccCCccceeecCCC-----ccccHhhHHHHhc--CCCccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLD--DHSTCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~--~~~~CP~C  163 (184)
                      |-||++.-.+++.+. . ||+     ...|..|+.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~~li-~-pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLI-S-PCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE---SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCcee-c-ccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999988766322 3 464     4799999999997  66779987

>PHA02862 5L protein; Provisional

Probab=97.62  E-value=3.7e-05  Score=53.06  Aligned_cols=45  Identities=24%  Similarity=0.736  Sum_probs=34.4

Q ss_pred             cccccCcccccCCccceeecCCC-----ccccHhhHHHHhc--CCCccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLD--DHSTCPLCRGRVRR  169 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~  169 (184)
                      +.|-||.++-.+  .+  - ||+     ..-|.+|+.+|+.  ++..||+||.+..-
T Consensus         3 diCWIC~~~~~e--~~--~-PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDE--RN--N-FCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCC--Cc--c-cccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            479999998543  22  3 354     6799999999997  56779999998753

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

Probab=97.51  E-value=6.5e-05  Score=44.26  Aligned_cols=39  Identities=31%  Similarity=0.784  Sum_probs=26.8

Q ss_pred             cccccCcccccCCccceee-cCCCccccHhhHHHHhc--CCCcccc
Q 045853          120 STCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLD--DHSTCPL  162 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~--~~~~CP~  162 (184)
                      ..|+|.+..|.+    ++. ..|||+|-++.|.+|++  ....||+
T Consensus        12 ~~CPiT~~~~~~----PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   12 LKCPITLQPFED----PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB-TTTSSB-SS----EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cCCCCcCChhhC----CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            479999999987    433 37999999999999994  4556998

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

Probab=97.30  E-value=9.3e-05  Score=53.82  Aligned_cols=44  Identities=23%  Similarity=0.582  Sum_probs=39.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      .|.||-.+|..    ++...|||.||..|.-.=.+...+|-+|-+...
T Consensus       198 ~C~iCKkdy~s----pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         198 LCGICKKDYES----PVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             eehhchhhccc----hhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            69999999999    777789999999999888888889999977553

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.30  E-value=0.00035  Score=49.23  Aligned_cols=52  Identities=23%  Similarity=0.729  Sum_probs=36.4

Q ss_pred             CCCCcccccCcccccCCccceeecCCCc---cccHhhHHHHhc--CCCcccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNH---IFHQTCMDDWLD--DHSTCPLCRGRVRRI  170 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H---~FH~~Ci~~Wl~--~~~~CP~CR~~i~~~  170 (184)
                      ...+..|-||.++..+  ...-. .|..   .-|.+|+++|+.  +...|++|+.+..-.
T Consensus         5 s~~~~~CRIC~~~~~~--~~~PC-~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          5 SLMDKCCWICKDEYDV--VTNYC-NCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCCeeEecCCCCCC--ccCCc-ccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4455689999988542  22211 3444   579999999997  466799999987543

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

Probab=97.26  E-value=0.00031  Score=39.53  Aligned_cols=45  Identities=29%  Similarity=0.716  Sum_probs=23.3

Q ss_pred             cccCcccccCCccceeec-CCCccccHhhHHHHhc-CCCccccccccc
Q 045853          122 CVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWLD-DHSTCPLCRGRV  167 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i  167 (184)
                      |++|.+++...+. ...| +||+..+..|...-+. ....||-||++.
T Consensus         1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999955443 3333 6899999999888886 578899999874

>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=97.21  E-value=0.0015  Score=43.40  Aligned_cols=35  Identities=20%  Similarity=0.663  Sum_probs=26.5

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHH
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMD  151 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~  151 (184)
                      ...++..|++|-..+..+ ...+. ||||+||..|++
T Consensus        74 ~i~~~~~C~vC~k~l~~~-~f~~~-p~~~v~H~~C~~  108 (109)
T PF10367_consen   74 VITESTKCSVCGKPLGNS-VFVVF-PCGHVVHYSCIK  108 (109)
T ss_pred             EECCCCCccCcCCcCCCc-eEEEe-CCCeEEeccccc
Confidence            345566899999999873 33334 699999999975

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 [].

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

Probab=97.17  E-value=0.00064  Score=59.31  Aligned_cols=43  Identities=30%  Similarity=0.709  Sum_probs=32.9

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV  167 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i  167 (184)
                      ...|..|-...+-.   .+...|||.||.+|+.   ..-..||-|+.+.
T Consensus       840 ~skCs~C~~~LdlP---~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLP---FVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccc---eeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            35799998887752   2333599999999998   5566799999844

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.15  E-value=0.0003  Score=52.90  Aligned_cols=54  Identities=11%  Similarity=0.329  Sum_probs=49.1

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~  173 (184)
                      .-|++|-+.+.+.-.+.+|.+|||+|..+|++........||+|-.++...++.
T Consensus       222 yiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  222 YICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             eecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            469999999999988889999999999999999999999999999999876644

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

Probab=97.13  E-value=0.00011  Score=57.45  Aligned_cols=52  Identities=25%  Similarity=0.643  Sum_probs=43.5

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      .....+|.+|-..|.+...+.   .|=|.||+.||-..|.....||.|...+-..
T Consensus        12 ~n~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cccceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            344558999999999976655   4889999999999999999999999877543

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

Probab=97.11  E-value=0.00021  Score=59.30  Aligned_cols=51  Identities=25%  Similarity=0.736  Sum_probs=41.4

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-----CCCcccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----DHSTCPLCRGRVR  168 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~i~  168 (184)
                      +......+|.+|-+.-++    .+...|.|.||.-|+.+++.     .+.+||.|-..+.
T Consensus       531 ~enk~~~~C~lc~d~aed----~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  531 DENKGEVECGLCHDPAED----YIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             ccccCceeecccCChhhh----hHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            444556789999998777    65667999999999999887     4678999988764

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

Probab=97.10  E-value=0.00031  Score=61.18  Aligned_cols=51  Identities=27%  Similarity=0.742  Sum_probs=40.6

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-------CCccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-------HSTCPLCRGRV  167 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~i  167 (184)
                      ....+|.||++.+...+.+--...|-|+||..||..|-+.       .=.||.|....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            3445899999999988877766678899999999999873       12499998543

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

Probab=97.09  E-value=0.00054  Score=52.37  Aligned_cols=54  Identities=28%  Similarity=0.509  Sum_probs=40.2

Q ss_pred             CcccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc--CCCcccccccccc
Q 045853          112 NDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRVR  168 (184)
Q Consensus       112 ~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i~  168 (184)
                      +......+.+|++|-+.-...   -+..+|||+||..||..-+.  ...+||.|-.+..
T Consensus       232 sss~~t~~~~C~~Cg~~PtiP---~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  232 SSSTGTSDTECPVCGEPPTIP---HVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccccccCCceeeccCCCCCCC---eeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            344456677999999886651   12235999999999988766  3468999988775

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

Probab=97.08  E-value=0.00069  Score=54.60  Aligned_cols=45  Identities=29%  Similarity=0.674  Sum_probs=35.1

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc--------CCCccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--------DHSTCPLCRG  165 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~  165 (184)
                      ..|.||+++.....-...+ ||+|+||..|+..++.        +.-+||-++-
T Consensus       185 f~C~ICf~e~~G~~c~~~l-pC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFL-PCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             ccceeeehhhcCcceeeec-ccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            4799999998776665656 5999999999999987        2345887653

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

Probab=97.07  E-value=0.0004  Score=55.06  Aligned_cols=50  Identities=30%  Similarity=0.646  Sum_probs=34.3

Q ss_pred             cccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       113 ~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      .........|.||+++..+    ....+|||+-+  |..--.. ..+||+||+.|..
T Consensus       299 ~~~~~~p~lcVVcl~e~~~----~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  299 FRELPQPDLCVVCLDEPKS----AVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIRL  348 (355)
T ss_pred             ccccCCCCceEEecCCccc----eeeecCCcEEE--chHHHhh-CCCCchhHHHHHH
Confidence            3344555679999999888    44446999855  5444333 3459999998853

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

Probab=97.04  E-value=0.00066  Score=53.71  Aligned_cols=50  Identities=22%  Similarity=0.453  Sum_probs=41.9

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..++..|+||+..-..    .+..||+|.-|..||.+-+-+.+.|=.|+..+..
T Consensus       419 ~sEd~lCpICyA~pi~----Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPIN----AVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CcccccCcceecccch----hhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            3567789999987665    3444699999999999999999999999998763

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

Probab=96.97  E-value=0.00034  Score=53.97  Aligned_cols=47  Identities=26%  Similarity=0.554  Sum_probs=41.1

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|-||-..|..    ++...|||.||..|...=++....|++|-+.+...
T Consensus       242 f~c~icr~~f~~----pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~  288 (313)
T KOG1813|consen  242 FKCFICRKYFYR----PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS  288 (313)
T ss_pred             cccccccccccc----chhhcCCceeehhhhccccccCCcceecccccccc
Confidence            359999999999    77778999999999999888889999999887543

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

Probab=96.92  E-value=0.00046  Score=53.35  Aligned_cols=45  Identities=31%  Similarity=0.644  Sum_probs=39.4

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      .|+||.+.+-.+....-..+|||..|..|+......+-+||+|.+
T Consensus       160 ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  160 NCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            499999998887766666679999999999999887799999988

>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=96.90  E-value=0.00071  Score=47.66  Aligned_cols=33  Identities=30%  Similarity=0.688  Sum_probs=23.7

Q ss_pred             CcccccCcccccCCccceeecC------------CCc-cccHhhHHHHhc
Q 045853          119 TSTCVICLEEFRDGDECKVRSK------------CNH-IFHQTCMDDWLD  155 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~------------C~H-~FH~~Ci~~Wl~  155 (184)
                      +..|+|||+--.+.    +|+-            |+- .-|.+|++++-+
T Consensus         2 d~~CpICme~PHNA----VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNA----VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCce----EEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            45799999988773    2222            442 469999999876

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.

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

Probab=96.87  E-value=5.4e-05  Score=60.32  Aligned_cols=53  Identities=25%  Similarity=0.622  Sum_probs=45.1

Q ss_pred             CCcccccCcccccCC-ccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          118 KTSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      -...|+||.+.+... +.+-.+ .|||.+|.+|+..|+.....||.||..+...+
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~-~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAI-VCGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHH-hhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            345799999999987 676666 49999999999999998889999999886544

>PHA03096 p28-like protein; Provisional

Probab=96.85  E-value=0.00053  Score=53.56  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=33.0

Q ss_pred             cccccCcccccCCc----cceeecCCCccccHhhHHHHhcC---CCccccccc
Q 045853          120 STCVICLEEFRDGD----ECKVRSKCNHIFHQTCMDDWLDD---HSTCPLCRG  165 (184)
Q Consensus       120 ~~C~ICl~~~~~~~----~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~  165 (184)
                      ..|.||++......    .--.++.|.|.|+..|+..|-..   +.+||.||.
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            47999999876431    22357789999999999999862   334555544

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.81  E-value=0.0014  Score=50.87  Aligned_cols=61  Identities=13%  Similarity=0.335  Sum_probs=47.5

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCCCC
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTT  177 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~~~  177 (184)
                      ......|+|...+|........+.+|||+|-..++...- ....||+|-.++...++....+
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp  170 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNP  170 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecC
Confidence            344567999999997666667777899999999999983 3567999999988766544433

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

Probab=96.75  E-value=0.006  Score=47.95  Aligned_cols=51  Identities=14%  Similarity=0.327  Sum_probs=38.5

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV  167 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i  167 (184)
                      ....+...|++|+..-.+...   +.--|-+||..|+-..+.....||+=-.+.
T Consensus       295 ~l~~~~~~CpvClk~r~Nptv---l~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  295 LLPPDREVCPVCLKKRQNPTV---LEVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             cCCCccccChhHHhccCCCce---EEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            334555689999999877422   222689999999999999999999855444

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

Probab=96.75  E-value=0.00053  Score=51.59  Aligned_cols=50  Identities=26%  Similarity=0.626  Sum_probs=35.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCC
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~  174 (184)
                      .|.-|..--. .+...++ .|+|+||..|...-..  ..||+||+.+.-..+..
T Consensus         5 hCn~C~~~~~-~~~f~LT-aC~HvfC~~C~k~~~~--~~C~lCkk~ir~i~l~~   54 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLT-ACRHVFCEPCLKASSP--DVCPLCKKSIRIIQLNR   54 (233)
T ss_pred             EeccccccCC-CCceeee-echhhhhhhhcccCCc--cccccccceeeeeeccc
Confidence            5776665444 6665655 6999999999866533  38999999976554433

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

Probab=96.68  E-value=0.001  Score=52.42  Aligned_cols=48  Identities=31%  Similarity=0.731  Sum_probs=39.1

Q ss_pred             cccccCcccccCC--ccceeecCCCccccHhhHHHHhcC-CCccccccccc
Q 045853          120 STCVICLEEFRDG--DECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~--~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i  167 (184)
                      .+|-||-++|..+  +.++..+.|||.|+..|+...+.. ...||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            4799999999977  445555679999999999888763 45699999985

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

Probab=96.66  E-value=0.0011  Score=47.43  Aligned_cols=29  Identities=38%  Similarity=1.100  Sum_probs=24.2

Q ss_pred             CCCccccHhhHHHHhcC-----------CCcccccccccc
Q 045853          140 KCNHIFHQTCMDDWLDD-----------HSTCPLCRGRVR  168 (184)
Q Consensus       140 ~C~H~FH~~Ci~~Wl~~-----------~~~CP~CR~~i~  168 (184)
                      .||.-||.-|+..||+.           -..||.|..++.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            69999999999999982           124999988874

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

Probab=96.51  E-value=0.00073  Score=47.65  Aligned_cols=31  Identities=35%  Similarity=0.794  Sum_probs=26.9

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccH
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQ  147 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~  147 (184)
                      ..+..||.||||++..+|++..|| |--+||+
T Consensus       174 ~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  174 KDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            445579999999999999999885 9999996

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.45  E-value=0.0035  Score=36.12  Aligned_cols=33  Identities=30%  Similarity=0.834  Sum_probs=29.8

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhH
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCM  150 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  150 (184)
                      ....|.+|-+.|.++|++.+.+.||-.+|..|-
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            345799999999999999999999999999994

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.36  E-value=0.0018  Score=37.36  Aligned_cols=44  Identities=20%  Similarity=0.433  Sum_probs=31.5

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      .|..|...-..    ..+.+|||+.+..|.+-+  +-+-||+|-+++...
T Consensus         9 ~~~~~~~~~~~----~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    9 PCVFCGFVGTK----GTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFD   52 (55)
T ss_pred             eEEEccccccc----cccccccceeeccccChh--hccCCCCCCCcccCC
Confidence            45555544333    444569999999998776  556799999988644

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

Probab=96.30  E-value=0.004  Score=49.27  Aligned_cols=60  Identities=25%  Similarity=0.543  Sum_probs=42.6

Q ss_pred             cccCCCCcccccCcccccCCccceeecCCCccccHhhHHHH--hcCCCcccccccccccccCCCCC
Q 045853          113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW--LDDHSTCPLCRGRVRRIAWPSFT  176 (184)
Q Consensus       113 ~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W--l~~~~~CP~CR~~i~~~~~~~~~  176 (184)
                      ++..+++.-|.||-+...-    .-++||+|..|--|.-+.  |..+..||+||..-...-+....
T Consensus        55 ddtDEen~~C~ICA~~~TY----s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e~V~fT~~~  116 (493)
T COG5236          55 DDTDEENMNCQICAGSTTY----SARYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASS  116 (493)
T ss_pred             cccccccceeEEecCCceE----EEeccCCchHHHHHHHHHHHHHhccCCCccccccceEEEecCC
Confidence            3444556679999988776    444579999999997543  44778899999976554444433

>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=96.20  E-value=0.0036  Score=34.55  Aligned_cols=41  Identities=34%  Similarity=0.918  Sum_probs=23.3

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhcCCC--ccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS--TCPLC  163 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~--~CP~C  163 (184)
                      |.+|-+-...+....-. .|+=.+|..|++.+++...  .||.|
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            56777776666554432 5888899999999998655  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.06  E-value=0.018  Score=50.87  Aligned_cols=40  Identities=20%  Similarity=0.365  Sum_probs=29.7

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD  155 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~  155 (184)
                      .....+++|.+|...+...-- .+. +|||.||.+|+.+-..
T Consensus       812 ~v~ep~d~C~~C~~~ll~~pF-~vf-~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  812 RVLEPQDSCDHCGRPLLIKPF-YVF-PCGHCFHRDCLIRHVL  851 (911)
T ss_pred             EEecCccchHHhcchhhcCcc-eee-eccchHHHHHHHHHHH
Confidence            345667789999988876422 233 6999999999987654

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

Probab=95.86  E-value=0.003  Score=55.13  Aligned_cols=55  Identities=25%  Similarity=0.629  Sum_probs=40.6

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcC--CCcccccccccccccCCCCCCCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD--HSTCPLCRGRVRRIAWPSFTTAD  179 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~i~~~~~~~~~~~~  179 (184)
                      ..|.||++ .   +...+. .|||.|+.+|+..-+..  ...||+||..+....+.+....+
T Consensus       455 ~~c~ic~~-~---~~~~it-~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~~~~~  511 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFIT-RCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSANPLP  511 (674)
T ss_pred             cccccccc-c---ccceee-cccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhccccc
Confidence            68999999 2   222334 59999999999988863  34699999998877765544433

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

Probab=95.55  E-value=0.0063  Score=47.96  Aligned_cols=46  Identities=20%  Similarity=0.565  Sum_probs=36.4

Q ss_pred             CCCCcccccCcccccCCccceeecCC--CccccHhhHHHHhcCCCccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKC--NHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C--~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..+-.+|+||.+.+..    ++. +|  ||+-|..|-.   +....||.||.++..
T Consensus        45 ~~~lleCPvC~~~l~~----Pi~-QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSP----PIF-QCDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             chhhccCchhhccCcc----cce-ecCCCcEehhhhhh---hhcccCCcccccccc
Confidence            3445689999999998    766 58  5999999975   346789999998863

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

Probab=95.54  E-value=0.023  Score=45.80  Aligned_cols=54  Identities=20%  Similarity=0.668  Sum_probs=34.4

Q ss_pred             cCCCCcccccCcccccC-------------CccceeecC-----CCccccHhhHHHHhc-------------CCCccccc
Q 045853          115 AVNKTSTCVICLEEFRD-------------GDECKVRSK-----CNHIFHQTCMDDWLD-------------DHSTCPLC  163 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~-------------~~~~~~l~~-----C~H~FH~~Ci~~Wl~-------------~~~~CP~C  163 (184)
                      ...+.+.|.=|+.+-.+             |...+..++     |.-..|.+|+.+|+.             ++..||+|
T Consensus       267 ~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtC  346 (358)
T PF10272_consen  267 SGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTC  346 (358)
T ss_pred             CccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCC
Confidence            44566678889875431             111112223     446679999999996             34469999


Q ss_pred             ccccc
Q 045853          164 RGRVR  168 (184)
Q Consensus       164 R~~i~  168 (184)
                      |+...
T Consensus       347 Ra~FC  351 (358)
T PF10272_consen  347 RAKFC  351 (358)
T ss_pred             cccce
Confidence            99764

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

>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=95.52  E-value=0.012  Score=45.56  Aligned_cols=58  Identities=21%  Similarity=0.493  Sum_probs=43.4

Q ss_pred             ccccCccc-ccCCccceeecCCCccccHhhHHHHhc-CCCcccccccccccccCCCCCCC
Q 045853          121 TCVICLEE-FRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAWPSFTTA  178 (184)
Q Consensus       121 ~C~ICl~~-~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~~~~~~~  178 (184)
                      .|++|-.+ |...+.....-+|||..|..|++..+. +...||-|-..+....+....-.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~fE   61 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTFE   61 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhcc
Confidence            48999866 555554444447999999999999986 66789999988877766554433

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

Probab=95.48  E-value=0.0078  Score=52.24  Aligned_cols=24  Identities=33%  Similarity=0.989  Sum_probs=21.5

Q ss_pred             cCCCccccHhhHHHHhcCCCcccc
Q 045853          139 SKCNHIFHQTCMDDWLDDHSTCPL  162 (184)
Q Consensus       139 ~~C~H~FH~~Ci~~Wl~~~~~CP~  162 (184)
                      ..|+|+.|..|...|++..-.||-
T Consensus      1046 g~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1046 GTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccccHHHHHHHHhcCCcCCC
Confidence            359999999999999998889984

