Citrus Sinensis ID: 031354

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-
Protein Sequence
MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHccccccHHHHHHcccEEEEccccccccccccccccEEccccccccEEEcccccccccccccHHHHHccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHccEEEEccccccccccccccEEEEEEcccccccEEEEcccccccccHHHHHHHHHcccccccccccccccccccccEcc
Coil and Loop (DISEMBL)
masqesqpfhwhytelddhnfqirGRTLFSIIVVFAVVLLVSFLFLYARWFCRrfshqnsnpdvpRAQQALtrgldlttintlpivlhrsekstkddkeeesecciclgvfedgdkvkilpkcrhcyhcecvdawlsarsscplcrnslrvdsalpsittq
Flexible Loop (DISEMBL)
masqesqpfhWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRfshqnsnpdvPRAQQALTRGLDlttintlpivlhrsekstkddkeeESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPlcrnslrvdsalpsittq
Low Complexity Region (SEG)
MASQESQPFHWHYTELDDHNFQIRGRTlfsiivvfavvllvsflflYARWFCRRFSHQNSNPDVPRAQQALTRGLDLTTINTLPIVLHRsekstkddkeeeseCCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ
Disordered region (IsUnstruct)
********FHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSH************ALTRGLDLTTINTLPIVLH**************ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL************
Disordered Region (DISOPRED)
*************************RTLFSIIVVFAVVLLVSFLFLYARWF***************************TINTLPIVLHRS********E**SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL************
Disordered Region (DISEMBL)
********FHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQALTRGLDLTTINTLPIVLHRS************ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ
Disordered Region (DISPRO)
*******************NFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFS****************RGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	161	2.2.26 [Sep-21-2011]
Q9SRM0	158	RING-H2 finger protein AT	yes	no	0.919	0.936	0.474	6e-30
O64763	378	E3 ubiquitin-protein liga	no	no	0.732	0.312	0.366	4e-18
Q8L9T5	304	RING-H2 finger protein AT	no	no	0.782	0.414	0.324	9e-18
Q8RXX9	398	E3 ubiquitin-protein liga	no	no	0.857	0.346	0.358	2e-17
Q7X843	349	RING-H2 finger protein AT	no	no	0.732	0.338	0.372	3e-17
Q9SG96	181	RING-H2 finger protein AT	no	no	0.763	0.679	0.366	9e-17
Q8GW38	369	RING-H2 finger protein AT	no	no	0.782	0.341	0.324	3e-16
Q9LZJ6	257	RING-H2 finger protein AT	no	no	0.844	0.529	0.309	4e-15
O64762	302	RING-H2 finger protein AT	no	no	0.757	0.403	0.364	4e-15
Q84W40	404	RING-H2 finger protein AT	no	no	0.720	0.287	0.357	5e-15

>sp|Q9SRM0|ATL66_ARATH RING-H2 finger protein ATL66 OS=Arabidopsis thaliana GN=ATL66 PE=2 SV=1

 Score =  129 bits (325), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 74/156 (47%), Positives = 99/156 (63%), Gaps = 8/156 (5%)

Query: 2   ASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQN-- 59
           + Q S   +WH  + DD NFQI GRTLF  + +F+VVL  + L LY    C      N  
Sbjct: 7   SPQASMLLYWHENQYDDRNFQIHGRTLFFALALFSVVLFFALLTLYIHRNCLPRDSINLH 66

Query: 60  -SNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVK 118
            S+PD  R  +  + GLD   I +LP+VL R E++ +++++E     ICLG FE+G+K+K
Sbjct: 67  ASSPD--RLTRCRSGGLDPAEIRSLPVVLCRRERAEEEEEKECC---ICLGGFEEGEKMK 121

Query: 119 ILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA 154
           +LP C HCYHCECVD WL   SSCPLCR S+RVDS+
Sbjct: 122 VLPPCSHCYHCECVDRWLKTESSCPLCRVSIRVDSS 157

Arabidopsis thaliana (taxid: 3702)

>sp|O64763|ATL9_ARATH E3 ubiquitin-protein ligase ATL9 OS=Arabidopsis thaliana GN=ATL9 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 48/131 (36%), Positives = 68/131 (51%), Gaps = 13/131 (9%)

Query: 31  IIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQA------------LTRGLDLT 78
           ++VV  V+ LV F  ++   FCRR + Q S   + R+  A              RGLD  
Sbjct: 51  VVVVITVLFLVIFFMVFGSIFCRRSNAQFSRSSIFRSTDADAESQVVRIRRLTARGLDAE 110

Query: 79  TINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA 138
            I T P  L+   K+ +  K    EC +CL  FED + ++++P C H +H +CVD WLS 
Sbjct: 111 AIETFPTFLYSEVKAVRIGKGG-VECAVCLCEFEDDETLRLMPPCCHVFHADCVDVWLSE 169

Query: 139 RSSCPLCRNSL 149
            S+CPLCR  L
Sbjct: 170 HSTCPLCRADL 180

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 89.4 bits (220), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 50/154 (32%), Positives = 81/154 (52%), Gaps = 28/154 (18%)

Query: 17  DDHNFQ------IRGRTLFS-IIVVFAVVLLVSFLFLYARWFCRRFSHQ----------- 58
           +D+NF       + G+ + S I+++F VV+L+ FL LYARW+  R   +           
Sbjct: 14  EDNNFSGSKTYAMSGKIMLSAIVILFFVVILMVFLHLYARWYLLRARRRHLRRRSRNRRA 73

Query: 59  -----NSNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFED 113
                 ++P         +RGLD   I +LP V   S+++ KD  E    C +CL  FE+
Sbjct: 74  TMVFFTADPSTAATSVVASRGLDPNVIKSLP-VFTFSDETHKDPIE----CAVCLSEFEE 128

Query: 114 GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN 147
            +  ++LP C+H +H +C+D W  + S+CPLCR+
Sbjct: 129 SETGRVLPNCQHTFHVDCIDMWFHSHSTCPLCRS 162

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 88.2 bits (217), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 57/159 (35%), Positives = 85/159 (53%), Gaps = 21/159 (13%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS 60
           +A+ +SQP   +      +N+   GR   ++ V+  VV+L++ LF    +F   F H + 
Sbjct: 26  LAASQSQPGPTN----QPYNY---GRLSPAMAVI--VVILIAALFFMG-FFSIYFRHCSG 75

Query: 61  NPDV---------PRAQ-QALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGV 110
            PD           RA   A  RGLD++ + T P  L+   K+ K  K E  EC ICL  
Sbjct: 76  VPDAGVSPAGGARSRATVNAAARGLDVSVVETFPTFLYSDVKTQKLGKGEL-ECAICLNE 134

Query: 111 FEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
           FED + +++LPKC H +H  C+DAWL A  +CP+CR +L
Sbjct: 135 FEDDETLRLLPKCDHVFHPHCIDAWLEAHVTCPVCRANL 173

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

 Score = 87.8 bits (216), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 48/129 (37%), Positives = 68/129 (52%), Gaps = 11/129 (8%)

Query: 29  FSIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDV-----PRAQQAL---TRGLDLTTI 80
            ++I+VF  VL + F FL          H N NPD+     P+ Q        GLD T I
Sbjct: 127 LALIIVFLGVLYLIFKFLRKSSTLFPIPHFNYNPDLFSFSSPQLQHLFFLHDSGLDQTAI 186

Query: 81  NTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS 140
           + LP+ L+    +     E+  +C +CL  F D DK+++LP C H +H  C+D WL + S
Sbjct: 187 DALPVFLY---GNVTISLEQPFDCAVCLNEFSDTDKLRLLPVCSHAFHLHCIDTWLLSNS 243

Query: 141 SCPLCRNSL 149
           +CPLCR SL
Sbjct: 244 TCPLCRRSL 252

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SG96|ATL72_ARATH RING-H2 finger protein ATL72 OS=Arabidopsis thaliana GN=ATL72 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 76/139 (54%), Gaps = 16/139 (11%)

Query: 30  SIIVVFAVVL--LVSFLFLYARWFC-----RRFSHQN-----SNPDVPRAQQALTRGLDL 77
           +++++ A +L  L+  L L +   C     RRF+  +     SN +    + A   GL  
Sbjct: 32  NMVIILAALLCALICALSLNSALRCVLRITRRFTSDDQVSNASNANANLGRLAAATGLKK 91

Query: 78  TTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS 137
             +  +P+ L+ S     D K   +EC ICLG FEDG+KV++LPKC H +H  C+D WL 
Sbjct: 92  QALKQIPVGLYGS--GIIDMKA--TECLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLL 147

Query: 138 ARSSCPLCRNSLRVDSALP 156
           +RSSCP CR SL ++   P
Sbjct: 148 SRSSCPTCRQSLLLEQPSP 166

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.3 bits (207), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 77/148 (52%), Gaps = 22/148 (14%)

Query: 20  NFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRF--------SHQNSNP---DVPRAQ 68
           N +I    LF I+++  +  + S L L  R++ ++         +  N NP   D    Q
Sbjct: 46  NNRISPIILFIIVLLSVIFFICSILHLLVRYYLKKKRSNLSSSPNESNQNPEFSDSDTYQ 105

Query: 69  QALTR-------GLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILP 121
           + L +       GLD   I+ LP+ L++  K TK    E  +C +CL  F + DK+++LP
Sbjct: 106 RQLQQLFHLHDSGLDQALIDALPVFLYKEIKGTK----EPFDCAVCLCEFSEDDKLRLLP 161

Query: 122 KCRHCYHCECVDAWLSARSSCPLCRNSL 149
            C H +H +C+D WL + S+CPLCR +L
Sbjct: 162 NCSHAFHIDCIDTWLLSNSTCPLCRGTL 189

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZJ6|ATL5_ARATH RING-H2 finger protein ATL5 OS=Arabidopsis thaliana GN=ATL5 PE=2 SV=1

 Score = 80.5 bits (197), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/152 (30%), Positives = 74/152 (48%), Gaps = 16/152 (10%)

Query: 11  WHYTELDDHNFQIRGRTLF-SIIVVFAVVLLVSFLFLYARWFCRRF---------SHQNS 60
           W         + + G+ +  S+I++F  V+L+     YARW  RR          +H  S
Sbjct: 12  WGNMNHGSSRYSLNGKIMLASVIILFVAVILILCFHSYARWLFRRQNRRIRRRISAHLRS 71

Query: 61  NPDV--PRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVK 118
                 P    +    LD T +  +PI ++    S K  +    EC +CL  FE+ D+ +
Sbjct: 72  LAAARDPTQSSSSLSPLDPTVLEKIPIFVY----SVKTHESPLEECSVCLSEFEEDDEGR 127

Query: 119 ILPKCRHCYHCECVDAWLSARSSCPLCRNSLR 150
           +LPKC H +H +C+D W  +RSSCPLCR  ++
Sbjct: 128 VLPKCGHVFHVDCIDTWFRSRSSCPLCRAPVQ 159

Arabidopsis thaliana (taxid: 3702)

>sp|O64762|ATL38_ARATH RING-H2 finger protein ATL38 OS=Arabidopsis thaliana GN=ATL38 PE=2 SV=1

 Score = 80.5 bits (197), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 47/129 (36%), Positives = 67/129 (51%), Gaps = 7/129 (5%)

Query: 27  TLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS-NP----DV-PRAQQALTRGLDLTTI 80
           TL  I ++   + +V    +  RW  R+F  Q S NP    DV  R      RGLD   I
Sbjct: 14  TLLVITIILFAIFIVGLASVCFRWTSRQFYSQESINPFTDSDVESRTSITAVRGLDEAII 73

Query: 81  NTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS 140
           N+ P  L+ SE   +       EC +C+  FED + ++++P+C H +H +CV  WLS  S
Sbjct: 74  NSFPTFLY-SEVKERRIGIGGVECAVCICEFEDHETLRLMPECCHVFHADCVSVWLSDHS 132

Query: 141 SCPLCRNSL 149
           +CPLCR  L
Sbjct: 133 TCPLCRVDL 141

Arabidopsis thaliana (taxid: 3702)

>sp|Q84W40|ATL11_ARATH RING-H2 finger protein ATL11 OS=Arabidopsis thaliana GN=ATL11 PE=2 SV=2

 Score = 80.5 bits (197), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 45/126 (35%), Positives = 68/126 (53%), Gaps = 10/126 (7%)

Query: 31  IIVVFAVVLLVSFLFLYARWFCRRFSHQN-SNPD------VPRAQQALTRGLDLTTINTL 83
           +IV+ +V   + F  +Y R    R    +  NP+          QQA  RGLD + I T 
Sbjct: 67  MIVLVSVFFFLGFFSVYIRRCLERVMGMDYGNPNDAGNWLATNRQQA--RGLDASIIETF 124

Query: 84  PIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCP 143
           P   + + K+ +  KE   EC +CL  FED + ++++PKC H +H  C+DAWL + ++CP
Sbjct: 125 PTFQYSTVKTLRIGKEAL-ECSVCLNEFEDDETLRLIPKCCHVFHPGCIDAWLRSHTTCP 183

Query: 144 LCRNSL 149
           LCR  L
Sbjct: 184 LCRADL 189

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	161
224101167	164	predicted protein [Populus trichocarpa]	1.0	0.981	0.530	6e-47
255574820	165	RING-H2 finger protein ATL2N, putative [	0.993	0.969	0.554	3e-42
388502780	173	unknown [Medicago truncatula]	0.987	0.919	0.490	4e-42
357461325	173	Zinc/RING finger protein [Medicago trunc	0.987	0.919	0.490	7e-42
356539989	175	PREDICTED: RING-H2 finger protein ATL66-	0.981	0.902	0.482	1e-41
255646665	175	unknown [Glycine max]	0.962	0.885	0.491	2e-41
356568178	175	PREDICTED: RING-H2 finger protein ATL66-	1.0	0.92	0.490	2e-40
449460935	168	PREDICTED: RING-H2 finger protein ATL66-	0.944	0.904	0.530	2e-39
356499217	173	PREDICTED: RING-H2 finger protein ATL66-	0.981	0.913	0.481	1e-36
356553773	221	PREDICTED: RING-H2 finger protein ATL66-	0.950	0.692	0.497	8e-33

>gi|224101167|ref|XP_002312167.1| predicted protein [Populus trichocarpa] gi|222851987|gb|EEE89534.1| predicted protein [Populus trichocarpa]

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 87/164 (53%), Positives = 121/164 (73%), Gaps = 3/164 (1%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS 60
           MASQ+SQPFHWHY ELD+++FQ+RGR LF +++V ++++L++ L +YARW C   +  N 
Sbjct: 1   MASQDSQPFHWHYEELDENDFQVRGRALFYVLIVGSMIILIALLSIYARWVCLENTRHNL 60

Query: 61  NPDVP--RAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEE-ESECCICLGVFEDGDKV 117
              +P   A +   RGL+ T I  LPI LH+S   T ++    ESECCICLGVFEDGD++
Sbjct: 61  PSRLPVHHAPRLPPRGLESTIIKALPITLHKSNLGTSNNGTAVESECCICLGVFEDGDRL 120

Query: 118 KILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           K+LP+C+HC+HC+CVD WL  +SSCPLCR S+R +SA+ SI T+
Sbjct: 121 KVLPQCQHCFHCDCVDKWLVTQSSCPLCRASIRAESAVLSIITE 164

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574820|ref|XP_002528317.1| RING-H2 finger protein ATL2N, putative [Ricinus communis] gi|223532272|gb|EEF34075.1| RING-H2 finger protein ATL2N, putative [Ricinus communis]

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 92/166 (55%), Positives = 115/166 (69%), Gaps = 6/166 (3%)

Query: 1   MASQE-SQPFHWHY-TELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQ 58
           M+SQE SQPFHWH+ TE  D+ F+I GRTLF ++V+FA+V+LV+ LFLYARW C    H 
Sbjct: 1   MSSQEYSQPFHWHFSTEPHDNGFEIHGRTLFFVVVLFALVILVTLLFLYARWVCHYQHHH 60

Query: 59  NSNPDVPRAQQALT---RGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGD 115
             +     A   L+   +GL  T I  + I LHRS  S+       +ECCICLGVFEDGD
Sbjct: 61  FPSSQANHAPHDLSPCHQGLHPTVIKAMSITLHRSSSSSLG-YYCTTECCICLGVFEDGD 119

Query: 116 KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           KVK+LP+C HC+H ECVD WL+A+SSCPLCR SL  DSA+ SI T+
Sbjct: 120 KVKVLPECSHCFHSECVDKWLTAQSSCPLCRASLHRDSAVISILTE 165

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502780|gb|AFK39456.1| unknown [Medicago truncatula]

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 113/165 (68%), Gaps = 6/165 (3%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSH--- 57
           M+S  S+  +WHYTELDD + +I+GRTLF +IV+F++ LLV  LF Y RW CR  +H   
Sbjct: 1   MSSPNSRSLNWHYTELDDRDLEIKGRTLFFVIVLFSIFLLVIVLFFYTRWVCRYHTHITT 60

Query: 58  -QNSNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDK 116
             +++   P AQ    +GLD   I  LPI+LH++    ++   EE+ECCICLG F DG+K
Sbjct: 61  TYSASIHAPPAQPP--QGLDPAAIKKLPIILHQAPTDPENGAWEETECCICLGEFRDGEK 118

Query: 117 VKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           +K+LP C H +HC+CVD WL+ +SSCPLCR SL+V+ + P I+ Q
Sbjct: 119 LKVLPGCEHYFHCDCVDKWLTHQSSCPLCRGSLKVEPSFPEISIQ 163

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461325|ref|XP_003600944.1| Zinc/RING finger protein [Medicago truncatula] gi|355489992|gb|AES71195.1| Zinc/RING finger protein [Medicago truncatula]

 Score =  174 bits (442), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 112/165 (67%), Gaps = 6/165 (3%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSH--- 57
           M+S  S+  +WHYTELDD + +I+GRTLF +IV+F++ LLV  LF Y RW CR  +H   
Sbjct: 1   MSSPNSRSLNWHYTELDDRDLEIKGRTLFFVIVLFSIFLLVIVLFFYTRWVCRYHTHITT 60

Query: 58  -QNSNPDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDK 116
             +++   P AQ    +GLD   I  LPI+LH++    ++   EE+ECCICLG F DG+K
Sbjct: 61  TYSASIHAPPAQPP--QGLDPAAIKKLPIILHQAPTDPENGAWEETECCICLGEFRDGEK 118

Query: 117 VKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           +K+LP C H +HC+CVD WL+ +SSCPLCR SL+V+ + P I  Q
Sbjct: 119 LKVLPGCEHYFHCDCVDKWLTHQSSCPLCRGSLKVEPSFPKILIQ 163

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539989|ref|XP_003538474.1| PREDICTED: RING-H2 finger protein ATL66-like [Glycine max]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 81/168 (48%), Positives = 114/168 (67%), Gaps = 10/168 (5%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS 60
           M++ +++ F+WHYTELDD + +IRGRTLF +IV+F+++LLV+ LF+Y RW CR   +Q  
Sbjct: 1   MSNPDTRSFNWHYTELDDRDLEIRGRTLFFVIVLFSIILLVTVLFIYTRWVCR---YQGR 57

Query: 61  NPDVPRAQQAL-------TRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFED 113
            P    +  A+        +GLD  +I  LPI+LH +     +   +E+ECCICLG F D
Sbjct: 58  LPTTAFSAAAVHAPPLAPPQGLDPASIKKLPIILHHAPADRDESAWDETECCICLGEFRD 117

Query: 114 GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           G+KVK+LP C H +HC+CVD WL+  SSCPLCR SL+V+S+ P I  Q
Sbjct: 118 GEKVKVLPACDHYFHCDCVDKWLTHHSSCPLCRASLKVESSFPKILIQ 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646665|gb|ACU23806.1| unknown [Glycine max]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 84/171 (49%), Positives = 114/171 (66%), Gaps = 16/171 (9%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS 60
           M+S +S+ F WHYTELDD + +IRGRTLF +IV+F+++LLV+ LF+Y RW CR   +Q  
Sbjct: 1   MSSPDSRSFSWHYTELDDRDLEIRGRTLFFVIVLFSIILLVTVLFIYTRWVCR---YQGR 57

Query: 61  NPDV----------PRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGV 110
            P            P AQ    +G+D  +I  LPI+LH +    ++   +E+ECCICLG 
Sbjct: 58  LPTTAFTAAAAHASPLAQ---PQGMDPASIKKLPIILHHAPSDREESAWDETECCICLGE 114

Query: 111 FEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           F DG+KVK+LP C H +HC+CVD WL+  SSCPLCR SL+V+S+ P I  Q
Sbjct: 115 FRDGEKVKVLPACDHYFHCDCVDKWLTHHSSCPLCRASLKVESSFPKILIQ 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568178|ref|XP_003552290.1| PREDICTED: RING-H2 finger protein ATL66-like [Glycine max]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 81/165 (49%), Positives = 111/165 (67%), Gaps = 4/165 (2%)

Query: 1   MASQESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNS 60
           M+S +S+ F WHYTELDD + +IRGRTLF +IV+F+++LLV+ LF+Y RW CR      +
Sbjct: 1   MSSPDSRSFSWHYTELDDRDLEIRGRTLFFVIVLFSIILLVTVLFIYTRWVCRYQGRLPT 60

Query: 61  NPDVPRAQQALT----RGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDK 116
                 A  A      +G+D  +I  LPI+LH +    ++   +E+ECCICLG F DG+K
Sbjct: 61  TAFTAAAAHAPPLAQPQGMDPASIKKLPIILHHAPSDREESAWDETECCICLGEFRDGEK 120

Query: 117 VKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           VK+LP C H +HC+CVD WL+  SSCPLCR SL+V+S+ P I  Q
Sbjct: 121 VKVLPACDHYFHCDCVDKWLTHHSSCPLCRASLKVESSFPKILIQ 165

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460935|ref|XP_004148199.1| PREDICTED: RING-H2 finger protein ATL66-like [Cucumis sativus] gi|449507803|ref|XP_004163133.1| PREDICTED: RING-H2 finger protein ATL66-like [Cucumis sativus]

 Score =  166 bits (421), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 87/164 (53%), Positives = 107/164 (65%), Gaps = 12/164 (7%)

Query: 1   MASQESQP-FHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQN 59
           MA+ +  P   WH+TELDD  FQIRGRT F + V+FAV+LLV+F+FLYARW CR   HQ 
Sbjct: 1   MATSQVPPSVPWHFTELDDRLFQIRGRTFFFVAVLFAVILLVTFIFLYARWVCR--FHQL 58

Query: 60  SNPDVPRAQQALT-----RGLDLTTINTLPIVLHRSEKSTKDDK----EEESECCICLGV 110
           +    P     L      +GL  TTI +LPI L++   + +D       +  EC ICLGV
Sbjct: 59  TTFSAPLPVHRLPSSPPQQGLGATTIISLPITLYKPPAAKEDAPGAAANDAGECSICLGV 118

Query: 111 FEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA 154
           FEDG+KVKILP CRHCYH ECVD WL + SSCPLCR SL +D +
Sbjct: 119 FEDGEKVKILPPCRHCYHSECVDRWLRSHSSCPLCRVSLCIDPS 162

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499217|ref|XP_003518438.1| PREDICTED: RING-H2 finger protein ATL66-like [Glycine max]

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 80/166 (48%), Positives = 106/166 (63%), Gaps = 8/166 (4%)

Query: 1   MASQESQPFHWHY-TELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQN 59
           M+ ++S+  +WHY TELDD   +IRGR LF +IV+F+++LL + LF++AR  CR      
Sbjct: 1   MSIRDSESLNWHYDTELDDETLEIRGRKLFFVIVLFSIILLFTALFVFARRICRHHHGLL 60

Query: 60  SNPDVPRAQQALT----RGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGD 115
               VP    +L+     GLD   I  LPIVLH           EE+ECCICLGVF DG+
Sbjct: 61  LPNAVPPRHASLSPPQNSGLDAEAIKRLPIVLHPRRNLAA---AEETECCICLGVFADGE 117

Query: 116 KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSITTQ 161
           K+K+LP C H +HCECVD WL+  S+CPLCR SL++DS+ P I  Q
Sbjct: 118 KLKVLPGCDHSFHCECVDKWLANHSNCPLCRASLKLDSSFPRILIQ 163

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553773|ref|XP_003545227.1| PREDICTED: RING-H2 finger protein ATL66-like [Glycine max]

 Score =  144 bits (364), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 83/167 (49%), Positives = 112/167 (67%), Gaps = 14/167 (8%)

Query: 1   MASQESQPFHWHY-TELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQN 59
           M+ ++S+  +WHY TELDD   +IRGR LF IIV+F+++LL + LF++AR  CRR  H +
Sbjct: 1   MSIRDSESLNWHYDTELDDETLEIRGRKLFFIIVLFSIILLFTALFVFARRICRRRHHHH 60

Query: 60  SN---PD-VPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGD 115
           +    PD VP  Q     GLD   I  LPIVLH      + ++  E+ECCICLG F DG+
Sbjct: 61  NGLLLPDAVPPPQNT---GLDSAAIKRLPIVLH-----PRCNRVAEAECCICLGAFADGE 112

Query: 116 KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD-SALPSITTQ 161
           K+K+LP C H +HCECVD WL+  S+CPLCR SL++D S+ P+I  Q
Sbjct: 113 KLKVLPGCDHSFHCECVDKWLTNHSNCPLCRASLKLDSSSFPAILIQ 159

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	161
TAIR|locus:2074678	158	AT3G11110 [Arabidopsis thalian	0.919	0.936	0.421	6.4e-28
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.577	0.513	0.391	4.7e-16
TAIR|locus:2097890	349	AT3G48030 "AT3G48030" [Arabido	0.559	0.257	0.386	1.5e-14
TAIR|locus:2044742	302	AT2G34990 [Arabidopsis thalian	0.621	0.331	0.373	4.8e-14
TAIR|locus:2096309	398	ATL6 "Arabidopsis toxicos en l	0.490	0.198	0.4	1.7e-13
TAIR|locus:2044757	378	ATL9 "Arabidopsis toxicos en l	0.590	0.251	0.354	1.9e-13
TAIR|locus:2057861	237	AT2G27940 [Arabidopsis thalian	0.484	0.329	0.404	3.4e-13
TAIR|locus:2118666	472	AT4G30400 [Arabidopsis thalian	0.472	0.161	0.405	4.3e-13
TAIR|locus:2206722	327	AT1G35330 [Arabidopsis thalian	0.478	0.235	0.397	4.4e-13
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.285	0.289	0.565	4.4e-13

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

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 64/152 (42%), Positives = 77/152 (50%)

Query:     4 QESQPFHWHYTELDDHNFQIRGRTXXXXXXXXXXXXXXXXXXXYARWFCRRFSHQNSNPD 63
             Q S   +WH  + DD NFQI GRT                   Y    C      N +  
Sbjct:     9 QASMLLYWHENQYDDRNFQIHGRTLFFALALFSVVLFFALLTLYIHRNCLPRDSINLHAS 68

Query:    64 VP-RAQQALTRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKILPK 122
              P R  +  + GLD   I +LP+VL R              CCICLG FE+G+K+K+LP 
Sbjct:    69 SPDRLTRCRSGGLDPAEIRSLPVVLCRRERAEEEEEKE---CCICLGGFEEGEKMKVLPP 125

Query:   123 CRHCYHCECVDAWLSARSSCPLCRNSLRVDSA 154
             C HCYHCECVD WL   SSCPLCR S+RVDS+
Sbjct:   126 CSHCYHCECVDRWLKTESSCPLCRVSIRVDSS 157

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2103162 DAFL1 "DAF-Like gene 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 38/97 (39%), Positives = 52/97 (53%)

Query:    60 SNPDVPRAQQALTRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKI 119
             SN +    + A   GL    +  +P+ L+               C ICLG FEDG+KV++
Sbjct:    74 SNANANLGRLAAATGLKKQALKQIPVGLY----GSGIIDMKATECLICLGDFEDGEKVRV 129

Query:   120 LPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP 156
             LPKC H +H  C+D WL +RSSCP CR SL ++   P
Sbjct:   130 LPKCNHGFHVRCIDTWLLSRSSCPTCRQSLLLEQPSP 166

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:2097890 AT3G48030 "AT3G48030" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 1.5e-14, P = 1.5e-14
 Identities = 39/101 (38%), Positives = 52/101 (51%)

Query:    57 HQNSNPDV-----PRAQQAL---TRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICL 108
             H N NPD+     P+ Q        GLD T I+ LP+ L+               C +CL
Sbjct:   155 HFNYNPDLFSFSSPQLQHLFFLHDSGLDQTAIDALPVFLY---GNVTISLEQPFDCAVCL 211

Query:   109 GVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
               F D DK+++LP C H +H  C+D WL + S+CPLCR SL
Sbjct:   212 NEFSDTDKLRLLPVCSHAFHLHCIDTWLLSNSTCPLCRRSL 252

GO:0001666 "response to hypoxia" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2044742 AT2G34990 [Arabidopsis thaliana (taxid:3702)]

 Score = 183 (69.5 bits), Expect = 4.8e-14, P = 4.8e-14
 Identities = 40/107 (37%), Positives = 54/107 (50%)

Query:    49 RWFCRRFSHQNS-NP----DVP-RAQQALTRGLDLTTINTLPIVLHRXXXXXXXXXXXXX 102
             RW  R+F  Q S NP    DV  R      RGLD   IN+ P  L+              
Sbjct:    36 RWTSRQFYSQESINPFTDSDVESRTSITAVRGLDEAIINSFPTFLY-SEVKERRIGIGGV 94

Query:   103 XCCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
              C +C+  FED + ++++P+C H +H +CV  WLS  S+CPLCR  L
Sbjct:    95 ECAVCICEFEDHETLRLMPECCHVFHADCVSVWLSDHSTCPLCRVDL 141

GO:0005576 "extracellular region" evidence=ISM

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

GO:0006863 "purine nucleobase transport" evidence=RCA

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

 Score = 182 (69.1 bits), Expect = 1.7e-13, P = 1.7e-13
 Identities = 32/80 (40%), Positives = 45/80 (56%)

Query:    70 ALTRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKILPKCRHCYHC 129
             A  RGLD++ + T P  L+               C ICL  FED + +++LPKC H +H 
Sbjct:    95 AAARGLDVSVVETFPTFLY-SDVKTQKLGKGELECAICLNEFEDDETLRLLPKCDHVFHP 153

Query:   130 ECVDAWLSARSSCPLCRNSL 149
              C+DAWL A  +CP+CR +L
Sbjct:   154 HCIDAWLEAHVTCPVCRANL 173

GO:0005576 "extracellular region" evidence=ISM

GO:0008270 "zinc ion binding" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

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

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

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

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2044757 ATL9 "Arabidopsis toxicos en levadura 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 1.9e-13, P = 1.9e-13
 Identities = 34/96 (35%), Positives = 49/96 (51%)

Query:    54 RFSHQNSNPDVPRAQQALTRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFED 113
             R +  ++   V R ++   RGLD   I T P  L+               C +CL  FED
Sbjct:    86 RSTDADAESQVVRIRRLTARGLDAEAIETFPTFLY-SEVKAVRIGKGGVECAVCLCEFED 144

Query:   114 GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
              + ++++P C H +H +CVD WLS  S+CPLCR  L
Sbjct:   145 DETLRLMPPCCHVFHADCVDVWLSEHSTCPLCRADL 180

GO:0005576 "extracellular region" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0010200 "response to chitin" evidence=IEP

GO:0050832 "defense response to fungus" evidence=IMP

GO:0048765 "root hair cell differentiation" evidence=RCA

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

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 34/84 (40%), Positives = 46/84 (54%)

Query:    73 RGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKILPKCRHCYHCECV 132
             RGLD   + +LP+  +               C ICL  FE+G+ VK++P C H +H +CV
Sbjct:   114 RGLDSQAVRSLPVYRY-----TKAAKQRNEDCVICLSDFEEGETVKVIPHCGHVFHVDCV 168

Query:   133 DAWLSARSSCPLCR-NSLRVDSAL 155
             D WLS+  +CPLCR N L  D  L
Sbjct:   169 DTWLSSYVTCPLCRSNQLFSDKDL 192

