Citrus Sinensis ID: 044807

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
RQQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHcccEEccccccccccccccccEEccccccccEEccccccccccccccHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHcccccccccccccccccccHHHHHHccEEEEEcccccccccccEEEEEEccccccccEEEcccccccccHHHHHHHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
rqqqlnstptavapqppimimgldectIKSFQKLVLeeskclpgpnssacsicLSEYlsqetikcipeckhcfhaecidewprlndkcpvcinsatpvhadyvnp
Flexible Loop (DISEMBL)
rqqqlnstptavapqppiMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINsatpvhadyvnp
Low Complexity Region (SEG)
RQQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP
Disordered region (IsUnstruct)
*****************IMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHA*****
Disordered Region (DISOPRED)
*********************GLDECTIKSFQKLVLEES*****PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINS***********
Disordered Region (DISEMBL)
***********VAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP
Disordered Region (DISPRO)
*******************IMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSA**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
RQQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	105	2.2.26 [Sep-21-2011]
Q9C7E9	299	RING-H2 finger protein AT	yes	no	0.828	0.290	0.517	3e-22
P0CH01	372	Putative RING-H2 finger p	no	no	0.914	0.258	0.505	1e-21
Q9SKK8	377	RING-H2 finger protein AT	no	no	0.819	0.228	0.505	2e-20
P0CH03	366	Putative RING-H2 finger p	no	no	0.8	0.229	0.517	1e-19
Q9FL42	159	Putative RING-H2 finger p	no	no	0.733	0.484	0.506	3e-19
P0CH02	362	Putative RING-H2 finger p	no	no	0.771	0.223	0.493	1e-18
Q8RX29	217	RING-H2 finger protein AT	no	no	0.704	0.341	0.448	6e-14
Q9M313	212	RING-H2 finger protein AT	no	no	0.761	0.377	0.393	2e-12
Q9FG21	197	Putative RING-H2 finger p	no	no	0.761	0.406	0.4	5e-12
O82353	214	RING-H2 finger protein AT	no	no	0.752	0.369	0.388	1e-11

>sp|Q9C7E9|ATL20_ARATH RING-H2 finger protein ATL20 OS=Arabidopsis thaliana GN=ATL20 PE=2 SV=2

 Score =  103 bits (258), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 45/87 (51%), Positives = 63/87 (72%)

Query: 10  TAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPEC 69
           T   P+  ++  GLD+ TI+S++K+ L ES+ LPG N   C ICLSEY S+ET++C+PEC
Sbjct: 213 TTQQPRGVVVTTGLDQSTIESYKKVELGESRRLPGTNGIICPICLSEYASKETVRCMPEC 272

Query: 70  KHCFHAECIDEWPRLNDKCPVCINSAT 96
            HCFH +CIDEW +++  CPVC NS +
Sbjct: 273 DHCFHVQCIDEWLKIHSSCPVCRNSRS 299

Arabidopsis thaliana (taxid: 3702)

>sp|P0CH01|AT21A_ARATH Putative RING-H2 finger protein ATL21A OS=Arabidopsis thaliana GN=ATL21A PE=3 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 49/97 (50%), Positives = 64/97 (65%), Gaps = 1/97 (1%)

Query: 4   QLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSS-ACSICLSEYLSQET 62
           Q N    A+ P   I+  GLDE  I+S++K  L ES+ LPG N    C ICLSEY S+ET
Sbjct: 273 QRNVAIAALQPNEVIVTTGLDESIIESYKKTELGESRRLPGNNDDIVCPICLSEYASKET 332

Query: 63  IKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH 99
           ++CIPEC HCFH+ECID W +++  CP+C NS +P  
Sbjct: 333 VRCIPECDHCFHSECIDVWLKIHGSCPLCRNSPSPAR 369

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SKK8|ATL22_ARATH RING-H2 finger protein ATL22 OS=Arabidopsis thaliana GN=ATL22 PE=2 SV=2

 Score = 97.8 bits (242), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/87 (50%), Positives = 63/87 (72%), Gaps = 1/87 (1%)

Query: 14  PQPPIMIMGLDECTIKSFQKLVLEESKCLP-GPNSSACSICLSEYLSQETIKCIPECKHC 72
           P   +  +GLDE TI+S++K+ L ES+ LP G N   C ICLSEY ++ET++C+PEC+HC
Sbjct: 290 PSNEVARIGLDESTIESYKKVELGESRRLPTGSNDVVCPICLSEYATKETVRCLPECEHC 349

Query: 73  FHAECIDEWPRLNDKCPVCINSATPVH 99
           FH ECID W +L+  CPVC ++ +P+ 
Sbjct: 350 FHTECIDAWLKLHSSCPVCRSNPSPLR 376

Arabidopsis thaliana (taxid: 3702)

>sp|P0CH03|AT21C_ARATH Putative RING-H2 finger protein ATL21C OS=Arabidopsis thaliana GN=ATL21C PE=3 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/87 (51%), Positives = 59/87 (67%), Gaps = 3/87 (3%)

Query: 11  AVAPQPPIMIM---GLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIP 67
           A   Q P  +M   GLD+ TI++F+K+ L ES+ L G N   C ICLSEY S+ET++ IP
Sbjct: 278 ATVMQQPREVMARRGLDQSTIETFKKMELGESRRLSGTNGIVCPICLSEYASKETVRFIP 337

Query: 68  ECKHCFHAECIDEWPRLNDKCPVCINS 94
           EC HCFH ECID W +++  CP+C NS
Sbjct: 338 ECDHCFHVECIDVWLKIHGSCPLCRNS 364

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FL42|ATL69_ARATH Putative RING-H2 finger protein ATL69 OS=Arabidopsis thaliana GN=ATL69 PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 56/77 (72%)

Query: 21  MGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDE 80
           +GLD   I+S+ ++VL +S+ LP PN+  CSICL +Y ++E ++CIPEC HCFH +C+DE
Sbjct: 65  LGLDRPVIESYPRIVLGDSRRLPRPNNGPCSICLCDYEAREPVRCIPECNHCFHTDCVDE 124

Query: 81  WPRLNDKCPVCINSATP 97
           W R +  CP+C NS  P
Sbjct: 125 WLRTSATCPLCRNSPAP 141

Arabidopsis thaliana (taxid: 3702)

>sp|P0CH02|AT21B_ARATH Putative RING-H2 finger protein ATL21B OS=Arabidopsis thaliana GN=ATL21B PE=3 SV=1

 Score = 91.3 bits (225), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/81 (49%), Positives = 57/81 (70%)

Query: 14  PQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCF 73
           P+  +   GLD+ TI+ ++ + L ES+  PG N   C ICLSEY+S+ET++ IPEC HCF
Sbjct: 280 PREVMATRGLDQSTIEKYKTMELGESRRPPGTNGIVCPICLSEYVSKETVRFIPECDHCF 339

Query: 74  HAECIDEWPRLNDKCPVCINS 94
           HA+CID W +++  CP+C NS
Sbjct: 340 HAKCIDVWLKIHGSCPLCRNS 360

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RX29|ATL70_ARATH RING-H2 finger protein ATL70 OS=Arabidopsis thaliana GN=ATL70 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 51/78 (65%), Gaps = 4/78 (5%)

Query: 22  GLDECTIKSFQKLVLEESKCLPGPNSSAC-SICLSEYLSQETIKCIPECKHCFHAECIDE 80
           GLDE TI+S+ K++  E+K   GP +++C +ICL +Y  +  ++ +P+C H FH +CID 
Sbjct: 121 GLDEDTIQSYPKILYSEAK---GPTTASCCAICLGDYKGKHLLRQLPDCNHLFHLKCIDT 177

Query: 81  WPRLNDKCPVCINSATPV 98
           W RLN  CPVC  S  P 
Sbjct: 178 WLRLNPTCPVCRTSPLPT 195

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M313|ATL68_ARATH RING-H2 finger protein ATL68 OS=Arabidopsis thaliana GN=ATL68 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 48/89 (53%), Gaps = 9/89 (10%)

Query: 18  IMIMGLDECTIKSFQKL--------VLEESKCLPGPNS-SACSICLSEYLSQETIKCIPE 68
           +++ GLD   I S+ K         V+       G    + CSICL EY+ +E ++ +PE
Sbjct: 95  VVVGGLDHSVINSYPKFHFTKDITAVVNGDGFHDGEGRETTCSICLCEYMEEEMLRMMPE 154

Query: 69  CKHCFHAECIDEWPRLNDKCPVCINSATP 97
           CKH FH  C+D W +LN  CPVC NS  P
Sbjct: 155 CKHYFHVYCLDAWLKLNGSCPVCRNSPLP 183

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG21|ATL71_ARATH Putative RING-H2 finger protein ATL71 OS=Arabidopsis thaliana GN=ATL71 PE=3 SV=1

 Score = 69.7 bits (169), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 48/85 (56%), Gaps = 5/85 (5%)

Query: 18  IMIMGLDECTIKSFQKLVLEESKC-----LPGPNSSACSICLSEYLSQETIKCIPECKHC 72
           + ++GL E  IK F KL  EE++           +S CSICL++Y   + I+ +P+C H 
Sbjct: 92  VEVLGLTEEVIKGFPKLPYEEARVSYSLQKESSTTSCCSICLADYKKMDMIRVLPDCNHL 151

Query: 73  FHAECIDEWPRLNDKCPVCINSATP 97
           FH  C+D W RL+  CPVC  S  P
Sbjct: 152 FHDNCVDPWLRLHPTCPVCRTSPLP 176

Arabidopsis thaliana (taxid: 3702)

>sp|O82353|ATL67_ARATH RING-H2 finger protein ATL67 OS=Arabidopsis thaliana GN=ATL67 PE=2 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 46/85 (54%), Gaps = 6/85 (7%)

Query: 19  MIMGLDECTIKSFQKLVLEESKCLPGPN------SSACSICLSEYLSQETIKCIPECKHC 72
           +++GLD+  I S+ K    +       +       + CSICL EY   E ++ +PECKH 
Sbjct: 101 VVVGLDQAVINSYPKFHFSKDTSAASSDGFGGGGDTTCSICLCEYKEAEMLRMMPECKHY 160

Query: 73  FHAECIDEWPRLNDKCPVCINSATP 97
           FH  C+D W +LN  CPVC NS  P
Sbjct: 161 FHLCCLDAWLKLNGSCPVCRNSPLP 185

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	105
224067976	373	predicted protein [Populus trichocarpa]	0.961	0.270	0.643	4e-32
224130536	297	predicted protein [Populus trichocarpa]	0.866	0.306	0.648	3e-29
356571242	506	PREDICTED: putative RING-H2 finger prote	0.838	0.173	0.659	3e-29
255564721	374	RING-H2 finger protein ATL3K, putative [	0.942	0.264	0.59	1e-27
225454522	372	PREDICTED: putative RING-H2 finger prote	0.857	0.241	0.623	7e-27
449432054	382	PREDICTED: putative RING-H2 finger prote	0.895	0.246	0.541	2e-25
449477933	382	PREDICTED: putative RING-H2 finger prote	0.895	0.246	0.541	2e-25
356560276	378	PREDICTED: putative RING-H2 finger prote	0.942	0.261	0.572	3e-25
356522514	372	PREDICTED: putative RING-H2 finger prote	1.0	0.282	0.518	2e-24
358345841	222	RING finger protein [Medicago truncatula	0.8	0.378	0.611	5e-24

>gi|224067976|ref|XP_002302627.1| predicted protein [Populus trichocarpa] gi|222844353|gb|EEE81900.1| predicted protein [Populus trichocarpa]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/101 (64%), Positives = 78/101 (77%)

Query: 4   QLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETI 63
           Q NST  AV+PQP I+++GLDE TI+SF KLVL ESK LPGPN S C+ICLSEY S+ET+
Sbjct: 272 QRNSTIAAVSPQPTILVLGLDESTIESFDKLVLGESKRLPGPNGSTCAICLSEYNSKETV 331

Query: 64  KCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVN 104
           + IPECKHCFHA+C+DEW R+N  CPVC  S +P H    N
Sbjct: 332 RIIPECKHCFHADCVDEWLRMNSTCPVCRKSPSPAHVRSSN 372

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130536|ref|XP_002320862.1| predicted protein [Populus trichocarpa] gi|222861635|gb|EEE99177.1| predicted protein [Populus trichocarpa]

 Score =  132 bits (332), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 72/91 (79%)

Query: 4   QLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETI 63
           Q N+    V+P+P I++MGLDE TI+SF KLVL ESK LPGPN S C+ICLSEY S+ET+
Sbjct: 205 QRNTATATVSPRPTILVMGLDESTIESFDKLVLGESKRLPGPNGSTCAICLSEYNSKETL 264

Query: 64  KCIPECKHCFHAECIDEWPRLNDKCPVCINS 94
           + IPECKHCFHA+C+DEW R+N  CPVC  S
Sbjct: 265 RMIPECKHCFHADCVDEWLRMNGTCPVCRKS 295

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571242|ref|XP_003553788.1| PREDICTED: putative RING-H2 finger protein ATL21A-like [Glycine max]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 58/88 (65%), Positives = 72/88 (81%)

Query: 7   STPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCI 66
           S P+A++PQP I  MGLD+ TI+S+QKLVL ES+ +PGPN   C+ICLSEY +++TI+CI
Sbjct: 405 SEPSAISPQPSIATMGLDDSTIESYQKLVLGESRRVPGPNDGCCTICLSEYKTKDTIRCI 464

Query: 67  PECKHCFHAECIDEWPRLNDKCPVCINS 94
           PEC HCFHAECIDEW R+N  CPVC NS
Sbjct: 465 PECAHCFHAECIDEWLRMNSTCPVCRNS 492

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255564721|ref|XP_002523355.1| RING-H2 finger protein ATL3K, putative [Ricinus communis] gi|223537443|gb|EEF39071.1| RING-H2 finger protein ATL3K, putative [Ricinus communis]

 Score =  126 bits (317), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 59/100 (59%), Positives = 75/100 (75%), Gaps = 1/100 (1%)

Query: 1   RQQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLP-GPNSSACSICLSEYLS 59
           R    NS   AV+P P I ++GLDE TI+S++K+VL ES  LP G N S C+ICL+EY S
Sbjct: 269 RTTNQNSATVAVSPLPNIAMVGLDESTIESYEKVVLGESMRLPAGRNDSTCAICLAEYRS 328

Query: 60  QETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH 99
           +ET++CIPECKHCFH ECIDEW ++N  CPVC NS +P+H
Sbjct: 329 KETLRCIPECKHCFHVECIDEWLKMNSSCPVCRNSPSPLH 368

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454522|ref|XP_002277387.1| PREDICTED: putative RING-H2 finger protein ATL21A [Vitis vinifera] gi|297745433|emb|CBI40513.3| unnamed protein product [Vitis vinifera]

 Score =  124 bits (311), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 58/93 (62%), Positives = 72/93 (77%), Gaps = 3/93 (3%)

Query: 13  APQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHC 72
           APQ P  +MGLDE TI+S+ K+VL ES+ +PG N S C ICLS+Y ++ET++CIP+C HC
Sbjct: 283 APQEPAAMMGLDESTIESYTKVVLGESRRVPGLNDSTCPICLSDYCTKETLRCIPDCGHC 342

Query: 73  FHAECIDEWPRLNDKCPVCINSATPVHADYVNP 105
           FHAECIDEW R+N  CPVC NS +PV   YVNP
Sbjct: 343 FHAECIDEWLRVNGSCPVCRNSPSPV---YVNP 372

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432054|ref|XP_004133815.1| PREDICTED: putative RING-H2 finger protein ATL21A-like [Cucumis sativus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 52/96 (54%), Positives = 72/96 (75%), Gaps = 2/96 (2%)

Query: 2   QQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQE 61
           +QQ+N  P     + P  + GL+E TI+S+QK++L ES+ LPGPN + CSICL EYL+++
Sbjct: 280 RQQVN--PAGSDLEAPTRLSGLNESTIESYQKVILGESRRLPGPNGTTCSICLGEYLTKD 337

Query: 62  TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP 97
           T++CIPECKHCFH +CID+W R+N  CP+C NS  P
Sbjct: 338 TVRCIPECKHCFHVDCIDQWLRVNSSCPLCRNSPNP 373

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449477933|ref|XP_004155166.1| PREDICTED: putative RING-H2 finger protein ATL21A-like [Cucumis sativus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 52/96 (54%), Positives = 72/96 (75%), Gaps = 2/96 (2%)

Query: 2   QQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQE 61
           +QQ+N  P     + P  + GL+E TI+S+QK++L ES+ LPGPN + CSICL EYL+++
Sbjct: 280 RQQVN--PAGSDLEAPTRLSGLNESTIESYQKVILGESRRLPGPNGTTCSICLGEYLTKD 337