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

Probab=95.46  E-value=0.0045  Score=52.72  Aligned_cols=42  Identities=26%  Similarity=0.564  Sum_probs=35.4

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      .|.||+..|.......+.+.|||+.|..|+..-.  +.+|| |+.
T Consensus        13 ~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly--n~scp-~~~   54 (861)
T KOG3161|consen   13 LCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY--NASCP-TKR   54 (861)
T ss_pred             hchHHHHHHHHHhcCcccccccchHHHHHHHhHh--hccCC-CCc
Confidence            6999999999887777778999999999998764  46788 654

>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=95.34  E-value=0.013  Score=32.65  Aligned_cols=41  Identities=24%  Similarity=0.659  Sum_probs=25.8

Q ss_pred             cccCcccccCCccceeecCCC-ccccHhhHHHHhcCCCcccccccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCN-HIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      |--|+-+...    .+  .|+ |..+..|+...+.+...||+|..++.
T Consensus         5 CKsCWf~~k~----Li--~C~dHYLCl~CLt~ml~~s~~C~iC~~~LP   46 (50)
T PF03854_consen    5 CKSCWFANKG----LI--KCSDHYLCLNCLTLMLSRSDRCPICGKPLP   46 (50)
T ss_dssp             --SS-S--SS----EE--E-SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred             ChhhhhcCCC----ee--eecchhHHHHHHHHHhccccCCCcccCcCc
Confidence            5556655444    33  486 99999999999999999999999874

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.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.32  E-value=0.014  Score=46.27  Aligned_cols=55  Identities=20%  Similarity=0.466  Sum_probs=37.7

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      .+++-|+.|++++...|+-..-.+||-..|.-|-...-+ -+.+||-||+......
T Consensus        12 deed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             cccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            344459999999998887665457996666666433322 3567999999775443

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.28  E-value=0.0087  Score=45.48  Aligned_cols=53  Identities=25%  Similarity=0.653  Sum_probs=36.4

Q ss_pred             cCCCCcccccCcccccCCccceeecCCC-----ccccHhhHHHHhcC--------CCccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLDD--------HSTCPLCRGRV  167 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~~--------~~~CP~CR~~i  167 (184)
                      +.+.+..|=||+..=+++-.--..-||.     |..|..|+..|+..        ...||-|++..
T Consensus        16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            3445567999998765543321222463     88999999999973        23599999875

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

Probab=95.17  E-value=0.039  Score=41.27  Aligned_cols=39  Identities=26%  Similarity=0.629  Sum_probs=29.1

Q ss_pred             cccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCcccccccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      |-.|-+.-..    .++.||.|+ +|..|-..    -..||+|+....
T Consensus       161 Cr~C~~~~~~----VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGEREAT----VLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCCce----EEeecccceEeccccccc----CccCCCCcChhh
Confidence            8888776555    555579985 99999765    346999998764

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

Probab=95.01  E-value=0.029  Score=49.22  Aligned_cols=57  Identities=21%  Similarity=0.535  Sum_probs=42.1

Q ss_pred             cCCCCcccccCcccccCCccceeecCCC---ccccHhhHHHHhc--CCCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCN---HIFHQTCMDDWLD--DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~---H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~~~  171 (184)
                      ..+++..|-||..+=..++.+-.-.+|.   ...|.+|+.+|+.  ....|-+|+.++.=.+
T Consensus         8 mN~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183           8 MNEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             CCccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            3455578999999988777765422343   4599999999997  5567999998875433

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

Probab=94.77  E-value=0.022  Score=45.18  Aligned_cols=52  Identities=25%  Similarity=0.701  Sum_probs=38.3

Q ss_pred             CcccccCcccccCCccceeecCCC-----ccccHhhHHHHhc--CCCcccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLD--DHSTCPLCRGRVRRI  170 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~~  170 (184)
                      +..|-||.++...........+|.     +..|..|++.|+.  ++..|.+|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            467999999876543212233464     6789999999998  677899999876544

>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=94.40  E-value=0.014  Score=43.98  Aligned_cols=57  Identities=21%  Similarity=0.611  Sum_probs=41.2

Q ss_pred             CcccccCccc-ccCCc-cceeecCCCccccHhhHHHHhc-CCCccc--ccccccccccCCCC
Q 045853          119 TSTCVICLEE-FRDGD-ECKVRSKCNHIFHQTCMDDWLD-DHSTCP--LCRGRVRRIAWPSF  175 (184)
Q Consensus       119 ~~~C~ICl~~-~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP--~CR~~i~~~~~~~~  175 (184)
                      +..|++|-.+ |-..+ .+.+-|.|-|.+|..|+++.+. ....||  -|.+-+....+...
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~q   71 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQ   71 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhccccc
Confidence            3479999977 44434 4445556999999999999997 567899  88776655555443

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

Probab=94.38  E-value=0.052  Score=42.33  Aligned_cols=43  Identities=26%  Similarity=0.568  Sum_probs=33.4

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRG  165 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~  165 (184)
                      ..|+.|-.-....-   ..+-|||.|+.+||..-|. ....||.|..
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            57999988877632   2245899999999997764 6778999965

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=94.22  E-value=0.05  Score=37.61  Aligned_cols=7  Identities=14%  Similarity=0.201  Sum_probs=2.5

Q ss_pred             HHHHHHh
Q 045853           43 YLFTQLY   49 (184)
Q Consensus        43 ~~~~~~~   49 (184)
                      +++.+++
T Consensus        20 ~~~~rRR   26 (130)
T PF12273_consen   20 YCHNRRR   26 (130)
T ss_pred             HHHHHHH
Confidence            3333333

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

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

Probab=93.76  E-value=0.036  Score=45.45  Aligned_cols=38  Identities=26%  Similarity=0.569  Sum_probs=28.6

Q ss_pred             CCCcccccCcccccCC-ccceeecCCCccccHhhHHHHhc
Q 045853          117 NKTSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLD  155 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~  155 (184)
                      ....+|.||+.+.... +.-. ...|+|.|+.+|..+.+.
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             cccccCccCccccccHhhhHH-HhcccchhhhHHhHHHhh
Confidence            3456899999555444 4544 446999999999998887

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

Probab=93.58  E-value=0.023  Score=44.44  Aligned_cols=46  Identities=33%  Similarity=0.685  Sum_probs=31.0

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      .|.-|--.+..  --|.. +|+|+||.+|...  ...+.||.|-..+.+..
T Consensus        92 fCd~Cd~PI~I--YGRmI-PCkHvFCl~CAr~--~~dK~Cp~C~d~VqrIe  137 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMI-PCKHVFCLECARS--DSDKICPLCDDRVQRIE  137 (389)
T ss_pred             eecccCCccee--eeccc-ccchhhhhhhhhc--CccccCcCcccHHHHHH
Confidence            46666554433  22555 5999999999743  34568999988776543

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

Probab=93.57  E-value=0.02  Score=52.54  Aligned_cols=47  Identities=30%  Similarity=0.655  Sum_probs=38.0

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i  167 (184)
                      ....|.||++.+..... + . .|||.++..|...|+..+..||+|+...
T Consensus      1152 ~~~~c~ic~dil~~~~~-I-~-~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGG-I-A-GCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhcCC-e-e-eechhHhhhHHHHHHHHhccCcchhhhh
Confidence            34479999999885332 2 2 4999999999999999999999998544

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.81  E-value=0.058  Score=41.91  Aligned_cols=29  Identities=21%  Similarity=0.688  Sum_probs=23.3

Q ss_pred             CCccccHhhHHHHhc-------------CCCccccccccccc
Q 045853          141 CNHIFHQTCMDDWLD-------------DHSTCPLCRGRVRR  169 (184)
Q Consensus       141 C~H~FH~~Ci~~Wl~-------------~~~~CP~CR~~i~~  169 (184)
                      |+...|.+|+.+|+.             ++.+||+||++..-
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            567789999999986             45679999998743

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

Probab=92.62  E-value=0.033  Score=48.24  Aligned_cols=51  Identities=27%  Similarity=0.758  Sum_probs=40.3

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcC---CCcccccccccccccCCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD---HSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~i~~~~~~~  174 (184)
                      .+|+||+..+..    +.+..|.|.|+..|+..-+..   ...||+|+..+.....+.
T Consensus        22 lEc~ic~~~~~~----p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~~E   75 (684)
T KOG4362|consen   22 LECPICLEHVKE----PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSLRE   75 (684)
T ss_pred             ccCCceeEEeec----cchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhccc
Confidence            489999999998    666689999999998776653   346999998876555443

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

Probab=92.42  E-value=0.1  Score=45.88  Aligned_cols=53  Identities=15%  Similarity=0.286  Sum_probs=38.3

Q ss_pred             CCCcccccCcccccCCcc-cee--ecCCCccccHhhHHHHhc------CCCccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDE-CKV--RSKCNHIFHQTCMDDWLD------DHSTCPLCRGRVRR  169 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~-~~~--l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR~~i~~  169 (184)
                      .+...|.+|..++.+.++ ...  +-.|+|.||..||..|..      .+..|++|...+..
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~s  155 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGS  155 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhh
Confidence            344578888888877332 222  225999999999999987      35569999987753

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=90.77  E-value=0.27  Score=33.95  Aligned_cols=21  Identities=14%  Similarity=0.230  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHhhHHHHh
Q 045853           35 LFLFYISYYLFTQLYSSRIQT   55 (184)
Q Consensus        35 ~~~~~i~~~~~~~~~~~r~~~   55 (184)
                      +++++++++++.+.+++|+++
T Consensus         9 i~~i~l~~~~~~~~~rRR~r~   29 (130)
T PF12273_consen    9 IVAILLFLFLFYCHNRRRRRR   29 (130)
T ss_pred             HHHHHHHHHHHHHHHHHHhhc
Confidence            334444456666666666554

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

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

Probab=90.40  E-value=0.45  Score=27.53  Aligned_cols=47  Identities=23%  Similarity=0.612  Sum_probs=35.4

Q ss_pred             ccccCcccccCCccceeecCCCc--cccHhhHHHHhcCCCccccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNH--IFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H--~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      .|-.|-.++..+..-...  |.+  .|+.+|.+.-|.  ..||.|-..+.+.+
T Consensus         7 nCE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l~--~~CPNCgGelv~RP   55 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI--CSFECTFCADCAETMLN--GVCPNCGGELVRRP   55 (57)
T ss_pred             CccccCCCCCCCCCcceE--EeEeCcccHHHHHHHhc--CcCcCCCCccccCC
Confidence            577888888776632322  764  699999999884  68999999887654

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

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=90.18  E-value=0.21  Score=37.27  Aligned_cols=41  Identities=32%  Similarity=0.814  Sum_probs=29.2

Q ss_pred             CcccccCccc-----ccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          119 TSTCVICLEE-----FRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       119 ~~~C~ICl~~-----~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      +..|-+|-++     |+. +.+...+.|+-+||..|..     +..||-|-+
T Consensus       152 GfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R  197 (202)
T PF13901_consen  152 GFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCAR  197 (202)
T ss_pred             CCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence            3468888753     222 3556677899999999975     267999954

>PF15050 SCIMP: SCIMP protein

Probab=89.50  E-value=0.76  Score=30.97  Aligned_cols=21  Identities=19%  Similarity=0.172  Sum_probs=10.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHH
Q 045853           16 LRLLVLTTPLVISSVVCLILF   36 (184)
Q Consensus        16 ~~~~~~~~~~~i~~~~~li~~   36 (184)
                      ..+|+++...++++.++|.++
T Consensus         6 ~nFWiiLAVaII~vS~~lglI   26 (133)
T PF15050_consen    6 DNFWIILAVAIILVSVVLGLI   26 (133)
T ss_pred             hchHHHHHHHHHHHHHHHHHH
Confidence            456666555544444444333

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

Probab=89.34  E-value=0.12  Score=45.36  Aligned_cols=45  Identities=24%  Similarity=0.543  Sum_probs=31.6

Q ss_pred             CcccccCcccccCC----ccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          119 TSTCVICLEEFRDG----DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       119 ~~~C~ICl~~~~~~----~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      +..|.-|.+.....    +.+.++ .|||+||+.|+..-..++. |-.|..
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~-~c~h~yhk~c~~~~~~~~~-~~~~~~  832 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVF-HCGHMYHKECLMMESLRNA-CNIESG  832 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEE-EccchhhhcccccHHHhcc-cChhhc
Confidence            34799999886633    344444 6999999999988776554 666544

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

Probab=88.73  E-value=0.22  Score=42.81  Aligned_cols=49  Identities=27%  Similarity=0.796  Sum_probs=39.6

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      .....+.|.||+.++    ..+..+ |.   |..|+..|+..+..||+|+..+...+
T Consensus       475 l~~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  475 LREPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             hhcccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccc
Confidence            345567899999999    236554 88   99999999999999999999886555

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

Probab=88.63  E-value=0.36  Score=27.59  Aligned_cols=43  Identities=28%  Similarity=0.543  Sum_probs=21.6

Q ss_pred             cccCcccccCCc------cceeecCCCccccHhhHHHHhcCCCcccccc
Q 045853          122 CVICLEEFRDGD------ECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR  164 (184)
Q Consensus       122 C~ICl~~~~~~~------~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  164 (184)
                      |.=|+..|....      .....+.|++.|+.+|=.---..-.+||-|-
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            445666666542      3455778999999999433223456799883

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.

>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]

Probab=88.39  E-value=5.5  Score=29.77  Aligned_cols=27  Identities=19%  Similarity=0.471  Sum_probs=14.9

Q ss_pred             CCccccHhhHHHHhc---CCCccccccccc
Q 045853          141 CNHIFHQTCMDDWLD---DHSTCPLCRGRV  167 (184)
Q Consensus       141 C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i  167 (184)
                      |.|.||..=+...-.   ....||.|+...
T Consensus       195 C~~C~hhngl~~~~ek~~~efiC~~Cn~~n  224 (251)
T COG5415         195 CPQCHHHNGLYRLAEKPIIEFICPHCNHKN  224 (251)
T ss_pred             cccccccccccccccccchheecccchhhc
Confidence            666555433322222   234699999866

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

Probab=88.28  E-value=0.45  Score=32.74  Aligned_cols=53  Identities=19%  Similarity=0.409  Sum_probs=36.8

Q ss_pred             CCcccccCcccccCCccc-eeecCCCccccHhhHHHHhc---CCCccccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDEC-KVRSKCNHIFHQTCMDDWLD---DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~-~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i~~~~  171 (184)
                      .-.+|.||-|...++--+ +-. =||=..+.-|-...|+   -+..||.|+.......
T Consensus        79 ~lYeCnIC~etS~ee~FLKPne-CCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNE-CCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCccc-ccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            446899999987664211 122 2887788888766666   5778999999876443

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=88.09  E-value=0.5  Score=37.54  Aligned_cols=56  Identities=25%  Similarity=0.439  Sum_probs=42.1

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~  175 (184)
                      ..|+||.+.....+...+=-+|||..|..|...-...+.+||.||++......+..
T Consensus       250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~t~~s~  305 (327)
T KOG2068|consen  250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERNTKKSE  305 (327)
T ss_pred             CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccCccccc
Confidence            68999999886554433222689889999988888899999999988765554443

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

Probab=88.08  E-value=0.17  Score=43.35  Aligned_cols=43  Identities=26%  Similarity=0.724  Sum_probs=27.4

Q ss_pred             CcccccCccc-----ccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          119 TSTCVICLEE-----FRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       119 ~~~C~ICl~~-----~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      ..-|.+|-..     |+ .+.++....|+++||..|..   ..+..||.|-+
T Consensus       511 gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~---r~s~~CPrC~R  558 (580)
T KOG1829|consen  511 GFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLR---RKSPCCPRCER  558 (580)
T ss_pred             eeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHh---ccCCCCCchHH
Confidence            3457788322     22 34445555799999999954   34555999944

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

Probab=87.85  E-value=0.34  Score=37.32  Aligned_cols=50  Identities=24%  Similarity=0.565  Sum_probs=37.0

Q ss_pred             CcccccCcccccCCccceee---cCCCccccHhhHHHHhc---------CCCcccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVR---SKCNHIFHQTCMDDWLD---------DHSTCPLCRGRVR  168 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l---~~C~H~FH~~Ci~~Wl~---------~~~~CP~CR~~i~  168 (184)
                      ..+|-+|..++.+.+..+..   +.|+-++|..|+..-+.         ....||.|++-+.
T Consensus       182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~~  243 (276)
T KOG3005|consen  182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFLS  243 (276)
T ss_pred             chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhceee
Confidence            35899999999666655542   36788899999999443         2346999998553

>smart00249 PHD PHD zinc finger

Probab=87.73  E-value=0.36  Score=26.18  Aligned_cols=30  Identities=33%  Similarity=0.739  Sum_probs=21.1

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHH
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDD  152 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  152 (184)
                      |.+|.... .++.+...-.|+..||..|+..
T Consensus         2 C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        2 CSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             cccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            77888776 3344444446899999999754

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

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

Probab=87.43  E-value=0.45  Score=41.82  Aligned_cols=45  Identities=22%  Similarity=0.433  Sum_probs=32.9

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccc--ccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPL--CRGRV  167 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~--CR~~i  167 (184)
                      .|.+|-.-...-  ......|||.-|..|+.+|+..+..||.  |-..-
T Consensus       781 ~CtVC~~vi~G~--~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~~c  827 (839)
T KOG0269|consen  781 KCTVCDLVIRGV--DVWCQVCGHGGHDSHLKSWFFKASPCAKSICPHLC  827 (839)
T ss_pred             Cceeecceeeee--EeecccccccccHHHHHHHHhcCCCCccccCCccc
Confidence            477776655442  2345579999999999999998888887  64433

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.37  E-value=0.64  Score=35.58  Aligned_cols=59  Identities=12%  Similarity=0.216  Sum_probs=43.0

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCCCC
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSFTT  177 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~~~  177 (184)
                      .....|+|=--+|..--.-..+.+|||+|-..-+.+.  ...+|++|-+.+...+.....+
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg  167 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNG  167 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeCC
Confidence            3444699877777664444556689999999888776  3578999999987776554443

>PF13974 YebO: YebO-like protein

Probab=86.97  E-value=2.2  Score=26.76  Aligned_cols=28  Identities=25%  Similarity=0.303  Sum_probs=13.0

Q ss_pred             HHHHHHHhhHHHHhhhHHHHhhhhHHHH
Q 045853           42 YYLFTQLYSSRIQTQNQDIEQGLSSQQQ   69 (184)
Q Consensus        42 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~   69 (184)
                      .|||.-+..-|.+.+..-.+.-.+++.+
T Consensus        14 vWFFVnRaSvRANEQI~LL~~ileqQKr   41 (80)
T PF13974_consen   14 VWFFVNRASVRANEQIELLEEILEQQKR   41 (80)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            4444445555555554444444433333

>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=86.68  E-value=0.3  Score=27.59  Aligned_cols=43  Identities=28%  Similarity=0.613  Sum_probs=29.1

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhc------CCCccccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD------DHSTCPLCRG  165 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR~  165 (184)
                      |.||.. ..+++.+...-.|+..||..|+..=..      ..-.||.|+.
T Consensus         2 C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    2 CPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             BTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             CcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            888988 334444455557888999999865543      2345888864

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 ....

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=86.61  E-value=3.3  Score=27.68  Aligned_cols=30  Identities=13%  Similarity=0.244  Sum_probs=19.4

Q ss_pred             eeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          136 KVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       136 ~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ...|.|+|..      .-+.+...|+.||+++.-++
T Consensus        70 V~CP~C~K~T------KmLGr~D~CM~C~~pLTLd~   99 (114)
T PF11023_consen   70 VECPNCGKQT------KMLGRVDACMHCKEPLTLDP   99 (114)
T ss_pred             eECCCCCChH------hhhchhhccCcCCCcCccCc
Confidence            3456787732      24445567999999986443

; GO: 0005887 integral to plasma membrane

>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []

Probab=86.28  E-value=2.2  Score=22.64  Aligned_cols=7  Identities=29%  Similarity=0.610  Sum_probs=2.5

Q ss_pred             HHHHHHH
Q 045853           39 YISYYLF   45 (184)
Q Consensus        39 ~i~~~~~   45 (184)
                      .+.+|.+
T Consensus        22 ~~~~YaC   28 (38)
T PF02439_consen   22 CMFYYAC   28 (38)
T ss_pred             HHHHHHH
Confidence            3333333

This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.