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

TAIR|locus:2118666 AT4G30400 [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 4.3e-13, P = 4.3e-13
 Identities = 32/79 (40%), Positives = 48/79 (60%)

Query:    74 GLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKILPKCRHCYHCECVD 133
             G+D + I+TLP+  ++              C +CL  FE  DK+++LPKC H +H +C+D
Sbjct:   107 GVDQSFIDTLPVFHYKSIIGLKNYPFD---CAVCLCEFETEDKLRLLPKCSHAFHMDCID 163

Query:   134 AWLSARSSCPLCRNSLRVD 152
              WL + S+CPLCR+SL  D
Sbjct:   164 TWLLSHSTCPLCRSSLLSD 182

GO:0005634 "nucleus" evidence=ISM

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

GO:0080167 "response to karrikin" evidence=IEP

TAIR|locus:2206722 AT1G35330 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 31/78 (39%), Positives = 44/78 (56%)

Query:    72 TRGLDLTTINTLPIVLHRXXXXXXXXXXXXXXCCICLGVFEDGDKVKILPKCRHCYHCEC 131
             +RGL    IN+ P  L+               C ICL  FED + ++++P C H +H  C
Sbjct:    97 SRGLGKDVINSFPSFLY-SQVKGLKIGKGGVECAICLNEFEDEETLRLMPPCSHAFHASC 155

Query:   132 VDAWLSARSSCPLCRNSL 149
             +D WLS+RS+CP+CR SL
Sbjct:   156 IDVWLSSRSTCPVCRASL 173

GO:0005576 "extracellular region" evidence=ISM

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

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

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 26/46 (56%), Positives = 34/46 (73%)

Query:   104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
             C ICLG F DG++V++LP C H +H  C+D WL + SSCP CR+SL
Sbjct:   105 CAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHSSCPNCRHSL 150

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SRM0	ATL66_ARATH	No assigned EC number	0.4743	0.9192	0.9367	yes	no

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: fgenesh4_pg.C_LG_VIII000612 hypothetical protein (164 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	161
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-12
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-08
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-08
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	8e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-05
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	7e-05
smart00184	40	smart00184, RING, Ring finger	6e-04
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	9e-04
PHA02926	242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.002
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.002

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

 Score = 58.6 bits (142), Expect = 1e-12
 Identities = 24/44 (54%), Positives = 32/44 (72%), Gaps = 1/44 (2%)

Query: 103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           EC ICL  FE G++V +LP C H +H EC+D WL + ++CPLCR
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 52.1 bits (125), Expect = 1e-08
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 81  NTLPIVLHRSEKSTKDDKEEESECCICL-GVFEDGDKVK---ILPKCRHCYHCECVDAWL 136
            T+P VL   EK     K++E  C IC+  V++   K     IL  C H +  EC+D W 
Sbjct: 156 KTIPSVLSEYEKLYNRSKDKE--CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWK 213

Query: 137 SARSSCPLCRN 147
             +++CP+CR 
Sbjct: 214 KEKNTCPVCRT 224

Length = 238

>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 = 46.7 bits (111), Expect = 4e-08
 Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 4/48 (8%)

Query: 103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSL 149
           EC ICL  F +     +L  C H +   C+D WL +   +CPLCR  +
Sbjct: 1   ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 50.8 bits (121), Expect = 4e-08
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 2/48 (4%)

Query: 103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSL 149
           EC IC+  F   D++++LP C H +H  CVD WL    + CP+CR ++
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 42.1 bits (99), Expect = 2e-06
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           EE EC ICL +  D     +L  C H +  EC+  +L  +S CP+CR
Sbjct: 1   EELECPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 44.3 bits (104), Expect = 8e-06
 Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 5/52 (9%)

Query: 103  ECCICLGVFEDGDKV---KILPKCRHCYHCECVDAWL--SARSSCPLCRNSL 149
            EC IC  V +  D+    K    C++ +H  C+  W   SARS+CPLCR+ +
Sbjct: 1471 ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

Length = 1525

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

 Score = 42.3 bits (99), Expect = 4e-05
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 11/67 (16%)

Query: 104 CCICL-GVFEDGD---------KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS 153
           C IC+  +F               K LP C H  H  C+  WL  + +CP+CR  +  D 
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIFDQ 348

Query: 154 ALPSITT 160
           + P+  +
Sbjct: 349 SSPTPAS 355

Length = 491

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

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 9/56 (16%)

Query: 100 EESECCICLGVFED---------GDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           E+  C IC   F+           D   +  +C H +H  C+  WL  R++CPLCR
Sbjct: 18  EDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 35.6 bits (82), Expect = 6e-04
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLC 145
           C ICL  +       ILP C H +   C+  WL + + +CP+C
Sbjct: 1   CPICLEEYLK--DPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 36.4 bits (84), Expect = 9e-04
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 103 ECCI-CLGVFEDGDKVKIL-PKCRHCYHCECVDAWLSARSSCPLCR 146
             C  C      GD+  ++   C H +H  C+  WL  +  CPL R
Sbjct: 32  GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 37.3 bits (86), Expect = 0.002
 Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 15/88 (17%)

Query: 76  DLTTINTLPIV--LHRSEKSTKDDKEEESECCICLGV-----FEDGDKVKILPKCRHCYH 128
           + TTI+ L I+  L + E   +  KE+E  C IC  V      E+     +L  C H + 
Sbjct: 145 NTTTISELDIIKILDKYEDVYRVSKEKE--CGICYEVVYSKRLENDRYFGLLDSCNHIFC 202

Query: 129 CECVDAWLSAR------SSCPLCRNSLR 150
             C++ W   R       +CP+CR   R
Sbjct: 203 ITCINIWHRTRRETGASDNCPICRTRFR 230

Length = 242

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 119 ILPKCRHCYHCECVDAWLSARSS---CPLCRNSLRV 151
           +  KC+H +H  C+  WL+  +S   CP+CR +   
Sbjct: 48  VWGKCKHNFHMHCILKWLATETSKGLCPMCRQTFVF 83

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	161
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.92
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.82
PHA02929	238	N1R/p28-like protein; Provisional	99.71
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.68
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.67
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.57
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.49
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.49
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.47
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.46
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.44
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.42
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.39
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.35
PHA02926	242	zinc finger-like protein; Provisional	99.33
PF14634	44	zf-RING_5: zinc-RING finger domain	99.32
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.26
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.24
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.23
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.22
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.2
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.16
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	99.07
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.05
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	99.04
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.04
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.98
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.98
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.82
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.82
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.81
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.78
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.72
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.71
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.71
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.69
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.67
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.65
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.63
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.62
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.49
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.48
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.46
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.34
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.34
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.27
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.26
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	98.09
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.01
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.95
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.94
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.9
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.88
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.85
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.8
PHA02862	156	5L protein; Provisional	97.72
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.56
KOG2660	331	consensus Locus-specific chromosome binding protei	97.51
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.5
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.47
KOG4739	233	consensus Uncharacterized protein involved in syna	97.47
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.42
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.41
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.38
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.31
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.19
COG5152	259	Uncharacterized conserved protein, contains RING a	97.19
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.15
PHA03096	284	p28-like protein; Provisional	97.15
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.14
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.12
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.03
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.91
PF04641	260	Rtf2: Rtf2 RING-finger	96.89
KOG1940	276	consensus Zn-finger protein [General function pred	96.88
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.87
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.78
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.74
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.68
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.51
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	96.28
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.12
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.11
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.04
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.96
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	95.89
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.84
KOG1001	674	consensus Helicase-like transcription factor HLTF/	95.76
PHA02975	69	hypothetical protein; Provisional	95.61
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.56
KOG1609	323	consensus Protein involved in mRNA turnover and st	95.27
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.22
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.22
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	95.13
PF08114	43	PMP1_2: ATPase proteolipid family; InterPro: IPR01	95.07
PHA02650	81	hypothetical protein; Provisional	95.03
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.9
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	94.78
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	94.29
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	94.29
KOG3053	293	consensus Uncharacterized conserved protein [Funct	94.01
PHA02819	71	hypothetical protein; Provisional	93.36
PHA02844	75	putative transmembrane protein; Provisional	93.31
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	93.22
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	93.06
PF12575	72	DUF3753: Protein of unknown function (DUF3753); In	92.71
PHA03054	72	IMV membrane protein; Provisional	92.47
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.29
KOG3002	299	consensus Zn finger protein [General function pred	92.19
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	92.14
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	91.8
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	91.47
KOG0825	1134	consensus PHD Zn-finger protein [General function	90.94
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	90.72
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	90.6
PHA02692	70	hypothetical protein; Provisional	90.58
PRK01844	72	hypothetical protein; Provisional	90.52
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	90.4
KOG1829	580	consensus Uncharacterized conserved protein, conta	90.34
KOG0269	839	consensus WD40 repeat-containing protein [Function	90.1
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.09
PF15102	146	TMEM154: TMEM154 protein family	90.06
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	89.61
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	89.53
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	89.49
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.04
PRK00523	72	hypothetical protein; Provisional	88.81
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	87.85
COG3763	71	Uncharacterized protein conserved in bacteria [Fun	87.4
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	87.34
PF05715	61	zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899	86.89
KOG3005	276	consensus GIY-YIG type nuclease [General function	86.69
PF03911	41	Sec61_beta: Sec61beta family; InterPro: IPR005609	86.64
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	86.28
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	85.22
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	85.01
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	84.74
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	84.15
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	83.18
KOG4367	699	consensus Predicted Zn-finger protein [Function un	83.03
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	82.51
KOG3457	88	consensus Sec61 protein translocation complex, bet	82.18
PF04710	416	Pellino: Pellino; InterPro: IPR006800 Pellino is i	81.84
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	81.41
TIGR01478	295	STEVOR variant surface antigen, stevor family. Thi	81.39
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	81.09
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	80.67
PF03672	64	UPF0154: Uncharacterised protein family (UPF0154);	80.37

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

Probab=99.92  E-value=7.9e-25  Score=165.21  Aligned_cols=81  Identities=35%  Similarity=0.826  Sum_probs=68.1

Q ss_pred             cCCCCHHHHhcCCcEeeecCCCCCCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC-CCcccccccc
Q 031354           72 TRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSLR  150 (161)
Q Consensus        72 ~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~  150 (161)
                      .+.+.+..+.++|...|.....  +...  +.||||||+|++||.+|.|| |+|.||..|||+||..+. .||+||+++.
T Consensus       204 ~~r~~k~~l~~~p~~~f~~~~~--~~~~--~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  204 RNRLIKRLLKKLPVRTFTKGDD--EDAT--DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             hhhhHHHHHhhCCcEEeccccc--cCCC--ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            3567788999999999987662  2222  79999999999999999999 999999999999998774 5999999998


Q ss_pred             CCCCCCC
Q 031354          151 VDSALPS  157 (161)
Q Consensus       151 ~~~~~~~  157 (161)
                      .....+.
T Consensus       279 ~~~~~~~  285 (348)
T KOG4628|consen  279 TDSGSEP  285 (348)
T ss_pred             CCCCCCC
Confidence            7665543

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

Probab=99.82  E-value=3.6e-21  Score=105.54  Aligned_cols=44  Identities=55%  Similarity=1.265  Sum_probs=40.7

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccc
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR  146 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  146 (161)
                      ++|+||+++|.+++.+..++ |||+||.+||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            47999999999999999999 999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.71  E-value=8.7e-18  Score=122.12  Aligned_cols=77  Identities=30%  Similarity=0.685  Sum_probs=59.6

Q ss_pred             cCCCCHHHHhcCCcEeeecCCCCCCCCCCCCccccccccccCCCe----eeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354           72 TRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDK----VKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus        72 ~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~~~CaICL~~f~~~~~----v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      .++..+..++.+|.+..+...  ......+.+|+||++++.+++.    +.++++|||.||.+||.+|+..+.+||+||.
T Consensus       147 k~~~~~~~i~~lp~vl~~~e~--~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~  224 (238)
T PHA02929        147 KGKNYKKFLKTIPSVLSEYEK--LYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT  224 (238)
T ss_pred             hcchhHHHHHhcchhhhhhhh--hhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCC
Confidence            456678889999988655433  2233457899999999876542    3345459999999999999999999999999


Q ss_pred             ccc
Q 031354          148 SLR  150 (161)
Q Consensus       148 ~l~  150 (161)
                      ++.
T Consensus       225 ~~~  227 (238)
T PHA02929        225 PFI  227 (238)
T ss_pred             Eee
Confidence            875

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

Probab=99.68  E-value=3.3e-17  Score=99.06  Aligned_cols=46  Identities=37%  Similarity=0.988  Sum_probs=36.9

Q ss_pred             CCCccccccccccC----------CCeeeecCCCCCccchhhHHHHHcCCCCCcccc
Q 031354          100 EESECCICLGVFED----------GDKVKILPKCRHCYHCECVDAWLSARSSCPLCR  146 (161)
Q Consensus       100 ~~~~CaICL~~f~~----------~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  146 (161)
                      .++.|+||+++|.+          +-.+...+ |||.||..||.+||+.+.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            35569999999943          23555567 999999999999999999999998

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

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

Probab=99.67  E-value=3.7e-17  Score=120.12  Aligned_cols=51  Identities=39%  Similarity=1.053  Sum_probs=46.9

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~  151 (161)
                      ...+||||+++|-++|.+++|| |.|.||..|+++|+. -+..||+||.++.+
T Consensus       322 ~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4589999999999999999999 999999999999998 56779999999875

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

Probab=99.57  E-value=1.5e-15  Score=114.55  Aligned_cols=55  Identities=31%  Similarity=0.849  Sum_probs=45.9

Q ss_pred             CCCCCCCCcccccccc-ccCCC---------eeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           95 KDDKEEESECCICLGV-FEDGD---------KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~-f~~~~---------~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ++..+++..|+||+|| |..+.         .-..|| |||+||-+|+..|++++++||+||.++.
T Consensus       281 eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         281 EQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhhcCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            3446778899999999 66542         335688 9999999999999999999999999964

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.49  E-value=1.9e-14  Score=100.79  Aligned_cols=57  Identities=26%  Similarity=0.716  Sum_probs=44.1

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----------------CCCCccccccccCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----------------RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~~~~  156 (161)
                      ....++.+|+||++.+++   ..+++ |||.||+.||.+|+..                +.+||+||.++......|
T Consensus        13 ~~~~~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP   85 (193)
T PLN03208         13 VDSGGDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP   85 (193)
T ss_pred             ccCCCccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence            344567899999999864   34577 9999999999999852                347999999997654443

>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=99.49  E-value=2.5e-14  Score=80.36  Aligned_cols=46  Identities=37%  Similarity=0.927  Sum_probs=39.9

Q ss_pred             CCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCcccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      +..|.||++...+   +..+| |||. |+..|+.+|++.+..||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999999665   77889 9999 999999999999999999999885

...

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

Probab=99.47  E-value=6.4e-14  Score=102.72  Aligned_cols=53  Identities=28%  Similarity=0.782  Sum_probs=45.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      ......|.+|||...+   ..-+| |||+||+.||.+|+..+..||+||....+...
T Consensus       236 ~~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            4455799999998654   66788 99999999999999999999999999877653

>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=99.46  E-value=4.9e-14  Score=75.01  Aligned_cols=39  Identities=38%  Similarity=1.049  Sum_probs=33.6

Q ss_pred             cccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  145 (161)
                      |+||++++.+  .+..++ |||+|+.+|+.+|++.+.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999876  556788 99999999999999998999998

>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=99.44  E-value=8.5e-14  Score=76.04  Aligned_cols=44  Identities=45%  Similarity=1.193  Sum_probs=37.7

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSL  149 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l  149 (161)
                      .|+||++.+  .+.+...+ |||.||..|++.|++. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  45566677 9999999999999987 77899999764

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

Probab=99.42  E-value=1.5e-13  Score=83.89  Aligned_cols=52  Identities=35%  Similarity=0.929  Sum_probs=39.8

Q ss_pred             CCCccccccccccC--------CCee-eecCCCCCccchhhHHHHHcC---CCCCccccccccC
Q 031354          100 EESECCICLGVFED--------GDKV-KILPKCRHCYHCECVDAWLSA---RSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~--------~~~v-~~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~l~~  151 (161)
                      +++.|.||...|..        |+.. .++..|+|.||..||.+|+..   +..||+||++...
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            47899999999883        3321 123349999999999999985   4679999998653

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

Probab=99.39  E-value=1.4e-13  Score=98.12  Aligned_cols=55  Identities=31%  Similarity=0.840  Sum_probs=43.7

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC---CCCccccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR---SSCPLCRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~~~~~~~  156 (161)
                      .....+|.||||.  .+|.| ++. |||.||+.||-+||+.+   +.||+||..+..+.-+|
T Consensus        44 ~~~~FdCNICLd~--akdPV-vTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP  101 (230)
T KOG0823|consen   44 DGGFFDCNICLDL--AKDPV-VTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP  101 (230)
T ss_pred             CCCceeeeeeccc--cCCCE-Eee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence            4667899999998  44555 444 99999999999999864   56999999997665444

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

Probab=99.35  E-value=2.9e-13  Score=110.34  Aligned_cols=55  Identities=33%  Similarity=0.777  Sum_probs=47.5

Q ss_pred             CCCCCCccccccccccCCCe--eeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354           97 DKEEESECCICLGVFEDGDK--VKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~--v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      ....++.|+||+|++..++.  ...+| |||+||..|+.+|++++++||+||..+...
T Consensus       287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  287 LALSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hhhcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            34558899999999998765  77889 999999999999999999999999955433

>PHA02926 zinc finger-like protein; Provisional

Probab=99.33  E-value=8.8e-13  Score=93.63  Aligned_cols=53  Identities=32%  Similarity=0.839  Sum_probs=41.1

Q ss_pred             CCCCCccccccccccCC-----CeeeecCCCCCccchhhHHHHHcCC------CCCcccccccc
Q 031354           98 KEEESECCICLGVFEDG-----DKVKILPKCRHCYHCECVDAWLSAR------SSCPLCRNSLR  150 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~-----~~v~~lp~C~H~FH~~Ci~~Wl~~~------~~CP~CR~~l~  150 (161)
                      ...+.+|+||+|..-++     ....+|++|+|.||..||..|...+      .+||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            45678999999986432     2344676799999999999999753      35999998875

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.32  E-value=1.5e-12  Score=71.05  Aligned_cols=44  Identities=23%  Similarity=0.782  Sum_probs=38.8

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      .|.||+++|.++...++++ |||+|+..|+.++......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4999999996667788888 9999999999999866678999985

>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=99.26  E-value=2.8e-12  Score=68.91  Aligned_cols=39  Identities=49%  Similarity=1.200  Sum_probs=33.2

Q ss_pred             cccccccccCCCeeeecCCCCCccchhhHHHHHc--CCCCCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS--ARSSCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~--~~~~CP~C  145 (161)
                      |+||++.+.+.  ++.++ |||.|+..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999997753  35788 999999999999998  45679998

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 ....

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

Probab=99.24  E-value=4.2e-12  Score=87.10  Aligned_cols=56  Identities=27%  Similarity=0.596  Sum_probs=45.3

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      .....-..|+|||+.+.+...+ -+. |||+||..||..-++....||+||..|..+.
T Consensus       126 ~~~~~~~~CPiCl~~~sek~~v-sTk-CGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  126 LRKEGTYKCPICLDSVSEKVPV-STK-CGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccccccCCCceecchhhcccc-ccc-cchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            3344458999999999876554 245 9999999999999999999999998776543

>smart00184 RING Ring finger

Probab=99.23  E-value=7.9e-12  Score=65.85  Aligned_cols=38  Identities=37%  Similarity=1.048  Sum_probs=32.7

Q ss_pred             cccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~C  145 (161)
                      |+||++.   ......++ |||.||..|++.|+. .+..||+|
T Consensus         1 C~iC~~~---~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899998   34577888 999999999999998 56779987

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

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

Probab=99.22  E-value=1.1e-11  Score=66.78  Aligned_cols=38  Identities=39%  Similarity=0.945  Sum_probs=29.2

Q ss_pred             cccccccccCCCeeeecCCCCCccchhhHHHHHcCC----CCCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR----SSCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~----~~CP~C  145 (161)
                      |+||++.|.+   -..|+ |||.|+..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999986   55788 99999999999999764    359988

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

Probab=99.20  E-value=8.6e-12  Score=74.18  Aligned_cols=52  Identities=29%  Similarity=0.749  Sum_probs=37.9

Q ss_pred             Ccccccccccc-----------CCCeee-ecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354          102 SECCICLGVFE-----------DGDKVK-ILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus       102 ~~CaICL~~f~-----------~~~~v~-~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      +.|+||...|-           .+++.. +-..|+|.||..||..||..+..||++|+......
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            56777765443           344332 22239999999999999999999999999876543

>smart00504 Ubox Modified RING finger domain

Probab=99.16  E-value=3.4e-11  Score=70.68  Aligned_cols=51  Identities=27%  Similarity=0.563  Sum_probs=42.9

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ..|+||++.+.+  . .+++ |||+|...||.+|++.+.+||+|+.++...+..+
T Consensus         2 ~~Cpi~~~~~~~--P-v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKD--P-VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCC--C-EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhhcee
Confidence            469999999876  3 3578 9999999999999998889999999986655444

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

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

Probab=99.07  E-value=2.9e-11  Score=88.00  Aligned_cols=56  Identities=21%  Similarity=0.657  Sum_probs=45.6

Q ss_pred             CCCCCCCccccccccccCCC-------eeeecCCCCCccchhhHHHHHc--CCCCCccccccccCC
Q 031354           96 DDKEEESECCICLGVFEDGD-------KVKILPKCRHCYHCECVDAWLS--ARSSCPLCRNSLRVD  152 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~-------~v~~lp~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~l~~~  152 (161)
                      ....++..||||-..+....       ....|. |+|+||..||.-|..  ++++||.|+..+..+
T Consensus       219 tkhl~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  219 TKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CCCCCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            34567889999988877655       667888 999999999999976  578999998877644

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.05  E-value=1.4e-10  Score=90.27  Aligned_cols=51  Identities=27%  Similarity=0.666  Sum_probs=43.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      ......|+||++.|.+   ..+++ |||.||..||..|+..+..||+||..+...
T Consensus        23 Le~~l~C~IC~d~~~~---Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFDV---PVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhhC---ccCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            4456799999999864   23678 999999999999999888899999988654

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

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

Probab=99.04  E-value=1.5e-10  Score=64.31  Aligned_cols=42  Identities=29%  Similarity=0.841  Sum_probs=33.0

Q ss_pred             ccccccccccCCCeeeecCCCC-----CccchhhHHHHHcC--CCCCcccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCR-----HCYHCECVDAWLSA--RSSCPLCR  146 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~-----H~FH~~Ci~~Wl~~--~~~CP~CR  146 (161)
                      .|.||+++.. ++...+.| |.     |.+|..|+++|+..  +.+||+|+
T Consensus         1 ~CrIC~~~~~-~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGD-EGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCC-CCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999444 44455789 85     99999999999965  45899995

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

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

Probab=99.04  E-value=3.2e-11  Score=71.18  Aligned_cols=50  Identities=32%  Similarity=0.923  Sum_probs=36.9

Q ss_pred             CCccccccccccC--------CCeee-ecCCCCCccchhhHHHHHcCC---CCCcccccccc
Q 031354          101 ESECCICLGVFED--------GDKVK-ILPKCRHCYHCECVDAWLSAR---SSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~--------~~~v~-~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~  150 (161)
                      ++.|-||...|..        ||..- ++--|.|.||..||.+|+...   ..||+||+...
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            3489999988874        33221 222399999999999999753   46999998754

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

Probab=98.98  E-value=2.3e-10  Score=83.26  Aligned_cols=51  Identities=27%  Similarity=0.676  Sum_probs=41.9

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHH-HHcCCCC-CccccccccCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDA-WLSARSS-CPLCRNSLRVDS  153 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~-Wl~~~~~-CP~CR~~l~~~~  153 (161)
                      ..+..|+||+++...   ...+| |||+|+..||.. |-.++.. ||+||+...++.
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            456789999998654   55677 999999999999 9877765 999999887654

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

Probab=98.98  E-value=1.7e-10  Score=90.28  Aligned_cols=51  Identities=29%  Similarity=0.853  Sum_probs=39.9

Q ss_pred             CCCccccccccccC---CC-------e----eeecCCCCCccchhhHHHHHc-CCCCCccccccccC
Q 031354          100 EESECCICLGVFED---GD-------K----VKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~---~~-------~----v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~  151 (161)
                      .-..|+||+.+..-   +.       .    -.++| |.|+||..|+.+|+. .+-.||+||+++.+
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            34689999987653   11       1    22458 999999999999999 56689999999864

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

Probab=98.82  E-value=3.4e-09  Score=57.04  Aligned_cols=38  Identities=29%  Similarity=0.768  Sum_probs=22.4

Q ss_pred             cccccccccC-CCeeeecCCCCCccchhhHHHHHcCC----CCCc
Q 031354          104 CCICLGVFED-GDKVKILPKCRHCYHCECVDAWLSAR----SSCP  143 (161)
Q Consensus       104 CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl~~~----~~CP  143 (161)
                      |+||.+ |.+ ...-.+|+ |||+|+.+||++++...    -.||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 755 34556799 99999999999999843    2477

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

Probab=98.82  E-value=1.8e-09  Score=85.11  Aligned_cols=52  Identities=29%  Similarity=0.749  Sum_probs=40.1

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC-----CCCccccccccCCCCCC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR-----SSCPLCRNSLRVDSALP  156 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~l~~~~~~~  156 (161)
                      +..|+|||++..    +-++..|||+||..||-+++...     ..||+||..|...+..|
T Consensus       186 ~~~CPICL~~~~----~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p  242 (513)
T KOG2164|consen  186 DMQCPICLEPPS----VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP  242 (513)
T ss_pred             CCcCCcccCCCC----cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence            789999999854    33333399999999999988642     46999999998755443

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

Probab=98.81  E-value=2.4e-09  Score=83.15  Aligned_cols=53  Identities=30%  Similarity=0.821  Sum_probs=43.3

Q ss_pred             CCCCCCCCccccccccccCCC-eeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           95 KDDKEEESECCICLGVFEDGD-KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~-~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      .....+.+.|+||||.+.+.- .++... |.|.||..|+.+|..  .+||+||....
T Consensus       169 ~~~~tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  169 PTGLTELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             CCCcccCCCcchhHhhcCccccceeeee-cccccchHHHhhccc--CcChhhhhhcC
Confidence            455667889999999987654 455666 999999999999964  67999998766

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

Probab=98.78  E-value=1.2e-09  Score=65.36  Aligned_cols=51  Identities=29%  Similarity=0.742  Sum_probs=24.6

Q ss_pred             CCccccccccccCCC--eeeecC--CCCCccchhhHHHHHcC----C-------CCCccccccccC
Q 031354          101 ESECCICLGVFEDGD--KVKILP--KCRHCYHCECVDAWLSA----R-------SSCPLCRNSLRV  151 (161)
Q Consensus       101 ~~~CaICL~~f~~~~--~v~~lp--~C~H~FH~~Ci~~Wl~~----~-------~~CP~CR~~l~~  151 (161)
                      +.+|.||.+.+.+++  ...+-+  .|++.||..||.+||+.    +       .+||.|+.+|.-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            458999999876333  223332  59999999999999963    1       259999998854

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.72  E-value=1.1e-08  Score=76.90  Aligned_cols=54  Identities=26%  Similarity=0.483  Sum_probs=40.0

Q ss_pred             CCcccccccc--ccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCC
Q 031354          101 ESECCICLGV--FEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSAL  155 (161)
Q Consensus       101 ~~~CaICL~~--f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  155 (161)
                      +..|++|..+  +.+.-.+.+.+ |||.||..|++..+.. ...||.|+.++....-.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            4689999995  32222334446 9999999999996654 56799999998877633

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).

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

Probab=98.71  E-value=4.4e-09  Score=79.13  Aligned_cols=51  Identities=27%  Similarity=0.682  Sum_probs=43.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      ...-..|.||.|.|..   -.++| |+|.||.-||...|..+..||.|+.++.+.
T Consensus        20 lD~lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             hHHHHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            3445689999999975   45677 999999999999999999999999887543

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

Probab=98.71  E-value=6.9e-09  Score=64.93  Aligned_cols=28  Identities=36%  Similarity=1.020  Sum_probs=25.7

Q ss_pred             CCCCccchhhHHHHHcCCCCCccccccc
Q 031354          122 KCRHCYHCECVDAWLSARSSCPLCRNSL  149 (161)
Q Consensus       122 ~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  149 (161)
                      .|+|.||-.||..||+.+..||+|.++-
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            3999999999999999999999998764

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

Probab=98.69  E-value=1.1e-08  Score=77.71  Aligned_cols=49  Identities=35%  Similarity=0.819  Sum_probs=41.8

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      +...+|.|||.+-.+   ..+|| |.|. .|..|-+...-.+..||+||+++..
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            446799999999665   77999 9997 9999999976567789999999864

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

Probab=98.67  E-value=8.8e-09  Score=78.72  Aligned_cols=48  Identities=25%  Similarity=0.803  Sum_probs=36.9

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC---CCCcccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR---SSCPLCRNS  148 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~  148 (161)
                      ...|.||.+-+.....+.-+..|||+||..|+.+|+..-   .+||.||-.
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik   54 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIK   54 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeec
Confidence            357999955555555666555699999999999999853   479999933

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

Probab=98.65  E-value=4.9e-09  Score=87.83  Aligned_cols=56  Identities=32%  Similarity=0.829  Sum_probs=40.7

Q ss_pred             CCCCCCCCccccccccccCCC---eeeecCCCCCccchhhHHHHHcC--CCCCcccccccc
Q 031354           95 KDDKEEESECCICLGVFEDGD---KVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNSLR  150 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~---~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~  150 (161)
                      .....+.++||||..-+..-|   .-...|+|.|-||..|+-+|++.  +.+||+||.++.
T Consensus      1463 ~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1463 DEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            445566889999988765211   11123348899999999999985  567999998764

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

Probab=98.63  E-value=2e-08  Score=60.68  Aligned_cols=54  Identities=28%  Similarity=0.546  Sum_probs=40.4

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~~  157 (161)
                      +...|+|+.+-|.+   -.++| +||.|-..||.+|+.. +.+||+|+.++...+.+|.
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn   57 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN   57 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence            34689999999875   44678 9999999999999998 7899999999987766553

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 ....