Query: 62  TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP 97
           T++CIPECKHCFH +CID+W R+N  CP+C NS  P
Sbjct: 338 TVRCIPECKHCFHVDCIDQWLRVNSSCPLCRNSPNP 373

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560276|ref|XP_003548419.1| PREDICTED: putative RING-H2 finger protein ATL21A-like [Glycine max]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 59/103 (57%), Positives = 78/103 (75%), Gaps = 4/103 (3%)

Query: 7   STPTA-VAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSAC-SICLSEYLSQETIK 64
           S P A ++P+P I   GLDE TI+S++K+VL ES+ +PGPN++ C  ICLSEY S+ETI+
Sbjct: 276 SAPAATISPEPQITTTGLDESTIESYEKVVLGESRRVPGPNNNGCCWICLSEYNSKETIR 335

Query: 65  CIPECKHCFHAECIDEWPRLNDKCPVCIN--SATPVHADYVNP 105
            IPECKHCFHA+CIDEW R+N  CPVC N  S +P+H   ++P
Sbjct: 336 LIPECKHCFHADCIDEWLRINTTCPVCRNSPSPSPIHVTSIDP 378

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522514|ref|XP_003529891.1| PREDICTED: putative RING-H2 finger protein ATL21A-like [Glycine max]

 Score =  116 bits (290), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/108 (51%), Positives = 77/108 (71%), Gaps = 3/108 (2%)

Query: 1   RQQQLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSAC-SICLSEYLS 59
           R    ++    ++P P I   GLDE TI+S++K+V+ ES+ +PGPN++ C  ICLSEY S
Sbjct: 265 RLTNRSALAATISPVPQIATTGLDESTIESYEKMVVGESRRVPGPNNNGCCWICLSEYNS 324

Query: 60  QETIKCIPECKHCFHAECIDEWPRLNDKCPVCIN--SATPVHADYVNP 105
           +ETI+ IPECKHCFHA+CIDEW R+N  CPVC N  S +P+H   ++P
Sbjct: 325 KETIRLIPECKHCFHADCIDEWLRINTTCPVCRNSPSPSPLHVTSIDP 372

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358345841|ref|XP_003636983.1| RING finger protein [Medicago truncatula] gi|355502918|gb|AES84121.1| RING finger protein [Medicago truncatula]

 Score =  114 bits (286), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 52/85 (61%), Positives = 67/85 (78%), Gaps = 1/85 (1%)

Query: 14  PQP-PIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHC 72
           PQP   +I GLDE TI+S++K+++ ES+ +PGPN   C ICL+EY S+ET++CIPECKHC
Sbjct: 128 PQPEATVIAGLDESTIESYEKVIIGESRRVPGPNDGCCWICLAEYNSKETVRCIPECKHC 187

Query: 73  FHAECIDEWPRLNDKCPVCINSATP 97
           FHA+CIDEW R+N  CPVC NS  P
Sbjct: 188 FHADCIDEWLRMNVTCPVCRNSPAP 212

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	105
TAIR|locus:2010489	299	AT1G28040 [Arabidopsis thalian	0.809	0.284	0.529	1.1e-23
TAIR|locus:2040085	377	AT2G25410 [Arabidopsis thalian	0.895	0.249	0.479	1e-22
TAIR|locus:2169399	159	AT5G07040 [Arabidopsis thalian	0.8	0.528	0.482	1.5e-21
TAIR|locus:2039170	217	AT2G35910 [Arabidopsis thalian	0.723	0.350	0.45	4.7e-16
TAIR|locus:2144088	197	AT5G06490 [Arabidopsis thalian	0.761	0.406	0.423	2.3e-14
TAIR|locus:2062892	214	AT2G46160 [Arabidopsis thalian	0.752	0.369	0.411	3e-14
TAIR|locus:2082762	212	AT3G61550 [Arabidopsis thalian	0.761	0.377	0.382	1.6e-13
TAIR|locus:2122348	132	AT4G09100 [Arabidopsis thalian	0.761	0.606	0.380	4.4e-13
TAIR|locus:2028436	219	AT1G49230 [Arabidopsis thalian	0.657	0.315	0.4	3.9e-12
TAIR|locus:2122363	345	AT4G09120 [Arabidopsis thalian	0.666	0.202	0.450	1.5e-11

TAIR|locus:2010489 AT1G28040 [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 45/85 (52%), Positives = 62/85 (72%)

Query:    10 TAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPEC 69
             T   P+  ++  GLD+ TI+S++K+ L ES+ LPG N   C ICLSEY S+ET++C+PEC
Sbjct:   213 TTQQPRGVVVTTGLDQSTIESYKKVELGESRRLPGTNGIICPICLSEYASKETVRCMPEC 272

Query:    70 KHCFHAECIDEWPRLNDKCPVCINS 94
              HCFH +CIDEW +++  CPVC NS
Sbjct:   273 DHCFHVQCIDEWLKIHSSCPVCRNS 297

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2040085 AT2G25410 [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 46/96 (47%), Positives = 69/96 (71%)

Query:     4 QLNSTPTAVAPQPPIMIMGLDECTIKSFQKLVLEESKCLP-GPNSSACSICLSEYLSQET 62
             +L+ + T+  P   +  +GLDE TI+S++K+ L ES+ LP G N   C ICLSEY ++ET
Sbjct:   281 RLSGSVTS-QPSNEVARIGLDESTIESYKKVELGESRRLPTGSNDVVCPICLSEYATKET 339

Query:    63 IKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV 98
             ++C+PEC+HCFH ECID W +L+  CPVC ++ +P+
Sbjct:   340 VRCLPECEHCFHTECIDAWLKLHSSCPVCRSNPSPL 375

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2169399 AT5G07040 [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 41/85 (48%), Positives = 59/85 (69%)

Query:    14 PQPPIMI-MGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHC 72
             P P   + +GLD   I+S+ ++VL +S+ LP PN+  CSICL +Y ++E ++CIPEC HC
Sbjct:    57 PSPAAEVKLGLDRPVIESYPRIVLGDSRRLPRPNNGPCSICLCDYEAREPVRCIPECNHC 116

Query:    73 FHAECIDEWPRLNDKCPVCINSATP 97
             FH +C+DEW R +  CP+C NS  P
Sbjct:   117 FHTDCVDEWLRTSATCPLCRNSPAP 141

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2039170 AT2G35910 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 36/80 (45%), Positives = 52/80 (65%)

Query:    19 MIMGLDECTIKSFQKLVLEESKCLPGPNS-SACSICLSEYLSQETIKCIPECKHCFHAEC 77
             ++ GLDE TI+S+ K++  E+K   GP + S C+ICL +Y  +  ++ +P+C H FH +C
Sbjct:   118 VVPGLDEDTIQSYPKILYSEAK---GPTTASCCAICLGDYKGKHLLRQLPDCNHLFHLKC 174

Query:    78 IDEWPRLNDKCPVCINSATP 97
             ID W RLN  CPVC  S  P
Sbjct:   175 IDTWLRLNPTCPVCRTSPLP 194

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2144088 AT5G06490 [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 36/85 (42%), Positives = 50/85 (58%)

Query:    18 IMIMGLDECTIKSFQKLVLEESKC---LPGPNS--SACSICLSEYLSQETIKCIPECKHC 72
             + ++GL E  IK F KL  EE++    L   +S  S CSICL++Y   + I+ +P+C H 
Sbjct:    92 VEVLGLTEEVIKGFPKLPYEEARVSYSLQKESSTTSCCSICLADYKKMDMIRVLPDCNHL 151

Query:    73 FHAECIDEWPRLNDKCPVCINSATP 97
             FH  C+D W RL+  CPVC  S  P
Sbjct:   152 FHDNCVDPWLRLHPTCPVCRTSPLP 176

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2062892 AT2G46160 [Arabidopsis thaliana (taxid:3702)]

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 35/85 (41%), Positives = 47/85 (55%)

Query:    19 MIMGLDECTIKSFQKLVLEE------SKCLPGPNSSACSICLSEYLSQETIKCIPECKHC 72
             +++GLD+  I S+ K    +      S    G   + CSICL EY   E ++ +PECKH 
Sbjct:   101 VVVGLDQAVINSYPKFHFSKDTSAASSDGFGGGGDTTCSICLCEYKEAEMLRMMPECKHY 160

Query:    73 FHAECIDEWPRLNDKCPVCINSATP 97
             FH  C+D W +LN  CPVC NS  P
Sbjct:   161 FHLCCLDAWLKLNGSCPVCRNSPLP 185

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

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2082762 AT3G61550 [Arabidopsis thaliana (taxid:3702)]

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 34/89 (38%), Positives = 49/89 (55%)

Query:    18 IMIMGLDECTIKSFQKLVLEE--SKCLPGPN-------SSACSICLSEYLSQETIKCIPE 68
             +++ GLD   I S+ K    +  +  + G          + CSICL EY+ +E ++ +PE
Sbjct:    95 VVVGGLDHSVINSYPKFHFTKDITAVVNGDGFHDGEGRETTCSICLCEYMEEEMLRMMPE 154

Query:    69 CKHCFHAECIDEWPRLNDKCPVCINSATP 97
             CKH FH  C+D W +LN  CPVC NS  P
Sbjct:   155 CKHYFHVYCLDAWLKLNGSCPVCRNSPLP 183

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2122348 AT4G09100 [Arabidopsis thaliana (taxid:3702)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 32/84 (38%), Positives = 46/84 (54%)

Query:    15 QPPIMIMGLDECTIKSFQKLVLEESKCL-PGPNSSACSICLSEYLSQETIKCIPECKHCF 73
             +PP    GLD   IKSF   V  E++ + PG     C +CL+E+   ET++ +P C H F
Sbjct:    52 RPP---RGLDAEAIKSFPSFVYTEARGIEPGIGELECVVCLNEFKDDETLRLVPPCVHVF 108

Query:    74 HAECIDEWPRLNDKCPVCINSATP 97
             HA+C+D W   +  CP+C     P
Sbjct:   109 HADCVDIWLSHSSTCPICRAKVVP 132

GO:0005576 "extracellular region" evidence=ISM

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

TAIR|locus:2028436 AT1G49230 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 28/70 (40%), Positives = 42/70 (60%)

Query:    22 GLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW 81
             G+    +KSFQ +       LPG ++  C+ICLSE++++E +K +P C H FH  CID+W
Sbjct:   104 GVKRKALKSFQTVSYSTELNLPGLDTE-CAICLSEFVAEERVKLLPTCHHGFHVRCIDKW 162

Query:    82 PRLNDKCPVC 91
                +  CP C
Sbjct:   163 LSSHSSCPTC 172

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

TAIR|locus:2122363 AT4G09120 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.5e-11, P = 1.5e-11
 Identities = 32/71 (45%), Positives = 41/71 (57%)

Query:    22 GLDECTIKSFQKLVLEESKCLP-GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDE 80
             GL++  I+SF   +  E K L  G     C+ICLSE+  QET++ +P C H FHA CID 
Sbjct:    94 GLEKEVIESFPTFLYSEVKGLKIGKGGVECAICLSEFEDQETLRWMPPCSHTFHANCIDV 153

Query:    81 WPRLNDKCPVC 91
             W      CPVC
Sbjct:   154 WLSSWSTCPVC 164

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	105
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	7e-08
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-07
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	6e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	6e-06
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	1e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.001

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

 Score = 44.7 bits (106), Expect = 7e-08
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C ICL E+   E +  +P C H FH EC+D+W R ++ CP+C
Sbjct: 3  CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLC 43

Length = 46

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

 Score = 46.1 bits (109), Expect = 4e-07
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 7/51 (13%)

Query: 50  CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND---KCPVCINSATP 97
           C+IC+S ++  + ++ +P C H FH  C+D+W  L     KCPVC  +A P
Sbjct: 326 CAICMSNFIKNDRLRVLP-CDHRFHVGCVDKW--LLGYSNKCPVC-RTAIP 372

Length = 374

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

 Score = 40.5 bits (95), Expect = 6e-06
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 9/51 (17%)

Query: 50 CSICLSEY---------LSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C+IC + +            +      EC H FH  CI  W +  + CP+C
Sbjct: 22 CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLC 72

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

 Score = 42.5 bits (100), Expect = 6e-06
 Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 6/47 (12%)

Query: 50  CSICLSEYLSQETIK-----CIPECKHCFHAECIDEWPRLNDKCPVC 91
           C+IC+ E +  + IK      +  C H F  ECID W +  + CPVC
Sbjct: 177 CAICM-EKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVC 222

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 = 38.6 bits (90), Expect = 2e-05
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEW-PRLNDKCPVC 91
          C ICL E+        +  C H F   CID+W     + CP+C
Sbjct: 2  CPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLC 41

Length = 45

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

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 50   CSIC---LSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSATPV 98
            C+IC   L         K    CK+ FH  C+ +W        CP+C +  T V
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITFV 1525

Length = 1525

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

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 11/52 (21%)

Query: 50  CSICLSEYL----------SQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
           C+IC+ E               T K +P C H  H  C+  W      CP+C
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPIC 340

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.77
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.74
PHA02929	238	N1R/p28-like protein; Provisional	99.68
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.63
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.51
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.5
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.47
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.44
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.44
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.41
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.4
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.38
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.37
PHA02926	242	zinc finger-like protein; Provisional	99.36
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.35
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.32
PF14634	44	zf-RING_5: zinc-RING finger domain	99.29
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.26
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.24
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.19
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.14
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.11
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.91
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.91
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.86
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.84
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.83
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.83
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.81
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.81
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.79
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.78
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.77
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.74
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.73
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.73
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.72
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.69
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.65
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.63
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.62
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.62
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.58
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.48
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.4
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.39
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.34
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.33
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.31
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.23
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	98.02
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.99
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.97
KOG2660	331	consensus Locus-specific chromosome binding protei	97.95
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.93
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.9
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.89
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.84
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.74
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.73
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.68
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.59
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.56
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.4
COG5152	259	Uncharacterized conserved protein, contains RING a	97.37
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.35
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.3
PHA03096	284	p28-like protein; Provisional	97.3
PF04641	260	Rtf2: Rtf2 RING-finger	97.28
PHA02862	156	5L protein; Provisional	97.24
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	97.14
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.12
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.04
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.02
KOG4739	233	consensus Uncharacterized protein involved in syna	97.02
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.95
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.93
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.93
KOG1940	276	consensus Zn-finger protein [General function pred	96.85
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.81
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.8
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.79
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.67
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.64
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.52
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.22
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.16
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.04
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	95.96
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	95.93
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	95.67
KOG3002	299	consensus Zn finger protein [General function pred	95.64
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.59
KOG3899	381	consensus Uncharacterized conserved protein [Funct	95.52
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.45
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.29
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.2
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.19
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.05
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.03
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	94.97
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.41
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	94.03
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	93.95
KOG4367	699	consensus Predicted Zn-finger protein [Function un	93.83
KOG1609	323	consensus Protein involved in mRNA turnover and st	93.1
KOG3053	293	consensus Uncharacterized conserved protein [Funct	92.7
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	92.27
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	92.12
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	92.0
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	91.16
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	90.97
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	90.58
KOG0825	1134	consensus PHD Zn-finger protein [General function	90.23
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	90.22
KOG1829	580	consensus Uncharacterized conserved protein, conta	90.19
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	89.52
KOG0269	839	consensus WD40 repeat-containing protein [Function	89.31
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	89.29
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	89.27
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	88.66
KOG3113	293	consensus Uncharacterized conserved protein [Funct	88.63
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.57
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	88.25
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	87.81
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	87.42
KOG2807	378	consensus RNA polymerase II transcription initiati	87.11
COG5109	396	Uncharacterized conserved protein, contains RING Z	85.49
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	85.08
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	83.99
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	83.57
KOG3005	276	consensus GIY-YIG type nuclease [General function	81.81
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	81.71
KOG2068	327	consensus MOT2 transcription factor [Transcription	81.59
cd00065	57	FYVE FYVE domain; Zinc-binding domain; targets pro	81.47
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	81.29
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	81.02
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	80.29
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	80.05

>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=99.77  E-value=8.1e-20  Score=93.87  Aligned_cols=44  Identities=45%  Similarity=1.127  Sum_probs=40.2

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      .+|+||++.|..++.++.++ |||.||.+||..|++++.+||+||
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            37999999999888999999 999999999999999999999997

...