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

Probab=85.96  E-value=0.49  Score=27.29  Aligned_cols=40  Identities=15%  Similarity=0.415  Sum_probs=29.0

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      |+-|-..+..++.+...  -|..||.+|+        +|-.|+++|....
T Consensus         1 C~~C~~~I~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~l~~~~   40 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKA--MGKFWHPECF--------KCSKCGKPLNDGD   40 (58)
T ss_dssp             BTTTSSBESSSSEEEEE--TTEEEETTTS--------BETTTTCBTTTSS
T ss_pred             CCCCCCCccCcEEEEEe--CCcEEEcccc--------ccCCCCCccCCCe
Confidence            66777777765554322  6788999884        7999999887654

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

>PF06716 DUF1201: Protein of unknown function (DUF1201); InterPro: IPR009591 This entry consists of several Beet yellows virus (BYV) putative membrane-binding proteins of around 54 residues in length

Probab=85.43  E-value=4.1  Score=22.56  Aligned_cols=31  Identities=19%  Similarity=0.335  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 045853           23 TPLVISSVVCLILFLFYISYYLFTQLYSSRI   53 (184)
Q Consensus        23 ~~~~i~~~~~li~~~~~i~~~~~~~~~~~r~   53 (184)
                      +++-..+++++.++.+.+.+++++++..-|.
T Consensus         9 L~~~F~~lIC~Fl~~~~~F~~F~~Kqilfr~   39 (54)
T PF06716_consen    9 LLLAFGFLICLFLFCLVVFIWFVYKQILFRN   39 (54)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            3444444555555555555566666655443

The function of this currently unknown.

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

Probab=85.28  E-value=0.78  Score=37.33  Aligned_cols=47  Identities=17%  Similarity=0.420  Sum_probs=33.6

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCC---Cccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH---STCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~i  167 (184)
                      ..|+|=-+.-.++.. +..+.|||+...+-+.+..++.   ..||.|=..-
T Consensus       335 F~CPVlKeqtsdeNP-Pm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  335 FICPVLKEQTSDENP-PMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             eecccchhhccCCCC-CeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            369985555554444 4444699999999999998754   4699995543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=85.01  E-value=0.51  Score=24.95  Aligned_cols=26  Identities=38%  Similarity=0.740  Sum_probs=17.3

Q ss_pred             ccccCcccccCCcc-------ceeecCCCcccc
Q 045853          121 TCVICLEEFRDGDE-------CKVRSKCNHIFH  146 (184)
Q Consensus       121 ~C~ICl~~~~~~~~-------~~~l~~C~H~FH  146 (184)
                      +|+=|-..|...++       ....+.|+|+|+
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            68888888875553       223556778775

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

Probab=84.20  E-value=0.68  Score=38.24  Aligned_cols=34  Identities=24%  Similarity=0.557  Sum_probs=28.4

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD  155 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~  155 (184)
                      ++..|+||..-|.+    ++.++|+|..|..|...-+.
T Consensus         3 eelkc~vc~~f~~e----piil~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYRE----PIILPCSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccC----ceEeecccHHHHHHHHhhcc
Confidence            44579999999998    66567999999999987765

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

Probab=83.96  E-value=0.77  Score=23.78  Aligned_cols=37  Identities=22%  Similarity=0.601  Sum_probs=25.4

Q ss_pred             cccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       122 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      |..|-..+..++.....  =+..||.+|+        .|..|+..+.
T Consensus         2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRA--LGKVWHPECF--------KCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEe--CCccccccCC--------CCcccCCcCc
Confidence            77788877775333222  4688999884        6888887763

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

>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world

Probab=83.60  E-value=4.6  Score=32.04  Aligned_cols=27  Identities=15%  Similarity=0.403  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 045853           18 LLVLTTPLVISSVVCLILFLFYISYYL   44 (184)
Q Consensus        18 ~~~~~~~~~i~~~~~li~~~~~i~~~~   44 (184)
                      ..+..+++++++++++++++.+|+.|.
T Consensus       256 t~I~aSiiaIliIVLIMvIIYLILRYR  282 (299)
T PF02009_consen  256 TAIIASIIAILIIVLIMVIIYLILRYR  282 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444333333443333

Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=83.03  E-value=0.7  Score=24.28  Aligned_cols=26  Identities=38%  Similarity=0.730  Sum_probs=17.3

Q ss_pred             ccccCcccccCCcc-c------eeecCCCcccc
Q 045853          121 TCVICLEEFRDGDE-C------KVRSKCNHIFH  146 (184)
Q Consensus       121 ~C~ICl~~~~~~~~-~------~~l~~C~H~FH  146 (184)
                      +|+=|...|..+|+ +      ...+.|||+|+
T Consensus         4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~   36 (36)
T PF13717_consen    4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF   36 (36)
T ss_pred             ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence            68888888886553 1      23456778774

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

Probab=82.98  E-value=0.7  Score=34.40  Aligned_cols=41  Identities=27%  Similarity=0.734  Sum_probs=33.2

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR  164 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  164 (184)
                      .|.+|-.-...+   +..-.||-.+|..|+...+++...||.|.
T Consensus       183 ~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~  223 (235)
T KOG4718|consen  183 NCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCG  223 (235)
T ss_pred             HHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchh
Confidence            699998887664   22335777899999999999988999993

>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=80.80  E-value=0.64  Score=28.05  Aligned_cols=35  Identities=20%  Similarity=0.483  Sum_probs=19.0

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHh
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL  154 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl  154 (184)
                      ..|.+|...|.--..-.....||++|+..|.....
T Consensus        10 ~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~   44 (69)
T PF01363_consen   10 SNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI   44 (69)
T ss_dssp             SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred             CcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence            47999999997644434455799999999986554

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 ....

>PTZ00370 STEVOR; Provisional

Probab=80.70  E-value=2.3  Score=33.26  Aligned_cols=27  Identities=30%  Similarity=0.433  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045853           24 PLVISSVVCLILFLFYISYYLFTQLYS   50 (184)
Q Consensus        24 ~~~i~~~~~li~~~~~i~~~~~~~~~~   50 (184)
                      |.-|..+|++++++++|++|+|..++|
T Consensus       256 Pygiaalvllil~vvliilYiwlyrrR  282 (296)
T PTZ00370        256 PYGIAALVLLILAVVLIILYIWLYRRR  282 (296)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444555666666666666777665544

>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=80.51  E-value=0.89  Score=22.07  Aligned_cols=23  Identities=30%  Similarity=0.540  Sum_probs=14.1

Q ss_pred             ccccCcccccCCccceeecCCCccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIF  145 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~F  145 (184)
                      .|+-|-.....+.  ...+.|||.|
T Consensus         2 ~CP~C~~~V~~~~--~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPESA--KFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhhc--CcCCCCCCCC
Confidence            4777776665432  3455688877

Several members are annotated as putative helicases.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-10
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		3e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		3e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		9e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-05
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-05
2ecm_A	55	Solution Structure Of The Ring Domain Of The Ring F		9e-04

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 24/50 (48%), Positives = 31/50 (62%)
Query: 115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           A++    C +CL E  DG+E +   +C H FH  C+D WL  HSTCPLCR
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 106 NNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           ++ S   ++ V     C +C E++  G+  + +  CNH+FH +C+  WL+ H +CP+CR
Sbjct: 2   SSGSSGTEEHVGSGLECPVCKEDYALGESVR-QLPCNHLFHDSCIVPWLEQHDSCPVCR 59

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA 171
           +N    C +CLE+F+  DE  +   C H FH+ C+  WL+    CPLC   V ++A
Sbjct: 12  LNLHELCAVCLEDFKPRDELGI-CPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA 66

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 111 QNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           ++  AV +   C IC  E+  GD       C+H FH+ C+  WL    TCP+CR
Sbjct: 32  EDHGAVGQEMCCPICCSEYVKGDV-ATELPCHHYFHKPCVSIWLQKSGTCPVCR 84

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           C ICL    +G++ + R  C H+FHQ C+D WL  +  CP+CR
Sbjct: 17  CTICLSILEEGEDVR-RLPCMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 105 INNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            N  +HQ++  +     CV+C+ +F      +V   CNH FH  C+D WL  + TCP+CR
Sbjct: 14  FNPNNHQSEQTL-----CVVCMCDFESRQLLRVL-PCNHEFHAKCVDKWLKANRTCPICR 67
Query: 165 G 165
Sbjct: 68  A 68

>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger And Chy Zinc Finger Domain-Containing Protein 1 From Mus Musculus Length = 55

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG 165
           +S C ICLE+            C H+ H+TC ++ L +   CPLC G
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSG 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	184
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-20
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-18
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	8e-18
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-17
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	5e-17
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	8e-17
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-14
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	4e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	4e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-13
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-12
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	4e-11
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	7e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-10
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	1e-09
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	7e-07
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	1e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	6e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-05
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	1e-05
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	3e-05
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	3e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	5e-05
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	5e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	6e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	7e-05
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	1e-04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	2e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	4e-04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	6e-04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	9e-04

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

 Score = 78.8 bits (195), Expect = 2e-20
 Identities = 24/46 (52%), Positives = 29/46 (63%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           C +CL E  DG+E +   +C H FH  C+D WL  HSTCPLCR  V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 73.1 bits (180), Expect = 3e-18
 Identities = 16/45 (35%), Positives = 22/45 (48%)

Query: 120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           S C ICLE+            C H+ H+TC ++ L +   CPLC 
Sbjct: 6   SGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 72.7 bits (179), Expect = 8e-18
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
           ++  ++ + CV+C+ +F      +V   CNH FH  C+D WL  + TCP+CR    
Sbjct: 17  NNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSG 71

>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 = 72.0 bits (177), Expect = 1e-17
 Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
             C ICL    +G++ +    C H+FHQ C+D WL  +  CP+CR  + 
Sbjct: 15  EKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIE 62

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

 Score = 72.1 bits (177), Expect = 2e-17
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 116 VNKTSTCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           +N    C +CLE+F+  DE  +    C H FH+ C+  WL+    CPLC   V
Sbjct: 12  LNLHELCAVCLEDFKPRDE--LGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

 Score = 70.9 bits (174), Expect = 5e-17
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 109 SHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           S   ++ V     C +C E++  G+  +    CNH+FH +C+  WL+ H +CP+CR
Sbjct: 5   SSGTEEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCR 59

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

 Score = 70.8 bits (174), Expect = 8e-17
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 111 QNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
           ++  AV +   C IC  E+  GD       C+H FH+ C+  WL    TCP+CR
Sbjct: 32  EDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

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

 Score = 64.0 bits (156), Expect = 2e-14
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 109 SHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
           S      +     C IC++   D     +   C H F Q C+D W D H  CP+CR ++ 
Sbjct: 5   SSGRVKQLTDEEECCICMDGRAD-----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59

Query: 169 RIAWPSFTTA 178
                S  ++
Sbjct: 60  GANESSGPSS 69

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

 Score = 63.4 bits (154), Expect = 4e-14
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C+ C  E +  D   V  +CNH FH  CM  W+  ++ CPLC+
Sbjct: 28  ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 62.8 bits (153), Expect = 4e-14
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI 170
             C ICLE+  +     +   C H F   C+  W+  + TCPLC+  V  +
Sbjct: 6   ERCPICLEDPSNYS---MALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV 53

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

 Score = 61.5 bits (149), Expect = 2e-13
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 117 NKTSTCVICLEEFRD---GDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           + T +C IC++ + +        V ++C H+F   C+ D L + +TCP CR ++
Sbjct: 13  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 59.5 bits (144), Expect = 9e-13
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 117 NKTSTCVICLEEFRD---GDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
           + T +C IC++ + +        V ++C H+F   C+ D L + +TCP CR ++  
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 63

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

 Score = 59.0 bits (143), Expect = 2e-12
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)

Query: 121 TCVICLEEFRD---GDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
           +C IC++ + +        V ++C H+F   C+ D L + +TCP CR ++  
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 56

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

 Score = 55.6 bits (134), Expect = 4e-11
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 112 NDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA 171
             +       C IC + F++     V +KC H F ++C  +       C +C      I 
Sbjct: 8   GSEEEEIPFRCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICDQPTGGIF 63

Query: 172 WP 173
            P
Sbjct: 64  NP 65

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

 Score = 54.8 bits (132), Expect = 7e-11
 Identities = 12/56 (21%), Positives = 20/56 (35%), Gaps = 3/56 (5%)

Query: 114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
             +     C IC     D       ++C H F ++C+       + CP C   V +
Sbjct: 10  SELTPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ 62

>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 = 53.7 bits (129), Expect = 3e-10
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 107 NKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRG 165
           +   Q+ +++ +   C IC+E+ RD   C     C+ +   +C+  WL +  + CP CR 
Sbjct: 10  HMDEQSVESIAEVFRCFICMEKLRDARLC---PHCSKLCCFSCIRRWLTEQRAQCPHCRA 66

Query: 166 RVR 168
            ++
Sbjct: 67  PLQ 69

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

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 4/47 (8%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
            C ICL+         V   C H+F   C+         C LCR  +
Sbjct: 17  ECAICLQTCVH----PVSLPCKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 52.4 bits (125), Expect = 3e-09
 Identities = 21/110 (19%), Positives = 46/110 (41%), Gaps = 8/110 (7%)

Query: 61  EQGLSSQQQQQQRVIINSTEYKVKEDPRASKFKKVSWTAFKRDIINNKSHQNDDAVNKTS 120
           E     ++  + +    +      ++   +K +K    A K +++++ +    D +    
Sbjct: 10  EHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMN----DVLENEL 65

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI 170
            C+IC E F +     V   C H F   C+++W+     CP+CR  ++  
Sbjct: 66  QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK 111

>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 = 49.8 bits (118), Expect = 1e-08
 Identities = 11/41 (26%), Positives = 13/41 (31%)

Query: 124 ICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
                    +       CNH FH  C+  WL     CPL  
Sbjct: 56  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 50.6 bits (120), Expect = 1e-08
 Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 3/56 (5%)

Query: 121 TCVICLEEFRDGDECK---VRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWP 173
           +C IC++ + +  +     V ++C H+F   C+ D L + +TCP CR ++    + 
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH 64

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

 Score = 46.7 bits (110), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 101 KRDIINNKSHQNDDAVNKTSTCVICLEEFRD---GDECKVRSKCNHIFHQTCMDDWLDDH 157
            R  IN+K +      + T +C IC++ + +        V ++C H+F   C+ D L + 
Sbjct: 54  CRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA 113

Query: 158 STCPLCR 164
           +TCP CR
Sbjct: 114 NTCPTCR 120

>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 = 48.8 bits (116), Expect = 1e-08
 Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 5/50 (10%)

Query: 117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH--STCPLCR 164
           +    C IC      G  C+    C    H  C+  +   +    CP C 
Sbjct: 13  DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCN 59

>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 = 49.5 bits (117), Expect = 2e-08
 Identities = 11/41 (26%), Positives = 13/41 (31%)

Query: 124 ICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
                    +       CNH FH  C+  WL     CPL  
Sbjct: 67  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 51.8 bits (123), Expect = 2e-08
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 15/73 (20%)

Query: 107 NKSHQNDDAVNKTSTCVICLEEFRDGDECKVR----SKCNHIFHQTCMDDWLDD------ 156
           +   + D+  N+   C IC     DG E  +     +KC    H  C+++W         
Sbjct: 296 SDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKT 355

Query: 157 -----HSTCPLCR 164
                   CP C+
Sbjct: 356 FLEVSFGQCPFCK 368

>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 = 49.0 bits (117), Expect = 2e-08
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
            CV+C   F D        +C H F +TC+  +L+    CP+C  +V +
Sbjct: 17  MCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHK 62

>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 = 51.7 bits (123), Expect = 2e-08
 Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 5/70 (7%)

Query: 101 KRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHST 159
              +   +     +  +    C IC E  +D         C H+   +C+  W + +   
Sbjct: 314 HIKVTQEQYELYCEMGSTFQLCKICAENDKDV----KIEPCGHLMCTSCLTSWQESEGQG 369

Query: 160 CPLCRGRVRR 169
           CP CR  ++ 
Sbjct: 370 CPFCRCEIKG 379

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

 Score = 47.5 bits (112), Expect = 8e-08
 Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 19/63 (30%)

Query: 121 TCVICLEEFRDGDECK--------------VRSKCNHIFHQTCMDDWL-----DDHSTCP 161
            C+IC+E+                        +KC+H FH  C+         D    CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 162 LCR 164
            C+
Sbjct: 87  SCK 89

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

 Score = 44.8 bits (106), Expect = 7e-07
 Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 3/56 (5%)

Query: 114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
             ++    C IC E F       +  +C+H +   C+  +L   + CP C   V  
Sbjct: 17  KTIDDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE 69

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

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 1/54 (1%)

Query: 112 NDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCR 164
           + DA      C +C+E     D       C +   + C      D +  CP CR
Sbjct: 4   SPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 57

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

 Score = 45.9 bits (108), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 5/70 (7%)

Query: 97  WTAFKRDIINNKSHQNDDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD 156
           +T   R I+  + +  +   +    C IC      G  C+    C    H  C+  +   
Sbjct: 158 FTLHGRAILEMEQYIRETYPDAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQS 214

Query: 157 H--STCPLCR 164
           +    CP C 
Sbjct: 215 NAEPRCPHCN 224

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

 Score = 42.6 bits (100), Expect = 6e-06
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCRGRVRRIAWPSFTTAD 179
            C IC+E   +     V   CNH   + C    ++  S  CP CR RV   +W  + T  
Sbjct: 17  QCGICMEILVE----PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS--SWTRYHTRR 70

Query: 180 DWSPD 184
           +   +
Sbjct: 71  NSLVN 75

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCRGRVRR 169
            C  C            +++C H F ++CM   L   S  C  C+  + +
Sbjct: 17  KCEKCHLVLCSP----KQTECGHRFCESCMAALLSSSSPKCTACQESIVK 62

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

 Score = 41.9 bits (98), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCRGRVRR 169
            C+ C E         + + C H   + C+D        +CP CR  + R
Sbjct: 54  QCICCQELVFR----PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR 99

>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* Length = 63

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFH-QTCMDDWLDDHSTCPLCRGRVRRI 170
           +D  N    C +C +  RDG    +  +  H+     C        ++CP+C+  ++ +
Sbjct: 1   EDCQNLLKPCSLCEKRPRDG--NIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLV 57

>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 Length = 112

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 7/52 (13%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH---STCPLCRGRVRR 169
            C ICLE  ++     V +KC+HIF + CM   L+     S CPLC+  + +
Sbjct: 23  ECPICLELIKE----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 117

 Score = 41.0 bits (96), Expect = 3e-05
 Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 5/49 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR 169
            C  C    R+         C HIF   C+ D +   + CP+C      
Sbjct: 24  RCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI 67

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 7/52 (13%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD---HSTCPLCRGRVRR 169
            C ICL+  +      V   C H F   C+    +       CPLC+  VR+
Sbjct: 22  ICPICLDILQK----PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRK 69

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94

 Score = 39.8 bits (93), Expect = 5e-05
 Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 5/53 (9%)

Query: 118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI 170
            +S C +CL E+   ++    ++C  IF   C+  +++      +  G    I
Sbjct: 4   GSSGCKLCLGEY-PVEQMTTIAQCQCIFCTLCLKQYVELL----IKEGLETAI 51

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 10/55 (18%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH------STCPLCRGRVRR 169
           TC ICLE  ++     V + CNH F + C+    + +        CP+CR     
Sbjct: 21  TCPICLELLKE----PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF 71

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

 Score = 39.0 bits (91), Expect = 6e-05
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 5/46 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCR 164
            C+IC +   D     V   C + +   C+   L   D  TCP C 
Sbjct: 17  LCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59

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

 Score = 39.5 bits (92), Expect = 7e-05
 Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 5/57 (8%)

Query: 113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVR 168
                K+ +C IC     D     V + C H+F + C+   L    S CP CR    
Sbjct: 17  PAHFVKSISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>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 Length = 64

 Score = 37.5 bits (87), Expect = 1e-04
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 3/56 (5%)

Query: 116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFH-QTCMDDWLDDHSTCPLCRGRVRRI 170
           +N    CVIC    ++G  C V  K  H+    TC       +  CP+CR  ++ I
Sbjct: 5   LNAIEPCVICQGRPKNG--CIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMI 58