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

Probab=98.62  E-value=1.2e-08  Score=75.57  Aligned_cols=55  Identities=25%  Similarity=0.800  Sum_probs=45.4

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----------------------CCCCccccccccCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----------------------RSSCPLCRNSLRVD  152 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----------------------~~~CP~CR~~l~~~  152 (161)
                      .......|+|||.-|.+++...+++ |.|+||..|+..+|..                       +..||+||..|..+
T Consensus       111 nn~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  111 NNHPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            3444669999999999999999999 9999999998877621                       23599999998755

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

Probab=98.49  E-value=6.6e-08  Score=71.50  Aligned_cols=49  Identities=22%  Similarity=0.483  Sum_probs=40.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ...-..|-||-+.|..   -..++ |||.||.-||...|..+..||+||.+..
T Consensus        22 LDs~lrC~IC~~~i~i---p~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          22 LDSMLRCRICDCRISI---PCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             chhHHHhhhhhheeec---ceecc-cccchhHHHHHHHhcCCCCCccccccHH
Confidence            4456689999887763   23455 9999999999999999999999998754

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

Probab=98.48  E-value=5.1e-08  Score=73.71  Aligned_cols=47  Identities=36%  Similarity=0.780  Sum_probs=40.6

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      ...+...|+||++.|.+-   .++| |||.|+..|+..++.....||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            445677999999999986   7889 9999999999999985567999993

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

Probab=98.46  E-value=2.7e-08  Score=82.04  Aligned_cols=53  Identities=25%  Similarity=0.470  Sum_probs=46.4

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      .....|++||..+.++......+ |+|+||..|++.|-+.-++||+||..+...
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            34568999999999888887777 999999999999999999999999887543

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

Probab=98.34  E-value=1.4e-07  Score=52.25  Aligned_cols=46  Identities=30%  Similarity=0.650  Sum_probs=34.3

Q ss_pred             CCccccccccccCCCeeeecCCCCCc-cchhhHHHHHc-CCCCCcccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLS-ARSSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~-~~~~CP~CR~~l~  150 (161)
                      +++|.||.|.-.+  .|  |..|||+ .+.+|-.+-++ -+..||+||+++.
T Consensus         7 ~dECTICye~pvd--sV--lYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD--SV--LYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch--HH--HHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            3899999997443  22  3349998 88888555444 6889999999875

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

Probab=98.34  E-value=1.5e-07  Score=72.52  Aligned_cols=52  Identities=31%  Similarity=0.730  Sum_probs=42.6

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC--CCCCccccccccCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNSLRVDSAL  155 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~  155 (161)
                      ..+.|-||-|.   +..|.+-| |||..|..|+..|-..  .++||.||.+|...+++
T Consensus       368 TFeLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  368 TFELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             hHHHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            35689999886   34588889 9999999999999854  57899999999766543

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

Probab=98.33  E-value=2.5e-07  Score=71.07  Aligned_cols=52  Identities=35%  Similarity=0.903  Sum_probs=40.9

Q ss_pred             CCCCccccccccccCCC----eeeecCCCCCccchhhHHHHHcC-------CCCCcccccccc
Q 031354           99 EEESECCICLGVFEDGD----KVKILPKCRHCYHCECVDAWLSA-------RSSCPLCRNSLR  150 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~----~v~~lp~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~l~  150 (161)
                      ..+.+|.||++...+..    ....||+|.|.|+..||+.|-..       .+.||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            55789999999876543    23456889999999999999843       357999998764

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

Probab=98.27  E-value=7e-07  Score=63.88  Aligned_cols=56  Identities=21%  Similarity=0.644  Sum_probs=46.8

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC--------CCCCccccccccCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA--------RSSCPLCRNSLRVDS  153 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~l~~~~  153 (161)
                      ..+.-...|..|-..++.||.+|..  |-|+||++|+++|-..        ...||-|..+|.++-
T Consensus        45 ~DsDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   45 QDSDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             hhcCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            3455667899999999999999876  9999999999999754        236999999998653

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

Probab=98.27  E-value=2e-07  Score=53.73  Aligned_cols=47  Identities=23%  Similarity=0.769  Sum_probs=23.0

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      -.|.+|.+-++  +.|.+.. |.|+|+..||..-+.  ..||+|+.+....+
T Consensus         8 LrCs~C~~~l~--~pv~l~~-CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILK--EPVCLGG-CEHIFCSSCIRDCIG--SECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--S--S-B---S-SS--B-TTTGGGGTT--TB-SSS--B-S-SS
T ss_pred             cCCcHHHHHhc--CCceecc-CccHHHHHHhHHhcC--CCCCCcCChHHHHH
Confidence            46999988865  3444444 999999999988443  45999999876543

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

Probab=98.26  E-value=6.3e-07  Score=69.19  Aligned_cols=49  Identities=29%  Similarity=0.864  Sum_probs=37.9

Q ss_pred             CCCccccccccccC-CCeeeecCCCCCccchhhHHHHHcC--CCCCcccccc
Q 031354          100 EESECCICLGVFED-GDKVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNS  148 (161)
Q Consensus       100 ~~~~CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~  148 (161)
                      ....|+|||++++- ++...+.+.|||.|-.+||++||-+  +..||.|...
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            45689999999985 5544455559999999999999963  2459999654

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

Probab=98.24  E-value=1.3e-07  Score=71.66  Aligned_cols=57  Identities=25%  Similarity=0.556  Sum_probs=45.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~~  157 (161)
                      ...+..|+|||+=++.   -+..+.|.|.||.+||.+-++. +.+||.||..+...-.+-+
T Consensus        40 ~~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~   97 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRI   97 (381)
T ss_pred             hhhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCC
Confidence            4457799999998775   4455569999999999999875 6789999999977655543

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

Probab=98.09  E-value=1.1e-06  Score=58.33  Aligned_cols=36  Identities=22%  Similarity=0.582  Sum_probs=30.5

Q ss_pred             CCccccccccccCCCeeeecCCCC------CccchhhHHHHHc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCR------HCYHCECVDAWLS  137 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~------H~FH~~Ci~~Wl~  137 (161)
                      ..+|+||++.+.+++.|..++ ||      |+||.+|+.+|-+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            569999999999966666677 87      9999999999943

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.

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

Probab=98.01  E-value=1.7e-06  Score=71.55  Aligned_cols=49  Identities=24%  Similarity=0.676  Sum_probs=39.0

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccccccccCCCC
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRVDSA  154 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~~~  154 (161)
                      -.|++|-+.+++   +.++. |||+||..|+.+-+. ++..||.|...+-.++-
T Consensus       644 LkCs~Cn~R~Kd---~vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  644 LKCSVCNTRWKD---AVITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             eeCCCccCchhh---HHHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            489999987665   43444 999999999999987 56779999888766543

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

Probab=98.01  E-value=3.3e-06  Score=62.92  Aligned_cols=50  Identities=22%  Similarity=0.511  Sum_probs=39.3

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVD  152 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  152 (161)
                      ....+|+||+-...   .-..|+ |+|.|+..||.--..+ +.+||+||+++...
T Consensus         5 ~~~~eC~IC~nt~n---~Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    5 TKKKECLICYNTGN---CPVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             ccCCcceeeeccCC---cCcccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            35678999988743   334677 9999999999987665 46799999999754

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

Probab=97.95  E-value=6.1e-06  Score=64.75  Aligned_cols=51  Identities=35%  Similarity=0.846  Sum_probs=43.1

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ....+.+|.||..-+.+   ..++| |||.|+..||++=+.....||.||.++..
T Consensus        80 ~~~sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   80 EIRSEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cccchhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            34667899999888765   55678 99999999999977777889999999875

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

Probab=97.94  E-value=5.2e-06  Score=65.48  Aligned_cols=56  Identities=34%  Similarity=0.724  Sum_probs=46.8

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ...+..|++|...+.+-  +..+. |||.|+..|+.+|+..+..||.|+..+.....+|
T Consensus        18 ~~~~l~C~~C~~vl~~p--~~~~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~   73 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDP--VQTTT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAEELP   73 (391)
T ss_pred             CcccccCccccccccCC--CCCCC-CCCcccccccchhhccCcCCcccccccchhhccC
Confidence            45667999999998753  32245 9999999999999999999999999998887776

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

Probab=97.90  E-value=6.6e-06  Score=72.32  Aligned_cols=54  Identities=28%  Similarity=0.685  Sum_probs=44.9

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC----------CCCccccccccC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR----------SSCPLCRNSLRV  151 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~----------~~CP~CR~~l~~  151 (161)
                      ....++.|.||+.|--.......|. |+|+||-.|...-|+++          .+||+|+.+|..
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            4566889999999877777888898 99999999998877653          269999998864

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

Probab=97.88  E-value=4.3e-06  Score=64.45  Aligned_cols=46  Identities=33%  Similarity=0.779  Sum_probs=38.2

Q ss_pred             CCCccccccccccCCC-eeeecCCCCCccchhhHHHHHcCC--CCCcccc
Q 031354          100 EESECCICLGVFEDGD-KVKILPKCRHCYHCECVDAWLSAR--SSCPLCR  146 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~-~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR  146 (161)
                      -+-.|-.|=+.+..++ .+.-|| |.|+||..|+.+.|.++  .+||-||
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            3557999988776544 677799 99999999999999876  5699998

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

Probab=97.85  E-value=1.6e-05  Score=45.44  Aligned_cols=44  Identities=30%  Similarity=0.562  Sum_probs=29.7

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC--CCCCcc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA--RSSCPL  144 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~  144 (161)
                      ......|+|.+..|+  +.|+-.. |||+|-.+.|.+|+.+  ...||+
T Consensus         8 ~~~~~~CPiT~~~~~--~PV~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    8 GTISLKCPITLQPFE--DPVKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB--SB-TTTSSB-S--SEEEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cEeccCCCCcCChhh--CCcCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            345678999999987  6777667 9999999999999954  346998

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

Probab=97.80  E-value=1.4e-05  Score=43.83  Aligned_cols=40  Identities=35%  Similarity=0.982  Sum_probs=27.8

Q ss_pred             cccccccccCCCeeeecCCCC-----CccchhhHHHHHc--CCCCCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCR-----HCYHCECVDAWLS--ARSSCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~-----H~FH~~Ci~~Wl~--~~~~CP~C  145 (161)
                      |-||+++-.+++.+ +.| |+     -..|.+|+.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~~l-i~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPL-ISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-E-E-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCce-ecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            67999987776633 567 75     4789999999997  45679987

>PHA02862 5L protein; Provisional

Probab=97.72  E-value=2.5e-05  Score=52.30  Aligned_cols=47  Identities=23%  Similarity=0.735  Sum_probs=35.7

Q ss_pred             CCccccccccccCCCeeeecCCCC-----CccchhhHHHHHcC--CCCCccccccccCC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCR-----HCYHCECVDAWLSA--RSSCPLCRNSLRVD  152 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~-----H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~~  152 (161)
                      .+.|=||+++-+  +.+  -| |.     ..-|.+|+.+|+..  +..||+|+.+....
T Consensus         2 ~diCWIC~~~~~--e~~--~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCD--ERN--NF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCC--CCc--cc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            467999999843  333  45 64     57899999999974  45799999988644

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

Probab=97.68  E-value=3.3e-05  Score=59.12  Aligned_cols=50  Identities=24%  Similarity=0.626  Sum_probs=37.0

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      .......+.|.||+++.++   ...+| |||+=+  |...-... .+||+||+.|..
T Consensus       299 ~~~~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs~~l-~~CPvCR~rI~~  348 (355)
T KOG1571|consen  299 FRELPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCSKHL-PQCPVCRQRIRL  348 (355)
T ss_pred             ccccCCCCceEEecCCccc---eeeec-CCcEEE--chHHHhhC-CCCchhHHHHHH
Confidence            4455667899999999877   66778 999944  66664332 459999988753

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

Probab=97.56  E-value=3.1e-05  Score=64.97  Aligned_cols=53  Identities=25%  Similarity=0.612  Sum_probs=42.7

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-------CCCCccccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-------RSSCPLCRNSL  149 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~l  149 (161)
                      .+....+|.||.+.+...+.+.--..|.|+||..||.+|-+.       ...||-|+...
T Consensus       187 l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  187 LSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             HhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            344566999999999988888776669999999999999864       23699998443

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

Probab=97.51  E-value=2.5e-05  Score=59.02  Aligned_cols=59  Identities=22%  Similarity=0.550  Sum_probs=48.3

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      .......|.+|-..|.+...+  .. |-|.||..||-+.|.....||+|...+....++..+
T Consensus        11 ~~n~~itC~LC~GYliDATTI--~e-CLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~ni   69 (331)
T KOG2660|consen   11 ELNPHITCRLCGGYLIDATTI--TE-CLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLNI   69 (331)
T ss_pred             hcccceehhhccceeecchhH--HH-HHHHHHHHHHHHHHHHhccCCccceeccCccccccC
Confidence            345677999999988875555  34 999999999999999999999999988777665554

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.50  E-value=0.00013  Score=53.14  Aligned_cols=56  Identities=14%  Similarity=0.279  Sum_probs=49.2

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSAL  155 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  155 (161)
                      ....|+||.+.+.+.-.+.+|.+|||+|..+|.++.+.....||+|-.++...+-+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            45689999999999888888888999999999999998889999999888766533

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

Probab=97.47  E-value=3.5e-05  Score=52.55  Aligned_cols=32  Identities=44%  Similarity=0.870  Sum_probs=28.4

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccch
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHC  129 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~  129 (161)
                      ...+..+|.||||+++.|+.+..|| |--+||+
T Consensus       173 L~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  173 LKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             hcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            3445669999999999999999999 9999996

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

Probab=97.47  E-value=4.2e-05  Score=55.62  Aligned_cols=53  Identities=30%  Similarity=0.684  Sum_probs=38.6

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCCC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSIT  159 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~~  159 (161)
                      .|..|. -+.+++...++. |+|+||..|...=..  ..||+||.++....-.++++
T Consensus         5 hCn~C~-~~~~~~~f~LTa-C~HvfC~~C~k~~~~--~~C~lCkk~ir~i~l~~slp   57 (233)
T KOG4739|consen    5 HCNKCF-RFPSQDPFFLTA-CRHVFCEPCLKASSP--DVCPLCKKSIRIIQLNRSLP   57 (233)
T ss_pred             Eecccc-ccCCCCceeeee-chhhhhhhhcccCCc--cccccccceeeeeecccccc
Confidence            466664 345588898888 999999999876322  38999999987655554443

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

Probab=97.42  E-value=9e-05  Score=59.48  Aligned_cols=60  Identities=27%  Similarity=0.666  Sum_probs=45.8

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----CCCCccccccccCCCCCCCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----RSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~l~~~~~~~~~  158 (161)
                      .....+..+|-+|-++-++   ..+.. |.|.||.-||.++...     +-+||.|...+..+...|.+
T Consensus       530 ~~enk~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~al  594 (791)
T KOG1002|consen  530 PDENKGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPAL  594 (791)
T ss_pred             CccccCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhh
Confidence            4445567799999887433   55666 9999999999888743     46799999999877666654

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.41  E-value=0.00017  Score=49.30  Aligned_cols=52  Identities=21%  Similarity=0.615  Sum_probs=38.4

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCC--C---ccchhhHHHHHcCC--CCCccccccccCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCR--H---CYHCECVDAWLSAR--SSCPLCRNSLRVDS  153 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~--H---~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~~  153 (161)
                      .+..+..|=||.++-.  +..  -| |.  .   .-|.+|+..|+..+  .+||+|+.+.....
T Consensus         4 ~s~~~~~CRIC~~~~~--~~~--~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~   62 (162)
T PHA02825          4 VSLMDKCCWICKDEYD--VVT--NY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK   62 (162)
T ss_pred             cCCCCCeeEecCCCCC--Ccc--CC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEE
Confidence            3556789999998843  222  46 65  3   57999999999753  56999999886553

>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=97.38  E-value=8.9e-05  Score=47.79  Aligned_cols=34  Identities=24%  Similarity=0.713  Sum_probs=28.1

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHH
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVD  133 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~  133 (161)
                      ......|++|-..+.. ..+.+.| |||+||..|++
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            3456789999999987 5666788 99999999975

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

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

Probab=97.31  E-value=0.0019  Score=47.89  Aligned_cols=53  Identities=23%  Similarity=0.434  Sum_probs=39.2

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC--CCCCcccccccc
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNSLR  150 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~  150 (161)
                      ......+.+|++|-+.-.  -.....+ |||+||.-||..=+.-  .-+||.|-.+..
T Consensus       233 ss~~t~~~~C~~Cg~~Pt--iP~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  233 SSTGTSDTECPVCGEPPT--IPHVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccccCCceeeccCCCCC--CCeeecc-ccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            344567889999966522  3344566 9999999999997663  357999988776

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

Probab=97.31  E-value=0.0009  Score=50.79  Aligned_cols=52  Identities=12%  Similarity=0.337  Sum_probs=40.4

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccc
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL  149 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  149 (161)
                      .........|+||+..-++.-.+.+   =|-+||..|+-+.+.+++.||+=..++
T Consensus       294 e~l~~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  294 ELLPPDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             ccCCCccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            4556677899999998766433322   589999999999999999999855443

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

Probab=97.19  E-value=1.4e-05  Score=61.61  Aligned_cols=57  Identities=25%  Similarity=0.586  Sum_probs=48.0

Q ss_pred             CCCCCCCCccccccccccCC-CeeeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354           95 KDDKEEESECCICLGVFEDG-DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~-~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      .........|+||.+.++.. +.+..+- |||.+|..||.+||..+..||.||+.+...
T Consensus       190 ~~~~slv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  190 QPTSSLVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             CchHHHHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            34455667999999999886 6777777 999999999999999988899999988643

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

Probab=97.19  E-value=0.0002  Score=50.53  Aligned_cols=45  Identities=20%  Similarity=0.471  Sum_probs=37.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL  149 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  149 (161)
                      ...|.||-.+|+.   -.++. |||.||..|...-++....|-+|....
T Consensus       196 PF~C~iCKkdy~s---pvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYES---PVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccc---hhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            4589999999985   33555 999999999999888889999997654

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

Probab=97.15  E-value=0.00039  Score=38.01  Aligned_cols=45  Identities=20%  Similarity=0.461  Sum_probs=20.9

Q ss_pred             cccccccccC-CCeeeecCCCCCccchhhHHHHHc-CCCCCccccccc
Q 031354          104 CCICLGVFED-GDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSL  149 (161)
Q Consensus       104 CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l  149 (161)
                      |++|.+++.. +..+.--+ ||+..+..|...-+. ....||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999833 22443344 778888888777665 367899999875

>PHA03096 p28-like protein; Provisional

Probab=97.15  E-value=0.00021  Score=53.95  Aligned_cols=48  Identities=19%  Similarity=0.462  Sum_probs=35.3

Q ss_pred             CccccccccccCC----CeeeecCCCCCccchhhHHHHHcCC---CC---Cccccccc
Q 031354          102 SECCICLGVFEDG----DKVKILPKCRHCYHCECVDAWLSAR---SS---CPLCRNSL  149 (161)
Q Consensus       102 ~~CaICL~~f~~~----~~v~~lp~C~H~FH~~Ci~~Wl~~~---~~---CP~CR~~l  149 (161)
                      -.|.||++...+.    ..-..|++|.|.|+..|+..|-..+   .+   ||.||..+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence            5799999987753    2444688899999999999998643   33   55555444

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

Probab=97.14  E-value=0.0002  Score=55.73  Aligned_cols=49  Identities=24%  Similarity=0.636  Sum_probs=39.0

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--------CCCccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--------SSCPLCRN  147 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--------~~CP~CR~  147 (161)
                      ......|-||+++..-.+....+| |+|+|+..|+..++...        -.||-+..
T Consensus       181 ~~slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  181 VNSLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             HhhcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            344568999999987668888999 99999999999998542        24877654

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

Probab=97.12  E-value=0.0002  Score=53.71  Aligned_cols=55  Identities=29%  Similarity=0.689  Sum_probs=42.0

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccc-cccccCCCCCCCCC
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLC-RNSLRVDSALPSIT  159 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~C-R~~l~~~~~~~~~~  159 (161)
                      ..|+.|-.-+.+  .++ +|.|||.|+.+||..-|. ....||.| |.++..+...|+++
T Consensus       275 LkCplc~~Llrn--p~k-T~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD~d  331 (427)
T COG5222         275 LKCPLCHCLLRN--PMK-TPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPDID  331 (427)
T ss_pred             ccCcchhhhhhC--ccc-CccccchHHHHHHhhhhhhccccCCCcccccchhhccCccHH
Confidence            579988665443  343 466999999999997766 45789999 77888888888764

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

Probab=97.03  E-value=0.00012  Score=54.66  Aligned_cols=43  Identities=28%  Similarity=0.685  Sum_probs=33.2

Q ss_pred             CCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ...|+||++.-.+   +..|+ |||. -+.+|-..    -..||+||+-+..
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKR----MNECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhccc----cccCchHHHHHHH
Confidence            6789999998554   77899 9996 66677544    2479999987754

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

Probab=96.97  E-value=0.0003  Score=52.56  Aligned_cols=47  Identities=19%  Similarity=0.398  Sum_probs=39.5

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ...|-||-..|..   -.++. |+|.|+..|-.+=+++...|++|.++...
T Consensus       241 Pf~c~icr~~f~~---pVvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYR---PVVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             Ccccccccccccc---chhhc-CCceeehhhhccccccCCcceeccccccc
Confidence            4579999999985   33455 99999999999989988999999887654

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

Probab=96.91  E-value=0.00079  Score=51.65  Aligned_cols=50  Identities=22%  Similarity=0.501  Sum_probs=41.3

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ...+++.|+||...-.   .-...| |+|.=|..||.+-+.+.+.|=.|+..+.
T Consensus       418 p~sEd~lCpICyA~pi---~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  418 PDSEDNLCPICYAGPI---NAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CCcccccCcceecccc---hhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            3467889999977522   244567 9999999999999999999999998876

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.89  E-value=0.0011  Score=49.73  Aligned_cols=58  Identities=16%  Similarity=0.381  Sum_probs=44.3

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSAL  155 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  155 (161)
                      .......|+|...+|........|-+|||+|-..++.+- .....||+|-.++...+-+
T Consensus       109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCCEE
Confidence            356677999999999665555555449999999999996 3356799999988755433

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

Probab=96.88  E-value=0.00061  Score=51.00  Aligned_cols=47  Identities=26%  Similarity=0.631  Sum_probs=39.2

Q ss_pred             CCCccccccccccCCC-eeeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354          100 EESECCICLGVFEDGD-KVKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~-~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      ....|+||.+.+-.+. .+..++ |||.-|..|..+-...+.+||+|..
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            3444999999887765 556788 9999999999998887799999987

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

Probab=96.87  E-value=0.001  Score=50.93  Aligned_cols=50  Identities=34%  Similarity=0.672  Sum_probs=38.2

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHH--HcCCCCCccccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW--LSARSSCPLCRNSL  149 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W--l~~~~~CP~CR~~l  149 (161)
                      ...++...|.||-+...-   +.++| |+|-.|..|--..  |-.++.||+||.+-
T Consensus        56 dtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          56 DTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            445566789999887554   77899 9999988896543  34578899999864

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.78  E-value=0.00072  Score=37.87  Aligned_cols=46  Identities=30%  Similarity=0.727  Sum_probs=32.4

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      .|..|...   +..-.++| |||+-+..|.+-  .+-.-||+|.+++...+.
T Consensus         9 ~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~--~rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen    9 PCVFCGFV---GTKGTVLP-CGHLICDNCFPG--ERYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             eEEEcccc---cccccccc-ccceeeccccCh--hhccCCCCCCCcccCCCC
Confidence            45555443   44455788 999999988776  345679999998876653

>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=96.74  E-value=0.00097  Score=35.78  Aligned_cols=41  Identities=27%  Similarity=0.727  Sum_probs=22.8

Q ss_pred             cccccccccCCCeeeecCCCCCccchhhHHHHHcCCC--CCccc
Q 031354          104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS--SCPLC  145 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~--~CP~C  145 (161)
                      |.+|-+-...|.....-. |+=.+|..|+..+++.+.  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            566766555555554334 888999999999998765  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.68  E-value=0.0016  Score=49.62  Aligned_cols=48  Identities=29%  Similarity=0.655  Sum_probs=39.4

Q ss_pred             CCccccccccccCCC---eeeecCCCCCccchhhHHHHHcCC-CCCccccccc
Q 031354          101 ESECCICLGVFEDGD---KVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSL  149 (161)
Q Consensus       101 ~~~CaICL~~f~~~~---~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l  149 (161)
                      ...|-||-++|..++   .-|+|. |||.|+..|+.+-+.+. ..||.||.+.
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            457999999999874   344566 99999999999987754 5699999986

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.51  E-value=0.0041  Score=34.83  Aligned_cols=35  Identities=34%  Similarity=0.842  Sum_probs=30.6

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHH
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDA  134 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~  134 (161)
                      ....|++|=+.|++++.+.+-|.||-.+|.+|-++
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            45689999999998888888999999999999654

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

Probab=96.28  E-value=0.0022  Score=53.81  Aligned_cols=22  Identities=32%  Similarity=0.915  Sum_probs=20.8

Q ss_pred             CCCccchhhHHHHHcCCCCCcc
Q 031354          123 CRHCYHCECVDAWLSARSSCPL  144 (161)
Q Consensus       123 C~H~FH~~Ci~~Wl~~~~~CP~  144 (161)
                      |+|+-|.+|..+|+.....||-
T Consensus      1048 C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1048 CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccHHHHHHHHhcCCcCCC
Confidence            9999999999999999999985

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

Probab=96.12  E-value=0.0027  Score=44.23  Aligned_cols=30  Identities=30%  Similarity=0.980  Sum_probs=24.5

Q ss_pred             CCCccchhhHHHHHcC----C-------CCCccccccccCC
Q 031354          123 CRHCYHCECVDAWLSA----R-------SSCPLCRNSLRVD  152 (161)
Q Consensus       123 C~H~FH~~Ci~~Wl~~----~-------~~CP~CR~~l~~~  152 (161)
                      ||.-||.-|+..||+.    +       ..||.|-.++..+
T Consensus       190 CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  190 CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            9999999999999964    1       2599998887543

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

Probab=96.11  E-value=0.003  Score=53.56  Aligned_cols=43  Identities=33%  Similarity=0.799  Sum_probs=31.5

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL  149 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  149 (161)
                      ...|..|-..++- ..|- .- |||.||.+|+.   .+...||-|+.++
T Consensus       840 ~skCs~C~~~Ldl-P~Vh-F~-CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDL-PFVH-FL-CGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcccc-ceee-ee-cccHHHHHhhc---cCcccCCccchhh
Confidence            4689999776543 2333 33 99999999999   4456799998744

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.04  E-value=0.0044  Score=33.51  Aligned_cols=30  Identities=30%  Similarity=0.765  Sum_probs=21.8

Q ss_pred             CC-CccchhhHHHHHcCCCCCccccccccCC
Q 031354          123 CR-HCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus       123 C~-H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      |. |+.+..|+..-+.+...||+|..+++..
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            86 9999999999999999999999988653

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.

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

Probab=95.96  E-value=0.0033  Score=45.47  Aligned_cols=41  Identities=32%  Similarity=0.697  Sum_probs=31.8

Q ss_pred             cccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccCC
Q 031354          104 CCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus       104 CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      |-.|-+.   +..|..+| |.|+ +|..|-..    -..||+|+.+....
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s~  202 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTSS  202 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhce
Confidence            8888665   56688999 9986 88899776    34599999876543

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

Probab=95.89  E-value=0.0037  Score=53.23  Aligned_cols=37  Identities=24%  Similarity=0.610  Sum_probs=29.8

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHH
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL  136 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl  136 (161)
                      ...++.|.+|--.+... .-.+.| |||.||++||.+-.
T Consensus       814 ~ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            45678999998777654 556788 99999999998876

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.84  E-value=0.0074  Score=46.25  Aligned_cols=55  Identities=24%  Similarity=0.481  Sum_probs=36.5

Q ss_pred             CCCCCCccccccccccCCCe-eeecCCCCCccchhhHHHHHc-CCCCCccccccccCC
Q 031354           97 DKEEESECCICLGVFEDGDK-VKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRVD  152 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~-v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~  152 (161)
                      .+.+++.|+.|+|++.-.|. ..-.| ||-..|.-|...--+ -+..||-||+-...+
T Consensus        10 sedeed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          10 SEDEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            45567789999999886553 33455 886655555333222 257899999987654

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

Probab=95.76  E-value=0.0042  Score=52.37  Aligned_cols=47  Identities=34%  Similarity=0.718  Sum_probs=37.2

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--CCCccccccccCCC
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--SSCPLCRNSLRVDS  153 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~~  153 (161)
                      ..|.||++    .+.....+ |||.|+.+|+.+-+...  ..||+||..+....
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            78999999    24455667 99999999999987643  45999999886553

>PHA02975 hypothetical protein; Provisional

Probab=95.61  E-value=0.012  Score=34.30  Aligned_cols=50  Identities=18%  Similarity=0.250  Sum_probs=27.2

Q ss_pred             CCCCCCCCCCCccc-----CCCCCccccccchHHHHHHHHHHHHHHHHHHHHHHH
Q 031354            1 MASQESQPFHWHYT-----ELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARW   50 (161)
Q Consensus         1 ~~~~~~~~~~~~~~-----~~~~~~~~~~~~~i~ii~~l~~~~l~~~~~~~~~~~   50 (161)
                      |+|.+.+.+.|.+.     ..+++.......+++++++++++++++++.++|.+.
T Consensus        13 msS~DdDF~nFI~vVksVLtdk~~~~~~~~~~~~~ii~i~~v~~~~~~~flYLK~   67 (69)
T PHA02975         13 LESNDSDFEDFIDTIMHVLTGKKEPKKKSSLSIILIIFIIFITCIAVFTFLYLKL   67 (69)
T ss_pred             cCCChHHHHHHHHHHHHHHcCCCCCCcCCchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            56666666666543     222223334444555555566666666666666554

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

Probab=95.56  E-value=0.0093  Score=46.48  Aligned_cols=55  Identities=25%  Similarity=0.716  Sum_probs=34.4

Q ss_pred             CCCCCCccccccccccC-------------CCeeeecCCCC-----CccchhhHHHHHcCC-------------CCCccc
Q 031354           97 DKEEESECCICLGVFED-------------GDKVKILPKCR-----HCYHCECVDAWLSAR-------------SSCPLC  145 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~-------------~~~v~~lp~C~-----H~FH~~Ci~~Wl~~~-------------~~CP~C  145 (161)
                      ...+.+.|.-|+.+-.+             |......+.|.     =+.|.+|+.+|+..+             -.||+|
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            44567789999875433             11111112233     457889999999543             269999


Q ss_pred             cccccC
Q 031354          146 RNSLRV  151 (161)
Q Consensus       146 R~~l~~  151 (161)
                      |+....
T Consensus       347 Ra~FCi  352 (358)
T PF10272_consen  347 RAKFCI  352 (358)
T ss_pred             ccccee
Confidence            997643

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

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

Probab=95.27  E-value=0.013  Score=44.84  Aligned_cols=52  Identities=25%  Similarity=0.627  Sum_probs=38.8

Q ss_pred             CCCccccccccccCCCe-eeecCCCC-----CccchhhHHHHHc--CCCCCccccccccCC
Q 031354          100 EESECCICLGVFEDGDK-VKILPKCR-----HCYHCECVDAWLS--ARSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~-v~~lp~C~-----H~FH~~Ci~~Wl~--~~~~CP~CR~~l~~~  152 (161)
                      ++..|=||.++...... ....| |.     +..|..|++.|+.  .+..|.+|.......
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            35789999998765432 34566 75     6789999999998  456799998876544

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

Probab=95.22  E-value=0.0052  Score=54.34  Aligned_cols=45  Identities=33%  Similarity=0.876  Sum_probs=37.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      ....|.||++.+.+.-.+.  . |||.++..|...|+..+..||+|+.
T Consensus      1152 ~~~~c~ic~dil~~~~~I~--~-cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIA--G-CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHhcCCee--e-echhHhhhHHHHHHHHhccCcchhh
Confidence            3459999999988544332  2 9999999999999999999999974

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

Probab=95.22  E-value=0.0075  Score=45.64  Aligned_cols=44  Identities=27%  Similarity=0.726  Sum_probs=30.6

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      .|.-|  +|--.-.-|.+| |.|+||.+|-..  ...+.||.|--.+..
T Consensus        92 fCd~C--d~PI~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen   92 FCDRC--DFPIAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQR  135 (389)
T ss_pred             eeccc--CCcceeeecccc-cchhhhhhhhhc--CccccCcCcccHHHH
Confidence            56665  333334457889 999999999765  446789999766543

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

Probab=95.13  E-value=0.029  Score=47.74  Aligned_cols=62  Identities=24%  Similarity=0.620  Sum_probs=46.0

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCC-----CccchhhHHHHHcC--CCCCcccccccc----CCCCCCCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCR-----HCYHCECVDAWLSA--RSSCPLCRNSLR----VDSALPSI  158 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~-----H~FH~~Ci~~Wl~~--~~~CP~CR~~l~----~~~~~~~~  158 (161)
                      .....+...|-||..|=..++++. -| |.     -+.|.+|+.+|+.-  +..|-+|+.++.    -.+.+|++
T Consensus         6 ~~mN~d~~~CRICr~e~~~d~pLf-hP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~~   78 (1175)
T COG5183           6 TPMNEDKRSCRICRTEDIRDDPLF-HP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQI   78 (1175)
T ss_pred             CCCCccchhceeecCCCCCCCcCc-cc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCcc
Confidence            344566689999999988777763 35 64     46999999999974  456999998874    34566654

>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase

Probab=95.07  E-value=0.045  Score=28.54  Aligned_cols=35  Identities=23%  Similarity=0.471  Sum_probs=27.1

Q ss_pred             ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 031354           22 QIRGRTLFSIIVVFAVVLLVSFLFLYARWFCRRFS   56 (161)
Q Consensus        22 ~~~~~~i~ii~~l~~~~l~~~~~~~~~~~~~~~~~   56 (161)
                      .+++..++++.+++.+.+.++.+++|.+|..|++.
T Consensus         5 ~lp~GVIlVF~lVglv~i~iva~~iYRKw~aRkr~   39 (43)
T PF08114_consen    5 TLPGGVILVFCLVGLVGIGIVALFIYRKWQARKRA   39 (43)
T ss_pred             cCCCCeeeehHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35667777777888888888888999998887743

Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].