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

Probab=99.74  E-value=1.3e-18  Score=122.08  Aligned_cols=76  Identities=26%  Similarity=0.625  Sum_probs=63.0

Q ss_pred             ccCCCCHHHHhhccchhhccccCCCCCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCC-CccccCCCCC
Q 044807           19 MIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDK-CPVCINSATP   97 (105)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~-CP~Cr~~~~~   97 (105)
                      ....+.+..+.++|...+........  ...|+||||+|..+++++.|| |+|.||..||..||...++ ||+|+.++..
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~--~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDA--TDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCC--CceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            44567788888888888876654322  269999999999999999999 9999999999999988755 9999997754

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.68  E-value=2.7e-17  Score=110.83  Aligned_cols=80  Identities=25%  Similarity=0.539  Sum_probs=60.3

Q ss_pred             CCCCHHHHhhccchhhccccCCCCCCcccccccccccccCCc----eeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           21 MGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQET----IKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~----~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      .+.....+..+|.+..+.........+.+|+||++.+.+...    +..++.|+|.||..||.+|+..+.+||+||..+.
T Consensus       148 ~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        148 GKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             cchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            345667778888876655444344567899999999866431    2344449999999999999999999999999987


Q ss_pred             CCCC
Q 044807           97 PVHA  100 (105)
Q Consensus        97 ~~~~  100 (105)
                      .+..
T Consensus       228 ~v~~  231 (238)
T PHA02929        228 SVIK  231 (238)
T ss_pred             EEee
Confidence            6543

>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=99.63  E-value=3.4e-16  Score=88.41  Aligned_cols=45  Identities=36%  Similarity=0.877  Sum_probs=35.8

Q ss_pred             cccccccccccccC----------CceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           47 SSACSICLSEYLSQ----------ETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        47 ~~~C~ICl~~~~~~----------~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      +..|+||++.|.+.          -.+...+ |||.||..||.+||..+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45699999999432          2344456 999999999999999999999997

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

>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=99.51  E-value=1.2e-14  Score=76.45  Aligned_cols=47  Identities=28%  Similarity=0.770  Sum_probs=40.3

Q ss_pred             cccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      +..|.||++...+   +..+| |||. ||..|+..|+.....||+||.++..
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~   49 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIES   49 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhcC
Confidence            5789999998654   67788 9999 9999999999999999999999865

...

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

Probab=99.50  E-value=1.5e-14  Score=99.43  Aligned_cols=52  Identities=35%  Similarity=1.030  Sum_probs=47.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ....+|+|||+.|..++.+..+| |.|.||..|+..|+.. +..||+||+++.+
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            34589999999999999999999 9999999999999984 7889999998864

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

Probab=99.47  E-value=1.9e-14  Score=101.31  Aligned_cols=51  Identities=29%  Similarity=0.867  Sum_probs=43.7

Q ss_pred             CCCcccccccccccccCC----------ceeEeCCCCCccchhhHHHHhcCCCCCccccCCC
Q 044807           44 GPNSSACSICLSEYLSQE----------TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSA   95 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~----------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   95 (105)
                      ..++..|.||||++...+          +.+.+| |||+||..|++.|++++.+||+||.++
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence            456889999999954332          456788 999999999999999999999999994

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.44  E-value=8.7e-14  Score=90.86  Aligned_cols=50  Identities=30%  Similarity=0.677  Sum_probs=40.7

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----------------CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----------------NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----------------~~~CP~Cr~~~~~   97 (105)
                      ..++.+|+||++.+.+   .++++ |||.||..||..|+..                ...||+||..+..
T Consensus        15 ~~~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         15 SGGDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCCccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            4567999999999865   35566 9999999999999842                3479999998864

>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=99.44  E-value=6.1e-14  Score=70.09  Aligned_cols=39  Identities=46%  Similarity=1.088  Sum_probs=32.6

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      |+||++.+.+  .++.++ |||.||.+||..|++.+..||+|
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            8999999866  346677 99999999999999998899987

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

Probab=99.41  E-value=1.1e-13  Score=94.48  Aligned_cols=51  Identities=31%  Similarity=0.742  Sum_probs=44.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      .....|.|||+...+   ...+| |||+||..||.+|......||+||..+.+..
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            456899999999766   46677 9999999999999999999999999887643

>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=99.40  E-value=2.6e-13  Score=68.86  Aligned_cols=44  Identities=39%  Similarity=1.066  Sum_probs=36.3

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSA   95 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~   95 (105)
                      +|+||++.+.  +.+...+ |||.||..|+..|+.. ...||+|+..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            5999999982  3345555 9999999999999987 77899999764

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

Probab=99.38  E-value=2.7e-13  Score=90.13  Aligned_cols=50  Identities=26%  Similarity=0.652  Sum_probs=40.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC---CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL---NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr~~~~~   97 (105)
                      .....+|.||||.-.+  .|+.+  |||.||+.||.+||..   ...||+|+..+..
T Consensus        44 ~~~~FdCNICLd~akd--PVvTl--CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD--PVVTL--CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI   96 (230)
T ss_pred             CCCceeeeeeccccCC--CEEee--cccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence            4667999999998544  35444  9999999999999975   4459999998754

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

Probab=99.37  E-value=5.2e-13  Score=85.65  Aligned_cols=54  Identities=26%  Similarity=0.626  Sum_probs=44.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ..+...|+|||+.+.....+ -.. |||+||..||+..+.....||+|++.|...+
T Consensus       128 ~~~~~~CPiCl~~~sek~~v-sTk-CGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEKVPV-STK-CGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccccCCCceecchhhcccc-ccc-cchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            45669999999998764322 234 9999999999999999999999998776543

>PHA02926 zinc finger-like protein; Provisional

Probab=99.36  E-value=2.8e-13  Score=89.83  Aligned_cols=56  Identities=27%  Similarity=0.694  Sum_probs=41.9

Q ss_pred             CCCcccccccccccccCC-----ceeEeCCCCCccchhhHHHHhcC------CCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQE-----TIKCIPECKHCFHAECIDEWPRL------NDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~-----~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~Cr~~~~~~~   99 (105)
                      ...+.+|+||||......     ...+|+.|+|.||..||..|...      ..+||+||..+..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~  233 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNIT  233 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeeec
Confidence            455789999999864421     22345559999999999999864      245999999876543

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

Probab=99.35  E-value=7.9e-13  Score=67.01  Aligned_cols=38  Identities=32%  Similarity=0.838  Sum_probs=29.0

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccc
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~C   91 (105)
                      |+||++.|.+   .+.++ |||.|+..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999977   57788 99999999999998763    369987

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

Probab=99.32  E-value=1.5e-12  Score=74.72  Aligned_cols=53  Identities=26%  Similarity=0.641  Sum_probs=40.1

Q ss_pred             CCccccccccccccc--------CC-ceeEeCCCCCccchhhHHHHhcC---CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLS--------QE-TIKCIPECKHCFHAECIDEWPRL---NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~--------~~-~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr~~~~~   97 (105)
                      ..+..|.||...|..        ++ -..+...|+|.||..||.+||..   +..||+||.+...
T Consensus        19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            347899999988862        22 22334459999999999999975   5679999998653

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.29  E-value=3.3e-12  Score=65.36  Aligned_cols=44  Identities=27%  Similarity=0.786  Sum_probs=37.4

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~   93 (105)
                      .|+||++.|.+.....+++ |||+||..|+..+......||+||+
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            5899999995555677777 9999999999999866778999984

>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=3.3e-12  Score=64.26  Aligned_cols=39  Identities=36%  Similarity=1.064  Sum_probs=32.8

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhc--CCCCCccc
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPR--LNDKCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~C   91 (105)
                      |+||++.+...  +..++ |||.||..||..|+.  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998664  34666 999999999999998  46679987

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 ....

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

Probab=99.24  E-value=2.5e-12  Score=95.99  Aligned_cols=50  Identities=34%  Similarity=0.795  Sum_probs=44.2

Q ss_pred             CCcccccccccccccCCc--eeEeCCCCCccchhhHHHHhcCCCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQET--IKCIPECKHCFHAECIDEWPRLNDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~--~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   95 (105)
                      ..+..|.||+|.+..+..  ...++ |+|+||..|+..|+++..+||+||..+
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence            457899999999987654  67788 999999999999999999999999944

>smart00184 RING Ring finger

Probab=99.19  E-value=1.9e-11  Score=59.92  Aligned_cols=38  Identities=42%  Similarity=1.140  Sum_probs=31.9

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhc-CCCCCccc
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-LNDKCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~C   91 (105)
                      |+||++..   .....++ |||.||..|+..|+. ....||+|
T Consensus         1 C~iC~~~~---~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999983   3366777 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)

>smart00504 Ubox Modified RING finger domain

Probab=99.14  E-value=5.3e-11  Score=64.98  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=40.1

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..|+||++.+.++   +.++ |||.|+..||..|+..+.+||+|+..+..
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            5799999998764   5567 99999999999999988899999988743

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.11  E-value=4.7e-11  Score=85.87  Aligned_cols=49  Identities=27%  Similarity=0.542  Sum_probs=42.4

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .....|+||++.|...   ++++ |||.||..||..|+.....||+|+..+..
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            4578999999998663   4567 99999999999999988899999998754

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

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

Probab=98.91  E-value=1e-09  Score=61.85  Aligned_cols=51  Identities=24%  Similarity=0.564  Sum_probs=37.5

Q ss_pred             ccccccccccccc-----------CC-ceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLS-----------QE-TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~-----------~~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      -..|+||...|..           ++ -.+....|.|.||..||.+||..++.||++|.+...
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            3677777665532           22 223333499999999999999999999999987653

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

Probab=98.91  E-value=9.5e-10  Score=55.81  Aligned_cols=33  Identities=27%  Similarity=0.837  Sum_probs=21.3

Q ss_pred             ccccccccccCC-ceeEeCCCCCccchhhHHHHhcC
Q 044807           50 CSICLSEYLSQE-TIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        50 C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      |+||.+ |...+ ..++|+ |||.|+.+||..++.+
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhc
Confidence            899999 75544 467788 9999999999999874

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

Probab=98.86  E-value=2.2e-09  Score=56.03  Aligned_cols=42  Identities=29%  Similarity=0.779  Sum_probs=32.5

Q ss_pred             cccccccccccCCceeEeCCCC-----CccchhhHHHHhcC--CCCCcccc
Q 044807           49 ACSICLSEYLSQETIKCIPECK-----HCFHAECIDEWPRL--NDKCPVCI   92 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~Cr   92 (105)
                      .|.||++ ....+.....| |.     |.||..|+..|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 33445556778 85     88999999999955  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

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

Probab=98.84  E-value=9.7e-10  Score=77.06  Aligned_cols=49  Identities=27%  Similarity=0.659  Sum_probs=43.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      +.-..|.||.+.|..   ..++| |+|.||.-||..+|..+..||.|+.++..
T Consensus        21 D~lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   21 DDLLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             HHHHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccch
Confidence            446799999999976   46677 99999999999999999999999998764

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

Probab=98.83  E-value=7.6e-10  Score=75.41  Aligned_cols=52  Identities=25%  Similarity=0.613  Sum_probs=41.4

Q ss_pred             CCCcccccccccccccCC-------ceeEeCCCCCccchhhHHHHh--cCCCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQE-------TIKCIPECKHCFHAECIDEWP--RLNDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~-------~~~~lp~C~H~Fh~~Ci~~wl--~~~~~CP~Cr~~~~   96 (105)
                      ..++..|+||-..+....       +...|. |+|.||..||..|-  .+..+||+|+..+.
T Consensus       221 hl~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            346789999988775543       566787 99999999999995  45789999987653

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

Probab=98.83  E-value=1.6e-09  Score=73.59  Aligned_cols=50  Identities=30%  Similarity=0.738  Sum_probs=40.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHH-HhcCCCC-CccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDE-WPRLNDK-CPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~-wl~~~~~-CP~Cr~~~~~~   98 (105)
                      ..+..|.||++....   ...++ |||+||..||.. |-..+.. ||+||+...+.
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            347899999998755   46677 999999999999 8766655 99999976653

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

Probab=98.81  E-value=5.1e-10  Score=62.63  Aligned_cols=51  Identities=29%  Similarity=0.608  Sum_probs=24.3

Q ss_pred             cccccccccccccCC-c-eeEe--CCCCCccchhhHHHHhcC-----------CCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQE-T-IKCI--PECKHCFHAECIDEWPRL-----------NDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~-~-~~~l--p~C~H~Fh~~Ci~~wl~~-----------~~~CP~Cr~~~~~   97 (105)
                      +.+|.||++.+...+ . ...-  +.|+..||..||.+||..           .+.||.|+.+|..
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            468999999876332 2 1222  249999999999999852           1259999998754

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.81  E-value=4.3e-09  Score=73.41  Aligned_cols=51  Identities=20%  Similarity=0.478  Sum_probs=36.9

Q ss_pred             Ccccccccccc-cccCCc-eeEeCCCCCccchhhHHHHhc-CCCCCccccCCCCC
Q 044807           46 NSSACSICLSE-YLSQET-IKCIPECKHCFHAECIDEWPR-LNDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~-~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~~~   97 (105)
                      ++..|+||... +..... +.+.+ |||.||..||...+. ....||.|+..+..
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            35789999995 333332 22335 999999999999654 45679999987754

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).

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

Probab=98.79  E-value=1.3e-09  Score=60.86  Aligned_cols=52  Identities=27%  Similarity=0.627  Sum_probs=38.1

Q ss_pred             Cccccccccccccc--------CC-ceeEeCCCCCccchhhHHHHhcC---CCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLS--------QE-TIKCIPECKHCFHAECIDEWPRL---NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~--------~~-~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr~~~~~   97 (105)
                      .+++|.||.-.|..        ++ -..++..|.|.||..||.+|+..   +..||+||.+...
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            45699999888853        22 22233349999999999999965   5569999987643

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

Probab=98.78  E-value=2.7e-09  Score=78.03  Aligned_cols=47  Identities=28%  Similarity=0.557  Sum_probs=37.4

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~~~~~   97 (105)
                      +..|+|||+....   ...+. |||+||..||.+++..     ...||+||..|..
T Consensus       186 ~~~CPICL~~~~~---p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCc---ccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            7899999998654   23344 9999999999987654     3569999998766

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

Probab=98.77  E-value=3e-09  Score=75.65  Aligned_cols=46  Identities=30%  Similarity=0.821  Sum_probs=34.0

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC---CCCCcccc
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL---NDKCPVCI   92 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr   92 (105)
                      ...|.||.+.+-....+.-+..|||+||..|+..|++.   +..||.|+
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            57899995544333333333349999999999999987   45799999

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

Probab=98.74  E-value=1.2e-08  Score=57.54  Aligned_cols=48  Identities=15%  Similarity=0.286  Sum_probs=37.9

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      +...|+|+.+.+.+   .++++ +||.|.+.+|..|+.. +.+||+++..+..
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            46789999999977   46788 9999999999999998 8899999988765

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 ....