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

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 12/65 (18%), Positives = 18/65 (27%), Gaps = 5/65 (7%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVRRIAWPSFTTAD 179
            C  C    R       +++C H +   C+   L      C  C          S   + 
Sbjct: 33  LCSACRNVLRRP----FQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESS 88

Query: 180 DWSPD 184
              PD
Sbjct: 89  SAFPD 93

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

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS---TCPLCRGRVR 168
            C IC+E F +         C H   + C++  L        CP C    R
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITR 67

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

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 5/45 (11%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCR 164
            C ICL   R+     V++ C H F + C+   + D    CP+  
Sbjct: 20  ECPICLMALREA----VQTPCGHRFCKACIIKSIRDAGHKCPVDN 60

>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite motif protein 34, interferon- responsive finger protein 1; NMR {Homo sapiens} Length = 79

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 11/56 (19%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHST-------CPLCRGRVRR 169
           TC ICLE   +     +   C H   + C+     +  T       CP+C      
Sbjct: 14  TCPICLELLTE----PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF 65

>2ecv_A Tripartite motif-containing protein 5; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 85

 Score = 35.7 bits (83), Expect = 9e-04
 Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 10/55 (18%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH------STCPLCRGRVRR 169
           TC ICLE         +   C H F Q C+             S+CP+CR   + 
Sbjct: 21  TCPICLELLTQ----PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.75
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.73
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.72
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.72
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.72
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.72
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.72
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.69
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.66
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.64
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.64
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.64
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.62
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.62
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.59
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.59
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.58
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.58
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.58
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.57
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.57
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.56
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.55
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.55
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.53
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.52
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.52
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.51
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.5
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.5
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.49
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.49
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.49
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.46
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.45
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.45
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.43
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.43
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.42
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.41
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.39
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.37
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.34
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.34
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.34
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.33
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.32
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.32
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.32
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.3
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.29
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.29
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.27
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.27
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.26
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.22
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.21
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.19
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.16
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.09
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.06
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.03
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.02
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.02
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.01
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.98
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.92
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.81
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.8
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.79
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.53
3nw0_A	238	Non-structural maintenance of chromosomes element	98.39
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.1
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	97.04
1we9_A	64	PHD finger family protein; structural genomics, PH	95.38
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.18
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.96
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	94.77
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.54
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	94.35
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	94.26
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	93.91
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	93.75
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.56
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	92.81
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	92.58
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	92.35
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	92.05
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	91.53
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.51
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	91.49
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	91.27
1wem_A	76	Death associated transcription factor 1; structura	91.12
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	90.77
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	90.71
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	90.53
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	90.26
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	90.07
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	89.89
1wee_A	72	PHD finger family protein; structural genomics, PH	89.83
2yt5_A	66	Metal-response element-binding transcription facto	89.08
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	88.62
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	88.57
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	88.19
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	88.17
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	87.96
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	87.94
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	87.79
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	87.68
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	87.31
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	87.28
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	87.04
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	86.52
1weu_A	91	Inhibitor of growth family, member 4; structural g	86.46
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	86.46
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	86.37
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	85.79
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	85.11
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	85.06
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	84.96
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	84.28
1wew_A	78	DNA-binding family protein; structural genomics, P	84.16
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	83.68
1z60_A	59	TFIIH basal transcription factor complex P44 subun	83.35
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	83.19
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	83.16
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	82.73
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	82.72
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	82.3
2co8_A	82	NEDD9 interacting protein with calponin homology a	81.52
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	81.05
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	80.92
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	80.89
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	80.73
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	80.54
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	80.24
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	80.18
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	80.08

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

Probab=99.75  E-value=4.3e-19  Score=104.29  Aligned_cols=52  Identities=46%  Similarity=1.057  Sum_probs=46.6

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      +++.+|+||++++..++.+..++.|||.||..||.+|++.+.+||+||+++.
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            4456899999999999888888679999999999999999999999999873

>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=99.73  E-value=3.8e-18  Score=104.90  Aligned_cols=55  Identities=33%  Similarity=0.896  Sum_probs=47.3

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ....+.+|+||++.|..++.++.+ +|||.||..||..|+..+.+||+||+.+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRL-PCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEEC-TTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEe-CCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            345567899999999888777777 5999999999999999889999999998643

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

Probab=99.72  E-value=4.6e-18  Score=107.01  Aligned_cols=61  Identities=30%  Similarity=0.843  Sum_probs=51.3

Q ss_pred             cccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCC
Q 045853          113 DDAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       113 ~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~  174 (184)
                      .+....+.+|+||++.|...+.+..+ +|||.||..||..|+..+.+||+||+.+.......
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~-~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A            9 EEHVGSGLECPVCKEDYALGESVRQL-PCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             CTTSSSSCCCTTTTSCCCTTSCEEEC-TTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCC
T ss_pred             cccCCCCCCCeeCCccccCCCCEEEe-CCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCC
Confidence            33445667899999999988877777 49999999999999999999999999997665443

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

Probab=99.72  E-value=3.5e-18  Score=108.31  Aligned_cols=54  Identities=35%  Similarity=0.756  Sum_probs=44.6

Q ss_pred             CCCcccccCcccccC-----------CccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          117 NKTSTCVICLEEFRD-----------GDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~-----------~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      .++..|+||+++|.+           ++.++.+++|||.||.+||++|+..+.+||+||+++...
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            345678888888864           455677778999999999999999999999999988543

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

Probab=99.72  E-value=6e-18  Score=105.41  Aligned_cols=56  Identities=38%  Similarity=0.915  Sum_probs=48.8

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ....+.+|+||++.|...+.++.++ |||.||..||..|++.+.+||+||+.+....
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             cCCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            3455678999999999988888774 9999999999999998889999999997544

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

Probab=99.72  E-value=3.7e-18  Score=110.63  Aligned_cols=54  Identities=37%  Similarity=0.861  Sum_probs=47.9

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ...++..|+||+++|..++.++.++ |||.||..||..|+..+.+||+||+.+.+
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            3456678999999999999888885 99999999999999999999999998853

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

Probab=99.72  E-value=2.4e-18  Score=107.53  Aligned_cols=53  Identities=36%  Similarity=0.928  Sum_probs=47.1

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..++.+|+||+++|..++.++.++ |||.||..||..|++.+.+||+||+++.+
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            345668999999999988888885 99999999999999989999999998854

>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=99.69  E-value=1.1e-17  Score=98.21  Aligned_cols=51  Identities=33%  Similarity=0.789  Sum_probs=43.7

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      ++.+|+||++++.+++.....++|||.||..||..|+..+.+||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            446899999999876655555679999999999999998899999999874

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

Probab=99.66  E-value=4.2e-17  Score=100.68  Aligned_cols=59  Identities=27%  Similarity=0.727  Sum_probs=47.1

Q ss_pred             CCCCcccccCcccccCC---ccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCC
Q 045853          116 VNKTSTCVICLEEFRDG---DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~---~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~  174 (184)
                      ..++.+|+||++.+.+.   +...+.++|||.||..||..|+..+.+||+||+.+....+..
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   68 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP   68 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhheee
Confidence            34556899999999763   233355579999999999999998899999999997665443

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

Probab=99.64  E-value=6.3e-17  Score=99.25  Aligned_cols=56  Identities=29%  Similarity=0.734  Sum_probs=44.9

Q ss_pred             ccCCCCcccccCcccccCC---ccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDG---DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~---~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ....+..+|+||++.+.+.   ....++++|||.||..||..|+..+.+||+||+.+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3345667899999999864   2223445799999999999999988999999998853

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

Probab=99.64  E-value=8.2e-17  Score=99.44  Aligned_cols=56  Identities=25%  Similarity=0.459  Sum_probs=46.2

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCC
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPS  174 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~  174 (184)
                      ...++.+|+||++.+.+    .+.++|||.||..||..|+..+.+||+||+.+....+..
T Consensus        11 ~~~~~~~C~IC~~~~~~----~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   66 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVH----PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLDS   66 (71)
T ss_dssp             SSSSCCBCSSSSSBCSS----EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHSC
T ss_pred             cCCCCCCCccCCcccCC----CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhccC
Confidence            34556789999999977    444469999999999999999999999999997655443

>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=99.64  E-value=1.2e-16  Score=105.90  Aligned_cols=51  Identities=29%  Similarity=0.664  Sum_probs=41.6

Q ss_pred             CCcccccCcccccCC--------------ccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          118 KTSTCVICLEEFRDG--------------DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~--------------~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      ++..|+||++.|...              +....+++|||.||..||..||..+.+||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            456899999999854              112344479999999999999999999999999853

>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=99.62  E-value=4.9e-16  Score=104.66  Aligned_cols=53  Identities=26%  Similarity=0.612  Sum_probs=42.0

Q ss_pred             CCcccccCcccccCCc--------------cceeecCCCccccHhhHHHHh-----cCCCcccccccccccc
Q 045853          118 KTSTCVICLEEFRDGD--------------ECKVRSKCNHIFHQTCMDDWL-----DDHSTCPLCRGRVRRI  170 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~--------------~~~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~i~~~  170 (184)
                      .+.+|+||+++|...+              .+..+++|||+||..||..|+     ..+.+||+||+.+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3458999999997643              233355799999999999999     5677999999988543

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

Probab=99.62  E-value=1.4e-16  Score=96.23  Aligned_cols=55  Identities=27%  Similarity=0.775  Sum_probs=44.4

Q ss_pred             CCcccccCcccccCC---ccceeecCCCccccHhhHHHHhcCCCcccccccccccccC
Q 045853          118 KTSTCVICLEEFRDG---DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~---~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~  172 (184)
                      ++.+|+||++.+.+.   ......++|||.||..|+.+|+..+.+||+||+.+....+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            345899999999863   2333444799999999999999989999999999876543

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

Probab=99.59  E-value=1.3e-15  Score=97.85  Aligned_cols=58  Identities=26%  Similarity=0.623  Sum_probs=47.5

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC---Cccccccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH---STCPLCRGRVRRIA  171 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~i~~~~  171 (184)
                      +...+..+|+||++.|.+++...+.++|||.||..|+..|+..+   .+||+||+.+...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             hhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            34456678999999999877645555799999999999999865   78999999886554

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

Probab=99.59  E-value=7.7e-16  Score=94.71  Aligned_cols=51  Identities=33%  Similarity=0.875  Sum_probs=43.8

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++.+.+    ..+ +|||.||..||..|+..+.+||+||+.+....
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LIL-PCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEE-TTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCCeeCCcCccC----ccc-CCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            4556789999999987    555 59999999999999999999999999987543

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

Probab=99.58  E-value=1.3e-15  Score=94.24  Aligned_cols=54  Identities=22%  Similarity=0.487  Sum_probs=44.3

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ...+...|+||++.+.+.   ..+.+|||.||..||..|+..+.+||+||+.+....
T Consensus        11 ~~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           11 ELTPYILCSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCCGGGSCTTTSSCCSSC---EECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             hcCCCCCCCCCChHHHCc---CEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            345566899999999871   233379999999999999998899999999997554

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

Probab=99.58  E-value=1.3e-15  Score=95.88  Aligned_cols=57  Identities=25%  Similarity=0.592  Sum_probs=45.2

Q ss_pred             cccCCCCcccccCcccccCCccceeecCCC-----ccccHhhHHHHhcCC--Cccccccccccccc
Q 045853          113 DDAVNKTSTCVICLEEFRDGDECKVRSKCN-----HIFHQTCMDDWLDDH--STCPLCRGRVRRIA  171 (184)
Q Consensus       113 ~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR~~i~~~~  171 (184)
                      .....++..|.||+++|.+++.+ ++ +|+     |.||..||++|+..+  .+||+||..+....
T Consensus         9 s~~~~~~~~C~IC~~~~~~~~~l-~~-pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A            9 SITPSSQDICRICHCEGDDESPL-IT-PCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CCCCTTSCCCSSSCCCCCSSSCE-EC-SSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCCCCeEcCccccCCCee-Ee-ccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            33445567899999999887765 45 596     999999999999854  58999999986433

>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=99.58  E-value=1.6e-16  Score=106.68  Aligned_cols=51  Identities=31%  Similarity=0.738  Sum_probs=0.9

Q ss_pred             CCcccccCcccccC-------------Ccc-ceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          118 KTSTCVICLEEFRD-------------GDE-CKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~~-------------~~~-~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      +++.|+||+++|.+             +++ .+..++|+|.||..||++|+..+.+||+||+++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            44689999999975             222 2333479999999999999999999999999863

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

Probab=99.57  E-value=1.7e-15  Score=95.80  Aligned_cols=51  Identities=24%  Similarity=0.621  Sum_probs=43.6

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      +.......|+||++.+.+    .+.++|||.||..||..|+....+||+||+.+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQN----PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCS----EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcC----eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            334556789999999977    555679999999999999998899999999985

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

Probab=99.57  E-value=2.2e-15  Score=91.56  Aligned_cols=52  Identities=21%  Similarity=0.538  Sum_probs=42.7

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++.+.+    .+..+|||.||..||..|+. .+.+||+||+.+....
T Consensus        12 ~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCS----PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEESS----CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCcCCCCCCCChHhcC----eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            4556789999999987    33347999999999999994 6678999999986543

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

Probab=99.56  E-value=4.1e-15  Score=92.15  Aligned_cols=53  Identities=30%  Similarity=0.695  Sum_probs=43.4

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~i~~~~  171 (184)
                      ...+...|+||++.+.+    .+..+|||.||..||..|+.   .+..||+||+.+...+
T Consensus        16 ~~~~~~~C~IC~~~~~~----~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           16 KLQEEVICPICLDILQK----PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCCBCTTTCSBCSS----EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             hCccCCEeccCCcccCC----eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            34566789999999987    44447999999999999997   4668999999986543

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

Probab=99.55  E-value=1.9e-15  Score=92.43  Aligned_cols=49  Identities=33%  Similarity=0.794  Sum_probs=41.1

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      .+.+|+||++.+.+.  . ...+|||.||..|+..|+..+.+||+||+.+..
T Consensus         4 ~~~~C~IC~~~~~~~--~-~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNY--S-MALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSC--E-EETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCC--c-EecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            445899999998752  2 344699999999999999988999999999864

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

Probab=99.55  E-value=3e-15  Score=93.10  Aligned_cols=54  Identities=24%  Similarity=0.541  Sum_probs=43.1

Q ss_pred             ccCCCCcccccCcccccCCccceeecC-CCccccHhhHHHHhcCC--Cccccccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSK-CNHIFHQTCMDDWLDDH--STCPLCRGRVRRIA  171 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~-C~H~FH~~Ci~~Wl~~~--~~CP~CR~~i~~~~  171 (184)
                      ....++..|+||++.|.+    .+.++ |||.||..||..|+..+  .+||+||+.+...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~----p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           10 DPIPDELLCLICKDIMTD----AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CCSCGGGSCSSSCCCCTT----CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             ccCCCCCCCcCCChHHhC----CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            344556789999999987    44456 99999999999999854  68999999765433

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

Probab=99.53  E-value=4.8e-15  Score=89.82  Aligned_cols=55  Identities=20%  Similarity=0.529  Sum_probs=43.6

Q ss_pred             CcccccCcc-cccCCccceeecCCCccccHhhHHHHhc-CCCcccccccccccccCC
Q 045853          119 TSTCVICLE-EFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       119 ~~~C~ICl~-~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~~  173 (184)
                      +..|+||++ .+.+.....++.+|||.||..||..|+. ....||+||+.+....+.
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   59 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccce
Confidence            457999999 7777655445557999999999999976 456799999999765543

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

Probab=99.52  E-value=4.6e-15  Score=103.20  Aligned_cols=47  Identities=32%  Similarity=0.921  Sum_probs=41.2

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|+||++.|.+    ++.++|||.||..||..|+..+.+||+||+++...
T Consensus        54 ~~C~iC~~~~~~----~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           54 LQCIICSEYFIE----AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             SBCTTTCSBCSS----EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             CCCcccCcccCC----ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            479999999987    45557999999999999999999999999998543

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

Probab=99.52  E-value=4.9e-15  Score=93.15  Aligned_cols=55  Identities=25%  Similarity=0.542  Sum_probs=44.8

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-------CCcccccccccccccCC
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-------HSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~i~~~~~~  173 (184)
                      ...+..+|+||++.|.+    .+.++|||.||..||..|+..       ...||+||+.+...++.
T Consensus         8 ~~~~~~~C~IC~~~~~~----p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~   69 (79)
T 2egp_A            8 NVQEEVTCPICLELLTE----PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQ   69 (79)
T ss_dssp             CCCCCCEETTTTEECSS----CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGG
T ss_pred             hcccCCCCcCCCcccCC----eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCC
Confidence            34566789999999987    444479999999999999986       67899999999765543

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

Probab=99.51  E-value=2.1e-14  Score=88.54  Aligned_cols=49  Identities=22%  Similarity=0.694  Sum_probs=42.1

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC--Ccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH--STCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~i~  168 (184)
                      +...+|+||.+.+..++...   .|+|.||..||.+||+.+  .+||+||+++.
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            34468999999999876554   699999999999999976  88999999875

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

Probab=99.50  E-value=1.7e-14  Score=91.73  Aligned_cols=54  Identities=30%  Similarity=0.668  Sum_probs=44.5

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC------CCcccccccccccccCC
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD------HSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~i~~~~~~  173 (184)
                      ..+...|+||++.+.+    .+.++|||.||..|+..|+..      ...||+||+.+....+.
T Consensus        16 ~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecw_A           16 IKEEVTCPICLELLKE----PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLK   75 (85)
T ss_dssp             CCTTTSCTTTCSCCSS----CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCE
T ss_pred             CccCCCCcCCChhhCc----ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCC
Confidence            4556789999999987    444579999999999999986      67899999998765443

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

Probab=99.50  E-value=2.2e-14  Score=91.25  Aligned_cols=55  Identities=31%  Similarity=0.628  Sum_probs=45.1

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC------CCcccccccccccccCC
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD------HSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~i~~~~~~  173 (184)
                      ...+..+|+||++.+.+    .+.++|||.||..|+..|+..      ...||+||+.+....+.
T Consensus        15 ~~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~   75 (85)
T 2ecv_A           15 NVKEEVTCPICLELLTQ----PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIR   75 (85)
T ss_dssp             CCCCCCCCTTTCSCCSS----CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCC
T ss_pred             HccCCCCCCCCCcccCC----ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcC
Confidence            34556789999999987    344479999999999999986      78899999999765543

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

Probab=99.49  E-value=2.3e-14  Score=89.93  Aligned_cols=52  Identities=25%  Similarity=0.541  Sum_probs=43.8

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++.|.+    .+..+|||.||..||..|+.. +.+||+||+.+....
T Consensus         5 ~~~~~~C~IC~~~~~~----Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            5 FPEYFRCPISLELMKD----PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             CSSSSSCTTTSCCCSS----EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CcccCCCCCccccccC----CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            3455689999999987    555579999999999999986 789999999986544

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

Probab=99.49  E-value=9.7e-15  Score=100.55  Aligned_cols=59  Identities=27%  Similarity=0.743  Sum_probs=47.0

Q ss_pred             CCCcccccCcccccCC---ccceeecCCCccccHhhHHHHhcCCCcccccccccccccCCCC
Q 045853          117 NKTSTCVICLEEFRDG---DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~---~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~  175 (184)
                      .++.+|+||++.|.+.   ....+.++|||.||..||.+|++.+.+||+||+.+........
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l   66 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI   66 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEEC
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccccccc
Confidence            3456899999999763   2333445799999999999999999999999999976665443

>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=99.49  E-value=1e-14  Score=95.86  Aligned_cols=51  Identities=27%  Similarity=0.776  Sum_probs=43.2

Q ss_pred             cccccCcccccCCccceee-cCCCccccHhhHHHHhcCC-CcccccccccccccCCC
Q 045853          120 STCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDH-STCPLCRGRVRRIAWPS  174 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~i~~~~~~~  174 (184)
                      ..|+||++.|.+    ++. ++|||.||..||..|+..+ .+||+||..+....+..
T Consensus        23 ~~C~IC~~~~~~----p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~   75 (100)
T 3lrq_A           23 FRCFICMEKLRD----ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVN   75 (100)
T ss_dssp             TBCTTTCSBCSS----EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEE
T ss_pred             CCCccCCccccC----ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHh
Confidence            479999999987    555 6899999999999999876 79999999997655443