>PHA02650 hypothetical protein; Provisional

Probab=95.03  E-value=0.022  Score=34.13  Aligned_cols=30  Identities=17%  Similarity=0.322  Sum_probs=18.3

Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031354           24 RGRTLFSIIVVFAVVLLVSFLFLYARWFCR   53 (161)
Q Consensus        24 ~~~~i~ii~~l~~~~l~~~~~~~~~~~~~~   53 (161)
                      ...+.++++++++++++++++++|.+...|
T Consensus        46 ~~~~~~~ii~i~~v~i~~l~~flYLK~~~r   75 (81)
T PHA02650         46 WFNGQNFIFLIFSLIIVALFSFFVFKGYTR   75 (81)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            344555666666666666666666665544

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

Probab=94.90  E-value=0.007  Score=50.02  Aligned_cols=45  Identities=27%  Similarity=0.509  Sum_probs=33.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNS  148 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  148 (161)
                      ...|.||+-.|....-.-+.+.|||..+..|+..-  .+.+|| |+++
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~D   55 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKRD   55 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCcc
Confidence            45799999998876654444459999999999984  457888 6443

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

Probab=94.78  E-value=0.015  Score=48.11  Aligned_cols=55  Identities=31%  Similarity=0.777  Sum_probs=45.3

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      +.....+.|++|+++.    ..+..+ |.   |.-|+.+|+..+..||+|+..+..++.....
T Consensus       474 ~l~~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~~~  528 (543)
T KOG0802|consen  474 QLREPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFLSKN  528 (543)
T ss_pred             hhhcccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcccccCcc
Confidence            4455678999999997    566777 88   9999999999999999999988877665543

>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=94.29  E-value=0.053  Score=37.23  Aligned_cols=35  Identities=20%  Similarity=0.517  Sum_probs=22.2

Q ss_pred             CCccccccccccCCCee---------eecCCCCC-ccchhhHHHHH
Q 031354          101 ESECCICLGVFEDGDKV---------KILPKCRH-CYHCECVDAWL  136 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v---------~~lp~C~H-~FH~~Ci~~Wl  136 (161)
                      +..|+||||--.+.--+         |-.- |+- .=|..|+|++-
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpym-c~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYM-CDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccc-cCCccchhHHHHHHH
Confidence            56899999975542211         1111 553 45889999975

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.

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

Probab=94.29  E-value=0.019  Score=45.41  Aligned_cols=41  Identities=29%  Similarity=0.611  Sum_probs=30.9

Q ss_pred             CCCCCcccccc-ccccCCCeeeecCCCCCccchhhHHHHHcCC
Q 031354           98 KEEESECCICL-GVFEDGDKVKILPKCRHCYHCECVDAWLSAR  139 (161)
Q Consensus        98 ~~~~~~CaICL-~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~  139 (161)
                      .....+|.||. +.....+...+.. |+|.|+.+|..+.+..+
T Consensus       143 ~~~~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  143 KLPKEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhhh
Confidence            34567999999 4444445666565 99999999999998754

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.01  E-value=0.026  Score=41.63  Aligned_cols=54  Identities=31%  Similarity=0.751  Sum_probs=38.7

Q ss_pred             CCCCCccccccccccCCCee-eecCCCC-----CccchhhHHHHHcCCC--------CCccccccccCC
Q 031354           98 KEEESECCICLGVFEDGDKV-KILPKCR-----HCYHCECVDAWLSARS--------SCPLCRNSLRVD  152 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v-~~lp~C~-----H~FH~~Ci~~Wl~~~~--------~CP~CR~~l~~~  152 (161)
                      ...+-.|-||+..=+++..- -+-| |.     |=-|..|+..|+..++        +||-|+.+....
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv   84 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIV   84 (293)
T ss_pred             cccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheee
Confidence            44566899999875553322 3456 63     7799999999996542        499999887543

>PHA02819 hypothetical protein; Provisional

Probab=93.36  E-value=0.085  Score=30.98  Aligned_cols=26  Identities=19%  Similarity=0.464  Sum_probs=14.8

Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHH
Q 031354           24 RGRTLFSIIVVFAVVLLVSFLFLYAR   49 (161)
Q Consensus        24 ~~~~i~ii~~l~~~~l~~~~~~~~~~   49 (161)
                      ...+.+++++++.++++++++++|.+
T Consensus        43 ~~~~~~~ii~l~~~~~~~~~~flYLK   68 (71)
T PHA02819         43 SFLRYYLIIGLVTIVFVIIFIIFYLK   68 (71)
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455555556666666666666554

>PHA02844 putative transmembrane protein; Provisional

Probab=93.31  E-value=0.053  Score=32.17  Aligned_cols=26  Identities=27%  Similarity=0.374  Sum_probs=14.5

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHH
Q 031354           25 GRTLFSIIVVFAVVLLVSFLFLYARW   50 (161)
Q Consensus        25 ~~~i~ii~~l~~~~l~~~~~~~~~~~   50 (161)
                      ..+..++++++++++++++.++|.+.
T Consensus        46 ~~~~~~ii~i~~v~~~~~~~flYLK~   71 (75)
T PHA02844         46 SSTKIWILTIIFVVFATFLTFLYLKA   71 (75)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhe
Confidence            34555555555666666666665543

>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=93.22  E-value=0.094  Score=35.06  Aligned_cols=23  Identities=30%  Similarity=0.537  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 031354           32 IVVFAVVLLVSFLFLYARWFCRR   54 (161)
Q Consensus        32 ~~l~~~~l~~~~~~~~~~~~~~~   54 (161)
                      +++++++++++++++++++.+||
T Consensus         4 l~~iii~~i~l~~~~~~~~~rRR   26 (130)
T PF12273_consen    4 LFAIIIVAILLFLFLFYCHNRRR   26 (130)
T ss_pred             eHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444443333

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 [].

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

Probab=93.06  E-value=0.69  Score=29.92  Aligned_cols=33  Identities=24%  Similarity=0.526  Sum_probs=22.7

Q ss_pred             cCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354          120 LPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus       120 lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      .|+|+|..      +-+-+...|+.|++++..+..+..-
T Consensus        72 CP~C~K~T------KmLGr~D~CM~C~~pLTLd~~legk  104 (114)
T PF11023_consen   72 CPNCGKQT------KMLGRVDACMHCKEPLTLDPSLEGK  104 (114)
T ss_pred             CCCCCChH------hhhchhhccCcCCCcCccCchhhcc
Confidence            35577762      2344556799999999988776543

; GO: 0005887 integral to plasma membrane

>PF12575 DUF3753: Protein of unknown function (DUF3753); InterPro: IPR009175 This group represents an uncharacterised conserved protein belonging to poxvirus family I2

Probab=92.71  E-value=0.091  Score=31.15  Aligned_cols=23  Identities=30%  Similarity=0.547  Sum_probs=12.1

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHH
Q 031354           26 RTLFSIIVVFAVVLLVSFLFLYA   48 (161)
Q Consensus        26 ~~i~ii~~l~~~~l~~~~~~~~~   48 (161)
                      +++++++.++++++++++.++|.
T Consensus        47 ~~~~~ii~ii~v~ii~~l~flYL   69 (72)
T PF12575_consen   47 NWIILIISIIFVLIIVLLTFLYL   69 (72)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHh
Confidence            34455555555555555555554

>PHA03054 IMV membrane protein; Provisional

Probab=92.47  E-value=0.13  Score=30.19  Aligned_cols=26  Identities=27%  Similarity=0.553  Sum_probs=14.3

Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHH
Q 031354           24 RGRTLFSIIVVFAVVLLVSFLFLYAR   49 (161)
Q Consensus        24 ~~~~i~ii~~l~~~~l~~~~~~~~~~   49 (161)
                      ...+.+++++++.+++++++.++|.+
T Consensus        45 ~~~~~~~ii~l~~v~~~~l~~flYLK   70 (72)
T PHA03054         45 CWGWYWLIIIFFIVLILLLLIYLYLK   70 (72)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33455555556566666656665543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.29  E-value=0.081  Score=39.92  Aligned_cols=28  Identities=25%  Similarity=0.746  Sum_probs=22.0

Q ss_pred             CCCccchhhHHHHHcC-------------CCCCcccccccc
Q 031354          123 CRHCYHCECVDAWLSA-------------RSSCPLCRNSLR  150 (161)
Q Consensus       123 C~H~FH~~Ci~~Wl~~-------------~~~CP~CR~~l~  150 (161)
                      |.-+.|.+|+.+|+..             +-+||+||....
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            5567889999999843             347999998764

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

Probab=92.19  E-value=0.11  Score=39.83  Aligned_cols=49  Identities=16%  Similarity=0.356  Sum_probs=35.3

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ....+-.+|+||.+.+..  .+.+-+ =||+-+..|=.+   ....||.||-++-
T Consensus        43 ~~~~~lleCPvC~~~l~~--Pi~QC~-nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   43 LLDLDLLDCPVCFNPLSP--PIFQCD-NGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             ccchhhccCchhhccCcc--cceecC-CCcEehhhhhhh---hcccCCccccccc
Confidence            345566799999999763  343333 479999888763   4567999998875

>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=92.14  E-value=0.62  Score=24.03  Aligned_cols=13  Identities=23%  Similarity=0.235  Sum_probs=5.1

Q ss_pred             hHHHHHHHHHHHH
Q 031354           27 TLFSIIVVFAVVL   39 (161)
Q Consensus        27 ~i~ii~~l~~~~l   39 (161)
                      ++-++.+++.+++
T Consensus         5 ~IaIIv~V~vg~~   17 (38)
T PF02439_consen    5 TIAIIVAVVVGMA   17 (38)
T ss_pred             hhhHHHHHHHHHH
Confidence            3334444433333

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.

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=91.80  E-value=0.12  Score=37.22  Aligned_cols=41  Identities=32%  Similarity=0.719  Sum_probs=29.2

Q ss_pred             CCCccccccc-----cccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccc
Q 031354          100 EESECCICLG-----VFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR  146 (161)
Q Consensus       100 ~~~~CaICL~-----~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  146 (161)
                      .+..|.+|-+     .|+.+ .+..-+.|+-+||..|..+     ..||-|-
T Consensus       151 kGfiCe~C~~~~~IfPF~~~-~~~~C~~C~~v~H~~C~~~-----~~CpkC~  196 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQID-TTVRCPKCKSVFHKSCFRK-----KSCPKCA  196 (202)
T ss_pred             CCCCCccCCCCCCCCCCCCC-CeeeCCcCccccchhhcCC-----CCCCCcH
Confidence            3568889975     34443 3444555999999999873     6699994

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=91.47  E-value=0.54  Score=31.11  Aligned_cols=16  Identities=25%  Similarity=0.088  Sum_probs=6.4

Q ss_pred             hHHHHHHHHHHHHHHH
Q 031354           27 TLFSIIVVFAVVLLVS   42 (161)
Q Consensus        27 ~i~ii~~l~~~~l~~~   42 (161)
                      ++.|++++.+.++.++
T Consensus        66 i~~Ii~gv~aGvIg~I   81 (122)
T PF01102_consen   66 IIGIIFGVMAGVIGII   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             eeehhHHHHHHHHHHH
Confidence            3334444444444333

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

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

Probab=90.94  E-value=0.14  Score=43.62  Aligned_cols=51  Identities=8%  Similarity=0.174  Sum_probs=35.8

Q ss_pred             CCCccccccccccC---CCeeeecCCCCCccchhhHHHHHcC------CCCCcccccccc
Q 031354          100 EESECCICLGVFED---GDKVKILPKCRHCYHCECVDAWLSA------RSSCPLCRNSLR  150 (161)
Q Consensus       100 ~~~~CaICL~~f~~---~~~v~~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~  150 (161)
                      ....|.+|.-++-+   +-.+..+.+|+|-||..||..|...      +..|++|...+.
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            34567777666665   3333333459999999999999853      345999988775

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

Probab=90.72  E-value=0.089  Score=44.70  Aligned_cols=48  Identities=27%  Similarity=0.470  Sum_probs=34.6

Q ss_pred             CCCCCCCccccccccccC-C---CeeeecCCCCCccchhhHHHHHcCCCCCccc
Q 031354           96 DDKEEESECCICLGVFED-G---DKVKILPKCRHCYHCECVDAWLSARSSCPLC  145 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~-~---~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  145 (161)
                      .....+..|.-|++..-. +   +.+.++. |||+||+.|+..-..+++ |-.|
T Consensus       779 v~v~~e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  779 VLVSVEERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             eeEeehhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChh
Confidence            334445689999886553 2   4677787 999999999988877655 5554

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

Probab=90.60  E-value=0.22  Score=33.19  Aligned_cols=55  Identities=22%  Similarity=0.418  Sum_probs=37.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc---CCCCCccccccccCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS---ARSSCPLCRNSLRVDSA  154 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~l~~~~~  154 (161)
                      .-.+|.||-|.-.+..-+.--.-||-..+-.|-...++   -+..||+|+......+.
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~  136 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS  136 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence            45589999987555332221112898888888766554   46789999998876554

>PHA02692 hypothetical protein; Provisional

Probab=90.58  E-value=0.29  Score=28.78  Aligned_cols=16  Identities=25%  Similarity=0.418  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHH
Q 031354           34 VFAVVLLVSFLFLYAR   49 (161)
Q Consensus        34 l~~~~l~~~~~~~~~~   49 (161)
                      ++.++++++++++|.+
T Consensus        53 ~~~~~~~vll~flYLK   68 (70)
T PHA02692         53 LIAAAIGVLLCFHYLK   68 (70)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            4555555555555543

>PRK01844 hypothetical protein; Provisional

Probab=90.52  E-value=1.6  Score=25.89  Aligned_cols=55  Identities=20%  Similarity=0.199  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCChhhHH---hhcCCCCHHHHhc
Q 031354           28 LFSIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQ---ALTRGLDLTTINT   82 (161)
Q Consensus        28 i~ii~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~   82 (161)
                      +.++++++++++-+++-|+..|.+..+.-..+++.+....+.   ...+..+++.+++
T Consensus         5 ~~I~l~I~~li~G~~~Gff~ark~~~k~lk~NPpine~mir~Mm~QMGqkPSekki~Q   62 (72)
T PRK01844          5 LGILVGVVALVAGVALGFFIARKYMMNYLQKNPPINEQMLKMMMMQMGQKPSQKKINQ   62 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccHHHHHH
Confidence            334444445555555555665555555233343333332222   3445555555543

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=90.40  E-value=0.61  Score=30.84  Aligned_cols=33  Identities=21%  Similarity=0.250  Sum_probs=22.0

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Q 031354           26 RTLFSIIVVFAVVLLVSFLFLYARWFCRRFSHQ   58 (161)
Q Consensus        26 ~~i~ii~~l~~~~l~~~~~~~~~~~~~~~~~~~   58 (161)
                      ..-.++.|++++++-++++++++.+..+|+++.
T Consensus        62 s~~~i~~Ii~gv~aGvIg~Illi~y~irR~~Kk   94 (122)
T PF01102_consen   62 SEPAIIGIIFGVMAGVIGIILLISYCIRRLRKK   94 (122)
T ss_dssp             S-TCHHHHHHHHHHHHHHHHHHHHHHHHHHS--
T ss_pred             cccceeehhHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            345677788888888888887777777664444

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

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

Probab=90.34  E-value=0.1  Score=43.26  Aligned_cols=44  Identities=23%  Similarity=0.609  Sum_probs=28.7

Q ss_pred             CCCCCccccccc-----cccCCCeeeecCCCCCccchhhHHHHHcCCCCCccc
Q 031354           98 KEEESECCICLG-----VFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLC  145 (161)
Q Consensus        98 ~~~~~~CaICL~-----~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~C  145 (161)
                      ......|.+|-.     .|+.....+-.. |+++||..|...   .+..||.|
T Consensus       508 ~~~gfiCe~Cq~~~iiyPF~~~~~~rC~~-C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  508 TGKGFICELCQHNDIIYPFETRNTRRCST-CLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             ccCeeeeeeccCCCcccccccccceeHHH-HHHHHHHHHHhc---cCCCCCch
Confidence            345667888822     344334444555 999999999654   33449999

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

Probab=90.10  E-value=0.24  Score=42.01  Aligned_cols=42  Identities=26%  Similarity=0.534  Sum_probs=31.1

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPL  144 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~  144 (161)
                      ...|++|-..+. |..+ .-+.|||.-|.+|+.+|+..+.-||.
T Consensus       779 ~~~CtVC~~vi~-G~~~-~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIR-GVDV-WCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hcCceeecceee-eeEe-ecccccccccHHHHHHHHhcCCCCcc
Confidence            347899955533 2333 23459999999999999999888876

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

Probab=90.09  E-value=0.27  Score=38.68  Aligned_cols=51  Identities=18%  Similarity=0.286  Sum_probs=39.7

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC---CCccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS---SCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~l  149 (161)
                      ...-..|||=-++=.++..-..|. |||+...+=+.+--++..   .||.|=.+-
T Consensus       331 fHSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ccceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            344568999888877777888898 999999999999766543   499994443

>PF15102 TMEM154: TMEM154 protein family

Probab=90.06  E-value=0.15  Score=34.62  Aligned_cols=7  Identities=29%  Similarity=0.999  Sum_probs=4.2

Q ss_pred             hHHHHHc
Q 031354          131 CVDAWLS  137 (161)
Q Consensus       131 Ci~~Wl~  137 (161)
                      =+|+|+.
T Consensus       129 eldkwm~  135 (146)
T PF15102_consen  129 ELDKWMN  135 (146)
T ss_pred             HHHhHHH
Confidence            3666764

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

Probab=89.61  E-value=0.093  Score=44.13  Aligned_cols=48  Identities=25%  Similarity=0.695  Sum_probs=37.1

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC---CCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR---SSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~~  151 (161)
                      ...+|+||+.-+.+.   ..+. |.|.|...|+..-|...   ..||+|++.+..
T Consensus        20 k~lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hhccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            345899999998764   3455 99999999988877643   469999977653

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=89.53  E-value=0.54  Score=36.03  Aligned_cols=58  Identities=26%  Similarity=0.561  Sum_probs=38.1

Q ss_pred             CCCCCCCCccccccccccC---------------CC-eeeecCCCCCccchhhHHHHHcC---------CCCCccccccc
Q 031354           95 KDDKEEESECCICLGVFED---------------GD-KVKILPKCRHCYHCECVDAWLSA---------RSSCPLCRNSL  149 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~---------------~~-~v~~lp~C~H~FH~~Ci~~Wl~~---------~~~CP~CR~~l  149 (161)
                      ++......+|++|+..=.-               |. .-...| |||+--++=..=|-+.         +..||+|-..|
T Consensus       335 e~~g~~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L  413 (429)
T KOG3842|consen  335 ENTGQRERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQL  413 (429)
T ss_pred             cccCcccCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhh
Confidence            4444557899999975211               11 122356 9999777777788754         24599998887


Q ss_pred             cCCC
Q 031354          150 RVDS  153 (161)
Q Consensus       150 ~~~~  153 (161)
                      ..+.
T Consensus       414 ~ge~  417 (429)
T KOG3842|consen  414 AGEQ  417 (429)
T ss_pred             ccCC
Confidence            6553

>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=89.49  E-value=0.41  Score=36.18  Aligned_cols=49  Identities=33%  Similarity=0.581  Sum_probs=34.2

Q ss_pred             cccccccc-ccCCC-eeeecCCCCCccchhhHHHHHcCC-CCCccccccccCC
Q 031354          103 ECCICLGV-FEDGD-KVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRVD  152 (161)
Q Consensus       103 ~CaICL~~-f~~~~-~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~  152 (161)
                      .|++|-.+ |-+.+ .+.+-| |||-.|..|++.-+... ..||-|-..+..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~-C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINE-CGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeecc-ccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            47777653 33333 333446 99999999999998764 5799997766543

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.04  E-value=0.46  Score=35.24  Aligned_cols=55  Identities=13%  Similarity=0.230  Sum_probs=41.1

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSAL  155 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  155 (161)
                      .....|+|=--+|........+-.|||+|-..=+.+-  ...+|++|.+.+...+-+
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvI  163 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVI  163 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeE
Confidence            4456899987777766666666669999998877773  357899999988766543

>PRK00523 hypothetical protein; Provisional

Probab=88.81  E-value=2.7  Score=24.99  Aligned_cols=53  Identities=6%  Similarity=-0.006  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCChhhHH---hhcCCCCHHHHhc
Q 031354           30 SIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQ---ALTRGLDLTTINT   82 (161)
Q Consensus        30 ii~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~~   82 (161)
                      ++++++++++-++.-++..|.+..+.-..+++.+....+.   ...+..+++.+++
T Consensus         8 I~l~i~~li~G~~~Gffiark~~~k~l~~NPpine~mir~M~~QMGqKPSekki~Q   63 (72)
T PRK00523          8 LGLGIPLLIVGGIIGYFVSKKMFKKQIRENPPITENMIRAMYMQMGRKPSESQIKQ   63 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHhCCCccHHHHHH
Confidence            3333444444444555555555554233344433332222   3445555555543

>smart00249 PHD PHD zinc finger

Probab=87.85  E-value=0.4  Score=25.14  Aligned_cols=31  Identities=23%  Similarity=0.588  Sum_probs=21.5

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHH
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDA  134 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~  134 (161)
                      .|.+|-.....+..+.-- .|+..||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~-~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCD-GCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECC-CCCchhhhhhCCC
Confidence            377887766444444434 4999999999865

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

>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.40  E-value=4.3  Score=23.99  Aligned_cols=52  Identities=15%  Similarity=0.114  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCChhhHH---hhcCCCCHHHHh
Q 031354           30 SIIVVFAVVLLVSFLFLYARWFCRRFSHQNSNPDVPRAQQ---ALTRGLDLTTIN   81 (161)
Q Consensus        30 ii~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~i~   81 (161)
                      +++++++.++.++.-++..|....+.-..+++.+....+.   ...++.++..++
T Consensus         7 il~ivl~ll~G~~~G~fiark~~~k~lk~NPpine~~iR~M~~qmGqKpSe~kI~   61 (71)
T COG3763           7 ILLIVLALLAGLIGGFFIARKQMKKQLKDNPPINEEMIRMMMAQMGQKPSEKKIN   61 (71)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCchHHHHH
Confidence            3444444444444444444444444233343333332221   344555555544

>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=87.34  E-value=0.32  Score=26.59  Aligned_cols=44  Identities=34%  Similarity=0.657  Sum_probs=30.3

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHc------CCCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS------ARSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~------~~~~CP~CR~  147 (161)
                      .|.||-....+++.|.=- .|+-.||..|+..=..      ..-.||.|+.
T Consensus         1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcCCCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            488998855555555444 4999999999765432      2456998863

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 ....

>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.89  E-value=0.45  Score=27.05  Aligned_cols=19  Identities=47%  Similarity=0.976  Sum_probs=14.3

Q ss_pred             CCCCccccccccCCCCCCC
Q 031354          139 RSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus       139 ~~~CP~CR~~l~~~~~~~~  157 (161)
                      +..||+|+..+...+..|+
T Consensus         2 k~~CPlCkt~~n~gsk~~p   20 (61)
T PF05715_consen    2 KSLCPLCKTTLNVGSKDPP   20 (61)
T ss_pred             CccCCcccchhhcCCCCCC
Confidence            4679999999877666554

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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse

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

Probab=86.69  E-value=0.53  Score=35.22  Aligned_cols=49  Identities=27%  Similarity=0.551  Sum_probs=35.0

Q ss_pred             CCccccccccccCCCeeee---cCCCCCccchhhHHHHHcC---------CCCCccccccc
Q 031354          101 ESECCICLGVFEDGDKVKI---LPKCRHCYHCECVDAWLSA---------RSSCPLCRNSL  149 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~---lp~C~H~FH~~Ci~~Wl~~---------~~~CP~CR~~l  149 (161)
                      ..+|-+|-.++.+.+..+.   -|.|+-++|..|+..-+..         ...||.|+.-+
T Consensus       182 ~~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~  242 (276)
T KOG3005|consen  182 NVECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL  242 (276)
T ss_pred             chhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence            4699999999954444433   2238889999999995432         23699998755

>PF03911 Sec61_beta: Sec61beta family; InterPro: IPR005609 This family consists of Sec61 subunit beta and homologues like archaeal SecG

Probab=86.64  E-value=1.5  Score=23.12  Aligned_cols=33  Identities=21%  Similarity=0.367  Sum_probs=17.3

Q ss_pred             CCCcccCCCCCccccccchHHHHHHHHHHHHHH
Q 031354            9 FHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLV   41 (161)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~i~ii~~l~~~~l~~   41 (161)
                      ..++|.+.+.++...+...++++.+.+++++++
T Consensus         4 gl~r~y~ed~~giki~P~~Vl~~si~fi~~V~~   36 (41)
T PF03911_consen    4 GLLRYYEEDAPGIKIDPKTVLIISIAFIAIVIL   36 (41)
T ss_dssp             ---------S-SS-BSCCHHHHHHHHHHHHHHH
T ss_pred             cceeeeeccCCcceeCCeehHHHHHHHHHHHHH
Confidence            456666668888999999998887777666654

This subunit is a component of the Sec61/SecYEG protein secretory system.; PDB: 2WWA_C 2WW9_C 3BO0_C 3KCR_C 3BO1_C 2YXR_C 3DKN_C 2YXQ_C 1RH5_C 1RHZ_C ....

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

Probab=86.28  E-value=0.49  Score=38.30  Aligned_cols=39  Identities=23%  Similarity=0.640  Sum_probs=31.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR  139 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~  139 (161)
                      .....+|-||.+.+..  .+..+. |||.|+..|....+..+
T Consensus        67 ~~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~k  105 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGTK  105 (444)
T ss_pred             CCccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhhe
Confidence            4566799999999876  455566 99999999999998653

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

Probab=85.22  E-value=1.6  Score=33.51  Aligned_cols=25  Identities=12%  Similarity=0.329  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Q 031354           30 SIIVVFAVVLLVSFLFLYARWFCRR   54 (161)
Q Consensus        30 ii~~l~~~~l~~~~~~~~~~~~~~~   54 (161)
                      +..++++++++++++++|.-+++||
T Consensus       259 ~aSiiaIliIVLIMvIIYLILRYRR  283 (299)
T PF02009_consen  259 IASIIAILIIVLIMVIIYLILRYRR  283 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333334444444444433

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 [].

>TIGR00622 ssl1 transcription factor ssl1

Probab=85.01  E-value=1.5  Score=28.55  Aligned_cols=46  Identities=20%  Similarity=0.459  Sum_probs=33.1

Q ss_pred             CCccccccccccCC----------CeeeecCCCCCccchhhHHHHHcCCCCCcccc
Q 031354          101 ESECCICLGVFEDG----------DKVKILPKCRHCYHCECVDAWLSARSSCPLCR  146 (161)
Q Consensus       101 ~~~CaICL~~f~~~----------~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR  146 (161)
                      ...|--|+..|.+.          .....-+.|++.|+.+|=.=+-+.-.+||-|-
T Consensus        55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~  110 (112)
T TIGR00622        55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI  110 (112)
T ss_pred             CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence            35699999988753          12234556999999999666655556799985

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

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

Probab=84.74  E-value=1.2  Score=24.46  Aligned_cols=42  Identities=19%  Similarity=0.507  Sum_probs=18.7

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----CCCCcccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----RSSCPLCRNS  148 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~  148 (161)
                      .|+|-...+.  -.+|... |.|.-+ -=++.|+..     ...||+|+++
T Consensus         4 ~CPls~~~i~--~P~Rg~~-C~H~~C-FDl~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIR--IPVRGKN-CKHLQC-FDLESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-S--SEEEETT---SS---EEHHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEE--eCccCCc-Ccccce-ECHHHHHHHhhccCCeECcCCcCc
Confidence            5777666543  4677776 988721 114556643     2469999864

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

>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=84.15  E-value=0.68  Score=27.06  Aligned_cols=38  Identities=21%  Similarity=0.370  Sum_probs=20.2

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHH
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL  136 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl  136 (161)
                      .+...|.+|-..|.--..-..-..||++|+.+|.....
T Consensus         7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~   44 (69)
T PF01363_consen    7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI   44 (69)
T ss_dssp             GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred             CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence            45678999999996544333444599999999987654

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 ....

>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=83.18  E-value=0.64  Score=21.93  Aligned_cols=23  Identities=22%  Similarity=0.511  Sum_probs=12.5

Q ss_pred             ccccccccccCCCeeeecCCCCCcc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCY  127 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~F  127 (161)
                      .|+-|-.+....  .+.-|.|||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            366665554332  33345677776

Several members are annotated as putative helicases.

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

Probab=83.03  E-value=0.62  Score=37.33  Aligned_cols=34  Identities=32%  Similarity=0.680  Sum_probs=27.6

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS  137 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~  137 (161)
                      ++..|+||..-|++   -.+|| |+|..+..|-..-+.
T Consensus         3 eelkc~vc~~f~~e---piil~-c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYRE---PIILP-CSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccC---ceEee-cccHHHHHHHHhhcc
Confidence            45689999988875   55789 999999999876553

>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=82.51  E-value=0.81  Score=33.75  Aligned_cols=50  Identities=32%  Similarity=0.578  Sum_probs=35.4

Q ss_pred             CCCCccccccccccCC-C-eeeecCCCCCccchhhHHHHHcCC-CCCc--ccccc
Q 031354           99 EEESECCICLGVFEDG-D-KVKILPKCRHCYHCECVDAWLSAR-SSCP--LCRNS  148 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~-~-~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP--~CR~~  148 (161)
                      ..+..|+||-.+---. + .+.+-|-|-|..|..|++.-+... ..||  -|..-
T Consensus         8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kI   62 (314)
T COG5220           8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKI   62 (314)
T ss_pred             hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHH
Confidence            3456899998764332 3 334445599999999999999875 4699  67543

>KOG3457 consensus Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones]

Probab=82.18  E-value=2.7  Score=25.80  Aligned_cols=47  Identities=11%  Similarity=0.123  Sum_probs=32.5

Q ss_pred             CCCCCCCCcccCCCCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031354            4 QESQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLVSFLFLYARWFC   52 (161)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~i~ii~~l~~~~l~~~~~~~~~~~~~   52 (161)
                      ..+++..|.+..+|..++-++...++++.+.+++.++  .+.++-++..
T Consensus        39 ~~~t~~mlkfYTDda~GlKV~PvvVLvmSvgFIasV~--~LHi~gK~~~   85 (88)
T KOG3457|consen   39 GGSTGGMLKFYTDDAPGLKVDPVVVLVMSVGFIASVF--ALHIWGKLTR   85 (88)
T ss_pred             CCCCCceeEEeecCCCCceeCCeeehhhhHHHHHHHH--HHHHHHHHhh
Confidence            3577789998888888888888887777766555443  3555544443

>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ]

Probab=81.84  E-value=0.44  Score=37.59  Aligned_cols=27  Identities=41%  Similarity=0.935  Sum_probs=0.0

Q ss_pred             eeeecCCCCCc--cchhhHHHHHcC------CCCCcccccc
Q 031354          116 KVKILPKCRHC--YHCECVDAWLSA------RSSCPLCRNS  148 (161)
Q Consensus       116 ~v~~lp~C~H~--FH~~Ci~~Wl~~------~~~CP~CR~~  148 (161)
                      .-..|. |||+  +|.     |-..      ..+||+||..
T Consensus       303 P~VYl~-CGHVhG~h~-----Wg~~~~~~~~~r~CPlCr~~  337 (416)
T PF04710_consen  303 PWVYLN-CGHVHGYHN-----WGQDSDRDPRSRTCPLCRQV  337 (416)
T ss_dssp             -----------------------------------------
T ss_pred             ceeecc-ccceeeecc-----cccccccccccccCCCcccc
Confidence            344566 9998  554     7542      3469999864

; PDB: 3EGB_B 3EGA_A.