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

Probab=98.73  E-value=4.2e-09  Score=71.91  Aligned_cols=44  Identities=30%  Similarity=0.662  Sum_probs=39.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      .+...|+||++.|...   .+++ |+|.||..||..++.....||.||
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            4678999999999886   6778 999999999999988556799999

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

Probab=98.73  E-value=4.9e-09  Score=72.30  Aligned_cols=49  Identities=24%  Similarity=0.459  Sum_probs=41.7

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      +.-..|-||-+.|...   ...+ |||.||.-||...|..+..||+||.+...
T Consensus        23 Ds~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          23 DSMLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             hhHHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHh
Confidence            3457999999998763   4556 99999999999999999999999997643

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

Probab=98.72  E-value=3e-09  Score=82.58  Aligned_cols=54  Identities=28%  Similarity=0.593  Sum_probs=40.7

Q ss_pred             CCCcccccccccccccCCc---eeEeCCCCCccchhhHHHHhcC--CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQET---IKCIPECKHCFHAECIDEWPRL--NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~---~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~~   97 (105)
                      -.+..+|+||...+..-+.   -...+.|.|.||..|+..|+..  +++||+||.++..
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence            4678999999987753221   1122239999999999999976  6679999988764

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

Probab=98.70  E-value=6.1e-09  Score=76.11  Aligned_cols=51  Identities=29%  Similarity=0.756  Sum_probs=39.4

Q ss_pred             CcccccccccccccCC--------------ceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQE--------------TIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~--------------~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ....|+|||.++..-.              .....| |.|+||..|+.+|... +-.||+||.++..
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            4579999999764211              122357 9999999999999995 5589999998864

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

Probab=98.69  E-value=2.6e-09  Score=56.08  Aligned_cols=47  Identities=23%  Similarity=0.542  Sum_probs=35.8

Q ss_pred             cccccccccccccCCceeEeCCCCCc-cchhhHHH-HhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHC-FHAECIDE-WPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~-wl~~~~~CP~Cr~~~~~   97 (105)
                      +.+|.||+|.-.+.  +. .. |||+ +|.+|-.+ |-..+..||+||+++..
T Consensus         7 ~dECTICye~pvds--Vl-Yt-CGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDS--VL-YT-CGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchH--HH-HH-cchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            47999999986543  32 33 9999 99999555 54578999999998754

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

Probab=98.65  E-value=9.8e-09  Score=74.16  Aligned_cols=50  Identities=34%  Similarity=0.818  Sum_probs=40.2

Q ss_pred             CCCcccccccccccccCCc-eeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQET-IKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      ..+..+|+||||.+..... +.... |.|.||..|+..|  ...+||+||.-..
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            3457899999999866543 45555 9999999999999  6678999998655

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

Probab=98.63  E-value=3.5e-09  Score=74.48  Aligned_cols=58  Identities=29%  Similarity=0.543  Sum_probs=45.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCCCcCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      ..+..|+|||+.+...   ...+.|.|.||..||..-+.. ++.||.||+.+.+.-...++|
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp   99 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDP   99 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCc
Confidence            4578999999998653   333459999999999888765 788999999988766655554

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

Probab=98.62  E-value=1.1e-08  Score=55.68  Aligned_cols=46  Identities=33%  Similarity=0.731  Sum_probs=23.4

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ...|++|.+.+..+   +.+.+|.|+||..||..-+.  ..||+|+.+...
T Consensus         7 lLrCs~C~~~l~~p---v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~   52 (65)
T PF14835_consen    7 LLRCSICFDILKEP---VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWI   52 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-
T ss_pred             hcCCcHHHHHhcCC---ceeccCccHHHHHHhHHhcC--CCCCCcCChHHH
Confidence            46899999998663   44445999999999988654  349999998644

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

Probab=98.62  E-value=2.3e-08  Score=70.51  Aligned_cols=50  Identities=26%  Similarity=0.691  Sum_probs=42.7

Q ss_pred             CCcccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      +...+|.|||.+..+   +.+|| |.|. .|..|.+..--.++.||+||.++...
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l  338 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEEL  338 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence            447899999999766   67899 9999 99999998766788999999988653

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

Probab=98.58  E-value=3e-08  Score=58.54  Aligned_cols=53  Identities=25%  Similarity=0.596  Sum_probs=38.9

Q ss_pred             CCCccccccccccccc-------------CCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLS-------------QETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~-------------~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      ......|+||...+.+             .+..+.-..|+|.||..||.+||+.++.||+|-.+-.
T Consensus        43 Di~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   43 DIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             eeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            3456899999765422             1223333349999999999999999999999977643

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

Probab=98.48  E-value=7.2e-08  Score=68.46  Aligned_cols=55  Identities=25%  Similarity=0.731  Sum_probs=41.7

Q ss_pred             CCCcccccccccccccCC----ceeEeCCCCCccchhhHHHHh--cC-----CCCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQE----TIKCIPECKHCFHAECIDEWP--RL-----NDKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~----~~~~lp~C~H~Fh~~Ci~~wl--~~-----~~~CP~Cr~~~~~~   98 (105)
                      ...+.+|.|||+.+.+..    ...++|+|.|.||..||..|-  ..     ...||.||.....+
T Consensus       158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            356899999999876543    123456699999999999997  33     46799999876543

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

Probab=98.40  E-value=4.7e-08  Score=74.89  Aligned_cols=54  Identities=26%  Similarity=0.466  Sum_probs=45.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      .....|++||..+.++....-.+ |+|.||..||..|-....+||+||.++..+.
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            45678889988887766555566 9999999999999999999999999886544

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

Probab=98.39  E-value=1e-07  Score=68.41  Aligned_cols=51  Identities=24%  Similarity=0.636  Sum_probs=40.3

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC--CCCCccccCCCCCCCCc
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSATPVHAD  101 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~~~  101 (105)
                      -..|.||-|.-   ..+.+-| |||..|..|+..|-..  ..+||.||.+|.-...-
T Consensus       369 FeLCKICaend---KdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  369 FELCKICAEND---KDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHHhhccC---CCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            46899998863   3377788 9999999999999744  67899999998644433

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

Probab=98.34  E-value=1.8e-07  Score=64.87  Aligned_cols=53  Identities=25%  Similarity=0.616  Sum_probs=43.8

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----------------------CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----------------------NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----------------------~~~CP~Cr~~~~~   97 (105)
                      ......|.|||.-|.+++....++ |.|.||..|+.++|..                       ...||+||..|..
T Consensus       112 n~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  112 NHPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            345789999999999999888888 9999999999998721                       2259999998753

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

Probab=98.33  E-value=2.1e-07  Score=64.45  Aligned_cols=48  Identities=23%  Similarity=0.395  Sum_probs=39.2

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ...+|+||+....-   ...|+ |+|.||.-||+.-+.+ ..+|++||.+|.+
T Consensus         6 ~~~eC~IC~nt~n~---Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    6 KKKECLICYNTGNC---PVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             cCCcceeeeccCCc---Ccccc-ccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            46799999998644   35677 9999999999987665 5679999999864

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

Probab=98.31  E-value=5e-07  Score=64.88  Aligned_cols=51  Identities=31%  Similarity=0.786  Sum_probs=38.1

Q ss_pred             Cccccccccccccc-CCceeEeCCCCCccchhhHHHHhcC--CCCCccccCCCC
Q 044807           46 NSSACSICLSEYLS-QETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~-~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      ...+|+|||+.+.. ++.-...+.|||.|...||+.||.+  ...||.|.....
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat   56 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT   56 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence            46799999998764 3333333449999999999999953  345999987654

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

Probab=98.23  E-value=9.5e-07  Score=63.94  Aligned_cols=49  Identities=24%  Similarity=0.638  Sum_probs=42.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+.+|.||+..+..   .+.+| |||.||..||.+-+.....||.||..+..
T Consensus        82 ~sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            568999999998866   45668 99999999999988888889999998874

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

Probab=98.11  E-value=2.7e-06  Score=57.09  Aligned_cols=52  Identities=27%  Similarity=0.673  Sum_probs=43.9

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--------CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--------NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~Cr~~~~~   97 (105)
                      .+....|..|-..+..++.+++.  |-|.||.+|+.+|...        ...||.|..+|++
T Consensus        47 sDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP  106 (299)
T KOG3970|consen   47 SDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFP  106 (299)
T ss_pred             cCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence            34578999999999999988765  9999999999999743        4469999999876

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

Probab=98.02  E-value=7e-06  Score=63.62  Aligned_cols=57  Identities=26%  Similarity=0.646  Sum_probs=42.1

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-------CCCCccccCCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-------NDKCPVCINSATPVHA  100 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-------~~~CP~Cr~~~~~~~~  100 (105)
                      .....+|.||++.+...+.+.--..|-|+||..||..|...       .-.||.|......+..
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~  251 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPK  251 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCCc
Confidence            45678999999998776655433338999999999999754       1249999865554433

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

Probab=97.99  E-value=3.1e-06  Score=61.37  Aligned_cols=52  Identities=31%  Similarity=0.574  Sum_probs=42.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      +.+..|+||+..+.+.-..  .. |||.||..|+..|+..+..||.|+..+....
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--TT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             cccccCccccccccCCCCC--CC-CCCcccccccchhhccCcCCcccccccchhh
Confidence            4578999999998775322  34 9999999999999999999999998876543

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

Probab=97.97  E-value=2.1e-06  Score=65.59  Aligned_cols=51  Identities=24%  Similarity=0.533  Sum_probs=39.8

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhc-CCCCCccccCCCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-LNDKCPVCINSATPVHA  100 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~  100 (105)
                      +-..|+.|-+-+.+   +++.. |||.||..||..-+. +...||.|-+.+..-+.
T Consensus       642 ~~LkCs~Cn~R~Kd---~vI~k-C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv  693 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD---AVITK-CGHVFCEECVQTRYETRQRKCPKCNAAFGANDV  693 (698)
T ss_pred             hceeCCCccCchhh---HHHHh-cchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence            45799999977654   33344 999999999999886 47889999888765443

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

Probab=97.95  E-value=1.8e-06  Score=60.52  Aligned_cols=51  Identities=25%  Similarity=0.544  Sum_probs=43.3

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ....+|.+|-..|.+..++.   .|-|.||..||...|....+||.|...+...
T Consensus        13 n~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            45789999999998865543   4999999999999999999999998877543

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

Probab=97.93  E-value=5.5e-06  Score=44.45  Aligned_cols=42  Identities=31%  Similarity=0.623  Sum_probs=27.6

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--CCCCcc
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPV   90 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~   90 (105)
                      -...|+|.+..|.++  +.... |||.|-++.|.+||.+  ...||+
T Consensus        10 ~~~~CPiT~~~~~~P--V~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDP--VKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSE--EEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCC--cCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            368999999998764  55455 9999999999999944  445998

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

Probab=97.90  E-value=3.4e-06  Score=53.91  Aligned_cols=40  Identities=25%  Similarity=0.526  Sum_probs=33.3

Q ss_pred             hhccccCCCCCCcccccccccccccCCceeEeCCCCCccch
Q 044807           35 VLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHA   75 (105)
Q Consensus        35 ~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~   75 (105)
                      .++.+.++..++..+|.||||++..++++..|| |-.+||+
T Consensus       165 rlsYNdDVL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  165 RLSYNDDVLKDDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             ccccccchhcccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            344445555677899999999999999999999 9999996

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

Probab=97.89  E-value=4.9e-06  Score=51.69  Aligned_cols=36  Identities=19%  Similarity=0.552  Sum_probs=30.1

Q ss_pred             CcccccccccccccCCceeEeCCCC------CccchhhHHHHh
Q 044807           46 NSSACSICLSEYLSQETIKCIPECK------HCFHAECIDEWP   82 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~------H~Fh~~Ci~~wl   82 (105)
                      ...+|.||++.+.+...++.++ ||      |+||.+|+.+|-
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            3689999999998855677676 75      899999999994

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

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

Probab=97.84  E-value=3.8e-06  Score=60.35  Aligned_cols=51  Identities=25%  Similarity=0.643  Sum_probs=40.0

Q ss_pred             CCcccccccccccccCC-ceeEeCCCCCccchhhHHHHhcCC--CCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQE-TIKCIPECKHCFHAECIDEWPRLN--DKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~   96 (105)
                      ..+..|..|-+.+.... ...-+| |.|+||..|+.+.|.++  .+||.||+-..
T Consensus       363 e~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~CrklrS  416 (518)
T KOG1941|consen  363 ETELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRKLRS  416 (518)
T ss_pred             HHhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHHHHh
Confidence            34678999998876543 456688 99999999999999764  46999995443

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

Probab=97.74  E-value=3.4e-05  Score=53.12  Aligned_cols=53  Identities=21%  Similarity=0.466  Sum_probs=40.7

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--CCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~~~~   99 (105)
                      ...+.+|++|-+.-..+  ....+ |+|+||..||..-+.-  ..+||.|-.+..++.
T Consensus       236 ~t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq  290 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ  290 (298)
T ss_pred             ccCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence            45678999999985443  34455 9999999999986543  578999988877554

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

Probab=97.73  E-value=1.8e-05  Score=64.72  Aligned_cols=54  Identities=28%  Similarity=0.608  Sum_probs=42.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC----------CCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----------DKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----------~~CP~Cr~~~~~~   98 (105)
                      .+.+..|.||+.+-......+.|. |+|+||..|...-|++.          -+||+|+.+|..+
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence            467889999998865556667787 99999999998877541          2699999987643

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

Probab=97.68  E-value=5.8e-05  Score=53.73  Aligned_cols=56  Identities=20%  Similarity=0.411  Sum_probs=42.4

Q ss_pred             ccccCCCCCCcccccccccccccCCceeEeCCCCCccchhhHHHH--hcCCCCCccccCCCC
Q 044807           37 EESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW--PRLNDKCPVCINSAT   96 (105)
Q Consensus        37 ~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w--l~~~~~CP~Cr~~~~   96 (105)
                      +.+......+...|.||-+.+.   ...++| |+|..|--|..+.  |-....||+||++-.
T Consensus        51 tsSaddtDEen~~C~ICA~~~T---Ys~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          51 TSSADDTDEENMNCQICAGSTT---YSARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cccccccccccceeEEecCCce---EEEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3344444567789999998753   256788 9999999997664  567889999999754

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

Probab=97.59  E-value=5.4e-05  Score=39.01  Aligned_cols=40  Identities=38%  Similarity=0.924  Sum_probs=26.3

Q ss_pred             ccccccccccCCceeEeCCCC-----CccchhhHHHHhc--CCCCCccc
Q 044807           50 CSICLSEYLSQETIKCIPECK-----HCFHAECIDEWPR--LNDKCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~C   91 (105)
                      |-||++.-.... ..+.| |+     -..|..||..|+.  ++.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999865544 34456 74     3589999999997  45679887

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

Probab=97.56  E-value=7.4e-05  Score=38.56  Aligned_cols=45  Identities=22%  Similarity=0.509  Sum_probs=22.4

Q ss_pred             ccccccccccCCceeEeC-CCCCccchhhHHHHhc-CCCCCccccCCC
Q 044807           50 CSICLSEYLSQETIKCIP-ECKHCFHAECIDEWPR-LNDKCPVCINSA   95 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp-~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~   95 (105)
                      |++|.+++...+.- ..| .||+.++..|...-++ ..+.||-||.+.
T Consensus         1 cp~C~e~~d~~d~~-~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKD-FYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT---SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCc-cccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78999998444322 223 2799999999988886 478899999864

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

Probab=97.40  E-value=6.4e-05  Score=56.15  Aligned_cols=49  Identities=27%  Similarity=0.548  Sum_probs=38.1

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~~~~   96 (105)
                      ..+..+|.+|-+.-.+   .+... |.|.||..||.+++..     +-+||+|...+.
T Consensus       533 nk~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             ccCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            5567899999987544   33344 9999999999999753     568999987664

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

Probab=97.37  E-value=6.2e-05  Score=49.75  Aligned_cols=45  Identities=29%  Similarity=0.581  Sum_probs=37.4

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSA   95 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   95 (105)
                      ...|.||-.+|..+   ++.. |||.||..|...-+.....|-+|.+..
T Consensus       196 PF~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         196 PFLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             ceeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            46899999999764   4455 999999999888888899999997653

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

Probab=97.35  E-value=0.0002  Score=51.14  Aligned_cols=53  Identities=23%  Similarity=0.497  Sum_probs=43.3

Q ss_pred             CCCCCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           41 CLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        41 ~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .....++..|+||...-..   .+..| |+|.=|+.||.+-+-+...|=+|++.+..
T Consensus       416 ~lp~sEd~lCpICyA~pi~---Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  416 DLPDSEDNLCPICYAGPIN---AVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CCCCcccccCcceecccch---hhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            3445788999999986433   35567 99999999999999999999999998763

>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=97.30  E-value=9.8e-05  Score=43.90  Aligned_cols=34  Identities=29%  Similarity=0.632  Sum_probs=27.7

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHH
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECID   79 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~   79 (105)
                      ..+...|++|-..+.. ......| |||.||..|+.
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            4567889999999866 4556678 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 [].