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

Probab=99.46  E-value=5.5e-14  Score=84.53  Aligned_cols=45  Identities=29%  Similarity=0.731  Sum_probs=37.6

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLC  163 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~C  163 (184)
                      ...++..|+||++.+.+    .+..+|||.||..||..|+.   .+.+||+|
T Consensus        16 ~~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQK----PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCSS----CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhCC----eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            34566789999999987    44447999999999999997   56689998

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

Probab=99.45  E-value=4e-14  Score=92.84  Aligned_cols=48  Identities=27%  Similarity=0.644  Sum_probs=41.4

Q ss_pred             cccccCcccccCCcccee-ecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          120 STCVICLEEFRDGDECKV-RSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~-l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..|+||++.|.+    .+ +++|||.||..||..|+..+.+||+||+.+....
T Consensus        23 ~~C~IC~~~~~~----p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   71 (99)
T 2y43_A           23 LRCGICFEYFNI----AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD   71 (99)
T ss_dssp             TBCTTTCSBCSS----EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             CCcccCChhhCC----cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhh
Confidence            479999999987    43 3379999999999999999999999999987543

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

Probab=99.45  E-value=6.5e-14  Score=82.71  Aligned_cols=45  Identities=29%  Similarity=0.909  Sum_probs=36.8

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHh---cCCCccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL---DDHSTCPLC  163 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl---~~~~~CP~C  163 (184)
                      ...+...|+||++.+.+    .+.++|||.||..||..|+   ..+.+||+|
T Consensus        11 ~~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKE----PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CSCCCCBCSSSCCBCSS----CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccccCCCCccCCcccCc----cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34566789999999987    3445799999999999995   466789998

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

Probab=99.43  E-value=2.8e-13  Score=84.72  Aligned_cols=57  Identities=18%  Similarity=0.372  Sum_probs=44.0

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCcccccccccccccC
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~  172 (184)
                      ..++.+|+||++.+...+....-.+|||.||..|+..|+. ....||.||+.+.....
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            4566789999999865444332225999999999999985 46789999999976654

>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=99.43  E-value=4.4e-14  Score=96.45  Aligned_cols=46  Identities=26%  Similarity=0.636  Sum_probs=39.8

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCC-Cccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVRR  169 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~i~~  169 (184)
                      ..|+||++.|.+    .+..+|||.||..||..|+..+ .+||+||+.+..
T Consensus        53 ~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           53 FQCICCQELVFR----PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             TBCTTTSSBCSS----EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCcCChHHcC----cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            479999999997    5555799999999999999844 489999999965

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

Probab=99.42  E-value=9.7e-14  Score=89.76  Aligned_cols=51  Identities=25%  Similarity=0.597  Sum_probs=42.2

Q ss_pred             ccCCCCcccccCcccccCCccceeecC-CCccccHhhHHHHhcC--CCcccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSK-CNHIFHQTCMDDWLDD--HSTCPLCRGRVR  168 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~-C~H~FH~~Ci~~Wl~~--~~~CP~CR~~i~  168 (184)
                      +...++..|+||++.|.+    .+..+ |||.||..||..|+..  +..||+||+.+.
T Consensus         8 ~~~~~~~~C~IC~~~~~~----p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A            8 DPIPDELLCLICKDIMTD----AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCCCTTTEETTTTEECSS----CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             ccCCcCCCCCCCChhhcC----ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            345566789999999987    55557 9999999999999963  468999999873

>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=99.41  E-value=9.7e-14  Score=92.46  Aligned_cols=49  Identities=31%  Similarity=0.716  Sum_probs=41.8

Q ss_pred             CCcccccCcccccCCccceee-cCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ++..|+||++.+.+    .+. .+|||.||..||..|+..+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~----p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID----ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS----EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC----cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            34579999999987    443 37999999999999999889999999998653

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

Probab=99.39  E-value=6.7e-14  Score=96.29  Aligned_cols=56  Identities=29%  Similarity=0.781  Sum_probs=45.4

Q ss_pred             CCCcccccCcccccCC---ccceeecCCCccccHhhHHHHhcCCCcccccccccccccC
Q 045853          117 NKTSTCVICLEEFRDG---DECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~---~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~  172 (184)
                      .+..+|+||++.+.+.   ....+.++|||.||..||++|++.+.+||+||+.+....+
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  128 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY  128 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGE
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcc
Confidence            4556899999999863   2233455799999999999999999999999999976653

>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=99.37  E-value=3.1e-13  Score=90.45  Aligned_cols=49  Identities=39%  Similarity=0.915  Sum_probs=40.7

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCC---CcccccccccccccCC
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH---STCPLCRGRVRRIAWP  173 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~i~~~~~~  173 (184)
                      .|+||++.+.+    .+..+|||.||..||..|+..+   .+||+||..+....+.
T Consensus        23 ~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~   74 (112)
T 1jm7_A           23 ECPICLELIKE----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQ   74 (112)
T ss_dssp             SCSSSCCCCSS----CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCB
T ss_pred             CCcccChhhcC----eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcC
Confidence            79999999977    4444799999999999999865   3899999998765543

>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=99.34  E-value=3e-13  Score=91.47  Aligned_cols=52  Identities=25%  Similarity=0.592  Sum_probs=42.9

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCC-ccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++.+.+    .+..+|||.||..||..|+..+. +||+||..+....
T Consensus        15 ~~~~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           15 LESKYECPICLMALRE----AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CCGGGBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCcCChhhcC----eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            4455689999999987    44457999999999999998654 9999999987543

>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=99.34  E-value=5e-13  Score=95.57  Aligned_cols=48  Identities=27%  Similarity=0.684  Sum_probs=40.0

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~  169 (184)
                      ...|+||++.|.+  . ..+++|||.||..||..|+.. +..||+||..+..
T Consensus        54 ~~~C~IC~~~~~~--p-~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           54 ELMCPICLDMLKN--T-MTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHBCTTTSSBCSS--E-EEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCcccChHhhC--c-CEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            3479999999987  2 233379999999999999986 7889999999853

>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=99.34  E-value=3e-13  Score=81.52  Aligned_cols=48  Identities=25%  Similarity=0.565  Sum_probs=40.2

Q ss_pred             CCcccccCcccccCCccceeec--CCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRS--KCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~--~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ++.+|.||++...+    .++.  +|||. |+..|+..|+..+..||+||+++..
T Consensus         7 ~~~~C~IC~~~~~~----~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKN----GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSC----EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCC----EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            34579999999877    4433  69999 8999999999988899999999853

>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=99.33  E-value=8.1e-13  Score=92.96  Aligned_cols=48  Identities=25%  Similarity=0.600  Sum_probs=41.1

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcCCC-cccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS-TCPLCRGRVRRI  170 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~i~~~  170 (184)
                      ...|+||++.|.+    .+.++|||.||..||..|+.... +||+||..+...
T Consensus        78 ~~~C~IC~~~~~~----pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQ----PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSS----EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcC----CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            3579999999987    55567999999999999998654 899999999765

>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=99.32  E-value=7.2e-13  Score=89.29  Aligned_cols=50  Identities=30%  Similarity=0.614  Sum_probs=42.5

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCcccccccccccccC
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIAW  172 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~~  172 (184)
                      ...|+||++.+.+    .+..+|||.||..||..|+.. +.+||+||..+....+
T Consensus        23 ~~~C~IC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           23 SISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HTBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCcHhcC----cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            3479999999987    554579999999999999985 7799999999876554

>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=99.32  E-value=3.8e-13  Score=93.69  Aligned_cols=49  Identities=18%  Similarity=0.510  Sum_probs=41.2

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC-Ccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVR  168 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~i~  168 (184)
                      ..+...|+||++.+.+    .+..+|||.||..||..|+... .+||+||.++.
T Consensus        28 l~~~~~C~IC~~~~~~----pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           28 LEAKYLCSACRNVLRR----PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CCGGGBCTTTCSBCSS----EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CCcCcCCCCCChhhcC----cEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            4555689999999988    5555799999999999999855 48999999864

>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=99.32  E-value=1.6e-13  Score=92.38  Aligned_cols=47  Identities=32%  Similarity=0.781  Sum_probs=40.1

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~  169 (184)
                      +..|+||++.+.+    .+.++|||.||..||..|+.. +.+||+||+.+..
T Consensus        15 ~~~C~iC~~~~~~----p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILVE----PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCSS----CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCccCCcccCc----eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            4579999999987    444479999999999999975 6789999999864

>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=99.30  E-value=6.1e-13  Score=79.89  Aligned_cols=49  Identities=20%  Similarity=0.589  Sum_probs=39.4

Q ss_pred             CcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..+|.||++...+.  +.+..+|||. |+..|+..|...+..||+||+++..
T Consensus         7 ~~~C~IC~~~~~~~--~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            7 LKPCSLCEKRPRDG--NIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GSBCTTTSSSBSCE--EEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             CCCCcccCCcCCCe--EEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            45799999987761  1222369998 9999999999888899999999853

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

Probab=99.29  E-value=2.6e-12  Score=81.74  Aligned_cols=52  Identities=13%  Similarity=0.086  Sum_probs=45.3

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++-|.+    ++..+|||.|+..||..|+..+.+||+||..+....
T Consensus        11 ~p~~~~CpI~~~~m~d----PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   62 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTD----PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESM   62 (85)
T ss_dssp             CCTTTBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CchheECcccCchhcC----CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHh
Confidence            3456789999999999    777789999999999999998899999999886543

>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=99.29  E-value=1.6e-12  Score=103.61  Aligned_cols=49  Identities=27%  Similarity=0.781  Sum_probs=42.6

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      ..+|+||++.+.+    .+..+|||.||..|+..|+. .+.+||+||+.+....
T Consensus       332 ~~~C~ICle~~~~----pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAENDKD----VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSBCC----EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCccCcCCCC----eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            3589999999977    55557999999999999998 7889999999987654

>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=99.27  E-value=4.2e-12  Score=83.20  Aligned_cols=52  Identities=15%  Similarity=0.102  Sum_probs=45.2

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++-|.+    ++..+|||.|+..||..|+..+.+||+||.++....
T Consensus        26 ~p~~~~CpI~~~~m~d----PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           26 APDEFRDPLMDTLMTD----PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             CSTTTBCTTTCSBCSS----EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             CcHhhCCcCccCcccC----CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            3456789999999999    776679999999999999998899999999986543

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

Probab=99.27  E-value=9.4e-13  Score=77.20  Aligned_cols=46  Identities=20%  Similarity=0.426  Sum_probs=37.7

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      .+...|+||++.|.+    .+.++|||.||..|+..|   ...||+||+.+..
T Consensus         4 ~~~~~C~IC~~~~~~----p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC----PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBC----CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCC----eEEcCCCCcccHHHHccC---CCCCCcCCcEeec
Confidence            445679999999987    444569999999999884   5689999998853

>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=99.26  E-value=6.5e-12  Score=81.98  Aligned_cols=52  Identities=13%  Similarity=0.007  Sum_probs=45.3

Q ss_pred             CCCCcccccCcccccCCccceeecCCC-ccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCN-HIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ..++..|+||++-|.+    ++..+|| |.|+..||..|+..+.+||+||+++....
T Consensus        19 ~p~~~~CpI~~~~m~d----PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCD----PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CCTTTBCTTTCSBCSS----EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             CcHhcCCcCccccccC----CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            3456689999999999    7777899 99999999999998899999999986543

>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=99.22  E-value=1.8e-12  Score=87.50  Aligned_cols=45  Identities=29%  Similarity=0.690  Sum_probs=38.8

Q ss_pred             cccccCcccccCCccceeec-CCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|+||++.|.+    .+.+ +|||.||..||..|+.  ..||+||..+...
T Consensus        23 ~~C~IC~~~~~~----pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           23 LRCSRCTNILRE----PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             TSCSSSCSCCSS----CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             CCCCCCChHhhC----ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccc
Confidence            479999999987    5544 7999999999999988  7899999998543

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

Probab=99.21  E-value=1.7e-12  Score=80.45  Aligned_cols=42  Identities=24%  Similarity=0.626  Sum_probs=36.7

Q ss_pred             cccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ..|+||++.+.+    .++.+|||. ||..|+..|    ..||+||+.+..
T Consensus        25 ~~C~iC~~~~~~----~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           25 KLCKICMDRNIA----IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             TBCTTTSSSBCC----EEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CCCCCCCCCCCC----EEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            379999999887    555579999 999999999    789999999864

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

Probab=99.19  E-value=3.5e-12  Score=99.15  Aligned_cols=52  Identities=29%  Similarity=0.786  Sum_probs=41.7

Q ss_pred             CCCcccccCcccccCCccce----eecCCCccccHhhHHHHhcCC-----------Ccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECK----VRSKCNHIFHQTCMDDWLDDH-----------STCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~----~l~~C~H~FH~~Ci~~Wl~~~-----------~~CP~CR~~i~  168 (184)
                      ....+|+||++.+.+++.++    ..++|||.||..|+.+||+..           .+||+||++|.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            45668999999999855544    234799999999999999732           46999999885

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

Probab=99.16  E-value=1.9e-11  Score=74.42  Aligned_cols=48  Identities=25%  Similarity=0.630  Sum_probs=39.2

Q ss_pred             ccCCCCcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       114 ~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ....+...|.||++...+    .++.||||. |+..|+..    ...||+||+.+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~----~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           10 PSEENSKDCVVCQNGTVN----WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CSCCCSSCCSSSSSSCCC----CEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             ccCCCCCCCCCcCcCCCC----EEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            344556789999999877    666679999 99999984    4789999999864

>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=99.09  E-value=3e-11  Score=86.64  Aligned_cols=52  Identities=25%  Similarity=0.588  Sum_probs=42.8

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC-Cccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++.+.+    ++..+|||.||..||..|+... .+||+||..+....
T Consensus        15 ~~~~~~C~IC~~~~~~----pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (170)
T 3hcs_A           15 LESKYECPICLMALRE----AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (170)
T ss_dssp             CCGGGBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCChhhcC----cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhh
Confidence            4455689999999988    5555799999999999999753 49999999987643

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

Probab=99.06  E-value=5.4e-11  Score=73.82  Aligned_cols=42  Identities=24%  Similarity=0.626  Sum_probs=35.3

Q ss_pred             cccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      .+|+||++.+.+    .++.+|||. ||..|+...    ..||+||+++..
T Consensus        26 ~~C~IC~~~~~~----~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   68 (75)
T 2ecg_A           26 KLCKICMDRNIA----IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   68 (75)
T ss_dssp             HSCSSSCSSCCC----BCCSSSCCCCBCHHHHHHC----SBCTTTCCBCCC
T ss_pred             CCCCcCCCCCCC----EEEecCCCHHHHHHHhhCC----CCCccCCceecC
Confidence            379999999877    555579999 999999653    789999999864

>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=99.03  E-value=2.1e-10  Score=88.14  Aligned_cols=53  Identities=11%  Similarity=0.184  Sum_probs=44.3

Q ss_pred             cCCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      ...+...|+||++-|.+    ++..+|||+|+..||..|+.. ..+||+||.++....
T Consensus       204 ~~~~~~~c~i~~~~~~d----Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          204 DIPDYLCGKISFELMRE----PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             CCCSTTBCTTTCSBCSS----EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CCCcccCCcCcCCHhcC----CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            34456789999999999    777789999999999999974 455999999986543

>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=2e-10  Score=67.96  Aligned_cols=48  Identities=31%  Similarity=0.821  Sum_probs=36.5

Q ss_pred             CCCcccccCcccccCCccceeecCCC--c---cccHhhHHHHhc--CCCcccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCN--H---IFHQTCMDDWLD--DHSTCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~--H---~FH~~Ci~~Wl~--~~~~CP~CR~~i~  168 (184)
                      ++...|.||+++.  ++.+ ++ ||.  |   .||..|+.+|+.  ++.+||+||..+.
T Consensus         4 ~~~~~CrIC~~~~--~~~l-~~-PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNER-FR-ACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEEC--SCCC-CC-SCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCC--CCce-ec-CcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            3456899999983  3333 34 464  4   899999999996  4788999999874

>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=99.02  E-value=1e-10  Score=75.69  Aligned_cols=49  Identities=24%  Similarity=0.641  Sum_probs=40.0

Q ss_pred             CCCcccccCcccccCCccceeec-CCCccccHhhHHHHhcCC------Ccccc--cccc-ccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWLDDH------STCPL--CRGR-VRR  169 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl~~~------~~CP~--CR~~-i~~  169 (184)
                      .+...|+||++.|.+    ++.. .|||+|+..||..|+..+      .+||+  |+.. +..
T Consensus         5 ~~~~~CPI~~~~~~d----PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK----PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SSCCBCTTTCSBCSS----EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             CcEeECcCcCchhcC----CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            344679999999998    7666 499999999999999753      58999  9866 543

>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=99.01  E-value=4.4e-11  Score=74.94  Aligned_cols=43  Identities=30%  Similarity=0.802  Sum_probs=36.6

Q ss_pred             cccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|.||++.+.+    .++.+|||. |+..|+..|    ..||+||+.+...
T Consensus        19 ~~C~IC~~~~~~----~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           19 MLCMVCCEEEIN----STFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             TBCTTTSSSBCC----EEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CEeEEeCcccCc----EEEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            379999999887    555679999 999999987    3899999998654

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

Probab=98.98  E-value=6e-10  Score=80.03  Aligned_cols=52  Identities=12%  Similarity=0.174  Sum_probs=43.8

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      ..+...|+||++-|.+    ++..+|||.|+..||..|+.. ..+||+||.++....
T Consensus       103 ip~~f~CPI~~elm~D----PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~  155 (179)
T 2f42_A          103 IPDYLCGKISFELMRE----PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQ  155 (179)
T ss_dssp             CCGGGBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CcHhhcccCccccCCC----CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhh
Confidence            4456789999999998    777789999999999999975 357999999886543

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.92  E-value=4e-10  Score=72.91  Aligned_cols=51  Identities=24%  Similarity=0.667  Sum_probs=40.4

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC--------CCcccc--cccc--cccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD--------HSTCPL--CRGR--VRRI  170 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~--i~~~  170 (184)
                      ..+|+||++++...+.+... +|||.||..|+..++..        ...||.  ||..  +.+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~-~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~   67 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIA-QCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN   67 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEET-TTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHH
T ss_pred             CcCCcccCcccccccceEcC-CCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHH
Confidence            45799999999876655544 59999999999999972        247999  9998  6443

>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=98.81  E-value=7.1e-10  Score=87.69  Aligned_cols=44  Identities=30%  Similarity=0.789  Sum_probs=38.0

Q ss_pred             CCcccccCcccccCCccceeecCCCcc-ccHhhHHHHhcCCCccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHI-FHQTCMDDWLDDHSTCPLCRGRVRR  169 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~i~~  169 (184)
                      ++..|+||++.+.+    .++.+|||. ||..|+..|    ..||+||.++..
T Consensus       294 ~~~~C~IC~~~~~~----~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS----VVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC----EEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc----eEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            45689999999987    665579999 999999998    689999999864

>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=98.80  E-value=1.6e-09  Score=64.26  Aligned_cols=50  Identities=20%  Similarity=0.293  Sum_probs=43.3

Q ss_pred             cccccCcccccCCccceeec-CCCccccHhhHHHHhcCCCcccccccccccccCC
Q 045853          120 STCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~  173 (184)
                      ..|+||++-+.+    .+.. +|||+|...||.+|+..+.+||+.++++...++.
T Consensus         4 ~~CpIs~~~m~d----PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Li   54 (61)
T 2bay_A            4 MLCAISGKVPRR----PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   54 (61)
T ss_dssp             CCCTTTCSCCSS----EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             EEecCCCCCCCC----CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcE
Confidence            369999999997    5555 7999999999999999888899999999766643

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.79  E-value=2.4e-09  Score=80.71  Aligned_cols=50  Identities=26%  Similarity=0.573  Sum_probs=41.1

Q ss_pred             CCcccccCcccccCCccceee-cCCCccccHhhHHHHhcCC--Ccccc--ccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDDH--STCPL--CRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~--~~CP~--CR~~i~~~~  171 (184)
                      ....|+||++.|.+    ++. ..|||.|+..||..|+..+  .+||+  ||+.+....
T Consensus       180 ~el~CPIcl~~f~D----PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~d  234 (267)
T 3htk_C          180 IELTCPITCKPYEA----PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRD  234 (267)
T ss_dssp             CCSBCTTTSSBCSS----EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGG
T ss_pred             eeeECcCccCcccC----CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhh
Confidence            34479999999988    664 3799999999999999854  57999  999886544