>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=81.41  E-value=1.3  Score=24.60  Aligned_cols=42  Identities=29%  Similarity=0.750  Sum_probs=20.6

Q ss_pred             cccccccccCC------CeeeecCCCCCccchhhHHHHHc-CCCCCcccc
Q 031354          104 CCICLGVFEDG------DKVKILPKCRHCYHCECVDAWLS-ARSSCPLCR  146 (161)
Q Consensus       104 CaICL~~f~~~------~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR  146 (161)
                      |.-|+..|..+      .....-|.|++.|+.+|= ...- .-.+||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD-~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCD-VFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHH-HTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcC-hhhhccccCCcCCC
Confidence            55677777664      245566779999998883 2222 224598874

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.

>TIGR01478 STEVOR variant surface antigen, stevor family

Probab=81.39  E-value=3.1  Score=31.53  Aligned_cols=24  Identities=29%  Similarity=0.585  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 031354           31 IIVVFAVVLLVSFLFLYARWFCRR   54 (161)
Q Consensus        31 i~~l~~~~l~~~~~~~~~~~~~~~   54 (161)
                      |.+++.+++.++++++|+++++||
T Consensus       263 iaalvllil~vvliiLYiWlyrrR  286 (295)
T TIGR01478       263 IAALVLIILTVVLIILYIWLYRRR  286 (295)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444444444444445555554444

This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=81.09  E-value=0.93  Score=22.54  Aligned_cols=19  Identities=37%  Similarity=0.742  Sum_probs=12.8

Q ss_pred             CCCccchhhHHHHHcCCCCCccccc
Q 031354          123 CRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus       123 C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      |||++-..-      ....||+|..
T Consensus         7 CGy~y~~~~------~~~~CP~Cg~   25 (33)
T cd00350           7 CGYIYDGEE------APWVCPVCGA   25 (33)
T ss_pred             CCCEECCCc------CCCcCcCCCC
Confidence            888765432      3457999965

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=80.67  E-value=1.1  Score=22.95  Aligned_cols=25  Identities=40%  Similarity=0.809  Sum_probs=14.1

Q ss_pred             ccccccccccCCC--------eeeecCCCCCccc
Q 031354          103 ECCICLGVFEDGD--------KVKILPKCRHCYH  128 (161)
Q Consensus       103 ~CaICL~~f~~~~--------~v~~lp~C~H~FH  128 (161)
                      .|+=|-..|+-.+        .++ -+.|+|+|+
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vr-C~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVR-CPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEE-CCCCCcEee
Confidence            4666666665433        333 334788875

>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised

Probab=80.37  E-value=6.4  Score=22.89  Aligned_cols=13  Identities=15%  Similarity=0.141  Sum_probs=6.8

Q ss_pred             hhcCCCCHHHHhc
Q 031354           70 ALTRGLDLTTINT   82 (161)
Q Consensus        70 ~~~~~~~~~~i~~   82 (161)
                      ...+..+++.++.
T Consensus        43 QMG~kpSekqi~Q   55 (64)
T PF03672_consen   43 QMGRKPSEKQIKQ   55 (64)
T ss_pred             HhCCCccHHHHHH
Confidence            4455555555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	161
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		6e-10
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		7e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-05
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		8e-04

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 34/48 (70%)
Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV 151
           C +CL   EDG++ + LP+C H +H ECVD WL + S+CPLCR ++ V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 3/54 (5%)
Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPS 157
           C ICL + E+G+ V+ LP C H +H  CVD WL     CP+CR  + +++ LPS
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR--VDIEAQLPS 67

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           C +C+  FE    +++LP C H +H +CVD WL A  +CP+CR
Sbjct: 26  CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67

>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 = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
           C +C   +  G+ V+ LP C H +H  C+  WL    SCP+CR SL
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	161
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-25
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-24
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	5e-22
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	6e-22
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-21
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-19
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	6e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	8e-16
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-10
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	4e-10
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	4e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	1e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-08
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	3e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	6e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	8e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	1e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	1e-07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	7e-07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	5e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	9e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	3e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	6e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	8e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	3e-04
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	3e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	4e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-04

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

 Score = 90.7 bits (226), Expect = 3e-25
 Identities = 25/53 (47%), Positives = 37/53 (69%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV 151
           ++  EC +CL   EDG++ + LP+C H +H ECVD WL + S+CPLCR ++ V
Sbjct: 3   DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

 Score = 88.9 bits (221), Expect = 2e-24
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 79  TINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA 138
           +   LP           +     + C +C+  FE    +++LP C H +H +CVD WL A
Sbjct: 5   SSGQLPSYRFNPNNHQSEQ----TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKA 59

Query: 139 RSSCPLCRNSLRVDSA 154
             +CP+CR      S 
Sbjct: 60  NRTCPICRADSGPSSG 75

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

 Score = 83.5 bits (207), Expect = 5e-22
 Identities = 23/78 (29%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 72  TRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCEC 131
                  +I+ LP +L   +        +E  C IC   +  GD    LP C H +H  C
Sbjct: 14  NPPASKESIDALPEILVTEDHGAVG---QEMCCPICCSEYVKGDVATELP-CHHYFHKPC 69

Query: 132 VDAWLSARSSCPLCRNSL 149
           V  WL    +CP+CR   
Sbjct: 70  VSIWLQKSGTCPVCRCMF 87

>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 = 82.4 bits (204), Expect = 6e-22
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 89  RSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNS 148
           + +     +++ E +C ICL + E+G+ V+ LP C H +H  CVD WL     CP+CR  
Sbjct: 2   KQDGEEGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVD 60

Query: 149 LRVDSALPS 157
           +       S
Sbjct: 61  IEAQLPSES 69

>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 = 80.9 bits (200), Expect = 3e-21
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
               T++      EC +C   +  G+ V+ LP C H +H  C+  WL    SCP+CR SL
Sbjct: 4   GSSGTEEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

Query: 150 RVDSA 154
              + 
Sbjct: 63  TGQNT 67

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

 Score = 76.7 bits (189), Expect = 1e-19
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
                  +      C +CL  F+  D++ I P C+H +H +C+  WL  R  CPLC   +
Sbjct: 4   GSSGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 66.9 bits (164), Expect = 6e-16
 Identities = 15/49 (30%), Positives = 17/49 (34%)

Query: 101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
            S C ICL        V  +  C H  H  C +  L     CPLC    
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 67.0 bits (164), Expect = 8e-16
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 5/56 (8%)

Query: 94  TKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL 149
                 +E ECCIC+    DG    ILP C H +  +C+D W     +CP+CR  +
Sbjct: 8   RVKQLTDEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQM 58

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

 Score = 60.7 bits (147), Expect = 3e-13
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           +    C  C    +  D V +  +C H +H  C+  W+   + CPLC+
Sbjct: 24  QVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 53.6 bits (129), Expect = 1e-10
 Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR 150
                C ICL    +      LP C H +   C+  W+    +CPLC+  + 
Sbjct: 3   TVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 54.5 bits (131), Expect = 1e-10
 Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 89  RSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRN 147
             ++ + +   E   C IC+    D    ++ P C       C+  WL+  R+ CP CR 
Sbjct: 10  HMDEQSVESIAEVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRA 66

Query: 148 SLRVDSALPS 157
            L++   +  
Sbjct: 67  PLQLRELVNC 76

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 3/67 (4%)

Query: 93  STKDDKEEESECCICLGVFEDGDKVKILP---KCRHCYHCECVDAWLSARSSCPLCRNSL 149
           +T         C IC+  + +  +   L    +C H +  +C+   L   ++CP CR  +
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

Query: 150 RVDSALP 156
                 P
Sbjct: 62  NHKRYHP 68

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

 Score = 52.2 bits (125), Expect = 4e-10
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 3/63 (4%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILP---KCRHCYHCECVDAWLSARSSCPLCR 146
               T         C IC+  + +  +   L    +C H +  +C+   L   ++CP CR
Sbjct: 4   GSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63

Query: 147 NSL 149
             +
Sbjct: 64  KKI 66

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

 Score = 53.3 bits (127), Expect = 4e-09
 Identities = 19/92 (20%), Positives = 30/92 (32%), Gaps = 15/92 (16%)

Query: 75  LDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKIL----PKCRHCYHCE 130
           L +  +   P+          ++  EE  C IC     DG +V ++     KC    H  
Sbjct: 282 LRMFDLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAV 341

Query: 131 CVDAWLSARSS-----------CPLCRNSLRV 151
           C++ W                 CP C+  L  
Sbjct: 342 CLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST 373

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

 Score = 49.0 bits (117), Expect = 6e-09
 Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 100 EESECCICLGVFED---GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP 156
               C IC+  + +     ++ +  +C H +  +C+   L   ++CP CR  +      P
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP 61

>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 = 49.4 bits (117), Expect = 1e-08
 Identities = 11/43 (25%), Positives = 14/43 (32%)

Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           C          +       C H +H  C+  WL  R  CPL  
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 48.7 bits (116), Expect = 2e-08
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 87  LHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           +HR+ +    +      C +C G F D      + +C H +   C+  +L     CP+C 
Sbjct: 1   MHRTTRIKITELNPHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICD 57

Query: 147 NSLRVDSALPSI 158
             +     L +I
Sbjct: 58  VQVHKTRPLLNI 69

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

 Score = 47.1 bits (112), Expect = 3e-08
 Identities = 12/65 (18%), Positives = 21/65 (32%), Gaps = 3/65 (4%)

Query: 96  DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSAL 155
            +      C IC G   D      + +C H +   C+       + CP C   +     L
Sbjct: 10  SELTPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL 66

Query: 156 PSITT 160
              ++
Sbjct: 67  SGPSS 71

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

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 4/63 (6%)

Query: 88  HRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN 147
                   D  E E +C IC   F +     +   C H +   C++ W+  +  CP+CR 
Sbjct: 51  EEVLSHMNDVLENELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRK 106

Query: 148 SLR 150
            ++
Sbjct: 107 DIK 109

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A* Length = 389

 Score = 49.8 bits (118), Expect = 6e-08
 Identities = 22/96 (22%), Positives = 34/96 (35%), Gaps = 6/96 (6%)

Query: 62  PDVPRAQQALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILP 121
           PD       LT   + T  + +  V     +   +       C IC    +D   VKI P
Sbjct: 294 PDGRNQNPDLTGLCEPTPQDHIK-VTQEQYELYCEMGSTFQLCKICAENDKD---VKIEP 349

Query: 122 KCRHCYHCECVDAWLSARS-SCPLCRNSLRVDSALP 156
            C H     C+ +W  +    CP CR  ++    + 
Sbjct: 350 -CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV 384

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 47.5 bits (112), Expect = 8e-08
 Identities = 11/43 (25%), Positives = 14/43 (32%)

Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
           C          +       C H +H  C+  WL  R  CPL  
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR 146
                 +++E    C IC   F++     ++ KCRH +   C      A   C +C 
Sbjct: 4   GSSGGSEEEEIPFRCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICD 56

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

 Score = 45.6 bits (108), Expect = 1e-07
 Identities = 14/64 (21%), Positives = 18/64 (28%), Gaps = 4/64 (6%)

Query: 93  STKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD 152
                     EC ICL          +   C+H +   CV         C LCR  +  D
Sbjct: 7   GNTAPSLTVPECAICLQTCVH----PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

Query: 153 SALP 156
               
Sbjct: 63  FLDS 66

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

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR 150
           ++   C IC   F       I+P+C H Y   C+  +LS ++ CP C  ++ 
Sbjct: 20  DDLLRCGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT 68

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 44.5 bits (105), Expect = 3e-07
 Identities = 12/54 (22%), Positives = 17/54 (31%), Gaps = 5/54 (9%)

Query: 98  KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL--SARSSCPLCRNSL 149
            +    C IC  +   G        C    H  CV  +   +A   CP C +  
Sbjct: 12  PDAVKICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

>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 = 44.8 bits (105), Expect = 7e-07
 Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 21/80 (26%)

Query: 86  VLHRSEKSTKDDKEEESECCICLGVFEDG--------------DKVKILPKCRHCYHCEC 131
           V+ +  +  K   EE+  C IC+                      V  L KC H +H  C
Sbjct: 12  VIRKYTEELKVAPEED--CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLC 69

Query: 132 VDAWLSARS-----SCPLCR 146
           + A     +      CP C+
Sbjct: 70  LLAMYCNGNKDGSLQCPSCK 89

>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 = 41.7 bits (98), Expect = 5e-06
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL--SARSSCPLCRN 147
                 D   +E  C IC  +  D     ++P C + Y  EC+   L  S   +CP C  
Sbjct: 4   GSSGEDDPIPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 60

Query: 148 SLRVDSAL 155
           +     AL
Sbjct: 61  NDVSPDAL 68

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

 Score = 40.9 bits (95), Expect = 9e-06
 Identities = 14/55 (25%), Positives = 20/55 (36%), Gaps = 1/55 (1%)

Query: 93  STKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCR 146
            + D KE+  EC +C+   E  D       C +     C     +     CP CR
Sbjct: 3   RSPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 57

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

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 99  EEESECCICLGVFEDGDKVKILP---KCRHCYHCECVDAWLSARSSCPLCRNSLR 150
                C IC+  + +  +   L    +C H +  +C+   L   ++CP CR  + 
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59

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

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 93  STKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL--SARSSCPLCR 146
           S  D   +E  C IC  +  D     ++P C + Y  EC+   L  S   +CP C 
Sbjct: 5   SEDDPIPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57

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

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKV-KILPKCRHCYHCECVDAWLSARS---SCPLC 145
                 D   E  EC IC+  F +     K+L  C H    +C++  L++      CP C
Sbjct: 4   GSSGNLDALREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFC 62

Query: 146 RNSLRVDSA 154
               R+ S 
Sbjct: 63  SKITRITSL 71

>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 = 39.6 bits (92), Expect = 6e-05
 Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNS 148
             +      EE  +C  C  +            C+H    +C+D    A+  SCP CR  
Sbjct: 41  PFQLFLSKVEETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYD 96

Query: 149 LRVDSALP 156
           L    A+ 
Sbjct: 97  LGRSYAMQ 104

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

 Score = 39.1 bits (91), Expect = 8e-05
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 10/66 (15%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCR-----NSLRVDS 153
           E+   C  C  +  +      L  C H +   CV   +   + CP+C        L+++ 
Sbjct: 20  EKLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINR 74

Query: 154 ALPSIT 159
            L S+ 
Sbjct: 75  QLDSMI 80

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 5/67 (7%)

Query: 90  SEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNS 148
              +     E+   C  C  +            C H    +C+     A+  SCP CR+ 
Sbjct: 67  EGPNFLKKLEQSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHD 122

Query: 149 LRVDSAL 155
           L  +  +
Sbjct: 123 LGQNYIM 129

>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 = 36.4 bits (84), Expect = 3e-04
 Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 96  DDKEEESECCICLGVFEDGDKVKILPKCRHCYHC-ECVDAWLSARSSCPLCR 146
           D +     C +C     DG    I  +  H   C  C      A +SCP+C+
Sbjct: 2   DCQNLLKPCSLCEKRPRDG--NIIHGRTGHLVTCFHCARRLKKAGASCPICK 51

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 10/69 (14%)

Query: 97  DKEEESECCICLGVFEDGDKVKILPKCRHCYHCEC-VDAWLSARSSCPLCR------NSL 149
               E  C ICL + ++        +C H +  +C + A  S    CP CR       SL
Sbjct: 50  SLHSELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 106

Query: 150 RVDSALPSI 158
           R D    ++
Sbjct: 107 RPDPNFDAL 115

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

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 5/51 (9%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL--SARSSCPLCRN 147
           +    C IC  +   G   +    C    H  CV  +   +A   CP C +
Sbjct: 178 DAVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	161
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.88
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.85
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.81
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.81
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.81
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.8
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.78
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.76
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.74
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.73
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.72
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.72
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.72
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.72
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.7
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.69
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.67
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.66
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.65
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.64
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.61
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.61
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.6
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.6
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.58
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.58
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.58
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.58
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.57
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.56
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.56
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.55
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.54
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.54
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.54
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.53
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.52
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.5
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.47
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.47
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.47
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.44
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.44
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.43
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.42
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.42
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.41
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.41
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.4
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.38
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.35
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.33
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.33
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.32
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.32
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.31
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.31
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.29
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.23
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.21
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.18
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.15
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.13
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.11
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.08
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.01
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.92
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.91
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.9
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.68
3nw0_A	238	Non-structural maintenance of chromosomes element	98.34
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.59
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	97.18
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.62
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.48
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	95.47
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	94.88
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	94.76
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	94.76
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	94.7
2yt5_A	66	Metal-response element-binding transcription facto	94.58
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	94.57
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	94.54
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	94.53
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	94.46
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	94.45
1we9_A	64	PHD finger family protein; structural genomics, PH	94.4
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.27
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	94.14
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	94.09
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	93.65
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	93.49
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	93.32
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	92.8
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	92.55
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	92.36
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	91.99
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	91.71
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	91.63
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	91.51
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	91.25
2l8s_A	54	Integrin alpha-1; transmembrane region, detergent	90.4
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	90.19
2knc_A	54	Integrin alpha-IIB; transmembrane signaling, prote	89.58
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	88.98
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	88.72
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	88.17
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	87.9
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	87.86
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	87.22
1wew_A	78	DNA-binding family protein; structural genomics, P	87.02
1wem_A	76	Death associated transcription factor 1; structura	86.96
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	86.87
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	86.76
2wwb_C	96	SEC61BETA, protein transport protein SEC61 subunit	86.74
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	86.2
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	85.99
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	85.73
1weu_A	91	Inhibitor of growth family, member 4; structural g	85.34
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	85.01
2k1a_A	42	Integrin alpha-IIB; single-PASS transmembrane segm	84.64
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	84.27
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	84.22
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	83.92
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	83.91
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	83.81
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	83.27
1wee_A	72	PHD finger family protein; structural genomics, PH	83.12
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	82.98
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	82.94
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	82.42
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	82.08
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	81.83
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	81.52
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	81.07
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	80.46
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	80.35

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

Probab=99.88  E-value=6.5e-23  Score=128.90  Aligned_cols=79  Identities=29%  Similarity=0.646  Sum_probs=69.0

Q ss_pred             HhhcCCCCHHHHhcCCcEeeecCCCCCCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccc
Q 031354           69 QALTRGLDLTTINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNS  148 (161)
Q Consensus        69 ~~~~~~~~~~~i~~lp~~~~~~~~~~~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  148 (161)
                      ....++++++.++.||.+.+....   .....+..|+||+++|.+++.++.+| |||.||..||++|+..+.+||+||..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~---~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~   86 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDH---GAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCM   86 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTC---SSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCB
T ss_pred             CcCCCCCCHHHHHhCCCeeecccc---cccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCcc
Confidence            345678999999999999877544   23456789999999999999999999 99999999999999999999999998


Q ss_pred             ccC
Q 031354          149 LRV  151 (161)
Q Consensus       149 l~~  151 (161)
                      +..
T Consensus        87 ~~~   89 (91)
T 2l0b_A           87 FPP   89 (91)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

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

Probab=99.85  E-value=3.9e-22  Score=120.95  Aligned_cols=70  Identities=33%  Similarity=0.820  Sum_probs=59.6

Q ss_pred             HHhcCCcEeeecCCCCCCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354           79 TINTLPIVLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus        79 ~i~~lp~~~~~~~~~~~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      .++.+|.+++....    ...+...|+||+++|.+++.++.+| |||+||..||.+|++.+.+||+||+++...+
T Consensus         5 ~i~~lp~~~~~~~~----~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            5 SSGQLPSYRFNPNN----HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPSS   74 (75)
T ss_dssp             CCSSCCCEEBCSSS----CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCCC
T ss_pred             hHhhCCcEEecCcc----ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCCC
Confidence            45678888776433    3456789999999999999999999 9999999999999999999999999987654

>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=99.81  E-value=3.1e-20  Score=110.72  Aligned_cols=59  Identities=37%  Similarity=0.986  Sum_probs=52.2

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      .........|+||++.|..++.++.+| |||+||..||.+|+..+.+||+||..+....+
T Consensus         8 ~~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A            8 GTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             CCSTTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             cCcCCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            344566789999999999988999999 99999999999999998999999999977654

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

Probab=99.81  E-value=1.3e-20  Score=107.43  Aligned_cols=52  Identities=46%  Similarity=1.188  Sum_probs=47.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      .++.+|+||+++|.+++.+..+|.|||.||.+||.+|++.+.+||+||+++.
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            4567899999999999988888779999999999999999999999999875

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

Probab=99.81  E-value=4.1e-20  Score=111.67  Aligned_cols=61  Identities=31%  Similarity=0.777  Sum_probs=53.8

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  157 (161)
                      .....+..|+||+++|.+++.++++| |||+||..||.+|++.+.+||+||.++.....++.
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (74)
T 2ep4_A           10 KELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSG   70 (74)
T ss_dssp             CCCCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCSCCC
T ss_pred             ccCCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccccccCC
Confidence            34456789999999999999999999 99999999999999988999999999987766554

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

Probab=99.80  E-value=5.4e-20  Score=112.23  Aligned_cols=62  Identities=32%  Similarity=0.790  Sum_probs=54.5

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  157 (161)
                      .........|+||+++|.+++.++.++ |||+||..||.+|++.+.+||+||..+......++
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A            9 EEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             CTTSSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             cccCCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            344566789999999999999999999 99999999999999999999999999987766544

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

Probab=99.78  E-value=7.1e-20  Score=112.50  Aligned_cols=53  Identities=32%  Similarity=0.764  Sum_probs=43.5

Q ss_pred             CCCccccccccccC-----------CCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCC
Q 031354          100 EESECCICLGVFED-----------GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~-----------~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      +++.|+||+++|.+           ++.+++++.|||+||.+||++|+..+.+||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            46678888888854           455666656999999999999999999999999997643

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

Probab=99.76  E-value=5.3e-19  Score=100.66  Aligned_cols=51  Identities=31%  Similarity=0.670  Sum_probs=44.6

Q ss_pred             CCCCccccccccccCC-CeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           99 EEESECCICLGVFEDG-DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~-~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      .+...|+||+++|.++ +.+..++ |||+||..||.+|++.+.+||+||.++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            4667899999999664 4577888 9999999999999998899999999874

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

Probab=99.74  E-value=1.2e-18  Score=106.32  Aligned_cols=62  Identities=24%  Similarity=0.626  Sum_probs=52.2

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCC-----CccchhhHHHHHcCC--CCCccccccccCCCCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCR-----HCYHCECVDAWLSAR--SSCPLCRNSLRVDSALPSIT  159 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~~~~~~~~  159 (161)
                      ....++..|+||+++|.+++.+ ++| |+     |.||.+||++|+..+  .+||+||.++.....+++..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~~P~~   78 (80)
T 2d8s_A           10 ITPSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLSGPS   78 (80)
T ss_dssp             CCCTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCSCCCC
T ss_pred             CCCCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCcccCCCC
Confidence            4455678999999999988877 689 96     999999999999865  58999999999887776653

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

Probab=99.73  E-value=2.1e-18  Score=103.16  Aligned_cols=58  Identities=21%  Similarity=0.578  Sum_probs=49.0

Q ss_pred             CCCCCCccccccccccC----CCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCC
Q 031354           97 DKEEESECCICLGVFED----GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSAL  155 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~----~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  155 (161)
                      ...+...|+||++.|.+    ++.+..++ |||.||..||.+|+..+.+||+||.++...+-.
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            34567899999999876    35567888 999999999999999999999999999866543

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

Probab=99.72  E-value=4.7e-18  Score=110.84  Aligned_cols=52  Identities=23%  Similarity=0.594  Sum_probs=43.1

Q ss_pred             CCCccccccccccCCC---------------eeeecCCCCCccchhhHHHHH-----cCCCCCccccccccCC
Q 031354          100 EESECCICLGVFEDGD---------------KVKILPKCRHCYHCECVDAWL-----SARSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~---------------~v~~lp~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~l~~~  152 (161)
                      .++.|+|||++|.+..               .++.++ |||+||..||++|+     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4569999999997643               445788 99999999999999     4567899999998644

>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=99.72  E-value=3.4e-18  Score=109.80  Aligned_cols=50  Identities=30%  Similarity=0.662  Sum_probs=43.4

Q ss_pred             CCCccccccccccCC---------------CeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354          100 EESECCICLGVFEDG---------------DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus       100 ~~~~CaICL~~f~~~---------------~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      +++.|+||+++|.+.               ..++.++ |+|.||..||++||..+.+||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            467899999999864               1366788 9999999999999999999999999854

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

Probab=99.72  E-value=3.7e-18  Score=101.47  Aligned_cols=55  Identities=20%  Similarity=0.541  Sum_probs=46.6

Q ss_pred             CCCCCCCccccccccccCC----CeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354           96 DDKEEESECCICLGVFEDG----DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~----~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ....+...|+||++.|.+.    ..+..++ |||+||..||++|+..+.+||+||.++..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCTTCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4456678999999999863    4457788 99999999999999998999999998754

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

Probab=99.72  E-value=4.9e-18  Score=101.36  Aligned_cols=57  Identities=33%  Similarity=0.848  Sum_probs=49.0

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      ...+...|+||++.+.+    ..+| |||.||..||.+|+..+.+||+||.++...+.....
T Consensus        11 ~~~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   67 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSGP   67 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCCCC
T ss_pred             cCCCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCccccC
Confidence            34567899999999876    5788 999999999999999999999999999877765544

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

Probab=99.70  E-value=3.9e-18  Score=99.90  Aligned_cols=53  Identities=21%  Similarity=0.585  Sum_probs=45.9

Q ss_pred             CCCccccccccccCC----CeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354          100 EESECCICLGVFEDG----DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~----~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      +..+|+||+++|.+.    +.+..++ |||.||..|+.+|+..+.+||+||.++...+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            467899999999753    4557788 9999999999999999999999999987654

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

Probab=99.69  E-value=2.6e-17  Score=98.73  Aligned_cols=60  Identities=22%  Similarity=0.461  Sum_probs=50.1

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      +...+...|+||++.|.+  .+.+++ |||.||..||.+|+..+.+||+||.++...+..+.+
T Consensus        10 ~~~~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A           10 SELTPYILCSICKGYLID--ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CCCCGGGSCTTTSSCCSS--CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCCC
T ss_pred             hhcCCCCCCCCCChHHHC--cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcccccccC
Confidence            344567799999999875  444457 999999999999999889999999999988777654

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

Probab=99.67  E-value=4.6e-17  Score=97.41  Aligned_cols=54  Identities=30%  Similarity=0.574  Sum_probs=45.6

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      ....+...|+||++.+.+   ...+| |||+||..||.+|+..+.+||+||..+....
T Consensus        10 ~~~~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           10 APSLTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             CSSSSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHHH
T ss_pred             ccCCCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHhh
Confidence            344567799999999865   45678 9999999999999999999999999987543

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus}

Probab=99.66  E-value=7.9e-18  Score=109.54  Aligned_cols=50  Identities=30%  Similarity=0.701  Sum_probs=1.0

Q ss_pred             CCCccccccccccCC-------------C--eeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354          100 EESECCICLGVFEDG-------------D--KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus       100 ~~~~CaICL~~f~~~-------------~--~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      .++.|+||+++|.+.             +  .+..++ |+|.||..||++||..+.+||+||++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            457999999999752             2  233356 9999999999999999999999999864

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

Probab=99.65  E-value=6.6e-17  Score=95.83  Aligned_cols=50  Identities=28%  Similarity=0.763  Sum_probs=43.4

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ..+..|+||++.+.+  .+..+| |||.||..|+.+|+..+.+||+||.++..
T Consensus         3 ~~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            3 TVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            456789999999864  356788 99999999999999988999999999864

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

Probab=99.64  E-value=2.1e-16  Score=98.27  Aligned_cols=56  Identities=30%  Similarity=0.694  Sum_probs=47.4

Q ss_pred             CCCCCCCccccccccccCCCe-eeecCCCCCccchhhHHHHHcCC---CCCccccccccCC
Q 031354           96 DDKEEESECCICLGVFEDGDK-VKILPKCRHCYHCECVDAWLSAR---SSCPLCRNSLRVD  152 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~-v~~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~~~  152 (161)
                      ....+...|+||++.|.+++. ...++ |||.||..|+.+|+..+   .+||+||..+...
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             hhccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            345567799999999998764 66788 99999999999999875   7899999988654

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

Probab=99.61  E-value=7.3e-16  Score=92.51  Aligned_cols=53  Identities=28%  Similarity=0.668  Sum_probs=43.7

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc---CCCCCccccccccCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS---ARSSCPLCRNSLRVDS  153 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~l~~~~  153 (161)
                      ...+...|+||++.|.+   ...++ |||.||..||.+|++   .+.+||+||.++..++
T Consensus        16 ~~~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           16 KLQEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             hCccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            34567799999999875   44568 999999999999997   4568999999987653

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

Probab=99.61  E-value=5.6e-16  Score=94.95  Aligned_cols=51  Identities=24%  Similarity=0.597  Sum_probs=43.6

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ........|+||++.|.+   ..+++ |||.||..||.+|+..+.+||+||.++.
T Consensus        10 ~~~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            344556799999999965   34688 9999999999999998899999999985

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

Probab=99.60  E-value=7.3e-16  Score=90.80  Aligned_cols=53  Identities=26%  Similarity=0.506  Sum_probs=43.2

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccccccccCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRVDS  153 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~~  153 (161)
                      ...+...|+||++.+.+.  + .++ |||.||..||.+|+. .+.+||+||.++..++
T Consensus        11 ~~~~~~~C~IC~~~~~~p--~-~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           11 TVEDKYKCEKCHLVLCSP--K-QTE-CGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             SCCCCEECTTTCCEESSC--C-CCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             cCCcCCCCCCCChHhcCe--e-ECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            345677999999998753  2 368 999999999999995 5678999999987653

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

Probab=99.60  E-value=7.9e-16  Score=92.71  Aligned_cols=56  Identities=30%  Similarity=0.649  Sum_probs=44.2

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--CCCccccccccCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--SSCPLCRNSLRVDSA  154 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~~~  154 (161)
                      +...+...|+||++.|.+  .+ ++|.|||.||..||..|+..+  .+||+||.++...+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~--p~-~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           10 DPIPDELLCLICKDIMTD--AV-VIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             CCSCGGGSCSSSCCCCTT--CE-ECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             ccCCCCCCCcCCChHHhC--Ce-EcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            344567799999999975  33 466699999999999999865  689999998655443

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

Probab=99.58  E-value=7.8e-16  Score=103.53  Aligned_cols=47  Identities=30%  Similarity=0.918  Sum_probs=41.7

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      +..|+||++.|.+   ..++| |||.||..||..|+..+.+||+||.++..
T Consensus        53 ~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            4579999999975   45788 99999999999999999999999999864

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

Probab=99.58  E-value=2.2e-15  Score=90.05  Aligned_cols=51  Identities=22%  Similarity=0.588  Sum_probs=43.8

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--CCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--SSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~  151 (161)
                      .....+|+||.+.+..++...  . |+|.||..||.+||+.+  .+||+||++...
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C~--~-C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSCE--T-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEECS--S-SCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             cCCCCcCcchhhHcccCCccC--C-CCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            445689999999999876664  5 99999999999999877  789999998763

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

Probab=99.58  E-value=7.5e-16  Score=102.60  Aligned_cols=55  Identities=20%  Similarity=0.559  Sum_probs=47.1