>PHA03096 p28-like protein; Provisional

Probab=97.30  E-value=0.00011  Score=51.35  Aligned_cols=45  Identities=27%  Similarity=0.473  Sum_probs=32.2

Q ss_pred             ccccccccccccCC----ceeEeCCCCCccchhhHHHHhcC---CCCCcccc
Q 044807           48 SACSICLSEYLSQE----TIKCIPECKHCFHAECIDEWPRL---NDKCPVCI   92 (105)
Q Consensus        48 ~~C~ICl~~~~~~~----~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr   92 (105)
                      ..|.|||+......    .-..|+.|.|.||..||..|...   ..+||.||
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~  230 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENR  230 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCcccc
Confidence            68999999765432    23457779999999999999743   33444443

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.28  E-value=0.00044  Score=47.68  Aligned_cols=60  Identities=23%  Similarity=0.439  Sum_probs=46.1

Q ss_pred             CCCcccccccccccccCCceeE-eCCCCCccchhhHHHHhcCCCCCccccCCCCCCCCcCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKC-IPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~-lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      ......|||...+|......+. .+ |||+|...+|.+.- ....||+|-.++...+.-.|||
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~-cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp  170 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRP-CGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNP  170 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcC-CCCEeeHHHHHhhc-ccccccccCCccccCCEEEecC
Confidence            4667899999999955554444 46 99999999999972 3567999999988766555554

>PHA02862 5L protein; Provisional

Probab=97.24  E-value=0.00024  Score=44.69  Aligned_cols=45  Identities=22%  Similarity=0.547  Sum_probs=33.3

Q ss_pred             cccccccccccccCCceeEeCCCC-----CccchhhHHHHhcC--CCCCccccCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECK-----HCFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      ...|-||.+.-.+.  .  -| |.     ..-|.+|+.+|+..  +.+|++|+.+..
T Consensus         2 ~diCWIC~~~~~e~--~--~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          2 SDICWICNDVCDER--N--NF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CCEEEEecCcCCCC--c--cc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            46899999984332  2  34 63     45899999999965  557999998764

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

Probab=97.14  E-value=0.00029  Score=45.95  Aligned_cols=53  Identities=28%  Similarity=0.622  Sum_probs=34.1

Q ss_pred             cccccccccccccCCce----eEeCCCCCccchhhHHHHhcC-----------CCCCccccCCCCCCCC
Q 044807           47 SSACSICLSEYLSQETI----KCIPECKHCFHAECIDEWPRL-----------NDKCPVCINSATPVHA  100 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~----~~lp~C~H~Fh~~Ci~~wl~~-----------~~~CP~Cr~~~~~~~~  100 (105)
                      ...|.||...-.++...    -... ||.-||.-|+..||..           -..||+|..++.....
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~q-CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS  232 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQ-CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS  232 (234)
T ss_pred             hhcccceeeeecCCccccccccccc-cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence            34566665543333211    1133 9999999999999964           2259999998765443

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

Probab=97.12  E-value=0.0003  Score=51.02  Aligned_cols=47  Identities=30%  Similarity=0.685  Sum_probs=37.0

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--------CCCCccccC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--------NDKCPVCIN   93 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~Cr~   93 (105)
                      ....|.||++...-...++.+| |+|.||..|+..++..        .-.||-+..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            4689999999975556788899 9999999999999842        224876654

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.04  E-value=0.0003  Score=37.19  Aligned_cols=45  Identities=20%  Similarity=0.457  Sum_probs=32.3

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ...|..|...-   ..-.++| |||..+..|..-  ++-+.||+|.+++..
T Consensus         7 ~~~~~~~~~~~---~~~~~~p-CgH~I~~~~f~~--~rYngCPfC~~~~~~   51 (55)
T PF14447_consen    7 EQPCVFCGFVG---TKGTVLP-CGHLICDNCFPG--ERYNGCPFCGTPFEF   51 (55)
T ss_pred             ceeEEEccccc---ccccccc-ccceeeccccCh--hhccCCCCCCCcccC
Confidence            44555555542   2345678 999999999664  467889999988765

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.02  E-value=0.00037  Score=49.62  Aligned_cols=58  Identities=19%  Similarity=0.434  Sum_probs=41.6

Q ss_pred             CCcccccccccccccCCce-eEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCCCcCC
Q 044807           45 PNSSACSICLSEYLSQETI-KCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVHADYV  103 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~~~  103 (105)
                      +++.-|+.|++.+...++- .-.| ||-..|.-|...--+. ++.||-||.........|+
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~   71 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV   71 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence            4556699999998776643 3345 9988888886554333 7789999998877665554

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

Probab=97.02  E-value=0.00029  Score=47.72  Aligned_cols=46  Identities=26%  Similarity=0.615  Sum_probs=32.4

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      .|.-|.-.-. ++...++. |+|+||..|...-  ....||+|+..+-.+
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~i   50 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRII   50 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceeeee
Confidence            5666665543 55566666 9999999998652  233899999986543

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

Probab=96.95  E-value=0.00064  Score=47.45  Aligned_cols=48  Identities=23%  Similarity=0.598  Sum_probs=38.5

Q ss_pred             cccccccccccccCC---ceeEeCCCCCccchhhHHHHhcC-CCCCccccCCC
Q 044807           47 SSACSICLSEYLSQE---TIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSA   95 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~---~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~   95 (105)
                      ...|-||-++|+..+   ..+.+. |||.|+..|+...+.. ...||.||...
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            468999999998764   245566 9999999999987765 44589999984

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.93  E-value=0.00098  Score=42.62  Aligned_cols=47  Identities=30%  Similarity=0.694  Sum_probs=34.3

Q ss_pred             CCcccccccccccccCCceeEeCCCC--C---ccchhhHHHHhcC--CCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECK--H---CFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~--H---~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      ..+..|-||.++-..  .  .-| |.  .   ..|.+|++.|+..  ...|++|.+++.
T Consensus         6 ~~~~~CRIC~~~~~~--~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          6 LMDKCCWICKDEYDV--V--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCCeeEecCCCCCC--c--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            457899999988432  1  235 64  3   4699999999975  456999998764

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

Probab=96.93  E-value=0.00061  Score=48.58  Aligned_cols=49  Identities=31%  Similarity=0.621  Sum_probs=35.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ......|.||+++..+   ...+| |||+-|  |..- .+...+||+||..|..+.
T Consensus       302 ~~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~c-s~~l~~CPvCR~rI~~~~  350 (355)
T KOG1571|consen  302 LPQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLC-SKHLPQCPVCRQRIRLVR  350 (355)
T ss_pred             cCCCCceEEecCCccc---eeeec-CCcEEE--chHH-HhhCCCCchhHHHHHHHH
Confidence            3456899999998765   56778 999955  5443 234555999999876443

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

Probab=96.85  E-value=0.00062  Score=47.27  Aligned_cols=48  Identities=23%  Similarity=0.578  Sum_probs=39.4

Q ss_pred             CCcccccccccccccCCc-eeEeCCCCCccchhhHHHHhcCCCCCccccC
Q 044807           45 PNSSACSICLSEYLSQET-IKCIPECKHCFHAECIDEWPRLNDKCPVCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~   93 (105)
                      .....|+||.+.+..... +..++ |||..|..|+.+....+-+||+|..
T Consensus       156 ~~~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  156 SSEFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cccCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            345569999998777654 45567 9999999999999877799999988

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

Probab=96.81  E-value=0.0013  Score=46.48  Aligned_cols=50  Identities=22%  Similarity=0.484  Sum_probs=39.1

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      ..+...|+||+....++..+. .  =|-+||..||..++.+.+.||+=-.++.
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~-v--SGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLE-V--SGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             CCccccChhHHhccCCCceEE-e--cceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            456789999999876642221 1  5899999999999999999998665543

>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=96.80  E-value=0.00081  Score=33.93  Aligned_cols=41  Identities=24%  Similarity=0.638  Sum_probs=21.9

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhcCCC--CCccc
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND--KCPVC   91 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~--~CP~C   91 (105)
                      |.+|.+....|..-.... |+=.+|..|+..++....  .||.|
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            567777665542221123 888999999999998755  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.79  E-value=0.00052  Score=47.85  Aligned_cols=46  Identities=24%  Similarity=0.467  Sum_probs=38.4

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..|-||-..|..+   ++.. |+|.||..|...=+.....|.+|-..+..
T Consensus       242 f~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccccc---hhhc-CCceeehhhhccccccCCcceeccccccc
Confidence            5699999999874   4455 99999999988888888999999876644

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.67  E-value=0.0025  Score=43.64  Aligned_cols=52  Identities=13%  Similarity=0.234  Sum_probs=44.2

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ....|+||.+.+.+......|..|||+|+.+|++..+..-..||+|-.++..
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd  271 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD  271 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence            4578999999998877666665599999999999999989999999887654

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

Probab=96.64  E-value=0.00018  Score=50.06  Aligned_cols=43  Identities=21%  Similarity=0.582  Sum_probs=32.6

Q ss_pred             cccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ...|.|||+...+   -+.|+ |||+ -|.+|-..    -+.||+||.-+..
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            6789999998655   46677 9998 67777543    3489999986644

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

Probab=96.52  E-value=0.0013  Score=51.47  Aligned_cols=45  Identities=29%  Similarity=0.701  Sum_probs=34.1

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      ....|..|-..+..+  .+.-- |||.||..|+.   .+...||-|+.++.
T Consensus       839 q~skCs~C~~~LdlP--~VhF~-CgHsyHqhC~e---~~~~~CP~C~~e~~  883 (933)
T KOG2114|consen  839 QVSKCSACEGTLDLP--FVHFL-CGHSYHQHCLE---DKEDKCPKCLPELR  883 (933)
T ss_pred             eeeeecccCCccccc--eeeee-cccHHHHHhhc---cCcccCCccchhhh
Confidence            347899998877554  33333 99999999998   46677999988554

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=96.22  E-value=0.0061  Score=39.01  Aligned_cols=35  Identities=20%  Similarity=0.657  Sum_probs=21.4

Q ss_pred             CcccccccccccccCCceeEe-----CC-----CC-CccchhhHHHHh
Q 044807           46 NSSACSICLSEYLSQETIKCI-----PE-----CK-HCFHAECIDEWP   82 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~l-----p~-----C~-H~Fh~~Ci~~wl   82 (105)
                      ++..|+||||..-+  .|.++     .+     |+ -.-|..|+.++-
T Consensus         1 ed~~CpICme~PHN--AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    1 EDVTCPICMEHPHN--AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CCccCceeccCCCc--eEEEEeccccCCccccccCCccchhHHHHHHH
Confidence            36799999998543  23222     01     33 225788999874

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

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

Probab=96.16  E-value=0.0033  Score=45.30  Aligned_cols=34  Identities=24%  Similarity=0.651  Sum_probs=25.3

Q ss_pred             CCCccchhhHHHHhcC-------------CCCCccccCCCCCCCCcC
Q 044807           69 CKHCFHAECIDEWPRL-------------NDKCPVCINSATPVHADY  102 (105)
Q Consensus        69 C~H~Fh~~Ci~~wl~~-------------~~~CP~Cr~~~~~~~~~~  102 (105)
                      |.-++|.+|+.+|+..             +-.||+||+.+...+.-+
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV~~  357 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDVCY  357 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeeeec
Confidence            4466899999999842             336999999987665433

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

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

Probab=96.04  E-value=0.0026  Score=49.27  Aligned_cols=44  Identities=30%  Similarity=0.659  Sum_probs=34.7

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcC--CCCCccccCCCC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      ..|.||++    .+.....+ |+|.||.+|+..-+..  ...||.||..+.
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~  500 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLK  500 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence            79999999    23355566 9999999999998765  235999998654

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

Probab=95.96  E-value=0.004  Score=48.59  Aligned_cols=28  Identities=39%  Similarity=0.838  Sum_probs=23.5

Q ss_pred             ceeEeCCCCCccchhhHHHHhcCCCCCcc
Q 044807           62 TIKCIPECKHCFHAECIDEWPRLNDKCPV   90 (105)
Q Consensus        62 ~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~   90 (105)
                      ..++.. |+|..|..|+.+|+.....||.
T Consensus      1042 s~~Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1042 SNFCGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             chhhcc-ccccccHHHHHHHHhcCCcCCC
Confidence            344555 9999999999999999988884

>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.93  E-value=0.0076  Score=42.05  Aligned_cols=47  Identities=32%  Similarity=0.713  Sum_probs=34.1

Q ss_pred             cccccccc-cccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCC
Q 044807           49 ACSICLSE-YLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSA   95 (105)
Q Consensus        49 ~C~ICl~~-~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~   95 (105)
                      .|++|-.+ |..++.......|+|..|..|+...+.. ...||.|-..+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            58899874 4444443333349999999999998866 55699997654

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

Probab=95.67  E-value=0.0056  Score=48.30  Aligned_cols=37  Identities=27%  Similarity=0.674  Sum_probs=28.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHh
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP   82 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl   82 (105)
                      ...+..|.+|.-.+... .-.+-| |||.||+.||..-.
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            35678999999887553 344556 99999999998764

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

Probab=95.64  E-value=0.0089  Score=42.15  Aligned_cols=47  Identities=21%  Similarity=0.578  Sum_probs=36.4

Q ss_pred             CCCcccccccccccccCCceeEeCCC--CCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPEC--KHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C--~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ..+-.+|+||.+.+..+  +.  . |  ||+-|..|=.   +..+.||.||.++..+
T Consensus        45 ~~~lleCPvC~~~l~~P--i~--Q-C~nGHlaCssC~~---~~~~~CP~Cr~~~g~~   93 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP--IF--Q-CDNGHLACSSCRT---KVSNKCPTCRLPIGNI   93 (299)
T ss_pred             chhhccCchhhccCccc--ce--e-cCCCcEehhhhhh---hhcccCCccccccccH
Confidence            45578999999998775  32  2 6  7999998864   4688899999998753

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

Probab=95.59  E-value=0.0005  Score=49.63  Aligned_cols=50  Identities=24%  Similarity=0.523  Sum_probs=40.8

Q ss_pred             CcccccccccccccC-CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           46 NSSACSICLSEYLSQ-ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~-~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      -...|+||.+.+... +.+..+- |||.+|..||..||.....||.|+.++.
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~  245 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELP  245 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence            357899999887654 3444454 9999999999999999889999998764

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.52  E-value=0.0048  Score=43.24  Aligned_cols=35  Identities=17%  Similarity=0.432  Sum_probs=27.1

Q ss_pred             CCCccchhhHHHHhc-------------CCCCCccccCCCCCCCCcCC
Q 044807           69 CKHCFHAECIDEWPR-------------LNDKCPVCINSATPVHADYV  103 (105)
Q Consensus        69 C~H~Fh~~Ci~~wl~-------------~~~~CP~Cr~~~~~~~~~~~  103 (105)
                      |.-++|.+|+.+|+.             ++-+||+||+.+...+..+|
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v  372 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCV  372 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEE
Confidence            567789999999983             34579999999877665554

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

Probab=95.45  E-value=0.0075  Score=30.91  Aligned_cols=29  Identities=24%  Similarity=0.701  Sum_probs=21.7

Q ss_pred             CC-CccchhhHHHHhcCCCCCccccCCCCC
Q 044807           69 CK-HCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        69 C~-H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      |+ |..|..|+...+.+...||+|..++..
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            85 999999999999999999999988754

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.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.29  E-value=0.028  Score=29.64  Aligned_cols=34  Identities=24%  Similarity=0.727  Sum_probs=29.2

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHH
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECID   79 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~   79 (105)
                      ....|.+|-+.|.+++.+++-|.||=-+|+.|..
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~   37 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE   37 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence            4678999999998888787777899999999954

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

Probab=95.20  E-value=0.012  Score=41.44  Aligned_cols=43  Identities=33%  Similarity=0.677  Sum_probs=33.5

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHh-cCCCCCccccC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWP-RLNDKCPVCIN   93 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~Cr~   93 (105)
                      ..|+.|...+...  +.. +-|+|.||.+||...| ..-..||.|..
T Consensus       275 LkCplc~~Llrnp--~kT-~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP--MKT-PCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc--ccC-ccccchHHHHHHhhhhhhccccCCCccc
Confidence            7899998877654  333 4489999999999875 45778999965

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

Probab=95.19  E-value=0.019  Score=41.71  Aligned_cols=49  Identities=14%  Similarity=0.354  Sum_probs=39.3

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC---CCCccccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN---DKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~Cr~~   94 (105)
                      .....|||=-+.-.+......|. |||++..+-|.+..++.   ..||+|=.+
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             cceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            35689999888877777778888 99999999999987664   369999443

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

Probab=95.05  E-value=0.0077  Score=43.86  Aligned_cols=39  Identities=21%  Similarity=0.590  Sum_probs=28.3

Q ss_pred             CCcccccccccccccC-CceeEeCCCCCccchhhHHHHhcC
Q 044807           45 PNSSACSICLSEYLSQ-ETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~-~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      ....+|.||+.+.... +..... .|+|.||..|+.+.++.
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             cccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhh
Confidence            3468999999544444 333334 49999999999998864

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

Probab=95.03  E-value=0.0071  Score=49.48  Aligned_cols=47  Identities=28%  Similarity=0.631  Sum_probs=38.3

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~   94 (105)
                      .+...|.||++.+.....+.  . |||.||..|+..|+..+..||.|+..
T Consensus      1151 ~~~~~c~ic~dil~~~~~I~--~-cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIA--G-CGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             hcccchHHHHHHHHhcCCee--e-echhHhhhHHHHHHHHhccCcchhhh
Confidence            34579999999987533332  2 99999999999999999999999743

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=94.97  E-value=0.0091  Score=40.82  Aligned_cols=49  Identities=29%  Similarity=0.626  Sum_probs=35.2

Q ss_pred             CCccccccccccc-ccCCc-eeEeCCCCCccchhhHHHHhcCCC-CCc--cccC
Q 044807           45 PNSSACSICLSEY-LSQET-IKCIPECKHCFHAECIDEWPRLND-KCP--VCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~-~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP--~Cr~   93 (105)
                      ..+..|+||..+. ..++. +.+-|.|-|.+|..|+.+-+.... .||  -|-+
T Consensus         8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            3467999998863 34443 334456999999999999987754 699  6643

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

Probab=94.41  E-value=0.01  Score=41.93  Aligned_cols=31  Identities=35%  Similarity=0.868  Sum_probs=23.4