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

Probab=98.53  E-value=5e-08  Score=62.38  Aligned_cols=48  Identities=25%  Similarity=0.484  Sum_probs=38.0

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      -|.+|--.+..  ..|.. ||+|+|+.+|+..|.+ ...+||.||.++....
T Consensus         3 fC~~C~~Pi~i--ygRmI-PCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMI-PCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSE--EEEEE-TTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeEE--Eeeec-cccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            47777766654  34666 5999999999999985 5788999999987654

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

Probab=98.39  E-value=2.5e-07  Score=69.49  Aligned_cols=50  Identities=20%  Similarity=0.554  Sum_probs=40.3

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC--Ccccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH--STCPLCRGRVRRI  170 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~i~~~  170 (184)
                      ...+|.||.+-...+..   .+.|+|.||..|+..|++.+  .+||.|+......
T Consensus       179 ~i~~C~iC~~iv~~g~~---C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCEE---CSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCcc---cCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            35689999999998644   33599999999999999854  4899999976443

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

Probab=97.04  E-value=0.00051  Score=40.85  Aligned_cols=48  Identities=23%  Similarity=0.517  Sum_probs=34.6

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCC----ccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS----TCPLCRGRV  167 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~i  167 (184)
                      ......|.||-+    ++++...-.|...||..|++..+....    .||.|+...
T Consensus         9 ~~~~~~C~vC~~----~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C            9 LAPGARCGVCGD----GTDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CCTTCCCTTTSC----CTTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCCcCCCCC----CCeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            344567999974    334455556889999999998886433    599998754

>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=95.38  E-value=0.0033  Score=36.99  Aligned_cols=50  Identities=20%  Similarity=0.489  Sum_probs=35.1

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-----CCCcccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----DHSTCPLCRGR  166 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~  166 (184)
                      .+...|+||...+.+++.....-.|...||..|+..-..     ..-.||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            344579999998876555454556888899999865332     34569999864

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

Probab=95.18  E-value=0.014  Score=37.31  Aligned_cols=35  Identities=14%  Similarity=0.379  Sum_probs=25.0

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHh
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL  154 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl  154 (184)
                      +..|.||.+++... .+.....|+|.|+..|+..+.
T Consensus         3 e~~C~~C~~~~~~~-av~~C~~C~~~~C~~Cl~~~h   37 (101)
T 2jun_A            3 KVLCQFCDQDPAQD-AVKTCVTCEVSYCDECLKATH   37 (101)
T ss_dssp             CCBCTTCCSSSCCB-CCEEETTTTEEECHHHHHHHS
T ss_pred             CCCCcCCCCCCCCC-ceEECCcCChHHhHHHCHHHh
Confidence            45799999875332 223335799999999999843

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

Probab=94.96  E-value=0.016  Score=33.62  Aligned_cols=47  Identities=21%  Similarity=0.656  Sum_probs=31.7

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCcccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGR  166 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  166 (184)
                      ...+..|.+|-..    ..+...-.|...||..|+..=+..    .=.||.|+..
T Consensus         8 ~~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            3445679999873    334444467788999999875442    2359999763

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=94.77  E-value=0.0078  Score=37.80  Aligned_cols=55  Identities=20%  Similarity=0.413  Sum_probs=36.5

Q ss_pred             cCCCCcccccCcccc-cCCccceeecCCCccccHhhHHHHhc--CCCccccccccccc
Q 045853          115 AVNKTSTCVICLEEF-RDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRVRR  169 (184)
Q Consensus       115 ~~~~~~~C~ICl~~~-~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i~~  169 (184)
                      ...++..|.||...- .+++.+...-.|.-.||..|+..-..  ..=.||.|+.....
T Consensus        21 ~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~   78 (88)
T 2l43_A           21 LIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR   78 (88)
T ss_dssp             CCCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTS
T ss_pred             cCCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccch
Confidence            345667899999764 33445555556778899999975332  23359999876543

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.54  E-value=0.01  Score=35.93  Aligned_cols=51  Identities=18%  Similarity=0.445  Sum_probs=34.7

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRVRR  169 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i~~  169 (184)
                      +...|.||-.... ++.....-.|.-.||..|+..-...    .-.||.|+..+..
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            3346999987754 3334444467788999999765442    3459999887643

>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=94.35  E-value=0.012  Score=42.04  Aligned_cols=48  Identities=27%  Similarity=0.492  Sum_probs=34.8

Q ss_pred             cccccCcccccCCcc---ceeecCCCccccHhhHHHH------hc-----CCCccccccccc
Q 045853          120 STCVICLEEFRDGDE---CKVRSKCNHIFHQTCMDDW------LD-----DHSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~---~~~l~~C~H~FH~~Ci~~W------l~-----~~~~CP~CR~~i  167 (184)
                      ..|+||-..|.+++.   ....-.|...||..|+..=      +.     ..-.||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            469999999998763   4555568899999997431      11     146799998753

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.26  E-value=0.0063  Score=34.75  Aligned_cols=46  Identities=22%  Similarity=0.644  Sum_probs=30.6

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRG  165 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  165 (184)
                      ...+..|.+|-..    ..+...-.|...||..|+..=+..    .=.||.|+.
T Consensus         6 ~~~~~~C~vC~~~----g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS----SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC----CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3445679999874    234444567789999999865442    224888864

>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=93.91  E-value=0.089  Score=32.32  Aligned_cols=36  Identities=19%  Similarity=0.517  Sum_probs=23.7

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ...+..|.||-. +..++..+ ..-|+-+||..|+.+-
T Consensus        12 ~~~D~~C~VC~~-~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVCEV-WTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTTCC-CCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCcccc-ccccceec-cccccccccHhhcccc
Confidence            345668999852 33333322 2237899999999997

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=93.75  E-value=0.083  Score=32.23  Aligned_cols=51  Identities=20%  Similarity=0.407  Sum_probs=33.9

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-----CCCcccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----DHSTCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~i~  168 (184)
                      .+...| ||-..+.++......-.|...||..|+.---.     ..-.||.|+..-.
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~   65 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccC
Confidence            334456 99988865444455556888999999853221     3456999987653

>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=93.56  E-value=0.018  Score=33.45  Aligned_cols=46  Identities=22%  Similarity=0.551  Sum_probs=30.5

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      .+..|.+|-+.    ..+...-.|...||..|+..-+..    .=.||.|+...
T Consensus         8 ~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC----CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            34579999852    333444467788999999864442    22499997654

>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=92.81  E-value=0.02  Score=41.71  Aligned_cols=46  Identities=26%  Similarity=0.543  Sum_probs=32.1

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCC----Cccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH----STCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~i  167 (184)
                      .+..|.+|-..    ..+...-.|...||..|+.+-+...    =.||.|+..-
T Consensus         6 ~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            6 NEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            34569999743    3345555678899999998766532    3599998754

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=92.58  E-value=0.043  Score=32.86  Aligned_cols=51  Identities=20%  Similarity=0.440  Sum_probs=34.1

Q ss_pred             CCCCcccccCcccc-cCCccceeecCCCccccHhhHHHHhc--CCCcccccccc
Q 045853          116 VNKTSTCVICLEEF-RDGDECKVRSKCNHIFHQTCMDDWLD--DHSTCPLCRGR  166 (184)
Q Consensus       116 ~~~~~~C~ICl~~~-~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~  166 (184)
                      ...+..|.||...- .+++.+...-.|.-.||..|+..-..  ..=.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            44556799998764 34455555557888999999975322  22348888764

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=92.35  E-value=0.094  Score=30.78  Aligned_cols=35  Identities=26%  Similarity=0.664  Sum_probs=26.2

Q ss_pred             CCCcccccCcccccCCccceeec-CCCccccHhhHH
Q 045853          117 NKTSTCVICLEEFRDGDECKVRS-KCNHIFHQTCMD  151 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~  151 (184)
                      .....|.+|...+.+++.....- .|.-.||..|+.
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            34457999999998877666665 688889999974

>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=92.05  E-value=0.032  Score=39.82  Aligned_cols=46  Identities=26%  Similarity=0.619  Sum_probs=32.0

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCcccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRVR  168 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i~  168 (184)
                      +..|.+|...    ..+...-.|...||..|+..-+..    .=.||.|+..-.
T Consensus         4 ~~~C~~C~~~----g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            4 EDWCAVCQNG----GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             CSSCTTTCCC----SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCccccCCCC----CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            3469999843    334555567789999998776653    235999987543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=91.53  E-value=0.079  Score=29.31  Aligned_cols=44  Identities=30%  Similarity=0.699  Sum_probs=28.8

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  165 (184)
                      .|.||...-.. +.+...-.|...||..|++.=+..    .=.||.|+.
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            48888876433 344445567889999999754432    224888864

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.51  E-value=0.042  Score=36.01  Aligned_cols=45  Identities=29%  Similarity=0.628  Sum_probs=30.9

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  165 (184)
                      .|.+|...-.+++.+...-.|...||..|++.-+..    .=.||.||.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            588888754444455555578899999999765542    225999875

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=91.49  E-value=0.026  Score=32.57  Aligned_cols=46  Identities=22%  Similarity=0.651  Sum_probs=31.5

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCcccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRVR  168 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i~  168 (184)
                      +..|.+|...    ..+...-.|...||..|+..=+..    .=.||.|+....
T Consensus         5 ~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            5 EDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CSSCTTTCCC----SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCcCCCCC----CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            4579999874    234445567889999999864442    234999977653

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=91.27  E-value=0.045  Score=32.23  Aligned_cols=46  Identities=22%  Similarity=0.551  Sum_probs=31.3

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      .+..|.||-+.    ..+...-.|...||..|+..=+..    .=.||.|+..-
T Consensus         7 ~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~~   56 (66)
T 1xwh_A            7 NEDECAVCRDG----GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQAT   56 (66)
T ss_dssp             CCCSBSSSSCC----SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHTC
T ss_pred             CCCCCccCCCC----CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccCcc
Confidence            44579999863    334445567789999999864442    22499997644

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=91.12  E-value=0.11  Score=31.47  Aligned_cols=46  Identities=22%  Similarity=0.460  Sum_probs=30.3

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHH---------hcCCCccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW---------LDDHSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W---------l~~~~~CP~CR~~i  167 (184)
                      ..| ||-..+..+. ....-.|...||..|+..-         ....-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~~~-MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           17 LYC-ICRQPHNNRF-MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCS-TTCCCCCSSC-EEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CEE-ECCCccCCCC-EEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            456 8988776433 3334468889999998521         12466799998754

>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=90.77  E-value=0.12  Score=45.87  Aligned_cols=51  Identities=14%  Similarity=0.062  Sum_probs=43.5

Q ss_pred             CCCcccccCcccccCCccceeecCCC-ccccHhhHHHHhcCCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCN-HIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      -+...|+|-++-|.+    ++..+-| +.|-...|.+|+..+.+||+=|+++....
T Consensus       889 P~~F~cPIs~~lM~D----PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          889 PDEFLDPLMYTIMKD----PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             CGGGBCTTTCSBCSS----EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             cHHhCCcchhhHHhC----CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            445579999999999    7777787 58999999999999999999999886544

>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=90.71  E-value=0.055  Score=30.23  Aligned_cols=44  Identities=20%  Similarity=0.434  Sum_probs=29.7

Q ss_pred             ccccCcccccCCccceeec-CCCccccHhhHHHHh----cCCCcccccc
Q 045853          121 TCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWL----DDHSTCPLCR  164 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl----~~~~~CP~CR  164 (184)
                      .|.+|...+.+++.....- .|.-.||..|+.--.    ..+-.||.|+
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            4789988886655545544 488889999975321    2456688885

>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=90.53  E-value=0.073  Score=33.56  Aligned_cols=50  Identities=22%  Similarity=0.410  Sum_probs=33.4

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      .+...|.||...-.. +.+...-.|...||..|+..=+..    .=.||.|+..-
T Consensus        14 ~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~~   67 (92)
T 2e6r_A           14 IDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAE   67 (92)
T ss_dssp             CCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHHH
T ss_pred             cCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCcc
Confidence            445579999877532 344555568889999999744432    22499998753

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=90.26  E-value=0.42  Score=31.10  Aligned_cols=34  Identities=21%  Similarity=0.513  Sum_probs=25.0

Q ss_pred             CCcccccCcccc-----cCCccceeecCCCccccHhhHH
Q 045853          118 KTSTCVICLEEF-----RDGDECKVRSKCNHIFHQTCMD  151 (184)
Q Consensus       118 ~~~~C~ICl~~~-----~~~~~~~~l~~C~H~FH~~Ci~  151 (184)
                      ....|.+|+..-     ..++++...-.|+..||..|+.
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            345799998763     2334566666899999999995

>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=90.07  E-value=0.088  Score=34.28  Aligned_cols=38  Identities=16%  Similarity=0.354  Sum_probs=26.5

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD  155 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~  155 (184)
                      ..+..|.||.+.=.. +.+.....|+..||..|+...+.
T Consensus         5 ~~~~~C~~C~~~g~~-~~ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            5 SSGANCAVCDSPGDL-LDQFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCSCBTTTCCCCCT-TTSEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCcCCCCCCCC-cCCeECCCCCCCcChHHhCCccc
Confidence            345679999876332 22344457889999999988765

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=89.89  E-value=0.075  Score=37.47  Aligned_cols=48  Identities=21%  Similarity=0.486  Sum_probs=33.5

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHh-----cCCCcccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL-----DDHSTCPLCRGR  166 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~  166 (184)
                      +...| +|...+.++......-.|...||..|+..-.     ...-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            44568 9998876555555555788899999985321     234569999874

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

Probab=89.83  E-value=0.062  Score=32.20  Aligned_cols=49  Identities=18%  Similarity=0.284  Sum_probs=32.4

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHh----cCCCccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWL----DDHSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl----~~~~~CP~CR~~i  167 (184)
                      +...| ||-..+.+++.....-.|...||..|+..--    ...-.||.|+..-
T Consensus        15 ~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           15 WKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             SEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             cceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            33468 7988766554444455688889999986432    1345699998643

>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=89.08  E-value=0.18  Score=29.42  Aligned_cols=51  Identities=27%  Similarity=0.638  Sum_probs=34.1

Q ss_pred             CCCcccccCcccccC-CccceeecCCCccccHhhHHHHhc-------CCCccccccccc
Q 045853          117 NKTSTCVICLEEFRD-GDECKVRSKCNHIFHQTCMDDWLD-------DHSTCPLCRGRV  167 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~-~~~~~~l~~C~H~FH~~Ci~~Wl~-------~~~~CP~CR~~i  167 (184)
                      .++..|.+|...... ++.+...-.|.-.||..|+..=+.       ..=.||.|+...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            345679999987543 344555557788999999875331       233599997654

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=88.62  E-value=0.17  Score=32.24  Aligned_cols=46  Identities=28%  Similarity=0.466  Sum_probs=30.2

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLCRG  165 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  165 (184)
                      +...| ||-.....+ .+...-.|.-.||..|+..=..   ..-.||.|+.
T Consensus        27 d~vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CBCCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CCEEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            34567 887766544 3344557888999999865322   2346999974

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.57  E-value=0.32  Score=30.29  Aligned_cols=46  Identities=26%  Similarity=0.653  Sum_probs=31.2

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCcccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGR  166 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  166 (184)
                      ..+..|.+|...   + .+...-.|.-.||..|+.+=+..    .-.||.|+..
T Consensus        23 ~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            344579999964   2 34444466778999999765543    2249999864

>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=88.19  E-value=0.26  Score=31.81  Aligned_cols=49  Identities=22%  Similarity=0.476  Sum_probs=34.5

Q ss_pred             cccccCcccccCCccceeec-CCCccccHhhHHHHh----------cCCCcccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRS-KCNHIFHQTCMDDWL----------DDHSTCPLCRGRVR  168 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl----------~~~~~CP~CR~~i~  168 (184)
                      ..|.||...+.+++.....- .|.-.||..|+.-=-          ...-.||.|+..-.
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~   63 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKE   63 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCC
Confidence            46999999997766655553 588889999975221          02345999987653

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=88.17  E-value=0.088  Score=31.38  Aligned_cols=44  Identities=30%  Similarity=0.643  Sum_probs=26.7

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC-----CCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-----HSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~  165 (184)
                      .|.+|...-. ++.+...-.|...||..|++.=+..     .=.||.|+.
T Consensus        20 ~C~~C~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGRQD-PDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCCSC-GGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCcCC-CCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            4667765422 2333444467789999999854431     225888865

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=87.96  E-value=0.11  Score=37.29  Aligned_cols=44  Identities=25%  Similarity=0.632  Sum_probs=30.0

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc----CCCccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD----DHSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~i  167 (184)
                      ..|.+|.+.   + .+...-.|...||..|+..=+.    ..-.||.|+..-
T Consensus         3 ~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            3 TICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCBTTTCCC---S-SCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CcCccCCCC---C-ceeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            469999844   2 3344456778999999975443    223599998764

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.94  E-value=0.075  Score=32.34  Aligned_cols=44  Identities=25%  Similarity=0.605  Sum_probs=28.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC-----CCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-----HSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~  165 (184)
                      .|.||...-. ++.+...-.|...||..|++.=+..     .=.||.|+.
T Consensus        28 ~C~vC~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHE-PNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCC-STTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCC-CCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            6888886432 3344444467789999999854331     225888864

>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=87.79  E-value=0.4  Score=29.85  Aligned_cols=55  Identities=18%  Similarity=0.291  Sum_probs=37.8

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-------CCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-------DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-------~~~~CP~CR~~i~~~~  171 (184)
                      .+...|.+|...|..-..--....||++|+..|......       ..+.|-.|-..+....
T Consensus         7 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~~~~   68 (88)
T 1wfk_A            7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTRGS   68 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHHCC
T ss_pred             CcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHHhcc
Confidence            444589999999986433233446999999999765431       2356888887776443

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=87.68  E-value=0.12  Score=30.55  Aligned_cols=47  Identities=23%  Similarity=0.566  Sum_probs=30.1

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc---CCCccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD---DHSTCPLCRG  165 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  165 (184)
                      .+...| ||-..+. ++.....-.|...||..|+..--.   ..-.||.|+.
T Consensus        17 ~~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           17 QGLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TTCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            344568 9987765 333344446888999999864321   2345888864

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=87.31  E-value=0.29  Score=26.25  Aligned_cols=6  Identities=33%  Similarity=1.104  Sum_probs=3.1

Q ss_pred             CCCCcc
Q 045853            9 TCPNDE   14 (184)
Q Consensus         9 ~~~~~~   14 (184)
                      .||.+.
T Consensus         2 gCp~~~    7 (44)
T 2ks1_B            2 GCPTNG    7 (44)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            466543

>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=87.28  E-value=0.52  Score=28.02  Aligned_cols=46  Identities=26%  Similarity=0.629  Sum_probs=28.1

Q ss_pred             CCCcccccCcccccCCccceeecC--CC-ccccHhhHHHHhcC----CCccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSK--CN-HIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      .+..-| ||-.... ++ ....-.  |. ..||..|+.  +..    +-.||.|+..-
T Consensus        14 ~~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           14 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             TSCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            344567 8987543 32 233334  55 689999997  432    33599997654

>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=87.04  E-value=0.39  Score=31.07  Aligned_cols=46  Identities=22%  Similarity=0.525  Sum_probs=28.3

Q ss_pred             CCCCcccccCcccccCCccceeec--CCCccccHhhHHHHhcCC----Cccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRS--KCNHIFHQTCMDDWLDDH----STCPLCRGRV  167 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~--~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~i  167 (184)
                      ...+..|.+|.+    +.++...-  .|...||..|+.  |...    =.||.|+-.+
T Consensus        12 ~~~~~~C~~C~~----~G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~   63 (107)
T 4gne_A           12 QMHEDYCFQCGD----GGELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDE   63 (107)
T ss_dssp             CSSCSSCTTTCC----CSEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTT
T ss_pred             CCCCCCCCcCCC----CCcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCc
Confidence            344557999983    23334332  377899999997  5422    2388775444

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=86.52  E-value=0.09  Score=32.84  Aligned_cols=52  Identities=21%  Similarity=0.526  Sum_probs=35.4