Q ss_pred             CCCCccccccccccCC----CeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354           99 EEESECCICLGVFEDG----DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~----~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      .+...|+||++.|.+.    +.+..++ |||.||..||.+|++.+.+||+||..+.....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            4567899999999763    5557888 99999999999999999999999999876543

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

Probab=99.58  E-value=2e-15  Score=91.77  Aligned_cols=56  Identities=25%  Similarity=0.487  Sum_probs=46.3

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~~  157 (161)
                      ..+...|+||++.|.+   -.+++ |||.||..||.+|+.. +.+||+||.++...+..|.
T Consensus         5 ~~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n   61 (78)
T 1t1h_A            5 FPEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             CSSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             CcccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccC
Confidence            4567899999999875   34568 9999999999999987 7889999999987655444

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

Probab=99.57  E-value=2.7e-15  Score=92.41  Aligned_cols=58  Identities=33%  Similarity=0.648  Sum_probs=47.1

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC------CCCCccccccccCCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA------RSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~~~~~~~~  158 (161)
                      ...+...|+||++.|.+   ...++ |||.||..|+..|+..      ...||+||..+...+..+..
T Consensus        15 ~~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~   78 (85)
T 2ecv_A           15 NVKEEVTCPICLELLTQ---PLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNR   78 (85)
T ss_dssp             CCCCCCCCTTTCSCCSS---CBCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSC
T ss_pred             HccCCCCCCCCCcccCC---ceeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccH
Confidence            34566799999999875   34578 9999999999999987      67899999999876555443

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

Probab=99.56  E-value=8.8e-16  Score=93.50  Aligned_cols=54  Identities=30%  Similarity=0.618  Sum_probs=44.6

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-------CCCCccccccccCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-------RSSCPLCRNSLRVDSA  154 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~l~~~~~  154 (161)
                      ...+...|+||++.|.+   ...+| |||.||..||.+|+..       ..+||+||.++...+.
T Consensus         8 ~~~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l   68 (79)
T 2egp_A            8 NVQEEVTCPICLELLTE---PLSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHL   68 (79)
T ss_dssp             CCCCCCEETTTTEECSS---CCCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGG
T ss_pred             hcccCCCCcCCCcccCC---eeECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhC
Confidence            34567899999999975   34578 9999999999999986       5689999999876543

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

Probab=99.56  E-value=3.1e-15  Score=92.13  Aligned_cols=55  Identities=25%  Similarity=0.650  Sum_probs=45.3

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC------CCCCccccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA------RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~~~~~~  156 (161)
                      ..+...|+||++.|.+   -..++ |||.||..||..|+..      ...||+||..+...+..+
T Consensus        16 ~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~   76 (85)
T 2ecw_A           16 IKEEVTCPICLELLKE---PVSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP   76 (85)
T ss_dssp             CCTTTSCTTTCSCCSS---CEECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEE
T ss_pred             CccCCCCcCCChhhCc---ceeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCc
Confidence            4567799999999875   23688 9999999999999987      678999999988664443

>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=99.55  E-value=1.5e-15  Score=96.76  Aligned_cols=52  Identities=27%  Similarity=0.698  Sum_probs=43.4

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC-CCCccccccccCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRVDS  153 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~~  153 (161)
                      .+...|+||++.|.+  .+..++ |||.||..||.+|+..+ .+||+||.++...+
T Consensus        20 ~~~~~C~IC~~~~~~--p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD--ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHHTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCccCCccccC--ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            345689999999974  444488 99999999999999977 69999999986544

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

Probab=99.54  E-value=3.2e-15  Score=87.74  Aligned_cols=56  Identities=21%  Similarity=0.463  Sum_probs=43.9

Q ss_pred             CCCccccccc-cccCCCee-eecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCC
Q 031354          100 EESECCICLG-VFEDGDKV-KILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       100 ~~~~CaICL~-~f~~~~~v-~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~  156 (161)
                      ++..|+||++ .|.+.... ..++ |||.||..||.+|+.. +.+||+||.++...+-.+
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   60 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV   60 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEE
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccccccee
Confidence            3568999999 77765433 4577 9999999999999765 467999999997765443

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

Probab=99.54  E-value=3e-15  Score=95.05  Aligned_cols=51  Identities=27%  Similarity=0.648  Sum_probs=43.1

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      +...|+||++.|.+  .+..++ |||.||..||.+|+..+.+||+||..+...+
T Consensus        21 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   71 (99)
T 2y43_A           21 DLLRCGICFEYFNI--AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD   71 (99)
T ss_dssp             HHTBCTTTCSBCSS--EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             CCCCcccCChhhCC--cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCChhh
Confidence            45689999999975  444447 9999999999999999899999999987643

>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=99.54  E-value=3.2e-15  Score=96.42  Aligned_cols=52  Identities=25%  Similarity=0.670  Sum_probs=44.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      .+...|+||++.|.+  .+..++ |||.||..||..|+..+.+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKTR   64 (108)
T ss_dssp             GGGTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSSC
T ss_pred             CCcCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCccccccC
Confidence            456789999999864  555458 9999999999999999899999999988654

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

Probab=99.53  E-value=9.5e-15  Score=85.16  Aligned_cols=46  Identities=28%  Similarity=0.688  Sum_probs=38.1

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc---CCCCCccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS---ARSSCPLC  145 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~---~~~~CP~C  145 (161)
                      +...+...|+||++.|.+   ..+++ |||.||..||.+|++   .+.+||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            344567899999999985   44568 999999999999998   45689998

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

Probab=99.52  E-value=3.1e-15  Score=99.54  Aligned_cols=55  Identities=22%  Similarity=0.632  Sum_probs=46.7

Q ss_pred             CCCCCccccccccccC----CCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCC
Q 031354           98 KEEESECCICLGVFED----GDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDS  153 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~----~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  153 (161)
                      ..+...|+||++.|.+    +.....++ |||+||..||++|+..+.+||+||.++..+.
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            3456789999999976    33446778 9999999999999999999999999997654

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

Probab=99.51  E-value=1.6e-14  Score=82.70  Aligned_cols=46  Identities=26%  Similarity=0.849  Sum_probs=37.5

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc---CCCCCccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS---ARSSCPLC  145 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~---~~~~CP~C  145 (161)
                      ....+...|+||++.|.+.   ..++ |||.||..||.+|+.   .+.+||+|
T Consensus        10 ~~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           10 ENLQVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCSCCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             hccccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            3345677999999999763   4578 999999999999954   56789998

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

Probab=99.50  E-value=2.1e-14  Score=94.78  Aligned_cols=49  Identities=29%  Similarity=0.554  Sum_probs=41.6

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC-CCccccccccCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~  152 (161)
                      +...|+||++.|.+   ...+| |||.||..||..|+..+. +||+||.++...
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  100 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGRS  100 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCCC
Confidence            45689999999985   44578 999999999999998554 899999999773

>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=99.47  E-value=3.1e-14  Score=92.20  Aligned_cols=53  Identities=28%  Similarity=0.608  Sum_probs=43.0

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC---CCccccccccCCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS---SCPLCRNSLRVDSALP  156 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~l~~~~~~~  156 (161)
                      ....|+||++.|.+   ...+| |||.||..||..|+..+.   +||+||.++...+..+
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE   75 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBC
T ss_pred             CCCCCcccChhhcC---eEECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCc
Confidence            34589999999875   33478 999999999999998654   8999999988765443

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

Probab=99.47  E-value=5.2e-14  Score=88.11  Aligned_cols=54  Identities=28%  Similarity=0.624  Sum_probs=42.7

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--CCCccccccccCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--SSCPLCRNSLRVD  152 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~  152 (161)
                      ....+...|+||++.|.+  . .++|.|||.||..||.+|+..+  .+||+||.++...
T Consensus         8 ~~~~~~~~C~IC~~~~~~--p-~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~   63 (92)
T 3ztg_A            8 DPIPDELLCLICKDIMTD--A-VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP   63 (92)
T ss_dssp             CCCCTTTEETTTTEECSS--C-EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCT
T ss_pred             ccCCcCCCCCCCChhhcC--c-eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCc
Confidence            345567899999999975  3 3566599999999999999743  5899999997433

>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=99.47  E-value=3e-14  Score=98.48  Aligned_cols=51  Identities=27%  Similarity=0.677  Sum_probs=42.8

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVD  152 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  152 (161)
                      .....|+||++.|.+  .+..++ |||.||..||.+|+.. +.+||+||.++...
T Consensus        52 ~~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           52 HSELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            345699999999975  555558 9999999999999997 77899999998543

>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=99.44  E-value=3.4e-14  Score=83.05  Aligned_cols=49  Identities=22%  Similarity=0.510  Sum_probs=41.1

Q ss_pred             CCCCCccccccccccCCCeeeec--CCCCCc-cchhhHHHHHcCCCCCcccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKIL--PKCRHC-YHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~l--p~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      ..++.+|+||++++.+   ...+  | |||+ |+.+|+..|...+..||+||+++.
T Consensus         5 ~~~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            5 LNAIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             CGGGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCCcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            3466789999998765   3344  9 9999 899999999998889999999885

>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=99.44  E-value=9.5e-14  Score=94.50  Aligned_cols=50  Identities=24%  Similarity=0.507  Sum_probs=42.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC-CCccccccccCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~~  153 (161)
                      +...|+||++.|.+   ..++| |||.||..||..|+.... +||+||.++....
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~  127 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQNY  127 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTC
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCCC
Confidence            45689999999875   34578 999999999999998754 8999999998763

>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=99.43  E-value=3.9e-14  Score=92.71  Aligned_cols=53  Identities=25%  Similarity=0.506  Sum_probs=44.2

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC-CCccccccccCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSLRVDS  153 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~~  153 (161)
                      ...+...|+||++.|.+   -..++ |||.||..||.+|+..+. +||+||.++....
T Consensus        14 ~~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           14 PLESKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CCCGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcCChhhcC---eEECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            44566799999999875   34578 999999999999998764 8999999987654

>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=99.42  E-value=8.9e-14  Score=90.70  Aligned_cols=52  Identities=25%  Similarity=0.483  Sum_probs=43.4

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSAL  155 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  155 (161)
                      +...|+||++.|.+   ...++ |||.||..||.+|+.. +.+||+||.++...+..
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   74 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhcc
Confidence            45689999999865   33478 9999999999999986 67899999998876543

>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=99.42  E-value=7.2e-14  Score=81.41  Aligned_cols=52  Identities=21%  Similarity=0.475  Sum_probs=41.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ......|.||++.+.+. .+..+| |||+ |+..|+.+|.+.+..||+||+++..
T Consensus         4 ~~~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            4 QNLLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGGGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             CCcCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            45567899999986541 122348 9998 9999999999888899999999853

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

Probab=99.41  E-value=7.1e-14  Score=79.54  Aligned_cols=50  Identities=24%  Similarity=0.550  Sum_probs=41.4

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      ..+...|+||++.|.+   ..++| |||.||..|+..|   ...||+||..+.....
T Consensus         3 e~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             SCCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             cccCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEeecCCc
Confidence            3466789999999986   46789 9999999999884   5679999999876544

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

Probab=99.41  E-value=3.6e-13  Score=81.61  Aligned_cols=56  Identities=27%  Similarity=0.442  Sum_probs=43.5

Q ss_pred             CCCCCccccccccccCCCe-eeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCC
Q 031354           98 KEEESECCICLGVFEDGDK-VKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSA  154 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~-v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~  154 (161)
                      ..++..|+||++.+...+. +..++ |||.||..|+..|+.. ...||+||.++.....
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            4567799999999865433 22356 9999999999999853 5689999999976543

>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=99.40  E-value=3.3e-14  Score=92.65  Aligned_cols=50  Identities=26%  Similarity=0.690  Sum_probs=41.9

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~  151 (161)
                      ..++..|+||++.|.+   ...++ |||.||..||.+|+.. +.+||+||..+..
T Consensus        12 ~~~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           12 SLSECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CHHHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3456789999999875   44568 9999999999999986 6789999999863

>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB: 2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A 2ldr_A*

Probab=99.38  E-value=2.4e-13  Score=104.63  Aligned_cols=50  Identities=32%  Similarity=0.722  Sum_probs=43.4

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccccccccCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~~  153 (161)
                      ....|+||++.+.+   ...+| |||.||..|+..|+. .+.+||+||.++....
T Consensus       331 ~~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          331 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            34799999999865   66788 999999999999998 7889999999987653

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

Probab=99.35  E-value=6.3e-13  Score=81.97  Aligned_cols=55  Identities=16%  Similarity=0.107  Sum_probs=46.6

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ......|+||++-|.+   -.+++ |||.|+..||.+|+..+.+||+||.++......|
T Consensus        11 ~p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~p   65 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEP   65 (85)
T ss_dssp             CCTTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             CchheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChHhcch
Confidence            4467899999999876   44688 9999999999999998899999999987665444

>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=99.33  E-value=1.3e-12  Score=82.95  Aligned_cols=56  Identities=16%  Similarity=0.110  Sum_probs=47.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  157 (161)
                      ......|+||++-|.+   -.++| |||.|+..||.+|+..+.+||+||.++......|.
T Consensus        26 ~p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn   81 (100)
T 2kre_A           26 APDEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPV   81 (100)
T ss_dssp             CSTTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEEC
T ss_pred             CcHhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhhceEC
Confidence            4557799999999875   44688 99999999999999988999999999987655443

>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=99.33  E-value=5.2e-13  Score=89.92  Aligned_cols=52  Identities=23%  Similarity=0.446  Sum_probs=42.4

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC-CCccccccccCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS-SCPLCRNSLRVD  152 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~  152 (161)
                      ...+...|+||++.|.+.   ..++ |||.||..||.+|+.... +||+||.++...
T Consensus        27 ~l~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             GCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             cCCcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            345677999999998753   4578 999999999999998654 899999987543

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

Probab=99.32  E-value=3.5e-13  Score=101.32  Aligned_cols=56  Identities=30%  Similarity=0.726  Sum_probs=43.2

Q ss_pred             CCCCCCccccccccccCCCeee----ecCCCCCccchhhHHHHHcCC-----------CCCccccccccCC
Q 031354           97 DKEEESECCICLGVFEDGDKVK----ILPKCRHCYHCECVDAWLSAR-----------SSCPLCRNSLRVD  152 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~----~lp~C~H~FH~~Ci~~Wl~~~-----------~~CP~CR~~l~~~  152 (161)
                      ......+|+||++.+.++..+-    ..+.|||.||..||.+||+..           .+||+||.++...
T Consensus       304 ~ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CCCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            4567889999999998844332    223499999999999999742           4699999998654

>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=99.32  E-value=2.1e-12  Score=81.61  Aligned_cols=55  Identities=20%  Similarity=0.200  Sum_probs=46.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCC-CccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCR-HCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ...+..|+||++-|.+   -.+++ || |.|+..||.+|+..+.+||+||.++......|
T Consensus        19 ~p~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~p   74 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRP   74 (98)
T ss_dssp             CCTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEE
T ss_pred             CcHhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceE
Confidence            3456799999999875   44678 99 99999999999998889999999998765544

>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=99.31  E-value=5.2e-13  Score=87.18  Aligned_cols=49  Identities=20%  Similarity=0.657  Sum_probs=40.6

Q ss_pred             CCCccccccccccCCCeeeec-CCCCCccchhhHHHHHcCCCCCccccccccCCCC
Q 031354          100 EESECCICLGVFEDGDKVKIL-PKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSA  154 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~l-p~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  154 (161)
                      +...|+||++.|.+  . ..+ + |||.||..||..|+.  ..||+||.++...+.
T Consensus        21 ~~~~C~IC~~~~~~--p-v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~   70 (117)
T 1jm7_B           21 KLLRCSRCTNILRE--P-VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQDL   70 (117)
T ss_dssp             HTTSCSSSCSCCSS--C-BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSSC
T ss_pred             hCCCCCCCChHhhC--c-cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCccccc
Confidence            45689999999965  3 345 7 999999999999998  789999999865443

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

Probab=99.31  E-value=4.2e-13  Score=80.64  Aligned_cols=44  Identities=30%  Similarity=0.716  Sum_probs=38.0

Q ss_pred             CCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ++..|+||++.+.+   ...+| |||. ||..|+..|    ..||+||.++..
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            45689999999765   56789 9999 999999999    789999998864

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

Probab=99.29  E-value=1.7e-12  Score=74.65  Aligned_cols=50  Identities=24%  Similarity=0.673  Sum_probs=39.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCC--C---ccchhhHHHHHcC--CCCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCR--H---CYHCECVDAWLSA--RSSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~--H---~FH~~Ci~~Wl~~--~~~CP~CR~~l~~  151 (161)
                      ..+...|.||+++.  ++.+ ++| |.  |   .||..|+++|+..  +.+||+||.++..
T Consensus         3 ~~~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            3 DEDVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            45677999999983  3444 688 76  4   8999999999974  5789999998753

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

Probab=99.23  E-value=8.6e-12  Score=73.57  Aligned_cols=50  Identities=28%  Similarity=0.695  Sum_probs=41.0

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      +....+...|.||++.+.+   +..+| |||. |+..|+..    ...||+||.++...
T Consensus         9 e~~~~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A            9 EPSEENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCSCCCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             cccCCCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            3445567899999998765   77899 9999 99999984    47899999998754

>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=99.21  E-value=4.5e-12  Score=87.91  Aligned_cols=54  Identities=24%  Similarity=0.482  Sum_probs=44.3

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC-CCCccccccccCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRVDSA  154 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~~~  154 (161)
                      ...+...|+||++.|.+  . ..++ |||.|+..||.+|+..+ .+||+||.++...+.
T Consensus        14 ~~~~~~~C~IC~~~~~~--p-v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   68 (170)
T 3hcs_A           14 PLESKYECPICLMALRE--A-VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQL   68 (170)
T ss_dssp             CCCGGGBCTTTCSBCSS--E-EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGC
T ss_pred             CCCCCCCCCCCChhhcC--c-EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchhhh
Confidence            34567799999999875  3 4578 99999999999999864 489999999876543

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

Probab=99.18  E-value=1.1e-11  Score=74.53  Aligned_cols=45  Identities=29%  Similarity=0.708  Sum_probs=37.2

Q ss_pred             CCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      +...|+||++.+.+   ...+| |||. ||..|+..    ...||+||.++...
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            34589999999765   56789 9999 99999975    37899999998654

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

Probab=99.15  E-value=2e-11  Score=76.58  Aligned_cols=49  Identities=24%  Similarity=0.626  Sum_probs=41.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC--------CCCCcc--cccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA--------RSSCPL--CRNS  148 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~  148 (161)
                      .+...|+||++++...+.+...+ |||.|+.+|+..++..        ...||.  |+..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            45678999999998877777778 9999999999999963        246999  9987

>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=99.13  E-value=1.3e-11  Score=77.46  Aligned_cols=53  Identities=23%  Similarity=0.470  Sum_probs=41.1

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC------CCCcc--cccc-ccCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR------SSCPL--CRNS-LRVDS  153 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~------~~CP~--CR~~-l~~~~  153 (161)
                      ......|+||++.|.+  .|.... |||.|+..||.+|+..+      .+||+  |+.. +...+
T Consensus         4 ~~~~~~CPI~~~~~~d--PV~~~~-cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKK--PVKNKV-CGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             CSSCCBCTTTCSBCSS--EEEESS-SCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGG
T ss_pred             CCcEeECcCcCchhcC--CEEcCC-CCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhh
Confidence            3466789999999874  554335 99999999999999753      48999  9866 55443

>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=99.11  E-value=1.7e-11  Score=74.39  Aligned_cols=44  Identities=27%  Similarity=0.640  Sum_probs=37.3

Q ss_pred             CCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      +...|+||++.+.+   ...+| |||. |+..|+..|    ..||+||.++..
T Consensus        17 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            34589999998765   66789 9999 999999987    489999998864

>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=99.08  E-value=4.5e-11  Score=88.65  Aligned_cols=57  Identities=18%  Similarity=0.254  Sum_probs=45.8

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~~  157 (161)
                      .......|+||++-|.+   -.++| |||.|+..||..|+.. ..+||+||.++......|.
T Consensus       204 ~~~~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n  261 (281)
T 2c2l_A          204 DIPDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN  261 (281)
T ss_dssp             CCCSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CCCcccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCccc
Confidence            34467799999999875   44688 9999999999999985 4559999999976655443

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

Probab=99.01  E-value=1.5e-10  Score=80.51  Aligned_cols=57  Identities=18%  Similarity=0.263  Sum_probs=46.0

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC-CCCccccccccCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~~~~~~  157 (161)
                      .......|+||++-|.+  .| ++| |||.|...||..|+..+ .+||+||.++......|.
T Consensus       102 ~ip~~f~CPI~~elm~D--PV-~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN  159 (179)
T 2f42_A          102 EIPDYLCGKISFELMRE--PC-ITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPN  159 (179)
T ss_dssp             CCCGGGBCTTTCSBCSS--EE-ECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEEC
T ss_pred             CCcHhhcccCccccCCC--Ce-ECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcch
Confidence            34567899999999875  44 568 99999999999999863 579999999877655543

>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=98.92  E-value=2.4e-10  Score=87.26  Aligned_cols=45  Identities=31%  Similarity=0.764  Sum_probs=38.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCc-cchhhHHHHHcCCCCCccccccccCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHC-YHCECVDAWLSARSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  152 (161)
                      ++..|+||++.+.+   ...+| |||. ||..|+..|    ..||+||.++...
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~  339 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKGT  339 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCEE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccCe
Confidence            35689999999865   66779 9999 999999998    6899999998643

>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=98.91  E-value=4.8e-10  Score=81.73  Aligned_cols=56  Identities=18%  Similarity=0.433  Sum_probs=44.7

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--CCCcc--ccccccCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--SSCPL--CRNSLRVDSALP  156 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--~~CP~--CR~~l~~~~~~~  156 (161)
                      ......|+||++.|.  +.|+.+. |||.|+..||.+|+..+  .+||+  ||..+...+..|
T Consensus       178 ~~~el~CPIcl~~f~--DPVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~p  237 (267)
T 3htk_C          178 GKIELTCPITCKPYE--APLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVR  237 (267)
T ss_dssp             SBCCSBCTTTSSBCS--SEEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEE
T ss_pred             CceeeECcCccCccc--CCeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCc
Confidence            345669999999985  6776667 99999999999999864  46999  999886654433

>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=98.90  E-value=3.5e-10  Score=65.10  Aligned_cols=53  Identities=13%  Similarity=0.234  Sum_probs=43.5

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ...|+||++-+.+  .|...+ +||+|-..||.+|++.+.+||+.+.++...+.+|
T Consensus         3 ~~~CpIs~~~m~d--PV~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip   55 (61)
T 2bay_A            3 HMLCAISGKVPRR--PVLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE   55 (61)
T ss_dssp             -CCCTTTCSCCSS--EEEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEE
T ss_pred             eEEecCCCCCCCC--CEEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEE
Confidence            3579999999884  453336 9999999999999998888999999998766554

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

Probab=98.68  E-value=1.6e-08  Score=62.75  Aligned_cols=48  Identities=19%  Similarity=0.445  Sum_probs=38.2

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDS  153 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~  153 (161)
                      -|.+|--.+  ....|.+| |+|+|+.+|+..|.++ .++||+||.++..-+
T Consensus         3 fC~~C~~Pi--~iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPI--KVYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBC--SEEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCe--EEEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            366775444  45788999 9999999999999865 688999999986543

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

Probab=98.34  E-value=3.4e-07  Score=66.49  Aligned_cols=50  Identities=22%  Similarity=0.597  Sum_probs=40.4

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCC--CCccccccccCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS--SCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~--~CP~CR~~l~~~  152 (161)
                      ....|+||.+-...|..+   ++|+|.||..|+.+|++.+.  +||.|+.+....
T Consensus       179 ~i~~C~iC~~iv~~g~~C---~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCEEC---SSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCccc---CccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            477999999988766444   34999999999999998654  899999886544

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

Probab=97.18  E-value=0.00044  Score=39.91  Aligned_cols=50  Identities=18%  Similarity=0.428  Sum_probs=36.1

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC----CCCccccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR----SSCPLCRNSL  149 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~l  149 (161)
                      +.......|.||-+.   ++.+ .-..|...||..|++..|...    ..||.|+...
T Consensus         7 ~~~~~~~~C~vC~~~---~~ll-~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C            7 QNLAPGARCGVCGDG---TDVL-RCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TCCCTTCCCTTTSCC---TTCE-ECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             cCCCCCCCcCCCCCC---CeEE-ECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            344556789999753   4444 444488999999999888653    3699997654

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

Probab=96.62  E-value=0.001  Score=41.49  Aligned_cols=35  Identities=23%  Similarity=0.370  Sum_probs=27.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      ++..|.||++++.......-+. |+|.|+..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            3468999998765445555588 9999999999983

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=96.48  E-value=0.0067  Score=36.21  Aligned_cols=38  Identities=16%  Similarity=0.460  Sum_probs=26.6

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      +....++.|.|| +.+..++... -..|+-+||..|+.+-
T Consensus        10 e~~~~D~~C~VC-~~~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           10 EPVVNDEMCDVC-EVWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             cCCCCCcccCcc-ccccccceec-cccccccccHhhcccc
Confidence            345578899999 5555444332 2238999999999995

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

Probab=95.47  E-value=0.011  Score=33.32  Aligned_cols=49  Identities=24%  Similarity=0.653  Sum_probs=34.4

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNS  148 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  148 (161)
                      .....+..|.+|-+.   ++.+. -..|...||..|++.=+..    ...||.|+..
T Consensus         6 ~~~~~~~~C~vC~~~---g~ll~-CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            6 YETDHQDYCEVCQQG---GEIIL-CDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CSSCCCSSCTTTSCC---SSEEE-CSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             ccCCCCCCCccCCCC---CcEEE-CCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            345667899999863   44444 3448889999999985543    3469999753

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.88  E-value=0.023  Score=34.45  Aligned_cols=58  Identities=24%  Similarity=0.515  Sum_probs=39.0

Q ss_pred             CCCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccccCCCCCC
Q 031354           95 KDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        95 ~~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~~~~~~~  156 (161)
                      ......+..|.+|.+.   ++.+ .-..|.-.||..|+++=+..    ...||.|+..-..++...
T Consensus        19 ~~~d~n~~~C~vC~~~---g~LL-~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~ke~~~   80 (88)
T 1fp0_A           19 GTLDDSATICRVCQKP---GDLV-MCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDV   80 (88)
T ss_dssp             CSSSSSSSCCSSSCSS---SCCE-ECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCCSST
T ss_pred             cccCCCCCcCcCcCCC---CCEE-ECCCCCCceecccCCCCCCCCcCCCcCCccccCCCccchhhc
Confidence            3445667799999864   4444 34448889999999876543    246999987655444443

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=94.76  E-value=0.0099  Score=37.67  Aligned_cols=48  Identities=23%  Similarity=0.524  Sum_probs=32.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCR  146 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR  146 (161)
                      ..+++.|.||.+.=+.++.+.-- .|+..||..|++..+..    ...||.|+
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~-~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCT-TCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECS-SSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCCcCCCCCCCCcCCeECC-CCCCCcChHHhCCccccccccCccCCcCC
Confidence            35778999998763323334434 49999999999987652    23466654

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=94.76  E-value=0.0073  Score=42.65  Aligned_cols=49  Identities=27%  Similarity=0.573  Sum_probs=35.2

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLR  150 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  150 (161)
                      ...++.|.+|-+.   |+ +....+|...||..|+.+-+..    ...||.|+..-.
T Consensus         4 d~~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~~   56 (207)
T 3u5n_A            4 DPNEDWCAVCQNG---GD-LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             CSSCSSBTTTCCC---EE-EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCCCCC---Cc-eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            3466789999754   33 4455558899999999887654    246999986543

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.70  E-value=0.0045  Score=34.28  Aligned_cols=47  Identities=28%  Similarity=0.682  Sum_probs=32.8

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      ....+..|.+|-+.   ++.+. -..|...||..|+++=+..    ...||.|+.
T Consensus         5 ~~~~~~~C~vC~~~---g~ll~-Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            5 SSGHEDFCSVCRKS---GQLLM-CDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CCSSCCSCSSSCCS---SCCEE-CSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             cCCCCCCCccCCCC---CeEEE-cCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            34567789999874   44444 3348899999999965543    235999964

>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=94.58  E-value=0.013  Score=33.42  Aligned_cols=52  Identities=21%  Similarity=0.483  Sum_probs=35.2

Q ss_pred             CCCCCcccccccccc-CCCeeeecCCCCCccchhhHHHHH-------cCCCCCccccccc
Q 031354           98 KEEESECCICLGVFE-DGDKVKILPKCRHCYHCECVDAWL-------SARSSCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~-~~~~v~~lp~C~H~FH~~Ci~~Wl-------~~~~~CP~CR~~l  149 (161)
                      ..++..|.||..... ++..+..-..|.-.||..|+..=+       .....||.|+...
T Consensus         3 ~~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            3 SGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            456789999997642 233444555588999999988633       2335699997543

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=94.57  E-value=0.044  Score=36.30  Aligned_cols=47  Identities=17%  Similarity=0.461  Sum_probs=33.8

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-----------CCCCCccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-----------ARSSCPLCRN  147 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR~  147 (161)
                      ....++.|.+|-+.   |+.+ .-..|-.+||..||+.=+.           ....||+|+.
T Consensus        59 ~Dg~~d~C~vC~~G---G~Ll-cCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           59 SDGMDEQCRWCAEG---GNLI-CCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TTSCBCSCSSSCCC---SSEE-ECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCCeecccCCC---CcEE-eCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            34567899999875   4444 4444889999999996552           2457999974

>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=94.54  E-value=0.0097  Score=33.55  Aligned_cols=48  Identities=23%  Similarity=0.552  Sum_probs=33.1

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l  149 (161)
                      ...+..|.||-+.   ++.+ .-.+|...||..|+..=+..    ...||.|+...
T Consensus         6 d~~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GELL-CCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---SSCB-CCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC---CCEE-EcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            4567789999753   4444 33348889999999865543    34599997654

>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=94.53  E-value=0.008  Score=41.60  Aligned_cols=47  Identities=26%  Similarity=0.620  Sum_probs=34.0

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLR  150 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  150 (161)
                      +++.|.+|-+.   |+.+ ...+|.-.||..|+.+-+..    ...||.|+..-.
T Consensus         3 ~~~~C~~C~~~---g~ll-~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG---GELL-CCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC---SSCE-ECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC---Ceee-ecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            56789999854   5544 44458899999999876654    246999987543

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.46  E-value=0.019  Score=30.98  Aligned_cols=44  Identities=25%  Similarity=0.628  Sum_probs=29.4

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      .|.||...-..++.+ .-..|...||..|++.=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll-~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEE-ECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588887654333444 44458899999999764433    235999964

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=94.45  E-value=0.0047  Score=34.73  Aligned_cols=49  Identities=27%  Similarity=0.653  Sum_probs=34.2

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccccCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~~~  152 (161)
                      .+..|.||-..   ++.+. -..|.-.||..|+.+=+..    ...||.|+......
T Consensus         4 ~~~~C~vC~~~---g~ll~-Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~   56 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLM-CDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKK   56 (60)
T ss_dssp             CCSSCTTTCCC---SSCEE-CSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHT
T ss_pred             CCCCCcCCCCC---CcEEE-cCCCCcCEECCcCCCCcCCCCCCceEChhccChhhch
Confidence            56789999874   44444 3448899999999965543    34599997665443

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

Probab=94.40  E-value=0.018  Score=32.65  Aligned_cols=51  Identities=20%  Similarity=0.473  Sum_probs=34.8

Q ss_pred             CCCCCccccccccccCCC-eeeecCCCCCccchhhHHHHHc-----CCCCCccccccc
Q 031354           98 KEEESECCICLGVFEDGD-KVKILPKCRHCYHCECVDAWLS-----ARSSCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~-~v~~lp~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~l  149 (161)
                      ..+...|+||...+.++. .|.-- .|..=||..|+.--..     .+-.||.|+..-
T Consensus         3 ~~e~~~C~~C~~~~~~~~~mI~Cd-~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            3 SGSSGQCGACGESYAADEFWICCD-LCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECS-SSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCCCCccCCCCCEEEcc-CCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            456678999998886444 55444 3888899999864322     245699997643