Q ss_pred             eEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           64 KCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        64 ~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      +.+| |.|+||.+|...  ..-+.||.|-..+..
T Consensus       105 RmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vqr  135 (389)
T KOG2932|consen  105 RMIP-CKHVFCLECARS--DSDKICPLCDDRVQR  135 (389)
T ss_pred             cccc-cchhhhhhhhhc--CccccCcCcccHHHH
Confidence            4578 999999999753  346689999765543

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

Probab=94.03  E-value=0.031  Score=37.48  Aligned_cols=40  Identities=28%  Similarity=0.737  Sum_probs=29.8

Q ss_pred             ccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCC
Q 044807           50 CSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      |-+|-+.   ...+.++| |.|. +|..|-..    -..||+|+.....
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhc
Confidence            8888775   34488899 9987 88888542    4569999987654

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

Probab=93.95  E-value=0.048  Score=34.00  Aligned_cols=52  Identities=23%  Similarity=0.459  Sum_probs=37.1

Q ss_pred             CcccccccccccccCCceeEeCC--CCCccchhhHHHHhc---CCCCCccccCCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPE--CKHCFHAECIDEWPR---LNDKCPVCINSATPVH   99 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~--C~H~Fh~~Ci~~wl~---~~~~CP~Cr~~~~~~~   99 (105)
                      .-.+|.||.|...+..  .+-|.  ||-..|..|....++   ....||+|++++-+..
T Consensus        79 ~lYeCnIC~etS~ee~--FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEER--FLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhh--cCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            5789999999754432  22221  899999999766443   3678999999986643

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

Probab=93.83  E-value=0.037  Score=41.02  Aligned_cols=36  Identities=22%  Similarity=0.453  Sum_probs=29.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      +++..|+||...|.+   .++|| |+|..|..|...-+..
T Consensus         2 eeelkc~vc~~f~~e---piil~-c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYRE---PIILP-CSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhccC---ceEee-cccHHHHHHHHhhccc
Confidence            357899999999977   57888 9999999998876644

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

Probab=93.10  E-value=0.064  Score=37.47  Aligned_cols=50  Identities=24%  Similarity=0.578  Sum_probs=36.0

Q ss_pred             cccccccccccccCCc-eeEeCCCC-----CccchhhHHHHhc--CCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQET-IKCIPECK-----HCFHAECIDEWPR--LNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~-~~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~Cr~~~~~   97 (105)
                      +..|-||.++...... ....| |.     ...|..|+..|+.  +...|.+|......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN  135 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence            5789999997654322 33445 64     5589999999997  56679999876543

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.70  E-value=0.047  Score=37.70  Aligned_cols=53  Identities=23%  Similarity=0.530  Sum_probs=36.3

Q ss_pred             CCcccccccccccccCCce-eEeCCC-----CCccchhhHHHHhcC--------CCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETI-KCIPEC-----KHCFHAECIDEWPRL--------NDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~-~~lp~C-----~H~Fh~~Ci~~wl~~--------~~~CP~Cr~~~~~~   98 (105)
                      +.+--|-||+..=++.... .+-| |     .|-.|..|+..|+..        .-+||.|+++...+
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv   84 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIV   84 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheee
Confidence            4567899999864443222 2345 6     377999999999843        12599999986543

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

Probab=92.27  E-value=0.37  Score=25.57  Aligned_cols=48  Identities=23%  Similarity=0.506  Sum_probs=33.1

Q ss_pred             ccccccccccccCCceeEeCCCC--CccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           48 SACSICLSEYLSQETIKCIPECK--HCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~--H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ..|-.|-.++.....-..+  |.  ..||..|....|  ++.||.|-.+|....
T Consensus         6 pnCE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l--~~~CPNCgGelv~RP   55 (57)
T PF06906_consen    6 PNCECCDKDLPPDSPEAYI--CSFECTFCADCAETML--NGVCPNCGGELVRRP   55 (57)
T ss_pred             CCccccCCCCCCCCCcceE--EeEeCcccHHHHHHHh--cCcCcCCCCccccCC
Confidence            4566777776554322222  65  469999999866  788999999887643

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

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

Probab=92.12  E-value=0.051  Score=42.02  Aligned_cols=40  Identities=28%  Similarity=0.654  Sum_probs=29.6

Q ss_pred             cccccccccccccCCc-eeEeCCCCCccchhhHHHHhcCCCCCc
Q 044807           47 SSACSICLSEYLSQET-IKCIPECKHCFHAECIDEWPRLNDKCP   89 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~~~CP   89 (105)
                      -..|.||+..|..... .+-+. |||..|..|++...  +.+||
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~-cghtic~~c~~~ly--n~scp   51 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQ-CGHTICGHCVQLLY--NASCP   51 (861)
T ss_pred             HhhchHHHHHHHHHhcCccccc-ccchHHHHHHHhHh--hccCC
Confidence            4689999988876543 33444 99999999998753  55677

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

Probab=92.00  E-value=0.087  Score=35.40  Aligned_cols=43  Identities=30%  Similarity=0.813  Sum_probs=35.1

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      .-..|.+|......+  +..-. |+-.||..|+..++.+...||.|
T Consensus       180 nlk~Cn~Ch~LvIqg--~rCg~-c~i~~h~~c~qty~q~~~~cphc  222 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG--IRCGS-CNIQYHRGCIQTYLQRRDICPHC  222 (235)
T ss_pred             HHHHHhHhHHHhhee--eccCc-ccchhhhHHHHHHhcccCcCCch
Confidence            457999999876443  44444 88889999999999999999999

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

Probab=91.16  E-value=0.12  Score=38.32  Aligned_cols=37  Identities=24%  Similarity=0.551  Sum_probs=29.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      .....|.||.+.+..  .+..+. |||.|+..|...++..
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            456899999998855  345566 9999999999998854

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

Probab=90.97  E-value=0.059  Score=41.86  Aligned_cols=47  Identities=21%  Similarity=0.582  Sum_probs=36.3

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC---CCCccccCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN---DKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~Cr~~~~   96 (105)
                      ...+|+||+..+...   ..+. |.|.|+..|+..-|...   ..||+|+..+.
T Consensus        20 k~lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   20 KILECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hhccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            468999999988775   4455 99999999987766553   35999986543

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

Probab=90.58  E-value=0.3  Score=39.04  Aligned_cols=53  Identities=28%  Similarity=0.711  Sum_probs=37.3

Q ss_pred             CCCcccccccccccccCCceeEeCCCC-----CccchhhHHHHhcCC--CCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECK-----HCFHAECIDEWPRLN--DKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~~~   98 (105)
                      .+++..|.||..+=..++.. .-| |.     -..|.+|+.+|+.-.  ..|-+|+.++...
T Consensus         9 N~d~~~CRICr~e~~~d~pL-fhP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk   68 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPL-FHP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFK   68 (1175)
T ss_pred             CccchhceeecCCCCCCCcC-ccc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeee
Confidence            45668999999875443333 334 64     338999999999754  4599999887543

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

Probab=90.23  E-value=0.19  Score=39.94  Aligned_cols=52  Identities=12%  Similarity=0.180  Sum_probs=35.9

Q ss_pred             CCccccccccccccc---CCceeEeCCCCCccchhhHHHHhcC------CCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLS---QETIKCIPECKHCFHAECIDEWPRL------NDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~---~~~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~Cr~~~~   96 (105)
                      .+...|.||..++.+   +-.+..+..|+|.||..||..|+.+      +-.|++|..-|.
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            345778888887776   2233333359999999999999854      345888876543

>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=90.22  E-value=0.33  Score=25.32  Aligned_cols=43  Identities=23%  Similarity=0.467  Sum_probs=20.3

Q ss_pred             ccccccccccCC------ceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           50 CSICLSEYLSQE------TIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        50 C~ICl~~~~~~~------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      |--|+..|..+.      ....-|.|++.||.+|=.--=+.-..||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            444555554431      2344556999999999443223455699883

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.

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

Probab=90.19  E-value=0.096  Score=40.10  Aligned_cols=43  Identities=26%  Similarity=0.769  Sum_probs=27.4

Q ss_pred             CCccccccccc-----ccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           45 PNSSACSICLS-----EYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        45 ~~~~~C~ICl~-----~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      .....|.||-.     .|.......... |+++||..|+..   ....||-|
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~~-C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFETRNTRRCST-CLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             cCeeeeeeccCCCcccccccccceeHHH-HHHHHHHHHHhc---cCCCCCch
Confidence            34577888832     122222344455 999999999764   45559999

>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=89.52  E-value=0.18  Score=25.76  Aligned_cols=43  Identities=26%  Similarity=0.644  Sum_probs=28.6

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhc------CCCCCcccc
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR------LNDKCPVCI   92 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~------~~~~CP~Cr   92 (105)
                      .|.||......++.+..-. |+-.||..|+..-..      ..-.||.|+
T Consensus         1 ~C~vC~~~~~~~~~i~C~~-C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCDS-CNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBST-TSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCCcCCCCCeEEcCC-CChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            3788888554445555554 999999999876432      134577764

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 ....

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

Probab=89.31  E-value=0.34  Score=38.22  Aligned_cols=42  Identities=19%  Similarity=0.380  Sum_probs=30.5

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCcc
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPV   90 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~   90 (105)
                      ...|.+|-..+. +..+ .-++|||.-|..|+..|+..+.-||.
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            357888876652 2222 23459999999999999998887765

>TIGR00622 ssl1 transcription factor ssl1

Probab=89.29  E-value=0.63  Score=28.26  Aligned_cols=46  Identities=24%  Similarity=0.394  Sum_probs=33.2

Q ss_pred             cccccccccccccCC----------ceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           47 SSACSICLSEYLSQE----------TIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~----------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      ...|--|+..|....          ....-+.|++.||.+|=.-+-+.-..||.|-
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            457999999885431          1222345999999999777767777799985

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

>smart00249 PHD PHD zinc finger

Probab=89.27  E-value=0.22  Score=24.29  Aligned_cols=31  Identities=26%  Similarity=0.676  Sum_probs=20.7

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHH
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDE   80 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~   80 (105)
                      .|.+|......+..+.... |...||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~~-C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCDG-CDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECCC-CCchhhhhhCCC
Confidence            3677877653333444444 999999999754

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

>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=88.66  E-value=0.24  Score=22.12  Aligned_cols=23  Identities=30%  Similarity=0.567  Sum_probs=11.4

Q ss_pred             cccccccccccCCceeEeCCCCCcc
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCF   73 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~F   73 (105)
                      .|+-|-..+...  ...-|.|||.|
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            466666655332  22234466666

Several members are annotated as putative helicases.

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.63  E-value=0.54  Score=32.57  Aligned_cols=58  Identities=16%  Similarity=0.174  Sum_probs=41.0

Q ss_pred             CCcccccccccccccCCce-eEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCCCcCCCC
Q 044807           45 PNSSACSICLSEYLSQETI-KCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      .....|+|=--++...... .+-+ |||+|-..-+.+.  ....|++|...+...+.-.+||
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~-CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg  167 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRC-CGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNG  167 (293)
T ss_pred             cceeecccccceecceEEEEEEec-cceeccHHHHHHh--hhccccccCCcccccCeEeeCC
Confidence            3457888876666544443 3345 9999999887774  4778999999887766655554

>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=88.57  E-value=0.41  Score=24.73  Aligned_cols=43  Identities=19%  Similarity=0.485  Sum_probs=19.0

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccCC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCINS   94 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~~   94 (105)
                      ..|+|-...+..+  ++... |.|.-|.+ +..||..     .-.||+|.++
T Consensus         3 L~CPls~~~i~~P--~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIP--VRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSE--EEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeC--ccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            4688877776543  45455 99985443 4555532     2359999763

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.

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

Probab=88.25  E-value=0.3  Score=35.74  Aligned_cols=44  Identities=23%  Similarity=0.421  Sum_probs=31.3

Q ss_pred             ccccccccccccc--CCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           47 SSACSICLSEYLS--QETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        47 ~~~C~ICl~~~~~--~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      -..|++|.-.+..  |-...+-. |||.||..|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence            4678888765433  32344445 99999999999998887777444

>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=87.81  E-value=0.27  Score=26.76  Aligned_cols=38  Identities=16%  Similarity=0.351  Sum_probs=19.2

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHh
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP   82 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl   82 (105)
                      .+...|.+|...|.....-..-..||++||..|.....
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            34689999999996544333333499999999976543

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 ....

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=87.42  E-value=0.45  Score=31.72  Aligned_cols=41  Identities=34%  Similarity=0.860  Sum_probs=27.7

Q ss_pred             Ccccccccccc-----cccCCceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           46 NSSACSICLSE-----YLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        46 ~~~~C~ICl~~-----~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      ....|-||-+.     |.. +.+..-+.|+-.||..|..     ...||-|.
T Consensus       151 kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~  196 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCA  196 (202)
T ss_pred             CCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcH
Confidence            45788888752     222 2333344599999999976     26799994

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

Probab=87.11  E-value=0.62  Score=33.41  Aligned_cols=49  Identities=29%  Similarity=0.524  Sum_probs=34.8

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCIN   93 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~   93 (105)
                      ......|-.|.++.........-. |.+.||.+|=.--=+.-..||.|-.
T Consensus       327 ~~~~~~Cf~C~~~~~~~~~y~C~~-Ck~~FCldCDv~iHesLh~CpgCeh  375 (378)
T KOG2807|consen  327 YNGSRFCFACQGELLSSGRYRCES-CKNVFCLDCDVFIHESLHNCPGCEH  375 (378)
T ss_pred             cCCCcceeeeccccCCCCcEEchh-ccceeeccchHHHHhhhhcCCCcCC
Confidence            344566999988776666666655 9999999995543344556999964

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

Probab=85.49  E-value=0.64  Score=33.26  Aligned_cols=46  Identities=17%  Similarity=0.360  Sum_probs=33.7

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC---CCCCcccc
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL---NDKCPVCI   92 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr   92 (105)
                      .-..||+=-+.-.+......|. |||++-.+-+....++   ...||+|=
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP  383 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCP  383 (396)
T ss_pred             ceeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence            4578888666655555566676 9999999988887654   34599993

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

Probab=85.08  E-value=0.35  Score=38.28  Aligned_cols=40  Identities=25%  Similarity=0.548  Sum_probs=28.9

Q ss_pred             CcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCC
Q 044807           46 NSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLND   86 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~   86 (105)
                      .+..|.-|.+.....    ..+.+.- |||+||..|+..-..++.
T Consensus       783 ~e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~  826 (846)
T KOG2066|consen  783 VEERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA  826 (846)
T ss_pred             ehhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc
Confidence            345899999876532    3466676 999999999887655443

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

Probab=83.99  E-value=0.64  Score=25.51  Aligned_cols=11  Identities=36%  Similarity=1.144  Sum_probs=8.2

Q ss_pred             cchhhHHHHhc
Q 044807           73 FHAECIDEWPR   83 (105)
Q Consensus        73 Fh~~Ci~~wl~   83 (105)
                      ||+.|+..|+.
T Consensus        12 FCRNCLskWy~   22 (68)
T PF06844_consen   12 FCRNCLSKWYR   22 (68)
T ss_dssp             --HHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999984

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

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

Probab=83.57  E-value=0.57  Score=33.01  Aligned_cols=39  Identities=18%  Similarity=0.375  Sum_probs=28.9

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      .-..|.+|.|.+++...|.+-..=.|.||+-|-.+-++.
T Consensus       267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~  305 (352)
T KOG3579|consen  267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQ  305 (352)
T ss_pred             CceeehhhhhhhccCceeecCCCcccceecccCHHHHHh
Confidence            347899999999876555321112799999999998865

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

Probab=81.81  E-value=0.91  Score=31.66  Aligned_cols=49  Identities=24%  Similarity=0.538  Sum_probs=34.1

Q ss_pred             cccccccccccccCCceeE---eCCCCCccchhhHHHHhcC---------CCCCccccCCC
Q 044807           47 SSACSICLSEYLSQETIKC---IPECKHCFHAECIDEWPRL---------NDKCPVCINSA   95 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~---lp~C~H~Fh~~Ci~~wl~~---------~~~CP~Cr~~~   95 (105)
                      ..+|-+|..++...+..+.   -+.|+-.+|..|+..-+..         ...||.|+..+
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            3699999999854443322   1248888999999985422         44699998743

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

Probab=81.71  E-value=0.88  Score=34.70  Aligned_cols=46  Identities=28%  Similarity=0.824  Sum_probs=36.2

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ......|.||+.+.    .....+ |.   |..|+..|+..+..||+|+..+..
T Consensus       476 ~~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~  521 (543)
T KOG0802|consen  476 REPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKE  521 (543)
T ss_pred             hcccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhc
Confidence            34568999999987    233344 77   899999999999999999886543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=81.59  E-value=1.5  Score=31.43  Aligned_cols=50  Identities=18%  Similarity=0.422  Sum_probs=37.1