Q ss_pred             CCcccccCcccccC-CccceeecCCCccccHhhHHHHhc--------CCCccccccccccc
Q 045853          118 KTSTCVICLEEFRD-GDECKVRSKCNHIFHQTCMDDWLD--------DHSTCPLCRGRVRR  169 (184)
Q Consensus       118 ~~~~C~ICl~~~~~-~~~~~~l~~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~i~~  169 (184)
                      .+..|.+|...-.. ++.+...-.|...||..|+..=+.        ..=.||.|+.....
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~   75 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhh
Confidence            34579999986443 244555557788999999986543        23359999876643

>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=86.46  E-value=0.57  Score=29.37  Aligned_cols=46  Identities=26%  Similarity=0.629  Sum_probs=28.4

Q ss_pred             CCCcccccCcccccCCccceeecC--CC-ccccHhhHHHHhcC----CCccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSK--CN-HIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      .+..-| ||-.... ++ ....-.  |. ..||..|+.  +..    +-.||.|+..-
T Consensus        34 ~e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~   86 (91)
T 1weu_A           34 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   86 (91)
T ss_dssp             CCCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCC
T ss_pred             CCCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcC
Confidence            344457 9987653 32 233334  55 689999997  332    34599998754

>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=86.46  E-value=0.11  Score=34.47  Aligned_cols=48  Identities=21%  Similarity=0.427  Sum_probs=33.4

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i  167 (184)
                      ..|..|-..|..-..--....||.+|+..|........+.|-.|-..+
T Consensus        20 ~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~   67 (120)
T 1y02_A           20 PSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFR   67 (120)
T ss_dssp             CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHHH
T ss_pred             CcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHHH
Confidence            479999999976433334557999999999877665667788886543

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=86.37  E-value=0.2  Score=32.83  Aligned_cols=34  Identities=26%  Similarity=0.412  Sum_probs=24.1

Q ss_pred             cccccCccccc------CCccceeecCCCccccHhhHHHH
Q 045853          120 STCVICLEEFR------DGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       120 ~~C~ICl~~~~------~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ..|.+|+..-.      +.+++...-.|+..||..|++..
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            36999987542      23455555578999999998754

>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=85.79  E-value=0.55  Score=28.00  Aligned_cols=33  Identities=21%  Similarity=0.470  Sum_probs=24.6

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHH
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDD  152 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  152 (184)
                      ..|.+|...|..-..--....||++|+..|...
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            479999999986433333447999999999753

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=85.11  E-value=0.97  Score=27.70  Aligned_cols=54  Identities=15%  Similarity=0.285  Sum_probs=36.1

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc--------CCCcccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD--------DHSTCPLCRGRVRRI  170 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~i~~~  170 (184)
                      .+...|.+|...|..-..--....||++|+..|......        ..+.|-.|-..+...
T Consensus        19 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~   80 (84)
T 1z2q_A           19 EDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACYLALRSS   80 (84)
T ss_dssp             TTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHHHHHHTS
T ss_pred             CCCCCCcCcCCccccchhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHHHHHhhc
Confidence            344579999999986543334457999999999765431        234577776665443

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=85.06  E-value=0.61  Score=28.49  Aligned_cols=51  Identities=25%  Similarity=0.517  Sum_probs=34.0

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhc------CCCcccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD------DHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR~~i~  168 (184)
                      +...|.+|...|.....--....||++|+..|....+.      ..+.|-.|-..+.
T Consensus        18 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~   74 (82)
T 2yw8_A           18 EATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLL   74 (82)
T ss_dssp             CCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEEECCTTCSSCEEECHHHHHHTT
T ss_pred             cCCcccCcCCcccCccccccCCCCCCEEChHHhCCeeecCCCCCcCEECHHHHHHHH
Confidence            34579999999986443334457999999999765431      2234777765553

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=84.96  E-value=0.3  Score=35.93  Aligned_cols=45  Identities=29%  Similarity=0.626  Sum_probs=25.5

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC-----CCcccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-----HSTCPLCRGR  166 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~  166 (184)
                      .|.+|-..-. ++.+...-.|...||..|+++=+..     .=.||.|+.+
T Consensus       176 ~C~vC~~~~~-~~~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          176 ACHLCGGRQD-PDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             SCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCcCCCCCCC-CCCeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            5778876432 2344445567889999999854432     2259999753

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=84.28  E-value=0.16  Score=30.81  Aligned_cols=45  Identities=29%  Similarity=0.633  Sum_probs=26.5

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC----C-Ccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----H-STCPLCRGR  166 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~-~~CP~CR~~  166 (184)
                      .|.+|-..-.. +.+...-.|...||..|++.-|..    . =.||.|+.+
T Consensus        28 ~C~vC~~~~d~-~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~d   77 (77)
T 3shb_A           28 ACHLCGGRQDP-DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   77 (77)
T ss_dssp             SBTTTCCCSCG-GGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC--
T ss_pred             cCCccCCCCCC-cceeEeCCCCCccCcccCCCcccCCCCCCceECcCcccc
Confidence            46666554322 333444467789999999865542    1 358988753

>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=84.16  E-value=0.55  Score=28.41  Aligned_cols=48  Identities=17%  Similarity=0.329  Sum_probs=30.2

Q ss_pred             CCcccccCcccccCCccceeec--CCCccccHhhHHHHhc---------CCCccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRS--KCNHIFHQTCMDDWLD---------DHSTCPLCRGRV  167 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~--~C~H~FH~~Ci~~Wl~---------~~~~CP~CR~~i  167 (184)
                      ....| ||-.....+ .....-  .|...||..|+.---.         .+-.||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T 1wew_A           15 IKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCccc
Confidence            44567 788874333 223333  5888999999863221         245699998754

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=83.68  E-value=0.59  Score=29.16  Aligned_cols=51  Identities=16%  Similarity=0.475  Sum_probs=35.5

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhc------CCCccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD------DHSTCPLCRGRVRR  169 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR~~i~~  169 (184)
                      ...|.+|...|..-..--....||++|+..|...+..      ..+.|-.|-..+..
T Consensus        20 ~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~~   76 (90)
T 3t7l_A           20 APNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETISK   76 (90)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEEEETTTTEEEEECHHHHHHHHH
T ss_pred             CCcCcCCCCcccchhhCccccCCCCEECCcccCCeeecCCCCCCCeECHHHHHHHHH
Confidence            3479999999986443344557999999999876542      23457777666643

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=83.35  E-value=0.71  Score=26.40  Aligned_cols=42  Identities=29%  Similarity=0.570  Sum_probs=30.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLC  163 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  163 (184)
                      .|.-|...+.+.. ....+.|++.|+.+|=.---..-.+||-|
T Consensus        17 ~C~~C~~~~~~~~-~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           17 FCYGCQGELKDQH-VYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             EETTTTEECTTSE-EECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             cccccCcccCCCc-cEECCccCcCcccchhHHHHhhccCCcCC
Confidence            5999999986432 24467899999999953333355679988

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.19  E-value=0.77  Score=27.23  Aligned_cols=41  Identities=17%  Similarity=0.411  Sum_probs=31.6

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ...|+-|-..+..++.+..   -+..||.+|+        +|..|+..|...
T Consensus         9 ~~~C~~C~~~I~~~~~v~a---~~~~~H~~CF--------~C~~C~~~L~~~   49 (76)
T 2cu8_A            9 ASKCPKCDKTVYFAEKVSS---LGKDWHKFCL--------KCERCSKTLTPG   49 (76)
T ss_dssp             CCBCTTTCCBCCTTTEEEE---TTEEEETTTC--------BCSSSCCBCCTT
T ss_pred             CCCCcCCCCEeECCeEEEE---CCeEeeCCCC--------CCCCCCCccCCC
Confidence            3579999999887665442   5788999884        699999988654

>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=83.16  E-value=0.4  Score=27.40  Aligned_cols=42  Identities=31%  Similarity=0.669  Sum_probs=26.2

Q ss_pred             CcccccCcccccCCccceeecC--CC-ccccHhhHHHHhcC----CCccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSK--CN-HIFHQTCMDDWLDD----HSTCPLCRG  165 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~  165 (184)
                      ..-| ||-.... + .....-.  |. ..||..|+.  +..    +-.||.|+.
T Consensus         9 ~~yC-~C~~~~~-g-~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            9 PTYC-LCHQVSY-G-EMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CEET-TTTEECC-S-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CcEE-ECCCCCC-C-CeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            3456 8987642 3 3333334  55 689999997  432    335999975

>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=82.73  E-value=0.64  Score=30.91  Aligned_cols=35  Identities=20%  Similarity=0.434  Sum_probs=25.8

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ...|.+|...|.....--....||++|+..|....
T Consensus        69 ~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           69 VQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            34799999999864333345579999999997544

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=82.72  E-value=0.17  Score=29.91  Aligned_cols=44  Identities=23%  Similarity=0.366  Sum_probs=26.4

Q ss_pred             cccccCcccccCCccceeec--CCCccccHhhHHHHhc--------CCCccccccc
Q 045853          120 STCVICLEEFRDGDECKVRS--KCNHIFHQTCMDDWLD--------DHSTCPLCRG  165 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~--~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~  165 (184)
                      ..| ||-.....+.. ...-  .|...||..|+.---.        .+-.||.||.
T Consensus        11 v~C-~C~~~~~~g~m-I~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~   64 (68)
T 2rsd_A           11 VRC-ICSSTMVNDSM-IQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRL   64 (68)
T ss_dssp             ECC-TTCCCSCCSCE-EECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHH
T ss_pred             EEe-ECCCCcCCCCE-EEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccC
Confidence            357 78765554433 2221  3888899999842111        1346999985

>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=82.30  E-value=0.43  Score=27.34  Aligned_cols=42  Identities=29%  Similarity=0.661  Sum_probs=25.7

Q ss_pred             CcccccCcccccCCccceeecC--CC-ccccHhhHHHHhcC----CCccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSK--CN-HIFHQTCMDDWLDD----HSTCPLCRG  165 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~  165 (184)
                      ..-| ||-.... + .....-.  |. ..||..|+.  +..    +-.||.|+.
T Consensus        10 ~~~C-~C~~~~~-g-~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A           10 PTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CEET-TTTEECC-S-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCEE-ECCCcCC-C-CEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            3456 8987642 3 3333334  44 579999997  442    335999865

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.52  E-value=1.1  Score=27.08  Aligned_cols=43  Identities=23%  Similarity=0.539  Sum_probs=32.3

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ....|+-|-..+...+.+..   =+..||.+|+        +|-.|+..|....
T Consensus        14 ~~~~C~~C~~~I~~~e~v~a---~~~~wH~~CF--------~C~~C~~~L~~~~   56 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLCV---NGHFFHRSCF--------RCHTCEATLWPGG   56 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCCB---TTBCCBTTTC--------BCSSSCCBCCTTS
T ss_pred             CCCCCcccCCCcccceEEEE---CCCeeCCCcC--------EEcCCCCCcCCCc
Confidence            44579999999877665542   4788999994        6888988886554

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.05  E-value=1.1  Score=26.15  Aligned_cols=41  Identities=20%  Similarity=0.433  Sum_probs=30.1

Q ss_pred             cccccCcccccC--CccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRD--GDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~--~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|+-|-..+..  ++.+...  -+..||.+|+        +|-.|+..|...
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a--~~~~wH~~CF--------~C~~C~~~L~~~   48 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISF--EERQWHNDCF--------NCKKCSLSLVGR   48 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEEC--SSCEECTTTC--------BCSSSCCBCTTS
T ss_pred             CCCcCCCccccCCCCcceEEE--CCcccCcccC--------EeccCCCcCCCC
Confidence            469999999886  3343322  5788999985        799999988643

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=80.92  E-value=1.8  Score=29.38  Aligned_cols=46  Identities=20%  Similarity=0.460  Sum_probs=30.9

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-----------CCCcccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----------DHSTCPLCRGR  166 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR~~  166 (184)
                      ..+..|.+|-+-    .++.-.-.|-.+||..|+.+=+.           ..=.||.|+..
T Consensus        61 g~~d~C~vC~~G----G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           61 GMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             SCBCSCSSSCCC----SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCeecccCCC----CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            345679999863    33344445778999999996653           23359999743

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.89  E-value=1.7  Score=25.62  Aligned_cols=43  Identities=19%  Similarity=0.509  Sum_probs=32.4

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      ...|+-|-..+..++.+...  -|..||.+|+        +|-.|++++....
T Consensus        11 ~~~C~~C~~~I~~~~~~~~a--~~~~~H~~CF--------~C~~C~~~L~~~~   53 (77)
T 1g47_A           11 SATCERCKGGFAPAEKIVNS--NGELYHEQCF--------VCAQCFQQFPEGL   53 (77)
T ss_dssp             CCBCSSSCCBCCSTTTCEEE--TTEEECTTTC--------CCTTTCCCCGGGC
T ss_pred             CCCchhcCCccCCCceEEEe--CccEeccccC--------eECCCCCCCCCCC
Confidence            45799999998866554433  5788999884        6889998887654

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.73  E-value=1.4  Score=26.97  Aligned_cols=35  Identities=20%  Similarity=0.391  Sum_probs=25.1

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHH
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDD  152 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  152 (184)
                      +...|.+|...|..-..---...||++|+..|...
T Consensus        13 ~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           13 NFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            34579999999975433223446999999999654

>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=80.54  E-value=0.77  Score=33.53  Aligned_cols=36  Identities=19%  Similarity=0.414  Sum_probs=26.6

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ++..|.+|...|.--..--....||++||..|....
T Consensus       160 ~~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~~  195 (220)
T 1dvp_A          160 DGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ  195 (220)
T ss_dssp             CCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCCccCCCCCccCCcccccccCCcCCEEChHHhCCe
Confidence            357899999999754433345579999999997543

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.24  E-value=0.86  Score=26.59  Aligned_cols=41  Identities=22%  Similarity=0.469  Sum_probs=30.5

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..|+-|-..+...+.+...  =+..||.+|+        +|-.|+..|...
T Consensus         6 ~~C~~C~~~I~~~~~~~~a--~~~~~H~~CF--------~C~~C~~~L~~~   46 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEY--KGSSWHETCF--------ICHRCQQPIGTK   46 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEE--TTEEEETTTT--------CCSSSCCCCCSS
T ss_pred             CCCccCCCcccCCceEEEE--CcCeecccCC--------cccccCCccCCC
Confidence            4699999998876544433  5778999885        688898888654

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=80.18  E-value=0.89  Score=30.62  Aligned_cols=50  Identities=18%  Similarity=0.465  Sum_probs=32.7

Q ss_pred             CCCcccccCccccc-CCccceeecCCCccccHhhHHHHhcC-C---Ccccccccc
Q 045853          117 NKTSTCVICLEEFR-DGDECKVRSKCNHIFHQTCMDDWLDD-H---STCPLCRGR  166 (184)
Q Consensus       117 ~~~~~C~ICl~~~~-~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~---~~CP~CR~~  166 (184)
                      .....|.+|...|. .+..-+....|+|.+|..|-..--.. +   =.|-+|++.
T Consensus        53 ~~~~~C~~C~~~~g~l~~~g~~C~~C~~~VC~~C~~~~~~~~~~~~W~C~vC~k~  107 (134)
T 1zbd_B           53 DGVNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQ  107 (134)
T ss_dssp             CSSSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEEECCCSSSSCCEEEHHHHHH
T ss_pred             CCCccccccCCCcccccCCCCCCCCCCcccccccCCccCCCCCccceechhhHHH
Confidence            34568999999994 33444667789999999985422111 1   137788764

>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=80.08  E-value=1.8  Score=26.21  Aligned_cols=35  Identities=26%  Similarity=0.585  Sum_probs=26.5

Q ss_pred             CCCcccccCcccccCCccceeecCC----CccccHhhHHHHhc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKC----NHIFHQTCMDDWLD  155 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C----~H~FH~~Ci~~Wl~  155 (184)
                      .....|.+|.+.+++.--    .+|    .|.|+..|-...++
T Consensus        13 ~a~l~CtlC~erLEdtHF----VQCPsv~~HkFCFpCsr~sIk   51 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHF----VQCPSVPSHKFCFPCSRESIK   51 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTS----EECSSCSSCEECHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCce----eeCCCccCCeeeccccHHHHH
Confidence            344579999999887322    135    48999999999987

---

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	184
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	4e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-12
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	6e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	4e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	6e-04
d1jm7b_	97	g.44.1.1 (B:) bard1 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 = 69.5 bits (170), Expect = 4e-17
 Identities = 25/53 (47%), Positives = 32/53 (60%)

Query: 115 AVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRV 167
           A++    C +CL E  DG+E +   +C H FH  C+D WL  HSTCPLCR  V
Sbjct: 1   AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI 170
           C ICLE+  +     +   C H F   C+  W+  + TCPLC+  V  +
Sbjct: 8   CPICLEDPSNYS---MALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV 53

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 3e-10
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 5/50 (10%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRR 169
            C IC E  +D         C H+   +C+  W + +   CP CR  ++ 
Sbjct: 25  LCKICAENDKDV----KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG 70

>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 = 50.1 bits (119), Expect = 2e-09
 Identities = 15/58 (25%), Positives = 16/58 (27%), Gaps = 14/58 (24%)

Query: 121 TCVICLEEFRDGDEC--------------KVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C IC     D                       CNH FH  C+  WL     CPL  
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>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 = 48.7 bits (116), Expect = 3e-09
 Identities = 9/48 (18%), Positives = 14/48 (29%), Gaps = 7/48 (14%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
            C  C  E +          C H     C++        CP+C+    
Sbjct: 8   RCQQCQAEAKCP----KLLPCLHTLCSGCLEAS---GMQCPICQAPWP 48

>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 = 49.0 bits (116), Expect = 3e-09
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 120 STCVICLEEFRDGDECKVR-SKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRR 169
             C  C          K+  + C H   ++C+D         CP C   +R+
Sbjct: 4   QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK 55

>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 = 47.0 bits (111), Expect = 1e-08
 Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 122 CVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHST-CPLCR 164
           C +C+E     D       C +   + C      D +  CP CR
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 46

>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 = 45.1 bits (106), Expect = 2e-07
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 7/59 (11%)

Query: 114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS---TCPLCRGRVRR 169
           +A+ K   C ICLE  ++     V +KC+HIF + CM   L+       CPLC+  + +
Sbjct: 16  NAMQKILECPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK 70

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH-STCPLCRGRVRR 169
           K+ +C IC     D     V + C H+F + C+   L    S CP CR     
Sbjct: 22  KSISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP 70

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 42.9 bits (100), Expect = 6e-07
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 121 TCVICLEEFRDGDECKVRSK-CNHIFHQTCMDDWLD--DHSTCPLCRGRVR 168
            C IC EE  +               H++C+  WL    ++ C +C     
Sbjct: 8   VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.5 bits (101), Expect = 1e-06
 Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 19/63 (30%)

Query: 121 TCVICLEEFRD--------------GDECKVRSKCNHIFHQTCMDDWL-----DDHSTCP 161
            C+IC+E+                        +KC+H FH  C+         D    CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 162 LCR 164
            C+
Sbjct: 87  SCK 89

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 9/54 (16%)

Query: 119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS--------TCPLCR 164
           +S C +CL E+       + ++C  IF   C+  +++           +CP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTI-AQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.3 bits (78), Expect = 6e-04
 Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 3/44 (6%)

Query: 121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCR 164
            C I  +  R         K   IF ++ ++ ++ D    P+  
Sbjct: 2   LCAISGKVPRRPVLSP---KSRTIFEKSLLEQYVKDTGNDPITN 42

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (77), Expect = 0.002
 Identities = 14/55 (25%), Positives = 20/55 (36%), Gaps = 5/55 (9%)

Query: 114 DAVNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR 168
           D + K   C  C    R+         C HIF   C+ D +   + CP+C     
Sbjct: 17  DRLEKLLRCSRCTNILREPVCL---GGCEHIFCSNCVSDCI--GTGCPVCYTPAW 66

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	184
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.86
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.74
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.7
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.67
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.66
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.63
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.54
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.53
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.49
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.45
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.41
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.29
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.27
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.24
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.07
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.95
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.22
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.52
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	94.81
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	94.81
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	94.27
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.46
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.22
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	92.97
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	92.67
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	92.08
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	91.77
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	90.07
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	89.64
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	89.29
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	88.34
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	87.34
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	86.1
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	85.51
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	85.51
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	83.14

>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=99.86  E-value=7.6e-23  Score=118.46  Aligned_cols=52  Identities=46%  Similarity=1.057  Sum_probs=47.6