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.27  E-value=0.015  Score=34.16  Aligned_cols=54  Identities=20%  Similarity=0.359  Sum_probs=36.2

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccccC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLRV  151 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~~  151 (161)
                      ...+...|.||-.....+..| .--.|.--||..|+..-...    ...||.|+..+..
T Consensus        14 ~~~~~~~C~~C~~~~~~~~mi-~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           14 WGNQIWICPGCNKPDDGSPMI-GCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             SSCEEECBTTTTBCCSSCCEE-ECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             cCCCCcCCCCCCCCCCCCCEE-EcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            345566799998765332344 34448888999999865442    3469999876643

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=94.14  E-value=0.022  Score=33.11  Aligned_cols=52  Identities=21%  Similarity=0.422  Sum_probs=35.1

Q ss_pred             CCCCCCccccccccc-cCCCeeeecCCCCCccchhhHHHHHcC--CCCCcccccc
Q 031354           97 DKEEESECCICLGVF-EDGDKVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNS  148 (161)
Q Consensus        97 ~~~~~~~CaICL~~f-~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~  148 (161)
                      ....+..|.||.+.- .+++.+..-..|.-.||..|+..-...  ...||.|+..
T Consensus        12 ~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           12 LIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            456678999998753 233445455558899999999853322  3469999653

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=94.09  E-value=0.0087  Score=34.30  Aligned_cols=47  Identities=23%  Similarity=0.637  Sum_probs=33.1

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNS  148 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  148 (161)
                      ...+..|.||-+.   ++.+ .-..|.-.||..|+..=+..    ...||.|...
T Consensus         5 ~~~~~~C~vC~~~---g~ll-~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            5 QKNEDECAVCRDG---GELI-CCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CSCCCSBSSSSCC---SSCE-ECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCCccCCCC---CCEE-EcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            4567899999864   4444 44448889999999865443    3459999653

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=93.65  E-value=0.037  Score=33.55  Aligned_cols=55  Identities=20%  Similarity=0.370  Sum_probs=36.5

Q ss_pred             CCCCCCccccccccc-cCCCeeeecCCCCCccchhhHHHHHcC--CCCCccccccccC
Q 031354           97 DKEEESECCICLGVF-EDGDKVKILPKCRHCYHCECVDAWLSA--RSSCPLCRNSLRV  151 (161)
Q Consensus        97 ~~~~~~~CaICL~~f-~~~~~v~~lp~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~  151 (161)
                      ...++..|.||.+.- .+++.+..-..|.-.||..|+..=+..  ...||.|......
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            345678999998753 233345455558889999999864322  3469999765443

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=93.49  E-value=0.084  Score=34.33  Aligned_cols=48  Identities=17%  Similarity=0.452  Sum_probs=33.1

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHH------c-----CCCCCcccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL------S-----ARSSCPLCRNS  148 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl------~-----~~~~CP~CR~~  148 (161)
                      ....++.|.||-+.   |+ +..-..|-.+||.+||..=+      .     ....|++|+..
T Consensus        53 ~Dg~~~~C~vC~dG---G~-LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           53 SDGMDEQCRWCAEG---GN-LICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             TTSCBSSCTTTCCC---SE-EEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCCCCcCeecCCC---Ce-eEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            34566789999864   33 43444588999999999742      1     23579999654

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=93.32  E-value=0.13  Score=32.49  Aligned_cols=47  Identities=23%  Similarity=0.513  Sum_probs=29.2

Q ss_pred             CCCcccccccccc-----CCCeeeecCCCCCccchhhHHHH------H-cCCCCCcccc
Q 031354          100 EESECCICLGVFE-----DGDKVKILPKCRHCYHCECVDAW------L-SARSSCPLCR  146 (161)
Q Consensus       100 ~~~~CaICL~~f~-----~~~~v~~lp~C~H~FH~~Ci~~W------l-~~~~~CP~CR  146 (161)
                      ....|.+|+..=.     .++++..-..|+..||..|+..+      + .....||-|+
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            4568999987631     22334344449999999999532      2 2344577664

>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=92.80  E-value=0.04  Score=38.15  Aligned_cols=48  Identities=25%  Similarity=0.537  Sum_probs=33.3

Q ss_pred             CCccccccccccCCCe---eeecCCCCCccchhhHHH------HHc-----CCCCCcccccc
Q 031354          101 ESECCICLGVFEDGDK---VKILPKCRHCYHCECVDA------WLS-----ARSSCPLCRNS  148 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~---v~~lp~C~H~FH~~Ci~~------Wl~-----~~~~CP~CR~~  148 (161)
                      +..|+||-..|.+++.   ......|..=||..|+.-      -+.     ..-.||.|+..
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~   63 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTER   63 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCC
Confidence            4579999999988762   333334889999999632      111     14689999865

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=92.55  E-value=0.032  Score=35.41  Aligned_cols=45  Identities=27%  Similarity=0.614  Sum_probs=30.4

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      .|.||-+.-.+++.+..-..|...||..|+++=|..    ...||.|+.
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            688887643333344444458899999999875543    246999974

>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=92.36  E-value=0.031  Score=33.90  Aligned_cols=55  Identities=16%  Similarity=0.447  Sum_probs=37.4

Q ss_pred             CCCccccccccccC-CCeeeecCCCCCccchhhHHHHHc--------CCCCCccccccccCCCC
Q 031354          100 EESECCICLGVFED-GDKVKILPKCRHCYHCECVDAWLS--------ARSSCPLCRNSLRVDSA  154 (161)
Q Consensus       100 ~~~~CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~l~~~~~  154 (161)
                      .+..|.||...-.. ++.+..--.|...||..|++.=|.        ....||.|+........
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~~~~   78 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQ   78 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCCSTT
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhhhcc
Confidence            45689999875322 234445555889999999987553        23569999876655443

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=91.99  E-value=0.077  Score=32.78  Aligned_cols=46  Identities=22%  Similarity=0.434  Sum_probs=31.6

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC---CCCCccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA---RSSCPLCRN  147 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~---~~~CP~CR~  147 (161)
                      +...| ||-.....+..|.--. |.--||..|+..=+..   ...||.|+.
T Consensus        27 d~vrC-iC~~~~~~~~mi~Cd~-C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDGYMICCDK-CSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CBCCC-TTSCCSCSSCEEEBTT-TCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CCEEe-ECCCccCCCcEEEcCC-CCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            34568 8877766666665444 8899999998753221   346999963

>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=91.71  E-value=0.028  Score=34.41  Aligned_cols=51  Identities=24%  Similarity=0.382  Sum_probs=33.9

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccc
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNS  148 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  148 (161)
                      ...+...|.||...-..+..+ .-..|...||..|+.+=|..    ...||.|+..
T Consensus        12 ~~~~~~~C~vC~~~~~~~~ll-~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           12 QFIDSYICQVCSRGDEDDKLL-FCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCCSSSCCSGGGGGCE-ECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             hccCCCCCccCCCcCCCCCEE-EcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            344556899998764333344 44458899999999854432    3459999764

>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=91.63  E-value=0.15  Score=32.37  Aligned_cols=45  Identities=24%  Similarity=0.476  Sum_probs=28.1

Q ss_pred             CccccccccccC------CCeeeecCCCCCccchhhHHHHH-------cCCCCCcccc
Q 031354          102 SECCICLGVFED------GDKVKILPKCRHCYHCECVDAWL-------SARSSCPLCR  146 (161)
Q Consensus       102 ~~CaICL~~f~~------~~~v~~lp~C~H~FH~~Ci~~Wl-------~~~~~CP~CR  146 (161)
                      +.|.+|+..-..      ++.+..-..|+..||..|++.+.       ...-.||.|+
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            579999875421      22333333499999999987542       1244577663

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=91.51  E-value=0.039  Score=38.34  Aligned_cols=46  Identities=30%  Similarity=0.657  Sum_probs=31.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  150 (161)
                      ++.|.+|.+.   |+.+. ..+|...||..|+.+=+..    ...||.|+..-.
T Consensus         2 ~~~C~~C~~~---g~ll~-Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~~   51 (189)
T 2ro1_A            2 ATICRVCQKP---GDLVM-CNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   51 (189)
T ss_dssp             CCCBTTTCCC---SSCCC-CTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSCC
T ss_pred             CCcCccCCCC---CceeE-CCCCCchhccccCCCCcccCCCCCCCCcCccCCCC
Confidence            5679999854   44443 3348889999999764432    246999986643

>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=91.25  E-value=0.27  Score=30.87  Aligned_cols=50  Identities=24%  Similarity=0.521  Sum_probs=32.8

Q ss_pred             CCCCCCCccccccccccCCCeeeecC--CCCCccchhhHHHHHcC----CCCCccccccccC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILP--KCRHCYHCECVDAWLSA----RSSCPLCRNSLRV  151 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp--~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~~  151 (161)
                      .....++.|.+|.+.   |+.+ .-.  .|-..||..|+.  |..    +..||-|+..+-.
T Consensus        10 ~~~~~~~~C~~C~~~---G~ll-~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C~   65 (107)
T 4gne_A           10 PKQMHEDYCFQCGDG---GELV-MCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDECS   65 (107)
T ss_dssp             CCCSSCSSCTTTCCC---SEEE-ECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTTC
T ss_pred             CcCCCCCCCCcCCCC---CcEe-EECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcCC
Confidence            345677889999842   4433 333  377899999998  543    2358887655543

>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}

Probab=90.40  E-value=1.3  Score=24.07  Aligned_cols=29  Identities=7%  Similarity=-0.025  Sum_probs=14.2

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 031354           25 GRTLFSIIVVFAVVLLVSFLFLYARWFCR   53 (161)
Q Consensus        25 ~~~i~ii~~l~~~~l~~~~~~~~~~~~~~   53 (161)
                      ..+++++.++.+.++++++.+++.+.-..
T Consensus         8 p~WiIi~svl~GLLLL~Lii~~LwK~GFF   36 (54)
T 2l8s_A            8 PLWVILLSAFAGLLLLMLLILALWKIGFF   36 (54)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence            34555555555555555444444444333

>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=90.19  E-value=0.15  Score=34.63  Aligned_cols=50  Identities=22%  Similarity=0.525  Sum_probs=31.9

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHH-----cCCCCCcccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL-----SARSSCPLCRNS  148 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~  148 (161)
                      ......| +|-....++.....-..|..-||..|+.--.     ...-.||.|+..
T Consensus         5 ~~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            5 SDTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             --CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            3456789 9988765444333334488899999985211     224579999764

>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=89.58  E-value=1.5  Score=23.78  Aligned_cols=26  Identities=12%  Similarity=-0.003  Sum_probs=12.0

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHH
Q 031354           25 GRTLFSIIVVFAVVLLVSFLFLYARW   50 (161)
Q Consensus        25 ~~~i~ii~~l~~~~l~~~~~~~~~~~   50 (161)
                      ..+++++.++.+.++++++.+++.+.
T Consensus        11 p~wiIi~svl~GLllL~li~~~LwK~   36 (54)
T 2knc_A           11 PIWWVLVGVLGGLLLLTILVLAMWKV   36 (54)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            33444555554444444444444433

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=88.98  E-value=0.057  Score=31.87  Aligned_cols=45  Identities=33%  Similarity=0.703  Sum_probs=28.0

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC----C-CCCcccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----R-SSCPLCRNS  148 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~-~~CP~CR~~  148 (161)
                      .|.||-..-..+ .+..--.|...||..|+++=|..    . -.||.|+.+
T Consensus        28 ~C~vC~~~~d~~-~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~d   77 (77)
T 3shb_A           28 ACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   77 (77)
T ss_dssp             SBTTTCCCSCGG-GEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC--
T ss_pred             cCCccCCCCCCc-ceeEeCCCCCccCcccCCCcccCCCCCCceECcCcccc
Confidence            566665543333 33344448899999999976643    2 469999763

>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=88.72  E-value=0.33  Score=41.67  Aligned_cols=56  Identities=21%  Similarity=0.288  Sum_probs=46.0

Q ss_pred             CCCCCccccccccccCCCeeeecCCCC-CccchhhHHHHHcCCCCCccccccccCCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCR-HCYHCECVDAWLSARSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  157 (161)
                      ..+...|+|=++-+.+   -.++| -| +.|=...|.+|+..+.+||+=|.++.....+|.
T Consensus       888 iP~~F~cPIs~~lM~D---PVilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN  944 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKD---PVILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPN  944 (968)
T ss_dssp             SCGGGBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CcHHhCCcchhhHHhC---CeEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCccccccc
Confidence            3456689999998765   44688 87 589999999999999999999999987766654

>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=88.17  E-value=0.51  Score=26.72  Aligned_cols=36  Identities=19%  Similarity=0.526  Sum_probs=24.7

Q ss_pred             CCCCCccccccccccCCCeeeecC-CCCCccchhhHH
Q 031354           98 KEEESECCICLGVFEDGDKVKILP-KCRHCYHCECVD  133 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp-~C~H~FH~~Ci~  133 (161)
                      ......|.+|...+.+++....-. .|.--||..|+.
T Consensus         5 ~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            5 SDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ----CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            445668999999987766554544 588889999963

>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=87.90  E-value=0.61  Score=27.36  Aligned_cols=50  Identities=18%  Similarity=0.406  Sum_probs=32.6

Q ss_pred             CCCCCcccccccccc-CCCeeeecCCCCCccchhhHHHHHc-----CCCCCccccccc
Q 031354           98 KEEESECCICLGVFE-DGDKVKILPKCRHCYHCECVDAWLS-----ARSSCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~-~~~~v~~lp~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~l  149 (161)
                      ......| ||-..+. .+..|.--- |..=||..|+.---.     ..-.||.|+...
T Consensus         9 ~~~~~~C-~C~~~~d~~~~MIqCd~-C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A            9 ALVPVYC-LCRQPYNVNHFMIECGL-CQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCCS-TTSCSCCSSSCEEEBTT-TCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             cCCccEE-EcCCccCCCCceEEcCC-CCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            3455677 8988875 344555444 888899999852211     245699998653

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.86  E-value=0.15  Score=30.08  Aligned_cols=46  Identities=26%  Similarity=0.653  Sum_probs=30.5

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----CCCCccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----RSSCPLCRN  147 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~  147 (161)
                      +..|.||...-..++.+ .-..|...||..|+++=|..     .-.||.|+.
T Consensus        26 ~c~C~vC~~~~~~~~ll-~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           26 SCSCRVCGGKHEPNMQL-LCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSSCSSSCCCCCSTTEE-ECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCCcCcCCcCCCCCEE-EcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            34789998643334444 44458899999999854432     245999965

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=87.22  E-value=0.54  Score=24.44  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 031354           34 VFAVVLLVSFLFLYARWFCRR   54 (161)
Q Consensus        34 l~~~~l~~~~~~~~~~~~~~~   54 (161)
                      ++.+++++...++++|.+.++
T Consensus        20 v~~v~ii~~~~~~~~RRRr~~   40 (44)
T 2l2t_A           20 LFILVIVGLTFAVYVRRKSIK   40 (44)
T ss_dssp             HHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHhhhhhhh
Confidence            444444555555666655544

>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=87.02  E-value=0.33  Score=28.50  Aligned_cols=51  Identities=22%  Similarity=0.392  Sum_probs=33.8

Q ss_pred             CCCCccccccccccCCCeeeec--CCCCCccchhhHHHHH---------cCCCCCccccccccC
Q 031354           99 EEESECCICLGVFEDGDKVKIL--PKCRHCYHCECVDAWL---------SARSSCPLCRNSLRV  151 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~l--p~C~H~FH~~Ci~~Wl---------~~~~~CP~CR~~l~~  151 (161)
                      .....| ||-.....+.+|.--  . |..=||..|+.---         ..+..||.|+..-..
T Consensus        14 ~~~~~C-iC~~~~~~g~MI~CD~~~-C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~~   75 (78)
T 1wew_A           14 EIKVRC-VCGNSLETDSMIQCEDPR-CHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGP   75 (78)
T ss_dssp             CCCCCC-SSCCCCCCSCEEECSSTT-TCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSC
T ss_pred             CCCEEe-ECCCcCCCCCEEEECCcc-CCccccCEEEccccccccccccCCCCEECCCCCcccCC
Confidence            355678 798775566666544  4 88889999986321         124569999765443

>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=86.96  E-value=0.51  Score=27.44  Aligned_cols=48  Identities=21%  Similarity=0.379  Sum_probs=32.6

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHH---------HcCCCCCcccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW---------LSARSSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W---------l~~~~~CP~CR~~l~  150 (161)
                      ...| ||-..+..+..|.--. |..=||..|+.--         ...+-.||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~MI~Cd~-C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCCCEEEeCC-CCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            4567 8988776555665444 8888999997421         124577999976543

>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=86.87  E-value=0.17  Score=31.77  Aligned_cols=47  Identities=23%  Similarity=0.512  Sum_probs=30.0

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCcccccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLR  150 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  150 (161)
                      .|.+|-..-.+...+ .-..|...||..|+++=+..    ...||.|+.--.
T Consensus        56 ~C~~C~~~~~~~~ll-~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c~~  106 (111)
T 2ysm_A           56 VCQNCKQSGEDSKML-VCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIS  106 (111)
T ss_dssp             CCTTTCCCSCCTTEE-ECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCCSC
T ss_pred             cccccCccCCCCCee-ECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCcCC
Confidence            466776653333344 34448899999999865443    345999976543

>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=86.76  E-value=0.11  Score=32.51  Aligned_cols=51  Identities=25%  Similarity=0.517  Sum_probs=33.3

Q ss_pred             CccccccccccCCCeeeecC-CCCCccchhhHHHH------H----cCCCCCccccccccCC
Q 031354          102 SECCICLGVFEDGDKVKILP-KCRHCYHCECVDAW------L----SARSSCPLCRNSLRVD  152 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp-~C~H~FH~~Ci~~W------l----~~~~~CP~CR~~l~~~  152 (161)
                      ..|.||...+.++.....-- .|.-=||..|+.-=      +    ..+..||.|+..-...
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~~~   65 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEGS   65 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTTTC
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCCCC
Confidence            46999999986654443442 47777999996421      1    0235699998765443

>2wwb_C SEC61BETA, protein transport protein SEC61 subunit beta; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Canis lupus familiaris}

Probab=86.74  E-value=0.8  Score=27.97  Aligned_cols=36  Identities=8%  Similarity=0.296  Sum_probs=20.8

Q ss_pred             CCCCCCcccCCCCCccccccchHHHHHHHHHHHHHH
Q 031354            6 SQPFHWHYTELDDHNFQIRGRTLFSIIVVFAVVLLV   41 (161)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~i~ii~~l~~~~l~~   41 (161)
                      +....|.|.++|..+.-++...++++.+++++++++
T Consensus        51 SsaGllRfY~dds~GlKV~P~~VLv~sl~Fi~~Vi~   86 (96)
T 2wwb_C           51 GTGGMWRFYTEDSPGLKVGPVPVLVMSLLFIASVFM   86 (96)
T ss_dssp             ----------CCSCCCCCSSCSHHHHHHHHHHHHHH
T ss_pred             CCcceeeeeecCCCceEECCEEehhhHHHHHHHHHH
Confidence            445778888878888999999888888777766654

>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=86.20  E-value=0.7  Score=26.62  Aligned_cols=47  Identities=28%  Similarity=0.665  Sum_probs=29.9

Q ss_pred             CCCCCccccccccccCCCeeeecCC--CC-CccchhhHHHHHcC----CCCCccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPK--CR-HCYHCECVDAWLSA----RSSCPLCRNSL  149 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~l  149 (161)
                      ..+...| ||-... .++.| .--+  |. .-||..|+.  |..    +..||.|+..-
T Consensus        13 ~~~~~~C-~C~~~~-~g~MI-~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           13 PNEPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             TTSCCCS-TTCCCS-CSSEE-CCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCCCEE-ECCCCC-CCCEe-EeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            3456678 797753 35544 3334  44 579999998  443    24599997654

>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=85.99  E-value=0.15  Score=29.36  Aligned_cols=44  Identities=34%  Similarity=0.720  Sum_probs=28.1

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----CCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----RSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~  147 (161)
                      .|.||...-..+ .+..-..|...||..|+++=|..     .-.||.|+.
T Consensus        20 ~C~~C~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCCSCGG-GEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCcCCCC-CEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            567776532223 34344458899999999854432     336999975

>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=85.73  E-value=0.086  Score=33.49  Aligned_cols=48  Identities=25%  Similarity=0.529  Sum_probs=31.9

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccccC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSLRV  151 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~~  151 (161)
                      .|.||-..-.+++.+. -..|...||..|+++=|..    ...||.|+..+..
T Consensus        60 ~C~~C~~~~~~~~ll~-Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~~~~~  111 (114)
T 2kwj_A           60 SCILCGTSENDDQLLF-CDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKE  111 (114)
T ss_dssp             CCTTTTCCTTTTTEEE-CSSSCCEEETTTSSSCCSSCCSSCCCCHHHHHHHHH
T ss_pred             ccCcccccCCCCceEE-cCCCCccccccccCCCccCCCCCCeECccccchhhc
Confidence            5888877544444444 3448899999999964433    2359999765543

>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=85.34  E-value=0.6  Score=28.36  Aligned_cols=48  Identities=27%  Similarity=0.644  Sum_probs=30.2

Q ss_pred             CCCCCccccccccccCCCeeeecCC--CC-CccchhhHHHHHcC----CCCCcccccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPK--CR-HCYHCECVDAWLSA----RSSCPLCRNSLR  150 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  150 (161)
                      ..+...| ||-... .++.| .--+  |. .-||..|+.  |..    +..||.|+..-.
T Consensus        33 ~~e~~yC-iC~~~~-~g~MI-~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           33 PNEPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             SCCCBCS-TTCCBC-CSCCC-CCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCCCcEE-ECCCCC-CCCEe-EecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            3455678 998754 24444 2333  44 569999998  433    346999976544

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=85.01  E-value=0.93  Score=27.25  Aligned_cols=54  Identities=20%  Similarity=0.291  Sum_probs=35.9

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-------CCCCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-------ARSSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-------~~~~CP~CR~~l~~  151 (161)
                      ..+...|.+|-..|..-..-.--..||++|+..|....+.       ....|-.|-..+..
T Consensus         6 ~~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~~   66 (88)
T 1wfk_A            6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILTR   66 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHHH
T ss_pred             CCcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHHh
Confidence            4455689999999875432223345999999999866431       12358888666543

>2k1a_A Integrin alpha-IIB; single-PASS transmembrane segment, alternative splicing, calcium, cell adhesion, cleavage on PAIR of basic residues; NMR {Homo sapiens} PDB: 2k9j_A

Probab=84.64  E-value=2  Score=22.04  Aligned_cols=21  Identities=14%  Similarity=0.080  Sum_probs=8.8

Q ss_pred             chHHHHHHHHHHHHHHHHHHH
Q 031354           26 RTLFSIIVVFAVVLLVSFLFL   46 (161)
Q Consensus        26 ~~i~ii~~l~~~~l~~~~~~~   46 (161)
                      .+++++.++...+++..+.+.
T Consensus        10 ~wiIi~s~l~GLllL~li~~~   30 (42)
T 2k1a_A           10 IWWVLVGVLGGLLLLTILVLA   30 (42)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444433333

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=84.27  E-value=0.87  Score=27.45  Aligned_cols=52  Identities=15%  Similarity=0.363  Sum_probs=34.2

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC------CCCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA------RSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~  151 (161)
                      +...|.+|-..|.--..-..-..||++|+..|...+...      ...|-.|-..+..
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~~   76 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETISK   76 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEEEETTTTEEEEECHHHHHHHHH
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCeeecCCCCCCCeECHHHHHHHHH
Confidence            345799999998754333334459999999998765421      2347777555543

>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=84.22  E-value=0.3  Score=27.93  Aligned_cols=50  Identities=20%  Similarity=0.407  Sum_probs=32.9

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHc---CCCCCccccc
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS---ARSSCPLCRN  147 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  147 (161)
                      ....+...| ||-..+..+..|.--. |..=||..|+.---.   ..-.||.|+.
T Consensus        14 ~~~~~~~~C-iC~~~~~~~~MIqCd~-C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           14 LYFQGLVTC-FCMKPFAGRPMIECNE-CHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             CTTTTCCCS-TTCCCCTTCCEEECTT-TCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCCCCceEe-ECCCcCCCCCEEECCC-CCccccccccCcCcccCCCcEECCCCCC
Confidence            344566788 9987765444665444 888899999864221   2346999964

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=83.92  E-value=0.94  Score=26.77  Aligned_cols=51  Identities=22%  Similarity=0.428  Sum_probs=33.0

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC------CCCCcccccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA------RSSCPLCRNSLR  150 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~  150 (161)
                      +...|.+|-..|.--..-.--..||.+|+..|....+..      ...|-.|-..|.
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            445799999999754322333459999999998764311      124777755544

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=83.91  E-value=1.6  Score=22.63  Aligned_cols=23  Identities=26%  Similarity=0.299  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 031354           32 IVVFAVVLLVSFLFLYARWFCRR   54 (161)
Q Consensus        32 ~~l~~~~l~~~~~~~~~~~~~~~   54 (161)
                      ..++..+++++++.+...++.++
T Consensus        15 ~gVVgGv~~~~ii~~~~~~~~RR   37 (44)
T 2ks1_B           15 TGMVGALLLLLVVALGIGLFMRR   37 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             eehhHHHHHHHHHHHHHHHHhhh
Confidence            33334344444444444444444

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=83.81  E-value=1.1  Score=26.53  Aligned_cols=54  Identities=19%  Similarity=0.363  Sum_probs=35.4

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc--------CCCCCccccccccCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS--------ARSSCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~l~~~~  153 (161)
                      +...|.+|-..|..-..-.--..||++|+..|......        ....|-.|-..+....
T Consensus        20 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~~~   81 (84)
T 1z2q_A           20 DAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACYLALRSSN   81 (84)
T ss_dssp             TCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHHHHHHTSC
T ss_pred             CCCCCcCcCCccccchhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHHHHHhhcc
Confidence            45689999999975432233345999999999876531        1235777766555443

>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=83.27  E-value=0.94  Score=29.12  Aligned_cols=36  Identities=19%  Similarity=0.358  Sum_probs=25.7

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      ....|.+|-..|.--..-..-..||++|+..|....
T Consensus        68 ~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           68 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            345899999998753322233459999999997654

>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=83.12  E-value=0.36  Score=27.81  Aligned_cols=50  Identities=18%  Similarity=0.317  Sum_probs=32.4

Q ss_pred             CCCCccccccccccCCC-eeeecCCCCCccchhhHHHHH----cCCCCCcccccccc
Q 031354           99 EEESECCICLGVFEDGD-KVKILPKCRHCYHCECVDAWL----SARSSCPLCRNSLR  150 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~-~v~~lp~C~H~FH~~Ci~~Wl----~~~~~CP~CR~~l~  150 (161)
                      .....| ||-....+++ .|.-- .|..=||..|+.---    ..+-.||.|+..-.
T Consensus        14 ~~~~~C-~C~~~~~~g~~mI~Cd-~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~~   68 (72)
T 1wee_A           14 NWKVDC-KCGTKDDDGERMLACD-GCGVWHHTRCIGINNADALPSKFLCFRCIELSG   68 (72)
T ss_dssp             SSEECC-TTCCCSCCSSCEEECS-SSCEEEETTTTTCCTTSCCCSCCCCHHHHHHCS
T ss_pred             CcceEe-eCCCccCCCCcEEECC-CCCCccCCeeeccCccccCCCcEECCCccCCCC
Confidence            345578 6988766664 55444 387779999986421    12346999976543

>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=82.98  E-value=0.19  Score=32.22  Aligned_cols=50  Identities=18%  Similarity=0.398  Sum_probs=31.5

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSL  149 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  149 (161)
                      ....|..|-..|..-..-....+||.+|+..|..........|-.|...+
T Consensus        18 ~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~   67 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFR   67 (120)
T ss_dssp             --CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHHH
T ss_pred             ccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHHH
Confidence            34689999998865322223345999999999877665566688885543

>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=82.94  E-value=1.1  Score=25.82  Aligned_cols=34  Identities=18%  Similarity=0.281  Sum_probs=24.3

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      ..|.+|-..|.--..-.--..||++|+..|....
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~~   45 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   45 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccCCe
Confidence            5899999998753322233459999999997543

>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=82.42  E-value=0.49  Score=25.37  Aligned_cols=44  Identities=18%  Similarity=0.264  Sum_probs=27.6

Q ss_pred             ccccccccccCCCeeeecC-CCCCccchhhHHHH----HcCCCCCcccc
Q 031354          103 ECCICLGVFEDGDKVKILP-KCRHCYHCECVDAW----LSARSSCPLCR  146 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp-~C~H~FH~~Ci~~W----l~~~~~CP~CR  146 (161)
                      .|.+|...+.+++....-. .|.-=||..|+.--    ...+..||.|+
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            4678888876544333333 38877999996521    12456799885

>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=82.08  E-value=0.36  Score=26.75  Aligned_cols=44  Identities=32%  Similarity=0.745  Sum_probs=27.8

Q ss_pred             CCCCccccccccccCCCeeeecCC--CC-CccchhhHHHHHcC----CCCCccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPK--CR-HCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      .+...| ||-... .|+.| .-.+  |. .-||..|+.  +..    +-.||.|+.
T Consensus         7 ~e~~yC-~C~~~~-~g~mi-~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            7 NEPTYC-LCHQVS-YGEMI-GCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             -CCEET-TTTEEC-CSEEE-ECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCcEE-ECCCCC-CCCee-EeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            345667 897753 34444 3444  54 589999998  443    345999964

>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=81.83  E-value=0.43  Score=34.01  Aligned_cols=46  Identities=30%  Similarity=0.674  Sum_probs=26.4

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHcC-----CCCCcccccc
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-----RSSCPLCRNS  148 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~  148 (161)
                      ..|.+|-..=..++ +..--.|...||..|+++=|..     .-.||.|+..
T Consensus       175 c~C~vC~~~~~~~~-lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          175 CACHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             TSCSSSCCCCC--C-CEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCCcCCCCCCCCCC-eEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            36888866422233 3344458899999999964432     2359999753

>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=81.52  E-value=0.37  Score=26.77  Aligned_cols=44  Identities=30%  Similarity=0.729  Sum_probs=27.1

Q ss_pred             CCCCccccccccccCCCeeeecCC--CC-CccchhhHHHHHcC----CCCCccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPK--CR-HCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      .+...| ||-... .|+.| .--+  |. .-||..|+.  |..    +..||.|+.
T Consensus         8 ~e~~~C-~C~~~~-~g~mi-~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            8 NEPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             -CCEET-TTTEEC-CSEEE-ECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCCEE-ECCCcC-CCCEE-EeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            345567 897753 24433 3344  43 579999998  443    245999964

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.07  E-value=1.4  Score=26.06  Aligned_cols=36  Identities=17%  Similarity=0.364  Sum_probs=25.0

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      +...|.+|-..|.--..-.--..||.+|+..|....
T Consensus        13 ~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~   48 (84)
T 1x4u_A           13 NFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSFK   48 (84)
T ss_dssp             CCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCEE
T ss_pred             CCCcCcCcCCccccchhhhhhcCCCcEEChhhcCCc
Confidence            445899999998653322223349999999997653

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=80.46  E-value=4.4  Score=20.93  Aligned_cols=21  Identities=14%  Similarity=0.191  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 031354           31 IIVVFAVVLLVSFLFLYARWF   51 (161)
Q Consensus        31 i~~l~~~~l~~~~~~~~~~~~   51 (161)
                      +..++.++++.+.++++.|.+
T Consensus        18 vVGvll~vi~~l~~~~~~RRR   38 (44)
T 2jwa_A           18 VVGILLVVVLGVVFGILIKRR   38 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhheehh
Confidence            333445555555555555443