Q ss_pred             CcccccccccccccCCceeE-eCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           46 NSSACSICLSEYLSQETIKC-IPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~-lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      ....|+||-+.....+...+ .| |++..|..|...-...+.+||.||++..
T Consensus       248 v~~s~p~~~~~~~~~d~~~lP~~-~~~~~~l~~~~t~~~~~~~~~~~rk~~~  298 (327)
T KOG2068|consen  248 VPPSCPICYEDLDLTDSNFLPCP-CGFRLCLFCHKTISDGDGRCPGCRKPYE  298 (327)
T ss_pred             cCCCCCCCCCccccccccccccc-ccccchhhhhhcccccCCCCCccCCccc
Confidence            34789999998744443222 34 7888888888887788999999997654

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

Probab=81.47  E-value=1.2  Score=23.09  Aligned_cols=37  Identities=16%  Similarity=0.346  Sum_probs=24.7

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhc
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR   83 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~   83 (105)
                      ...|.+|-..|.....-..-..||++|+..|......
T Consensus         2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~   38 (57)
T cd00065           2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIP   38 (57)
T ss_pred             cCcCcccCccccCCccccccCcCcCCcChHHcCCeee
Confidence            3578888887765432222224999999999876543

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

Probab=81.29  E-value=2.3  Score=24.15  Aligned_cols=51  Identities=25%  Similarity=0.486  Sum_probs=20.6

Q ss_pred             CCcccccccccccccC---Cc-eeEeCCCCCccchhhHHHHh-cCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQ---ET-IKCIPECKHCFHAECIDEWP-RLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~---~~-~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~Cr~~~~   96 (105)
                      .....|-||-+++...   +. +... .|+--.|+.|++-=. ..+..||.|++...
T Consensus         7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~-eC~fPvCr~CyEYErkeg~q~CpqCkt~yk   62 (80)
T PF14569_consen    7 LNGQICQICGDDVGLTENGEVFVACH-ECAFPVCRPCYEYERKEGNQVCPQCKTRYK   62 (80)
T ss_dssp             -SS-B-SSS--B--B-SSSSB--S-S-SS-----HHHHHHHHHTS-SB-TTT--B--
T ss_pred             cCCcccccccCccccCCCCCEEEEEc-ccCCccchhHHHHHhhcCcccccccCCCcc
Confidence            4568999999886543   22 2223 377778999987544 44778999998764

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

Probab=81.02  E-value=1.2  Score=20.66  Aligned_cols=36  Identities=25%  Similarity=0.519  Sum_probs=21.8

Q ss_pred             ccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCC
Q 044807           50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSA   95 (105)
Q Consensus        50 C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   95 (105)
                      |..|-..+...+.....  =+..||..|+        .|..|...|
T Consensus         2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~L   37 (39)
T smart00132        2 CAGCGKPIRGGELVLRA--LGKVWHPECF--------KCSKCGKPL   37 (39)
T ss_pred             ccccCCcccCCcEEEEe--CCccccccCC--------CCcccCCcC
Confidence            67777777554233222  3567888775        377776655

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

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

Probab=80.29  E-value=1.2  Score=31.68  Aligned_cols=50  Identities=24%  Similarity=0.555  Sum_probs=39.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .....|-||...+......   .+|+|.|+..|...|....+-||.|+.-+..
T Consensus       103 ~~~~~~~~~~g~l~vpt~~---qg~w~qf~~~~p~~~~~~~~~~~d~~~~~~p  152 (324)
T KOG0824|consen  103 QDHDICYICYGKLTVPTRI---QGCWHQFCYVCPKSNFAMGNDCPDCRGKISP  152 (324)
T ss_pred             CCccceeeeeeeEEecccc---cCceeeeeecCCchhhhhhhccchhhcCcCc
Confidence            4457888888877654332   3499999999999999999999999886654

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.05  E-value=2.6  Score=23.60  Aligned_cols=27  Identities=26%  Similarity=0.590  Sum_probs=21.3

Q ss_pred             CCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           70 KHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        70 ~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      .|.||..|.+.-  -+..||.|-.++...
T Consensus        28 EcTFCadCae~~--l~g~CPnCGGelv~R   54 (84)
T COG3813          28 ECTFCADCAENR--LHGLCPNCGGELVAR   54 (84)
T ss_pred             eeehhHhHHHHh--hcCcCCCCCchhhcC
Confidence            488999998864  367899998887643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	105
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		3e-06
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		5e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-04
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-04

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          +   C++CL+E    E  + +P C H FHAEC+D W   +  CP+C
Sbjct: 4  DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP 97
          C +C+ ++ S++ ++ +P C H FHA+C+D+W + N  CP+C   + P
Sbjct: 26 CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGP 72

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C+ICLS     E ++ +P C H FH  C+D+W   N KCP+C
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPIC 57

>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 = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT 96
          C +C  +Y   E+++ +P C H FH  CI  W   +D CPVC  S T
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	105
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-15
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	5e-14
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-13
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	3e-12
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-11
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-11
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	1e-11
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-11
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-08
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-07
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-07
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	7e-07
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-06
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-06
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-05
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	7e-05
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-04
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	4e-04
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-04
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	5e-04
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-04

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

 Score = 64.1 bits (157), Expect = 1e-15
 Identities = 18/42 (42%), Positives = 26/42 (61%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C++CL+E    E  + +P C H FHAEC+D W   +  CP+C
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

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

 Score = 60.8 bits (148), Expect = 5e-14
 Identities = 17/54 (31%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP 97
              + C +C+ ++ S++ ++ +P C H FHA+C+D+W + N  CP+C   + P
Sbjct: 20 QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGP 72

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

 Score = 59.3 bits (144), Expect = 2e-13
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 22 GLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW 81
             + +I +  ++++ E     G     C IC SEY+  +    +P C H FH  C+  W
Sbjct: 16 PASKESIDALPEILVTEDHGAVG-QEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIW 73

Query: 82 PRLNDKCPVC 91
           + +  CPVC
Sbjct: 74 LQKSGTCPVC 83

>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 = 55.8 bits (135), Expect = 3e-12
 Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C+ICLS     E ++ +P C H FH  C+D+W   N KCP+C
Sbjct: 17 CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPIC 57

>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 = 54.7 bits (132), Expect = 1e-11
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C +C  +Y   E+++ +P C H FH  CI  W   +D CPVC
Sbjct: 18 CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVC 58

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

 Score = 54.9 bits (132), Expect = 1e-11
 Identities = 14/42 (33%), Positives = 23/42 (54%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C  C +E   ++ +    EC H FH  C+  W + N++CP+C
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLC 70

>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 = 53.8 bits (130), Expect = 1e-11
 Identities = 14/46 (30%), Positives = 22/46 (47%)

Query: 46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
           SS C ICL +  +   +  +  C H  H  C +E  +   +CP+C
Sbjct: 4  GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49

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

 Score = 54.4 bits (131), Expect = 1e-11
 Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C++CL ++  ++ +   P CKH FH +C+ +W  +   CP+C
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58

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

 Score = 47.0 bits (112), Expect = 1e-08
 Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 3/45 (6%)

Query: 47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          +  C ICL +  +         C H F   CI  W R N  CP+C
Sbjct: 5  AERCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLC 46

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

 Score = 45.5 bits (108), Expect = 3e-08
 Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 5/42 (11%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C IC+           I  C H F  +CID+W   +  CP+C
Sbjct: 18 CCICMDGR-----ADLILPCAHSFCQKCIDKWSDRHRNCPIC 54

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

 Score = 43.0 bits (101), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 50 CSICLSEY---LSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C IC+  Y   +    +    EC H F ++C+ +  +  + CP C
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 62

>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 = 43.7 bits (102), Expect = 5e-07
 Identities = 12/42 (28%), Positives = 16/42 (38%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C    +   S+E       C H FH  CI  W +    CP+ 
Sbjct: 54 CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 95

>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 = 43.3 bits (101), Expect = 7e-07
 Identities = 12/42 (28%), Positives = 16/42 (38%)

Query: 50  CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
           C    +   S+E       C H FH  CI  W +    CP+ 
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 106

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

 Score = 41.3 bits (97), Expect = 2e-06
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 3/45 (6%)

Query: 50 CSICLSEY---LSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C IC+  Y   +    +    EC H F ++C+ +  +  + CP C
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 50

>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 = 41.4 bits (97), Expect = 2e-06
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 46 NSSACSICLSEY---LSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
           + +C IC+  Y   +    +    EC H F ++C+ +  +  + CP C
Sbjct: 9  GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 57

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

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          CSIC   YL   T   I EC H F   CI      +++CP C
Sbjct: 18 CSICK-GYLIDATT--ITECLHTFCKSCIVRHFYYSNRCPKC 56

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 39.4 bits (92), Expect = 2e-05
 Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 3/42 (7%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C +C   Y    T   I EC H F   CI  +   +  CP+C
Sbjct: 18 CVLCG-GYFIDATT--IIECLHSFCKTCIVRYLETSKYCPIC 56

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

 Score = 38.3 bits (89), Expect = 3e-05
 Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 4/43 (9%)

Query: 49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
           C IC   +        + +C+H F   C  E  R   +C +C
Sbjct: 17 RCFICRQAF----QNPVVTKCRHYFCESCALEHFRATPRCYIC 55

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

 Score = 39.1 bits (90), Expect = 7e-05
 Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 15/57 (26%)

Query: 50  CSICLSEYLSQETIKCI----PECKHCFHAECIDEW-----------PRLNDKCPVC 91
           C+IC +  L    +  +     +C    HA C++EW                +CP C
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

>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 = 36.4 bits (84), Expect = 2e-04
 Identities = 11/43 (25%), Positives = 15/43 (34%), Gaps = 4/43 (9%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEW-PRLNDKCPVC 91
          C IC+ +       +  P C       CI  W      +CP C
Sbjct: 25 CFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHC 64

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

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C IC  EY +   I  IP+C H + + CI ++     +CP C
Sbjct: 25 CGICF-EYFNIAMI--IPQCSHNYCSLCIRKFLSYKTQCPTC 63

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

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 5/44 (11%)

Query: 50  CSICLSEYLSQETIKCIPECKHCFHAECIDEW--PRLNDKCPVC 91
           C+IC S  +  +   C   C    H  C+ ++       +CP C
Sbjct: 183 CNICHSLLI--QGQSC-ETCGIRMHLPCVAKYFQSNAEPRCPHC 223

>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 = 36.7 bits (84), Expect = 5e-04
 Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 5/47 (10%)

Query: 46  NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDK-CPVC 91
               C IC       + +K  P C H     C+  W     + CP C
Sbjct: 331 TFQLCKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFC 373

>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 = 34.9 bits (80), Expect = 5e-04
 Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 5/44 (11%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEW--PRLNDKCPVC 91
          C+IC S  +     +    C    H  C+ ++       +CP C
Sbjct: 18 CNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHC 58

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

 Score = 34.8 bits (80), Expect = 6e-04
 Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 4/53 (7%)

Query: 39 SKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
              P      C+ICL              CKH F   C+     L  +C +C
Sbjct: 7  GNTAPSLTVPECAICLQTC----VHPVSLPCKHVFCYLCVKGASWLGKRCALC 55

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.87
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.8
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.79
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.77
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.77
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.77
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.74
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.71
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.71
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.7
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.7
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.69
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.68
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.67
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.66
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.66
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.65
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.63
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.62
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.62
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.61
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.6
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.6
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.58
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.58
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.57
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	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
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.54
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.54
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.53
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.53
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.53
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.53
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.52
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.52
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.52
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.51
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.5
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.49
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.48
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.47
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.46
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.46
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.45
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.44
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.44
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.44
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.41
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.39
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.38
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.38
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.38
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.36
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.34
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.33
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.31
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.29
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.25
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.23
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.21
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.21
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.2
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.17
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.11
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.08
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	99.02
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.99
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.88
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.71
3nw0_A	238	Non-structural maintenance of chromosomes element	98.56
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.34
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.75
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.71
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	94.73
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.55
1we9_A	64	PHD finger family protein; structural genomics, PH	94.51
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.74
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.71
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	93.64
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	93.62
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	92.76
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	92.71
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	92.63
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	92.52
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	92.44
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	92.01
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	91.86
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	91.85
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	91.81
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.78
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.54
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	91.53
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	91.41
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	91.11
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	90.95
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	90.36
2yt5_A	66	Metal-response element-binding transcription facto	90.04
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	89.27
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	89.19
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	89.04
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	88.56
1z60_A	59	TFIIH basal transcription factor complex P44 subun	88.31
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	88.16
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	88.12
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	88.12
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	87.9
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	87.72
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	87.43
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.2
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	86.99
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	86.63
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	86.53
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	86.32
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	86.21
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	86.01
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	85.86
1weu_A	91	Inhibitor of growth family, member 4; structural g	85.8
2d8v_A	67	Zinc finger FYVE domain-containing protein 19; zfy	85.46
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	85.19
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	84.26
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	82.65
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	82.29
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	82.0
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	81.61
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	81.57
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	81.56
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	81.27
2a20_A	62	Regulating synaptic membrane exocytosis protein 2;	80.69

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

Probab=99.87  E-value=4.8e-22  Score=115.91  Aligned_cols=84  Identities=24%  Similarity=0.544  Sum_probs=70.9

Q ss_pred             CCCCCccccCCCCHHHHhhccchhhccccCCCCCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           12 VAPQPPIMIMGLDECTIKSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      ..........+++++.+..||...+...... ..++..|+||++.|..++.+..++ |||.||..||..|+..+.+||+|
T Consensus         6 ~~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~C   83 (91)
T 2l0b_A            6 HHHSHMVANPPASKESIDALPEILVTEDHGA-VGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVC   83 (91)
T ss_dssp             CCSCCSSCCCCCCHHHHHTSCEEECCTTCSS-SSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTT
T ss_pred             ccCCCCcCCCCCCHHHHHhCCCeeecccccc-cCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCc
Confidence            3444567778999999999998887654432 356789999999999888888899 99999999999999999999999


Q ss_pred             cCCCCC
Q 044807           92 INSATP   97 (105)
Q Consensus        92 r~~~~~   97 (105)
                      |..+..
T Consensus        84 r~~~~~   89 (91)
T 2l0b_A           84 RCMFPP   89 (91)
T ss_dssp             CCBSSC
T ss_pred             CccCCC
Confidence            998764

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

Probab=99.80  E-value=5.3e-21  Score=107.61  Aligned_cols=67  Identities=25%  Similarity=0.811  Sum_probs=54.4

Q ss_pred             hhccchhhccccCCCCCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           29 KSFQKLVLEESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ..+|...+.....  ..++..|+||++.|..++.+..++ |+|.||..||..|+..+.+||+||.++...
T Consensus         7 ~~lp~~~~~~~~~--~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            7 GQLPSYRFNPNNH--QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SSCCCEEBCSSSC--SSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hhCCcEEecCccc--cCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3455555443322  356789999999999888888899 999999999999999999999999988764

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

Probab=99.79  E-value=1.3e-19  Score=96.10  Aligned_cols=52  Identities=35%  Similarity=0.889  Sum_probs=46.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      +++.+|+||++.|..++.+..++.|||.||..||..|+..+.+||+||.++.
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            4578999999999888877777669999999999999999999999999874

>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=99.77  E-value=3.8e-19  Score=98.39  Aligned_cols=54  Identities=35%  Similarity=0.831  Sum_probs=48.3

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ......|+||++.|..+..+..++ |||.||..||..|+..+.+||+||..+...
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            456789999999998877888898 999999999999999999999999998754

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

Probab=99.77  E-value=3.8e-19  Score=99.61  Aligned_cols=56  Identities=25%  Similarity=0.751  Sum_probs=49.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHA  100 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  100 (105)
                      ...+..|+||++.|..+..+..++ |+|.||..||..|+..+.+||+||..+..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccccc
Confidence            355789999999998888888888 99999999999999998999999999876543

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

Probab=99.77  E-value=6.5e-19  Score=99.60  Aligned_cols=55  Identities=35%  Similarity=0.827  Sum_probs=48.9

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      .....+|+||++.|..+..+..++ |+|.||..||..|+..+.+||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             CCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            355789999999998888888888 9999999999999999999999999987644

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

Probab=99.74  E-value=1.7e-18  Score=98.80  Aligned_cols=53  Identities=26%  Similarity=0.773  Sum_probs=42.8

Q ss_pred             CCccccccccccccc-----------CCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLS-----------QETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~-----------~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .++..|+||++.|..           ++.++.++.|+|.||..||.+||..+.+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            356778888888854           34354554599999999999999999999999998764