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      +++.+|+||+++|.+++.++.++.|||.||..||.+|++.+.+||+||++|.
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            4556899999999999999888789999999999999999999999999874

>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=99.74  E-value=3.6e-19  Score=101.72  Aligned_cols=49  Identities=22%  Similarity=0.502  Sum_probs=42.5

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRR  169 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~  169 (184)
                      +|+||+++|..++......+|||.||..|+++|+.. +.+||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            799999999988776666579999999999999985 5579999998854

>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=99.70  E-value=2.9e-18  Score=103.48  Aligned_cols=50  Identities=32%  Similarity=0.788  Sum_probs=41.7

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..++|+||++.+.+  .++ .++|||.||..||.+|++.+.+||+||+++...
T Consensus         4 ~~d~C~IC~~~~~~--~~~-~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~~   53 (68)
T d1chca_           4 VAERCPICLEDPSN--YSM-ALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEE-ETTTTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCccCCcCccC--CcE-EeCCCCcCcHHHHHHHHHhCCcCCCCCcchHhh
Confidence            34579999999965  233 346999999999999999999999999998643

>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=99.67  E-value=1.3e-17  Score=99.54  Aligned_cols=55  Identities=18%  Similarity=0.436  Sum_probs=42.5

Q ss_pred             CCcccccCcccccCC-ccceeecCCCccccHhhHHHHhc-CCCcccccccccccccC
Q 045853          118 KTSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~  172 (184)
                      ++..|+||++++..+ +.....++|||.||..||..|+. .+.+||+||+.+...++
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~   58 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccc
Confidence            346899999986543 33334457999999999999995 46689999999866554

>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=2.3e-17  Score=104.45  Aligned_cols=51  Identities=29%  Similarity=0.627  Sum_probs=41.2

Q ss_pred             CCcccccCcccccCCcc--------------ceeecCCCccccHhhHHHHhcCCCcccccccccc
Q 045853          118 KTSTCVICLEEFRDGDE--------------CKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVR  168 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~--------------~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~  168 (184)
                      .++.|+||++++.+...              ...+++|||+||..||.+||+.+.+||+||++..
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            34569999998875321              2344579999999999999999999999999864

>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=99.64  E-value=7e-17  Score=100.04  Aligned_cols=48  Identities=27%  Similarity=0.813  Sum_probs=40.5

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      ..|+||++.+.+    .+.++|||.||..||..|+. ++.+||+||+.|....
T Consensus        24 ~~C~IC~~~~~~----~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          24 QLCKICAENDKD----VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TBCTTTSSSBCC----EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCccCCCcCCC----eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            469999999877    45557999999999999997 5678999999997544

>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=99.63  E-value=1.6e-16  Score=105.52  Aligned_cols=54  Identities=24%  Similarity=0.548  Sum_probs=41.2

Q ss_pred             CCcccccCcccccCC--------------ccceeecCCCccccHhhHHHHhcC-----CCccccccccccccc
Q 045853          118 KTSTCVICLEEFRDG--------------DECKVRSKCNHIFHQTCMDDWLDD-----HSTCPLCRGRVRRIA  171 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~--------------~~~~~l~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~i~~~~  171 (184)
                      .+..|+||++++...              +..+.+++|||+||.+||..|++.     +.+||+||+.+....
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            345799999998642              233445579999999999999973     347999999885443

>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=99.54  E-value=7.7e-16  Score=88.97  Aligned_cols=51  Identities=18%  Similarity=0.306  Sum_probs=44.2

Q ss_pred             ccccCcccccCCcccee-ecCCCccccHhhHHHHhcCCCcccccccccccccCCCC
Q 045853          121 TCVICLEEFRDGDECKV-RSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAWPSF  175 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~-l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~~~~  175 (184)
                      .|+||++.+.+    .+ ++.|||+||..||.+|++.+.+||+||+++...++...
T Consensus         2 ~C~Ic~~~~~~----Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipi   53 (56)
T d2baya1           2 LCAISGKVPRR----PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI   53 (56)
T ss_dssp             CCTTTCSCCSS----EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEEC
T ss_pred             CCccCCchHHh----cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeC
Confidence            49999999988    54 45699999999999999999999999999987765443

>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=99.53  E-value=3.4e-15  Score=93.32  Aligned_cols=50  Identities=30%  Similarity=0.600  Sum_probs=42.8

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCcccccccccccccCC
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIAWP  173 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~~~  173 (184)
                      ..|+||++.+.+    ++..+|||.|+..||.+|++ ++.+||+||.++...++.
T Consensus        24 l~C~IC~~~~~~----pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          24 ISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             TBCTTTCSBCSS----EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCCccCCcchhc----ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            479999999988    66667999999999999997 567899999998766644

>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=99.49  E-value=1.6e-15  Score=87.31  Aligned_cols=45  Identities=20%  Similarity=0.414  Sum_probs=37.1

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhcCCCcccccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRI  170 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~  170 (184)
                      ..+|+||++.|.+    .+.++|||.||..||++|   +.+||+||+++...
T Consensus         6 ~l~C~IC~~~~~~----p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAKC----PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBC----CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccCC----CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            3589999999987    444469999999999876   66899999999643

>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=99.45  E-value=1.9e-14  Score=93.51  Aligned_cols=48  Identities=40%  Similarity=0.935  Sum_probs=40.2

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCC---CcccccccccccccC
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDH---STCPLCRGRVRRIAW  172 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~i~~~~~  172 (184)
                      +|+||++.|.+    ++..+|||.||..||..|+..+   ..||+||.++...++
T Consensus        23 ~CpIC~~~~~~----pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l   73 (103)
T d1jm7a_          23 ECPICLELIKE----PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSL   73 (103)
T ss_dssp             SCSSSCCCCSS----CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTC
T ss_pred             CCCccCchhCC----eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhC
Confidence            69999999987    4445799999999999999754   479999999876554

>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=5.5e-14  Score=82.22  Aligned_cols=52  Identities=21%  Similarity=0.489  Sum_probs=38.3

Q ss_pred             CCCcccccCcccccCCccce-eecCCCccccHhhHHHHhc--CCCcccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECK-VRSKCNHIFHQTCMDDWLD--DHSTCPLCRGRVR  168 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~-~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~i~  168 (184)
                      ++...|.||++++.+....+ ....|+|.||..||..|+.  ++.+||+||+++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            34567999999987542221 1123469999999999995  6678999999864

>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=99.29  E-value=2.5e-13  Score=87.11  Aligned_cols=47  Identities=28%  Similarity=0.672  Sum_probs=38.4

Q ss_pred             cccccCcccccCCcccee-ecCCCccccHhhHHHHhcCCCcccccccccccccC
Q 045853          120 STCVICLEEFRDGDECKV-RSKCNHIFHQTCMDDWLDDHSTCPLCRGRVRRIAW  172 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~-l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~~  172 (184)
                      .+|+||++.|.+    .+ +++|||.||..||..|+.  ..||.||.++...++
T Consensus        23 l~C~IC~~~~~~----pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l   70 (97)
T d1jm7b_          23 LRCSRCTNILRE----PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (97)
T ss_dssp             TSCSSSCSCCSS----CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             CCCccCCchhhc----CceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhC
Confidence            379999999987    33 347999999999999985  469999998865443

>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=99.27  E-value=1.5e-12  Score=80.40  Aligned_cols=51  Identities=12%  Similarity=0.156  Sum_probs=43.2

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhc-CCCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-DHSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~i~~~~  171 (184)
                      -++..|+||++-|.+    ++..+|||.|+..||..|+. .+.+||.||.++....
T Consensus         5 P~~l~CpIc~~l~~d----Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           5 PDYLCGKISFELMRE----PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             CSTTBCTTTCSBCSS----EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             CccccCcCcCchhhh----hcccCCcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            345679999999999    66678999999999999996 5668999999886544

>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=99.24  E-value=3e-12  Score=78.63  Aligned_cols=51  Identities=25%  Similarity=0.551  Sum_probs=43.1

Q ss_pred             CCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-CCccccccccccccc
Q 045853          117 NKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-HSTCPLCRGRVRRIA  171 (184)
Q Consensus       117 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~i~~~~  171 (184)
                      -++..|+||++-|.+    .+..+|||.|+..||..|+.. ..+||.||.++....
T Consensus         6 P~~l~CpIc~~~m~d----PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           6 PEYFRCPISLELMKD----PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSSCTTTSCCCSS----EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             CccCCCcCcCchhhC----ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            455689999999998    666679999999999999975 567999999986544

>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=99.07  E-value=7.9e-11  Score=75.19  Aligned_cols=52  Identities=13%  Similarity=0.007  Sum_probs=43.9

Q ss_pred             CCCCcccccCcccccCCccceeecCCC-ccccHhhHHHHhcCCCccccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCN-HIFHQTCMDDWLDDHSTCPLCRGRVRRIA  171 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~i~~~~  171 (184)
                      .-++..|+||.+-|.+    ++..+|+ |.|...||..|+..+.+||+||+++....
T Consensus        19 ~P~~f~CPI~~~lm~d----PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~   71 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCD----PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             CCTTTBCTTTCSBCSS----EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             CcHHhCCcCchhHHHH----HHhcccccchhhHHHHHHHHHhcCCcccccccccchh
Confidence            3446789999999999    7666676 57999999999999999999999986544

>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=98.95  E-value=1.3e-10  Score=73.60  Aligned_cols=46  Identities=24%  Similarity=0.657  Sum_probs=36.1

Q ss_pred             CCcccccCcccccCCccceeecCCCccccHhhHHHHhcC--------CCcccccc
Q 045853          118 KTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD--------HSTCPLCR  164 (184)
Q Consensus       118 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR  164 (184)
                      ...+|+||++++..++.... ++|||.||.+|+..|+..        ..+||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTI-AQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEE-TTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEE-CCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            34589999999987666554 469999999999999971        23699864

>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=96.22  E-value=0.00043  Score=39.46  Aligned_cols=48  Identities=21%  Similarity=0.506  Sum_probs=35.3

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHHhc-----CCCcccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD-----DHSTCPLCRGR  166 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~  166 (184)
                      ...|.+|...+.+++.....-.|+..||..|+..=..     ..-.||.|+..
T Consensus         6 ~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           6 SGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            3479999998877776566667999999999863111     23469999864

>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=95.52  E-value=0.0025  Score=34.30  Aligned_cols=44  Identities=30%  Similarity=0.708  Sum_probs=30.8

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCC----ccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS----TCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  165 (184)
                      .|.||-..-.. +.+...-.|+..||..|++.-+....    .||.||.
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            58889765433 34455557889999999988765322    4999975

>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=94.81  E-value=0.014  Score=34.16  Aligned_cols=36  Identities=22%  Similarity=0.597  Sum_probs=26.3

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ...+..|.|| +-+..++..+= .-|+-+||..|+.+-
T Consensus        12 v~~D~mC~vC-~v~t~~~l~pC-RvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLFPC-RVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCSSC-SSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccccceecc-eeecchhhHHHHHHh
Confidence            4456689999 66766655432 237899999999998

>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=94.81  E-value=0.035  Score=32.44  Aligned_cols=48  Identities=19%  Similarity=0.406  Sum_probs=33.1

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHH--HHh-c--CCCcccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMD--DWL-D--DHSTCPLCRGRVR  168 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~--~Wl-~--~~~~CP~CR~~i~  168 (184)
                      .+.||-..+..++.....-.|+-.||..|+.  ..- .  .+-.||.|+....
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            4449998877666555566788899999985  221 1  2357999987543

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.27  E-value=0.0024  Score=38.61  Aligned_cols=50  Identities=18%  Similarity=0.483  Sum_probs=33.3

Q ss_pred             CcccccCcccccCC-ccceeecCCCccccHhhHHHHhc--------CCCcccccccccc
Q 045853          119 TSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLD--------DHSTCPLCRGRVR  168 (184)
Q Consensus       119 ~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~i~  168 (184)
                      ...|.||......+ ..+...-.|+..||..|+...+.        ..-.||.|+....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            34699998754433 34454557888999999874332        1345999987554

>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=93.46  E-value=0.0092  Score=33.25  Aligned_cols=44  Identities=25%  Similarity=0.631  Sum_probs=30.3

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcC----CCccccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD----HSTCPLCRGRV  167 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~i  167 (184)
                      ..|.+|.+    +..+...-.|.-.||..|+...+..    .-.||.|+..-
T Consensus        10 ~~C~~C~~----~g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_          10 EFCRVCKD----GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCTTTCC----CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCC----CCeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            35999974    2334545567789999999766553    23599998654

>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=93.22  E-value=0.031  Score=31.86  Aligned_cols=43  Identities=28%  Similarity=0.659  Sum_probs=29.6

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCC----ccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHS----TCPLCRGRV  167 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~i  167 (184)
                      .|.+|.+   .+ .+...-.|...||..|+...+....    .||.|+..-
T Consensus         9 ~C~~C~~---~~-~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           9 ICRVCQK---PG-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             CCSSSCS---SS-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCC---cC-EEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            5666653   23 3455557889999999998776333    499997644

>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=92.97  E-value=0.0058  Score=32.88  Aligned_cols=45  Identities=22%  Similarity=0.491  Sum_probs=31.8

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLCRG  165 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  165 (184)
                      .|.+|...|.....-.....||++|+..|....-...+.|..|.+
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            588999998865544455579999999998766555667888864

>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=92.67  E-value=0.01  Score=34.22  Aligned_cols=46  Identities=20%  Similarity=0.337  Sum_probs=32.2

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhc----CCCcccccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLD----DHSTCPLCRGR  166 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~  166 (184)
                      ..| ||......++.....-.|...||..|+..=..    ..-.||.|+..
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            357 78877766666666667888999999754221    33459999765

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.08  E-value=0.045  Score=31.32  Aligned_cols=43  Identities=30%  Similarity=0.736  Sum_probs=24.8

Q ss_pred             cccccCcccccCCccceee-cCCC-ccccHhhHHHHhcC----CCcccccccc
Q 045853          120 STCVICLEEFRDGDECKVR-SKCN-HIFHQTCMDDWLDD----HSTCPLCRGR  166 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l-~~C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~  166 (184)
                      .-| ||..... ++.+... -.|- ..||..|+.  +..    .-.||.||..
T Consensus        17 ~~C-iC~~~~~-~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVSY-GEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCCC-SSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCCC-CCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            345 9987543 2332321 1344 469999985  332    3359999764

>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=91.77  E-value=0.064  Score=29.26  Aligned_cols=43  Identities=28%  Similarity=0.570  Sum_probs=31.0

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHHhcCCCccccc
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDDHSTCPLC  163 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  163 (184)
                      ..|.=|...+.+ ..+...+.|++.|+.+|=----..-.+||-|
T Consensus        16 ~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          16 RFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            469999988864 3345677899999999953333355679987

>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=90.07  E-value=0.032  Score=27.00  Aligned_cols=27  Identities=19%  Similarity=0.625  Sum_probs=23.2

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhH
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCM  150 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  150 (184)
                      ..|++|-..+.+    +++.-.|-.||..|+
T Consensus         9 EkC~~C~~~I~d----riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           9 EKCATCSQPILD----RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CBCTTTCCBCCS----CCEEETTEEECTTTC
T ss_pred             HHHHHhchHHHH----HHHHHhCCCCCCCCC
Confidence            469999999998    777778999999884

>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=89.64  E-value=0.17  Score=29.21  Aligned_cols=48  Identities=17%  Similarity=0.410  Sum_probs=30.5

Q ss_pred             CcccccCcccccCCccceee-cCCCccccHhhHHH----Hhc-----CCCccccccccc
Q 045853          119 TSTCVICLEEFRDGDECKVR-SKCNHIFHQTCMDD----WLD-----DHSTCPLCRGRV  167 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~----Wl~-----~~~~CP~CR~~i  167 (184)
                      ...| ||-.....+..+... ..|+..||..|+.-    .-.     ..-.||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            3457 899877665544322 14889999999842    111     124699998643

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.29  E-value=0.089  Score=24.69  Aligned_cols=28  Identities=14%  Similarity=0.482  Sum_probs=24.0

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhH
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCM  150 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  150 (184)
                      .|+-|...+...|.++..  =+++||..|+
T Consensus         4 ~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             ccccccCcCChhHhheec--ccceeeeccC
Confidence            599999999999988865  4799999984

>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=88.34  E-value=0.26  Score=28.05  Aligned_cols=45  Identities=22%  Similarity=0.534  Sum_probs=28.2

Q ss_pred             ccccCcccccCCccceeecCCCccccHhhHH----H-----HhcCCCccccccccc
Q 045853          121 TCVICLEEFRDGDECKVRSKCNHIFHQTCMD----D-----WLDDHSTCPLCRGRV  167 (184)
Q Consensus       121 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~----~-----Wl~~~~~CP~CR~~i  167 (184)
                      .| ||-..... +.....-.|.=.||..|+.    .     -....-.||.|+..-
T Consensus        18 ~C-iC~~~~~~-~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          18 YC-ICRQPHNN-RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CS-TTCCCCCS-SCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             EE-ECCCccCC-CeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            47 88766543 3344445677789999983    1     112346799997543

>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=87.34  E-value=0.15  Score=29.09  Aligned_cols=35  Identities=20%  Similarity=0.421  Sum_probs=26.6

Q ss_pred             CcccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          119 TSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       119 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      +..|.+|-..|..-..-.....||++|+..|....
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~~   47 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ   47 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCCc
Confidence            34799999999865544455579999999997544

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=86.10  E-value=0.1  Score=33.10  Aligned_cols=49  Identities=16%  Similarity=0.360  Sum_probs=32.7

Q ss_pred             CcccccCcccccCC-ccceeecCCCccccHhhHHHHhc----CCCccccccccc
Q 045853          119 TSTCVICLEEFRDG-DECKVRSKCNHIFHQTCMDDWLD----DHSTCPLCRGRV  167 (184)
Q Consensus       119 ~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~i  167 (184)
                      ...|.+|...|..- ..-.....||+.||..|-..-..    ....|.+|....
T Consensus        48 ~~~C~~C~~~f~~~~~~~~~C~~C~~~~C~~C~~~~~~~~~~~~w~C~~C~k~r  101 (124)
T d1zbdb_          48 VNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQR  101 (124)
T ss_dssp             SSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEEECCCSSSSCCEEEHHHHHHH
T ss_pred             CCcCcccCCcccCCCCCCCcCccCCcccccCCCCCccCCCCCCCEECccCcchH
Confidence            35799999998743 33345668999999999432111    124588887754

>d1wfka_ g.50.1.1 (A:) Zinc finger FYVE domain containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Zinc finger FYVE domain containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.51  E-value=0.054  Score=32.39  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=38.2

Q ss_pred             CCCCcccccCcccccCCccceeecCCCccccHhhHHHHhcC-------CCcccccccccccc
Q 045853          116 VNKTSTCVICLEEFRDGDECKVRSKCNHIFHQTCMDDWLDD-------HSTCPLCRGRVRRI  170 (184)
Q Consensus       116 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~i~~~  170 (184)
                      ...+..|.+|-.+|..-..-.....||-+|+..|...+...       .+.|..|-..+...
T Consensus         6 ~~~~s~C~~C~~~Fs~~~rrhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~RVC~~C~~~l~~~   67 (88)
T d1wfka_           6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTRG   67 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHHC
T ss_pred             CcccCcCcccCchhccccccccccccChhhChHHhCCccccCCCCCCCCeECHHHHHHHHhc
Confidence            34456899999999765444445578899999998765431       23599997666543

>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=85.51  E-value=0.28  Score=27.40  Aligned_cols=34  Identities=21%  Similarity=0.424  Sum_probs=25.2

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ..|.+|-..|..-..--....||.+|+..|...+
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             cccccCCCcccCcccccccccCCCEecccccCCc
Confidence            4699999999764433344469999999997544

>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=83.14  E-value=0.32  Score=26.87  Aligned_cols=34  Identities=21%  Similarity=0.447  Sum_probs=25.2

Q ss_pred             cccccCcccccCCccceeecCCCccccHhhHHHH
Q 045853          120 STCVICLEEFRDGDECKVRSKCNHIFHQTCMDDW  153 (184)
Q Consensus       120 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  153 (184)
                      ..|.+|-..|..-..--....||++|+..|....
T Consensus         9 ~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           9 QNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             CBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CcCcCcCCcccCCccccchhhhCCeecccccCCc
Confidence            4699999999765433334579999999996544