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=80.35  E-value=0.45  Score=26.64  Aligned_cols=44  Identities=30%  Similarity=0.649  Sum_probs=27.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCC---CccchhhHHHHHcC----CCCCccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCR---HCYHCECVDAWLSA----RSSCPLCRN  147 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~---H~FH~~Ci~~Wl~~----~~~CP~CR~  147 (161)
                      .+...| ||-... .|+.| .--+|.   .-||..|+.  |..    +-.||.|+.
T Consensus         9 ~e~~yC-~C~~~~-~g~MI-~CD~c~C~~~WfH~~Cvg--l~~~p~~~w~Cp~C~~   59 (62)
T 2g6q_A            9 NEPTYC-LCNQVS-YGEMI-GCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRG   59 (62)
T ss_dssp             -CCEET-TTTEEC-CSEEE-ECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHT
T ss_pred             CCCcEE-ECCCCC-CCCee-eeeCCCCCcccEecccCC--cCcCCCCCEECcCccc
Confidence            445677 897753 35444 333433   689999998  333    346999965

---

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	161
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-18
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	9e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-04
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	4e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	4e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.001
d1wewa_	78	g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale c	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 = 71.8 bits (176), Expect = 3e-18
 Identities = 25/53 (47%), Positives = 37/53 (69%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV 151
           ++  EC +CL   EDG++ + LP+C H +H ECVD WL + S+CPLCR ++ V
Sbjct: 3   DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 52.3 bits (125), Expect = 1e-10
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 3/48 (6%)

Query: 103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR 150
            C ICL    +     +   C H +   C+  W+    +CPLC+  + 
Sbjct: 7   RCPICLEDPSNYS---MALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 47.7 bits (113), Expect = 9e-09
 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 5/66 (7%)

Query: 86  VLHRSEKSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSS-CPL 144
           V     +   +       C IC    +D   VKI P C H     C+ +W  +    CP 
Sbjct: 8   VTQEQYELYCEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPF 63

Query: 145 CRNSLR 150
           CR  ++
Sbjct: 64  CRCEIK 69

>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 = 46.3 bits (109), Expect = 4e-08
 Identities = 14/61 (22%), Positives = 16/61 (26%), Gaps = 14/61 (22%)

Query: 100 EESECCICLGVFEDGDK--------------VKILPKCRHCYHCECVDAWLSARSSCPLC 145
               C IC     D                       C H +H  C+  WL  R  CPL 
Sbjct: 20  VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 79

Query: 146 R 146
            
Sbjct: 80  N 80

>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 = 45.5 bits (107), Expect = 4e-08
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 2/53 (3%)

Query: 100 EESECCICLGVFEDGDKVKILP-KCRHCYHCECVDAWLSARS-SCPLCRNSLR 150
           ++  C  C         +K++   C H     CVD      + +CP C   LR
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

>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 = 45.3 bits (107), Expect = 5e-08
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 7/62 (11%)

Query: 97  DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP 156
           ++ +   C  C    +     K+LP C H     C++A       CP+C+    + +  P
Sbjct: 2   EEFQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADTP 54

Query: 157 SI 158
           ++
Sbjct: 55  AL 56

>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 = 44.7 bits (105), Expect = 7e-08
 Identities = 12/51 (23%), Positives = 16/51 (31%), Gaps = 1/51 (1%)

Query: 103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLCRNSLRVD 152
           EC +C+   E  D       C +     C     +     CP CR     D
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 41.6 bits (97), Expect = 3e-06
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 92  KSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS---SCPLCRNS 148
           ++  +  ++  EC ICL + ++     +  KC H +   C+   L+ +     CPLC+N 
Sbjct: 12  QNVINAMQKILECPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

Query: 149 LRVDSALPSIT 159
           +   S   S  
Sbjct: 68  ITKRSLQESTR 78

>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 = 41.2 bits (95), Expect = 5e-06
 Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 21/80 (26%)

Query: 86  VLHRSEKSTKDDKEEESECCICLGVFED--------------GDKVKILPKCRHCYHCEC 131
           V+ +  +  K   EE+  C IC+                      V  L KC H +H  C
Sbjct: 12  VIRKYTEELKVAPEED--CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLC 69

Query: 132 VDAWLSARS-----SCPLCR 146
           + A     +      CP C+
Sbjct: 70  LLAMYCNGNKDGSLQCPSCK 89

>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 = 38.7 bits (89), Expect = 2e-05
 Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 3/58 (5%)

Query: 97  DKEEESECCICLGVFEDGDKVKILPK-CRHCYHCECVDAWLSAR--SSCPLCRNSLRV 151
           + E+   C IC     +               H  C+  WL+    ++C +C      
Sbjct: 2   EDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT 59

>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 = 36.7 bits (84), Expect = 1e-04
 Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 6/70 (8%)

Query: 92  KSTKDDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSC---PLCRNS 148
           ++  D  E+   C  C  +  +      L  C H +   CV   +         P     
Sbjct: 13  RAALDRLEKLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQD 69

Query: 149 LRVDSALPSI 158
           L+++  L S+
Sbjct: 70  LKINRQLDSM 79

>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 = 35.7 bits (82), Expect = 4e-04
 Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 5/56 (8%)

Query: 96  DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSS-CPLCRNSLR 150
               +   C IC  +  D     +   C+H +   C+   L    S CP CR    
Sbjct: 18  AHFVKSISCQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 69

>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 = 35.8 bits (82), Expect = 4e-04
 Identities = 11/56 (19%), Positives = 18/56 (32%), Gaps = 9/56 (16%)

Query: 99  EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARS--------SCPLCR 146
              S C +CLG +       I   C+  +   C+  ++            SCP   
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 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 = 33.6 bits (76), Expect = 0.001
 Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 3/53 (5%)

Query: 104 CCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP 156
           C I   V          PK R  +    ++ ++    + P+    L ++  + 
Sbjct: 3   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE 52

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

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]

 Score = 33.6 bits (76), Expect = 0.002
 Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 12/77 (15%)

Query: 90  SEKSTKDDKEEESE--CCICLGVFEDGDKVKIL-PKCRHCYHCECV---------DAWLS 137
           S  S+ +D  +      C+C    E    ++   P+C    H  CV         +  L 
Sbjct: 2   SSGSSGEDPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLP 61

Query: 138 ARSSCPLCRNSLRVDSA 154
               C +CR +    S 
Sbjct: 62  ESFYCEICRLTSGPSSG 78

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	161
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.89
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.78
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.76
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.75
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.72
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.71
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.67
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.62
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.53
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.52
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.42
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.39
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.35
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.2
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.13
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.54
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.13
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	95.98
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	95.6
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.48
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	93.5
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	93.43
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	92.78
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	92.2
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.47
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	91.29
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	91.09
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	88.97
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	86.54
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	86.07
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	85.85
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	85.27
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	84.45
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	83.4
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	82.99
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	82.76
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	81.97
d2co8a2	36	Nedd9 interacting protein with calponin homology,	80.64

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.89  E-value=2.1e-24  Score=121.39  Aligned_cols=52  Identities=46%  Similarity=1.188  Sum_probs=47.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCcccccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLR  150 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  150 (161)
                      +++.+|+||+++|.+++.++.+|.|||.||.+||++|++++.+||+||++|.
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            3556799999999999999888669999999999999999999999999875

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.78  E-value=4.1e-20  Score=108.33  Aligned_cols=50  Identities=28%  Similarity=0.763  Sum_probs=43.5

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      ...++|+||++.|.+  .++.+| |||.||.+||.+|++.+.+||+||+++..
T Consensus         3 ~~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           3 TVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            356789999999964  466788 99999999999999999999999998853

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=9.1e-20  Score=101.12  Aligned_cols=48  Identities=23%  Similarity=0.393  Sum_probs=41.1

Q ss_pred             ccccccccccCCCee-eecCCCCCccchhhHHHHHcCC-CCCccccccccC
Q 031354          103 ECCICLGVFEDGDKV-KILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRV  151 (161)
Q Consensus       103 ~CaICL~~f~~~~~v-~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  151 (161)
                      +|+||+++|.+++.+ ..++ |||.||.+|+++|++.+ .+||+||+++..
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            799999999877654 4567 99999999999999864 579999999865

>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=99.75  E-value=4.8e-19  Score=108.83  Aligned_cols=51  Identities=29%  Similarity=0.649  Sum_probs=43.0

Q ss_pred             CCCccccccccccCCC---------------eeeecCCCCCccchhhHHHHHcCCCCCccccccccC
Q 031354          100 EESECCICLGVFEDGD---------------KVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~---------------~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  151 (161)
                      .++.|+||++++.+..               .+..++ |||+||.+||.+||+.+.+||+||++...
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            4567999999887632               366778 99999999999999999999999998753

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.4e-18  Score=104.52  Aligned_cols=53  Identities=30%  Similarity=0.696  Sum_probs=45.3

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~  156 (161)
                      ....|+||++++.+   .+++| |||.||..||..|+.. +.+||+||.+|.....+.
T Consensus        22 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i~   75 (79)
T d1fbva4          22 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV   75 (79)
T ss_dssp             CTTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCSS
T ss_pred             CCCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCceee
Confidence            44579999999865   67899 9999999999999985 578999999998777654

>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=99.72  E-value=2.4e-18  Score=99.69  Aligned_cols=53  Identities=25%  Similarity=0.491  Sum_probs=42.3

Q ss_pred             CCCccccccccccCC--CeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCC
Q 031354          100 EESECCICLGVFEDG--DKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDS  153 (161)
Q Consensus       100 ~~~~CaICL~~f~~~--~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~  153 (161)
                      ++..|+||++++..+  ..+.+++ |||.||.+||.+|+.. +.+||+||.++...+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            467899999986543  2445677 9999999999999965 467999999986554

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=2.3e-18  Score=110.79  Aligned_cols=52  Identities=23%  Similarity=0.534  Sum_probs=42.0

Q ss_pred             CCCccccccccccC---------------CCeeeecCCCCCccchhhHHHHHcCC-----CCCccccccccCC
Q 031354          100 EESECCICLGVFED---------------GDKVKILPKCRHCYHCECVDAWLSAR-----SSCPLCRNSLRVD  152 (161)
Q Consensus       100 ~~~~CaICL~~f~~---------------~~~v~~lp~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~l~~~  152 (161)
                      .++.|+||+++|.+               ...+++++ |||+||..||++||..+     .+||+||+.+..+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            45689999999864               33566778 99999999999999743     4799999988554

>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=99.67  E-value=6.2e-18  Score=94.71  Aligned_cols=53  Identities=25%  Similarity=0.575  Sum_probs=44.6

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~~  158 (161)
                      ....+|+||++.|.+   .+++| |||+||..||++|   +.+||+||+++......|.+
T Consensus         4 ~~~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~~~aL   56 (56)
T d1bora_           4 FQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADTPAL   56 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSSCCCC
T ss_pred             cCCCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCCCCCC
Confidence            345689999999976   56789 9999999999876   56799999999988877753

>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=99.62  E-value=4.6e-17  Score=91.37  Aligned_cols=51  Identities=14%  Similarity=0.250  Sum_probs=43.5

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      .|+||++.|+  +.|.... |||+||.+||.+|++.+.+||+||.++..++-+|
T Consensus         2 ~C~Ic~~~~~--~Pv~~~~-cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLip   52 (56)
T d2baya1           2 LCAISGKVPR--RPVLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE   52 (56)
T ss_dssp             CCTTTCSCCS--SEEEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEE
T ss_pred             CCccCCchHH--hcCccCC-CCCcccHHHHHHHHhhccCCCccCCcCCHHhcee
Confidence            5999999986  4554444 9999999999999999999999999998876654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=5.6e-16  Score=93.96  Aligned_cols=53  Identities=25%  Similarity=0.476  Sum_probs=43.8

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~  156 (161)
                      +...|+||++.|.+   ..+++ |||.|+..||.+|++. +.+||+||.++...+..+
T Consensus        22 ~~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhhccC
Confidence            34579999999875   56788 9999999999999974 467999999987665444

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.7e-15  Score=94.46  Aligned_cols=52  Identities=31%  Similarity=0.625  Sum_probs=41.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC---CCCccccccccCCCCCC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR---SSCPLCRNSLRVDSALP  156 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~~~~~~~  156 (161)
                      ...|+||++.|.+   ...++ |||.||..||.+|+..+   ..||+||.++...+--+
T Consensus        21 ~l~CpIC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~   75 (103)
T d1jm7a_          21 ILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE   75 (103)
T ss_dssp             HTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBC
T ss_pred             CcCCCccCchhCC---eEEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCc
Confidence            3479999999975   34578 99999999999999764   37999999987655333

>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=99.52  E-value=3.5e-15  Score=84.77  Aligned_cols=54  Identities=19%  Similarity=0.419  Sum_probs=39.4

Q ss_pred             CCCCCccccccccccCCCeee-ecCCCCCccchhhHHHHHc--CCCCCccccccccC
Q 031354           98 KEEESECCICLGVFEDGDKVK-ILPKCRHCYHCECVDAWLS--ARSSCPLCRNSLRV  151 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~-~lp~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~l~~  151 (161)
                      .++...|.||++++.+..... ...+|+|.||..||.+|+.  .+.+||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            456778999999986532221 1112459999999999995  45789999998764

>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=99.42  E-value=1.9e-14  Score=89.57  Aligned_cols=51  Identities=20%  Similarity=0.578  Sum_probs=40.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccccccCCCCCC
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRNSLRVDSALP  156 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~  156 (161)
                      ...|+||++.|.+  .+...+ |||.||..||.+|+.  ..||.||.++...+..+
T Consensus        22 ~l~C~IC~~~~~~--pv~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~   72 (97)
T d1jm7b_          22 LLRCSRCTNILRE--PVCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKI   72 (97)
T ss_dssp             TTSCSSSCSCCSS--CBCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCC
T ss_pred             cCCCccCCchhhc--CceeCC-CCCchhHHHHHHHHh--ccccccCCcCchhhCcc
Confidence            4589999999964  454557 999999999999985  45999999887655443

>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=99.39  E-value=2e-13  Score=81.39  Aligned_cols=58  Identities=26%  Similarity=0.509  Sum_probs=47.4

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC-CCCccccccccCCCCCCCC
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR-SSCPLCRNSLRVDSALPSI  158 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~~~~~~~  158 (161)
                      ...++..|+||++-|.+  .| +++ |||.|+..||.+|+..+ .+||.|+.++......|..
T Consensus         4 eiP~~l~CpIc~~~m~d--PV-~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~   62 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKD--PV-IVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             CCSSSSSCTTTSCCCSS--EE-EET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CCCccCCCcCcCchhhC--ce-Ecc-CCCcchHHHHHHHHHHCCCCCCcccccCCcccccchH
Confidence            34577899999999975  34 678 99999999999999864 6799999999877665543

>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=99.35  E-value=2.7e-13  Score=81.23  Aligned_cols=54  Identities=17%  Similarity=0.271  Sum_probs=44.4

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC-CCCCccccccccCCCCCC
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA-RSSCPLCRNSLRVDSALP  156 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~  156 (161)
                      .++..|+||++-|.+  .| +++ |||.|+..||.+|+.. +.+||+||.++...+..|
T Consensus         5 P~~l~CpIc~~l~~d--Pv-~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~p   59 (80)
T d2c2la2           5 PDYLCGKISFELMRE--PC-ITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIP   59 (80)
T ss_dssp             CSTTBCTTTCSBCSS--EE-ECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEE
T ss_pred             CccccCcCcCchhhh--hc-ccC-CcCeecHHHHHHHHhcCCccCCCcccccccccccc
Confidence            466789999999875  44 688 9999999999999974 568999999987665444

>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=99.20  E-value=1.2e-11  Score=76.61  Aligned_cols=56  Identities=20%  Similarity=0.202  Sum_probs=46.5

Q ss_pred             CCCCCccccccccccCCCeeeecCCCC-CccchhhHHHHHcCCCCCccccccccCCCCCCC
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCR-HCYHCECVDAWLSARSSCPLCRNSLRVDSALPS  157 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~~~  157 (161)
                      ..++..|+||++-|.+   -.++| || |.|...||.+||..+.+||+||.++......|.
T Consensus        19 ~P~~f~CPI~~~lm~d---PV~~~-~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN   75 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             CCTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             CcHHhCCcCchhHHHH---HHhcc-cccchhhHHHHHHHHHhcCCcccccccccchhhcch
Confidence            3457899999999876   55788 55 589999999999999999999999987765554

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=1.3e-11  Score=75.86  Aligned_cols=49  Identities=22%  Similarity=0.524  Sum_probs=40.1

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC--------CCCccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR--------SSCPLCRN  147 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~--------~~CP~CR~  147 (161)
                      .....+|+||++++..++.+..++ |||.||.+|+..|+..+        .+||.|+.
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           2 SSGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CCSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            346679999999998878887777 99999999999999531        25998653

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.00049  Score=36.14  Aligned_cols=44  Identities=25%  Similarity=0.610  Sum_probs=31.2

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCC----CCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR----SSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~----~~CP~CR~  147 (161)
                      .|.||-..-..+..| .-..|...||..|++.-+...    -.||.||.
T Consensus         2 ~C~vC~~~~~~~~~i-~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEE-EcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588887654444444 444589999999999876542    35999975

>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=96.13  E-value=0.00092  Score=36.79  Aligned_cols=51  Identities=20%  Similarity=0.461  Sum_probs=36.0

Q ss_pred             CCCCCccccccccccCCCeeeecCCCCCccchhhHHHHH---c--CCCCCcccccc
Q 031354           98 KEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL---S--ARSSCPLCRNS  148 (161)
Q Consensus        98 ~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl---~--~~~~CP~CR~~  148 (161)
                      ......|.+|.....+++....-..|+.-||..|+..=.   .  .+-.||.|+..
T Consensus         3 ~~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            345678999998877766544555699999999986311   1  23469999754

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.98  E-value=0.0023  Score=35.86  Aligned_cols=52  Identities=27%  Similarity=0.590  Sum_probs=34.8

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHcCC----CCCccccccccCCCCC
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSAR----SSCPLCRNSLRVDSAL  155 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~l~~~~~~  155 (161)
                      ....|.+|-+   .++.+ .-..|...||..|+...+...    ..||.|+..-...+..
T Consensus         6 ~c~~C~~C~~---~~~ll-~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~~~~   61 (70)
T d1fp0a1           6 SATICRVCQK---PGDLV-MCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEED   61 (70)
T ss_dssp             SSSCCSSSCS---SSCCE-ECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCCSS
T ss_pred             CCCCCCCCCC---cCEEE-ECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccCccc
Confidence            4456777754   35544 444489999999999887543    3599997665544433

>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=95.60  E-value=0.0012  Score=36.01  Aligned_cols=47  Identities=23%  Similarity=0.560  Sum_probs=32.6

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhhHHHHHcC----CCCCccccccc
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSA----RSSCPLCRNSL  149 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l  149 (161)
                      ...+.|.+|.+.   ++.| .-..|.-.||..|++.-+..    .-.||.|+..-
T Consensus         7 ~~~~~C~~C~~~---g~lv-~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELL-CCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCB-CCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEE-EeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            455689999753   4444 33448899999999866553    23699997654

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.48  E-value=0.0059  Score=34.79  Aligned_cols=60  Identities=22%  Similarity=0.480  Sum_probs=38.9

Q ss_pred             CCCCCCCccccccccccCCCeeeecCCCCCccchhhHHHH--HcC--------------CCCCccccc--cccCCCCCCC
Q 031354           96 DDKEEESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW--LSA--------------RSSCPLCRN--SLRVDSALPS  157 (161)
Q Consensus        96 ~~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W--l~~--------------~~~CP~CR~--~l~~~~~~~~  157 (161)
                      +....+..|.|| +.|..++.. -...|+-+||..|+.+-  ++.              ..+|+.|..  .+..++.+.+
T Consensus        10 e~v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl~~LLtEeem~s   87 (89)
T d1wila_          10 EPVVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNINLLLTEESGPS   87 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCCCSSSCCCCCCC
T ss_pred             cCCCcCcccccc-Cccccccee-cceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcchhhhhcHhhhhc
Confidence            446678899999 777655433 22237899999999986  211              126999942  3444555544

>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=93.50  E-value=0.013  Score=34.05  Aligned_cols=50  Identities=18%  Similarity=0.534  Sum_probs=32.6

Q ss_pred             CCccccccccccC-CCeeeecCCCCCccchhhHHHHH-----cC---CCCCcccccccc
Q 031354          101 ESECCICLGVFED-GDKVKILPKCRHCYHCECVDAWL-----SA---RSSCPLCRNSLR  150 (161)
Q Consensus       101 ~~~CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl-----~~---~~~CP~CR~~l~  150 (161)
                      ...|.||...... +..+..-..|+..||..|+...+     ..   ...||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            4579999865432 23344444588999999987433     21   356999976544

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=93.43  E-value=0.047  Score=30.79  Aligned_cols=51  Identities=22%  Similarity=0.474  Sum_probs=33.0

Q ss_pred             CCCccccccccccCCCeeeec-CCCCCccchhhHHH----H--Hc---CCCCCccccccccC
Q 031354          100 EESECCICLGVFEDGDKVKIL-PKCRHCYHCECVDA----W--LS---ARSSCPLCRNSLRV  151 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~l-p~C~H~FH~~Ci~~----W--l~---~~~~CP~CR~~l~~  151 (161)
                      ....| ||-....++..+..- ..|..=||..|+.-    .  ..   .+..||.|+..-.+
T Consensus        15 ~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~p   75 (78)
T d1wewa_          15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGP   75 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCSC
T ss_pred             CccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCCC
Confidence            34578 899887766666443 13888899999841    1  11   13569999765433

>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=92.78  E-value=0.031  Score=25.62  Aligned_cols=28  Identities=21%  Similarity=0.462  Sum_probs=24.1

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhh
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCEC  131 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~C  131 (161)
                      ..|+-|...+...|-|+.-  =+++||.+|
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~C   30 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKC   30 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGG
T ss_pred             cccccccCcCChhHhheec--ccceeeecc
Confidence            3699999999999988876  479999998

>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=92.20  E-value=0.054  Score=30.03  Aligned_cols=46  Identities=30%  Similarity=0.699  Sum_probs=27.7

Q ss_pred             CCCCccccccccccCCCeeeec-CCCCC-ccchhhHHHHHcC----CCCCcccccc
Q 031354           99 EEESECCICLGVFEDGDKVKIL-PKCRH-CYHCECVDAWLSA----RSSCPLCRNS  148 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~l-p~C~H-~FH~~Ci~~Wl~~----~~~CP~CR~~  148 (161)
                      .+...| ||.... +++.+... .+|-+ -||..|+.  |..    +-.||.|+..
T Consensus        14 ~e~~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          14 NEPTYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             SSCCCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCCEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            344567 898653 34444432 22544 59999985  333    2359999754

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.47  E-value=0.18  Score=28.25  Aligned_cols=48  Identities=19%  Similarity=0.418  Sum_probs=30.8

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHH--HHH-cC--CCCCccccccc
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVD--AWL-SA--RSSCPLCRNSL  149 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~--~Wl-~~--~~~CP~CR~~l  149 (161)
                      ...| ||-..+..++....-..|.--||..|+.  ..- ..  +-.||.|+...
T Consensus        12 pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            3456 9988765554333444588889999984  222 22  35799997643

>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=91.29  E-value=0.011  Score=30.78  Aligned_cols=45  Identities=18%  Similarity=0.471  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeeecCCCCCccchhhHHHHHcCCCCCccccc
Q 031354          103 ECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLSARSSCPLCRN  147 (161)
Q Consensus       103 ~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~  147 (161)
                      .|.+|-..|..-..-..-..||.+|+.+|....-.....|..|..
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            578888888754433334459999999997665444456888853

>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=91.09  E-value=0.21  Score=27.56  Aligned_cols=48  Identities=21%  Similarity=0.456  Sum_probs=30.2

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHH------HH---HcCCCCCccccccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVD------AW---LSARSSCPLCRNSL  149 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~------~W---l~~~~~CP~CR~~l  149 (161)
                      ....| ||-....++..|. -..|.=-||..|+.      ..   ...+-.||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~~~mi~-Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          15 NALYC-ICRQPHNNRFMIC-CDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSSCEEE-CSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CcCEE-ECCCccCCCeEEE-ECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            34467 8877665545554 33487889999982      11   12346899996543

>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=88.97  E-value=0.064  Score=29.63  Aligned_cols=47  Identities=19%  Similarity=0.395  Sum_probs=30.6

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHHHc----CCCCCccccccc
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS----ARSSCPLCRNSL  149 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~l  149 (161)
                      ..| ||-....+++....-..|..-||..|+..=..    ..-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~   67 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcC
Confidence            457 78776666654444445888999999754211    234699997653

>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=86.54  E-value=0.2  Score=26.38  Aligned_cols=44  Identities=27%  Similarity=0.677  Sum_probs=30.3

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHHc-CCCCCccc
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWLS-ARSSCPLC  145 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl~-~~~~CP~C  145 (161)
                      ....|--|...+.+ ..+..-|.|++.|+.+|=. ... .-.+||-|
T Consensus        14 ~~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~-fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDV-FVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTT-SEEECCTTTTCCBCHHHHH-TTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCC-CceEECcCCCCccccccch-hhhhhhcCCCCC
Confidence            45679999988865 4455666799999988832 222 22468877

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=86.07  E-value=0.31  Score=23.01  Aligned_cols=27  Identities=26%  Similarity=0.579  Sum_probs=17.0

Q ss_pred             CeeeecCCCCCccchhhHHHHHcCCCCCcccccc
Q 031354          115 DKVKILPKCRHCYHCECVDAWLSARSSCPLCRNS  148 (161)
Q Consensus       115 ~~v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  148 (161)
                      +.+.+-+.|||++-.       ..-..||+|..+
T Consensus         3 ~~~~vC~vCGyi~~g-------~~Pe~CPvCg~~   29 (36)
T d1yuza2           3 DKFHLCPICGYIHKG-------EDFEKCPICFRP   29 (36)
T ss_dssp             CCEEECSSSCCEEES-------SCCSBCTTTCCB
T ss_pred             CCEEECCCCCCEeeC-------CCCCcCCCCCCc
Confidence            455666679998542       122469999754

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {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: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.85  E-value=0.2  Score=24.31  Aligned_cols=27  Identities=30%  Similarity=0.678  Sum_probs=19.0

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhh
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCEC  131 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~C  131 (161)
                      ...|..|-+- -.|+.+...   +|.||..|
T Consensus        15 G~~C~~C~~~-ItG~V~~Ag---~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQF-IEGEVVSAL---GKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCB-CCSCCEEET---TEEECTTT
T ss_pred             CcccccccCE-eeeeeeEec---CcccCCCC
Confidence            4689999554 467766543   48899988

>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=85.27  E-value=0.33  Score=29.63  Aligned_cols=51  Identities=14%  Similarity=0.321  Sum_probs=32.0

Q ss_pred             CCCCccccccccccC-CCeeeecCCCCCccchhhHHHHH-cC---CCCCccccccc
Q 031354           99 EEESECCICLGVFED-GDKVKILPKCRHCYHCECVDAWL-SA---RSSCPLCRNSL  149 (161)
Q Consensus        99 ~~~~~CaICL~~f~~-~~~v~~lp~C~H~FH~~Ci~~Wl-~~---~~~CP~CR~~l  149 (161)
                      .+...|++|...|.. ...-..-..||+.||..|-..=. ..   ...|.+|....
T Consensus        46 ~~~~~C~~C~~~f~~~~~~~~~C~~C~~~~C~~C~~~~~~~~~~~~w~C~~C~k~r  101 (124)
T d1zbdb_          46 DGVNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLEQR  101 (124)
T ss_dssp             CSSSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEEECCCSSSSCCEEEHHHHHHH
T ss_pred             cCCCcCcccCCcccCCCCCCCcCccCCcccccCCCCCccCCCCCCCEECccCcchH
Confidence            345679999999874 23333445599999999943211 11   13588886543

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.45  E-value=0.44  Score=25.45  Aligned_cols=37  Identities=19%  Similarity=0.337  Sum_probs=26.1

Q ss_pred             CCCccccccccccCCCeeeecCCCCCccchhhHHHHH
Q 031354          100 EESECCICLGVFEDGDKVKILPKCRHCYHCECVDAWL  136 (161)
Q Consensus       100 ~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~Wl  136 (161)
                      +...|.+|-..|..-..-.--..||++|+..|...+.
T Consensus         7 ~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~~   43 (64)
T d1joca1           7 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNA   43 (64)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEE
T ss_pred             cCCcCcCcCCcccCCccccchhhhCCeecccccCCce
Confidence            4457999999987643323334599999999976544

>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=83.40  E-value=0.38  Score=26.39  Aligned_cols=35  Identities=14%  Similarity=0.321  Sum_probs=25.7

Q ss_pred             CCccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          101 ESECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       101 ~~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      .+.|.+|-..|.--..-..-..||++|+..|....
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            45799999998764433344459999999997654

>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=82.99  E-value=0.53  Score=25.36  Aligned_cols=34  Identities=18%  Similarity=0.281  Sum_probs=24.6

Q ss_pred             CccccccccccCCCeeeecCCCCCccchhhHHHH
Q 031354          102 SECCICLGVFEDGDKVKILPKCRHCYHCECVDAW  135 (161)
Q Consensus       102 ~~CaICL~~f~~~~~v~~lp~C~H~FH~~Ci~~W  135 (161)
                      +.|.+|-..|..-..-.--..||.+|+..|...+
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            4799999998754333333459999999997554

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {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: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.76  E-value=0.45  Score=21.89  Aligned_cols=31  Identities=26%  Similarity=0.501  Sum_probs=24.7

Q ss_pred             CCCCccccccccccCCCeeeecCCCCCccchhh
Q 031354           99 EEESECCICLGVFEDGDKVKILPKCRHCYHCEC  131 (161)
Q Consensus        99 ~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~C  131 (161)
                      .....|.-|-+.|++.+.+.-.  =|-++|..|
T Consensus         5 L~~~~C~RC~~gF~p~EkiVNS--nGEl~H~qC   35 (35)
T d1g47a1           5 LASATCERCKGGFAPAEKIVNS--NGELYHEQC   35 (35)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEE--TTEEECTTT
T ss_pred             HHHHHHHHHccCCCchHHhhcC--CCccccccC
Confidence            4566899999999998877443  688899887

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=81.97  E-value=0.62  Score=22.03  Aligned_cols=25  Identities=32%  Similarity=0.550  Sum_probs=16.3

Q ss_pred             eeecCCCCCccchhhHHHHHcCCCCCcccccc
Q 031354          117 VKILPKCRHCYHCECVDAWLSARSSCPLCRNS  148 (161)
Q Consensus       117 v~~lp~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  148 (161)
                      +.+-+.|||++-.       ..=..||+|..+
T Consensus         5 ~~~C~vCG~i~~g-------~~P~~CPvCg~~   29 (37)
T d1nnqa2           5 VYICPICGYTAVD-------EAPEYCPVCGAP   29 (37)
T ss_dssp             EEECTTTCCEEES-------CCCSBCTTTCCB
T ss_pred             EEECCCCCCEecC-------CCCCcCCCCCCc
Confidence            4555669998753       122469999654

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.64  E-value=0.72  Score=21.64  Aligned_cols=32  Identities=16%  Similarity=0.365  Sum_probs=20.7

Q ss_pred             CCCCCCccccccccccCCCeeeecCCCCCccchhh
Q 031354           97 DKEEESECCICLGVFEDGDKVKILPKCRHCYHCEC  131 (161)
Q Consensus        97 ~~~~~~~CaICL~~f~~~~~v~~lp~C~H~FH~~C  131 (161)
                      .....+.|++|-...-.=+.+   ..=|++||..|
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl---~a~g~~yHk~C   35 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERL---CVNGHFFHRSC   35 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBC---CBTTBCCBTTT
T ss_pred             cCCCCCcccccCCEEeeeeEE---EecCcEecccc
Confidence            345678999996654332322   21478999998