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

Probab=99.71  E-value=4.7e-18  Score=94.27  Aligned_cols=55  Identities=22%  Similarity=0.603  Sum_probs=46.3

Q ss_pred             CCCcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ..++..|+||++.|.+.    ..+..++ |||.||..||..|+..+.+||+||..+....
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            35678999999998763    4456677 9999999999999999999999999987543

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

Probab=99.71  E-value=4.8e-18  Score=94.14  Aligned_cols=56  Identities=27%  Similarity=0.720  Sum_probs=49.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCCCcCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      .+...|+||++.+.+    ..++ |||.||..||..|+....+||+||..+......++.|
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~   68 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSGPS   68 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCCCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCccccCC
Confidence            457899999999865    5678 9999999999999999999999999998877776654

>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=99.70  E-value=1e-17  Score=88.68  Aligned_cols=51  Identities=29%  Similarity=0.783  Sum_probs=43.7

Q ss_pred             CCcccccccccccccCC-ceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQE-TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~-~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      .++..|+||++.|.+++ .+..++ |||.||..||..|+....+||+||..+.
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            45789999999986644 466677 9999999999999998899999999864

>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=99.70  E-value=2.3e-17  Score=99.27  Aligned_cols=53  Identities=21%  Similarity=0.437  Sum_probs=42.5

Q ss_pred             CcccccccccccccCC---------------ceeEeCCCCCccchhhHHHHh-----cCCCCCccccCCCCCCC
Q 044807           46 NSSACSICLSEYLSQE---------------TIKCIPECKHCFHAECIDEWP-----RLNDKCPVCINSATPVH   99 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~Cr~~~~~~~   99 (105)
                      .+..|+|||+.|..+.               .+.+++ |+|.||..||..|+     ..+.+||+||..+....
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCC
Confidence            4579999999996543               233667 99999999999999     45778999999886543

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

Probab=99.69  E-value=1.5e-17  Score=91.57  Aligned_cols=53  Identities=23%  Similarity=0.632  Sum_probs=44.6

Q ss_pred             CCCcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+...|+||++.|.+.    ..+..++ |||.||..||..|+..+.+||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            35578999999998764    3346677 99999999999999999999999998753

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

Probab=99.68  E-value=1.3e-17  Score=90.65  Aligned_cols=53  Identities=23%  Similarity=0.610  Sum_probs=44.9

Q ss_pred             CcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           46 NSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ++.+|+||++.+.+.    ..+..++ |||.||..||..|+..+.+||+||..+...+
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            467999999998763    3456777 9999999999999999999999999987543

>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=99.67  E-value=5.6e-17  Score=96.82  Aligned_cols=51  Identities=25%  Similarity=0.578  Sum_probs=43.2

Q ss_pred             CCcccccccccccccCC---------------ceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQE---------------TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      .++..|+||++.|...-               .+..++ |+|.||..||..||..+.+||+||.++.
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            45789999999987541               255677 9999999999999999999999999864

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

Probab=99.66  E-value=5.2e-17  Score=89.41  Aligned_cols=51  Identities=33%  Similarity=0.772  Sum_probs=43.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ..+..|+||++.+.+.  +..++ |||.||..||..|+..+.+||+||..+...
T Consensus         3 ~~~~~C~IC~~~~~~~--~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            3 TVAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCCeeCCccccCC--cEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            3467999999998643  46677 999999999999999999999999988653

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

Probab=99.66  E-value=7.5e-17  Score=89.62  Aligned_cols=50  Identities=26%  Similarity=0.656  Sum_probs=43.4

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+...|+||++.+.+   .+.++ |||.||..||..|+..+..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           12 SLTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SSSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            3457899999999865   46678 99999999999999999999999998764

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

Probab=99.65  E-value=1.8e-16  Score=88.34  Aligned_cols=53  Identities=23%  Similarity=0.447  Sum_probs=43.9

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ..+...|+||++.|.+.  +.+++ |||.||..||..|+..+..||+||..+...+
T Consensus        12 ~~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           12 LTPYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             CCGGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             cCCCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            34578999999998763  33347 9999999999999998999999999987543

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

Probab=99.63  E-value=4.5e-16  Score=89.43  Aligned_cols=53  Identities=19%  Similarity=0.539  Sum_probs=44.6

Q ss_pred             CCCcccccccccccccCCc-eeEeCCCCCccchhhHHHHhcCC---CCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQET-IKCIPECKHCFHAECIDEWPRLN---DKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~-~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~Cr~~~~~   97 (105)
                      ..+...|+||++.|.+.+. .+.++ |||.||..||..|+...   ..||+||..+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             ccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            3557899999999987654 66777 99999999999999865   789999998754

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

Probab=99.62  E-value=5.7e-16  Score=86.74  Aligned_cols=54  Identities=26%  Similarity=0.519  Sum_probs=43.3

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC--CCCccccCCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN--DKCPVCINSATPVHA  100 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~~  100 (105)
                      ..+...|+||++.|.+.   +.++.|||.||..||..|+..+  ..||+||..+...+.
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           12 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             SCGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             CCCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            34578999999999763   4465599999999999999764  689999998665443

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

Probab=99.62  E-value=2e-16  Score=98.24  Aligned_cols=48  Identities=27%  Similarity=0.758  Sum_probs=42.5

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      +..|+||++.|.+   ++.++ |||.||..||..|+..+.+||+||.++...
T Consensus        53 ~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            5689999999865   46788 999999999999999999999999998653

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

Probab=99.61  E-value=5.2e-16  Score=88.30  Aligned_cols=53  Identities=23%  Similarity=0.600  Sum_probs=43.8

Q ss_pred             CCCcccccccccccccCCceeEeCCCC-----CccchhhHHHHhcCC--CCCccccCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECK-----HCFHAECIDEWPRLN--DKCPVCINSATPV   98 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~-----H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~~~   98 (105)
                      ..++..|.||+++|..++.+ ++| |+     |.||..||.+||..+  .+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            34568999999999776665 578 96     999999999999764  5899999988653

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

Probab=99.60  E-value=6e-16  Score=87.92  Aligned_cols=48  Identities=23%  Similarity=0.500  Sum_probs=42.2

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      .....|+||++.|.+   .++++ |||.||..||..|+.....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            456899999999865   45677 9999999999999998999999999875

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

Probab=99.60  E-value=1.8e-15  Score=84.14  Aligned_cols=50  Identities=30%  Similarity=0.541  Sum_probs=41.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhc---CCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR---LNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~Cr~~~~~~   98 (105)
                      .+...|+||++.|.+   .+.++ |||.||..||..|+.   ....||+||..+...
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            457899999999865   45567 999999999999997   456899999988653

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

Probab=99.58  E-value=1.4e-16  Score=96.44  Aligned_cols=52  Identities=25%  Similarity=0.542  Sum_probs=1.6

Q ss_pred             CCcccccccccccccCC---------------ceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQE---------------TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+..|+||++.|....               .+..++ |+|.||..||..||..+.+||+||.++..
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CCC-----------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            45689999999996521               233346 99999999999999999999999998643

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

Probab=99.58  E-value=2e-15  Score=82.65  Aligned_cols=50  Identities=24%  Similarity=0.447  Sum_probs=41.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhc-CCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-LNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~~~~   98 (105)
                      .+...|+||++.+.+.   +.++ |||.||..||..|+. ....||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4578999999998764   3367 999999999999995 567899999988653

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

Probab=99.57  E-value=1.4e-15  Score=93.04  Aligned_cols=53  Identities=23%  Similarity=0.632  Sum_probs=45.4

Q ss_pred             CCcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      .+...|+||++.|.+.    ..++.++ |||.||..||..|+..+.+||+||..+...
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            4578999999998764    3457777 999999999999999999999999988653

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

Probab=99.56  E-value=4.8e-15  Score=83.51  Aligned_cols=49  Identities=16%  Similarity=0.368  Sum_probs=42.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+   .+.++ |||.||..||..|+.. +.+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            457899999999876   45678 9999999999999987 7889999998864

>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=1.2e-15  Score=90.02  Aligned_cols=48  Identities=21%  Similarity=0.526  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCceeE-eCCCCCccchhhHHHHhcCC-CCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKC-IPECKHCFHAECIDEWPRLN-DKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~-lp~C~H~Fh~~Ci~~wl~~~-~~CP~Cr~~~~~   97 (105)
                      +...|+||++.|.+   .+. ++ |||.||..||..|+... .+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           21 EVFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            46899999999965   344 77 99999999999999887 699999998754

>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=7.9e-15  Score=80.00  Aligned_cols=51  Identities=20%  Similarity=0.461  Sum_probs=41.0

Q ss_pred             Cccccccccc-ccccCCce-eEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           46 NSSACSICLS-EYLSQETI-KCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~-~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ++..|+||++ .+.+.... ..++ |||.||..||..|+.. ...||+||..+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   55 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccc
Confidence            4678999999 77665443 3466 9999999999999765 5679999998864

>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=99.54  E-value=4.6e-15  Score=90.48  Aligned_cols=48  Identities=21%  Similarity=0.438  Sum_probs=41.0

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC-CCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN-DKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~Cr~~~~~   97 (105)
                      +...|+||++.|.+   .+.++ |||.||..||..|+... ..||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45789999999975   45677 99999999999999864 489999999865

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

Probab=99.54  E-value=2.3e-15  Score=84.85  Aligned_cols=49  Identities=27%  Similarity=0.543  Sum_probs=41.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-------CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-------NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-------~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+.   +.++ |||.||..||..|+..       ...||+||..+..
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            4578999999998663   4467 9999999999999976       5689999998864

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

Probab=99.53  E-value=4e-15  Score=87.46  Aligned_cols=48  Identities=25%  Similarity=0.651  Sum_probs=41.5

Q ss_pred             CcccccccccccccCCceeEe-CCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCI-PECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      +...|+||++.|.+   .+.+ + |||.||..||..|+..+.+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhCC---cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            36799999999876   3444 6 99999999999999999999999998764

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

Probab=99.53  E-value=1.1e-14  Score=78.95  Aligned_cols=44  Identities=32%  Similarity=0.599  Sum_probs=37.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhc---CCCCCccc
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR---LNDKCPVC   91 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~C   91 (105)
                      ..++..|+||++.|.+   .+.++ |||.||..||..|+.   ....||+|
T Consensus        17 ~~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            3457899999999875   45567 999999999999997   46689998

>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=99.53  E-value=7e-15  Score=87.69  Aligned_cols=49  Identities=22%  Similarity=0.585  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCceeEe-CCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCI-PECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      +...|+||++.|.+   .+.+ + |||.||..||..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID---ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC---cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            47899999999865   3444 7 999999999999999999999999988653

>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=99.53  E-value=3.6e-15  Score=94.95  Aligned_cols=77  Identities=21%  Similarity=0.356  Sum_probs=51.6

Q ss_pred             cccCCCCHHHHhhccchhhccccC-----CCCCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccc
Q 044807           18 IMIMGLDECTIKSFQKLVLEESKC-----LPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVC   91 (105)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~C   91 (105)
                      ....++....+...+.........     ....+...|+||++.|.+.  +.+++ |||.||..||..|+.. ...||+|
T Consensus        20 ~~~~~l~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~C   96 (165)
T 2ckl_B           20 SKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTC   96 (165)
T ss_dssp             -CCCCCCHHHHHCCCCCCCCSCCEEC----CCHHHHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTT
T ss_pred             CccccCCHHHHhcCchhhhccccccccchhhCCCCCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCC
Confidence            344566666665544332222111     0122456999999998762  33347 9999999999999987 7789999


Q ss_pred             cCCCCC
Q 044807           92 INSATP   97 (105)
Q Consensus        92 r~~~~~   97 (105)
                      |..+..
T Consensus        97 r~~~~~  102 (165)
T 2ckl_B           97 RKKLVS  102 (165)
T ss_dssp             CCBCCS
T ss_pred             CCcCCC
Confidence            998854

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

Probab=99.52  E-value=9.8e-15  Score=84.61  Aligned_cols=50  Identities=26%  Similarity=0.551  Sum_probs=41.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--CCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      ..+...|+||++.|.+.   +.++.|||.||..||..|+..  ...||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            35678999999998763   455549999999999999964  368999999874

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

Probab=99.52  E-value=9.7e-15  Score=83.08  Aligned_cols=49  Identities=27%  Similarity=0.525  Sum_probs=41.7

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC------CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL------NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+.   ..++ |||.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            4578999999998663   4677 9999999999999976      6689999998764

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

Probab=99.52  E-value=2.1e-14  Score=80.35  Aligned_cols=54  Identities=22%  Similarity=0.522  Sum_probs=43.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC--CCCccccCCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN--DKCPVCINSATPVHA  100 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~~  100 (105)
                      .+...+|+||.+.|..++  .... |+|.||..||..||+.+  .+||+||.++.....
T Consensus        12 ~~~i~~C~IC~~~i~~g~--~C~~-C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQ--SCET-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSE--ECSS-SCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCC
T ss_pred             cCCCCcCcchhhHcccCC--ccCC-CCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCC
Confidence            455689999999997653  3334 99999999999999887  889999998765433

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

Probab=99.51  E-value=1.3e-14  Score=82.54  Aligned_cols=49  Identities=29%  Similarity=0.666  Sum_probs=41.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC------CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL------NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.+.+.   ..++ |||.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            4578999999998653   4567 9999999999999976      7789999998864

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

Probab=99.50  E-value=1.9e-14  Score=76.57  Aligned_cols=43  Identities=35%  Similarity=0.796  Sum_probs=36.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHh---cCCCCCccc
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP---RLNDKCPVC   91 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl---~~~~~CP~C   91 (105)
                      .+...|+||++.+.+.   +.++ |||.||..||..|+   .....||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4578999999998764   4567 99999999999995   456789998

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

Probab=99.49  E-value=8.3e-15  Score=89.60  Aligned_cols=55  Identities=24%  Similarity=0.652  Sum_probs=45.8

Q ss_pred             CCCcccccccccccccC----CceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           44 GPNSSACSICLSEYLSQ----ETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~----~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ..+...|+||++.|...    ..+..++ |||.||..||.+|+..+.+||+||..+...+
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            35678999999998763    2346677 9999999999999999999999999987543

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

Probab=99.48  E-value=7.6e-14  Score=78.92  Aligned_cols=59  Identities=17%  Similarity=0.295  Sum_probs=44.6

Q ss_pred             CCcccccccccccccCCce-eEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCCCcCCC
Q 044807           45 PNSSACSICLSEYLSQETI-KCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVHADYVN  104 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~~~~  104 (105)
                      .++.+|+||++.+...+.. .-++ |||.||..|+..++.. ...||+||..+......+.+
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~~~   69 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYKP   69 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCCCS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhhcc
Confidence            5678999999988544332 2245 9999999999998754 67899999998766555443

>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=99.47  E-value=3.2e-14  Score=89.54  Aligned_cols=49  Identities=18%  Similarity=0.382  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC-CCccccCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND-KCPVCINSATPV   98 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~Cr~~~~~~   98 (105)
                      +...|+||++.|.+   .+.++ |||.||..||..|+.... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45789999999866   45578 999999999999998754 899999998754

>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=99.46  E-value=2e-14  Score=78.44  Aligned_cols=51  Identities=20%  Similarity=0.363  Sum_probs=42.7

Q ss_pred             CCcccccccccccccCCceeEe--CCCCCc-cchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCI--PECKHC-FHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~l--p~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      .++.+|.||++.+.+   +..+  | |||. ||..|+..|+..+..||+||.++..+.
T Consensus         6 ~~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~i   59 (64)
T 2vje_A            6 NAIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQMIV   59 (64)
T ss_dssp             GGGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCEEE
T ss_pred             CCcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhceE
Confidence            456799999998755   3444  8 9999 899999999998899999999987543

>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=99.46  E-value=1.2e-14  Score=87.70  Aligned_cols=50  Identities=28%  Similarity=0.545  Sum_probs=42.1

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVH   99 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~   99 (105)
                      +...|+||++.+.+   .+.++ |||.||..||..|+.. ..+||+||..+....
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            35789999999865   35577 9999999999999986 778999999987543

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

Probab=99.45  E-value=1e-14  Score=87.78  Aligned_cols=49  Identities=20%  Similarity=0.563  Sum_probs=41.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      .++..|+||++.|.+   .+.++ |||.||..||..|+.. ...||+||..+..
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            446899999999865   45667 9999999999999977 6789999998753

>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=99.44  E-value=5.5e-14  Score=83.96  Aligned_cols=47  Identities=28%  Similarity=0.589  Sum_probs=39.8

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC---CCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND---KCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~---~CP~Cr~~~~~   97 (105)
                      ...|+||++.|.+.   ..++ |||.||..||..|+....   +||+||..+..
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            57999999998653   4467 999999999999998654   89999998764

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

Probab=99.44  E-value=2e-13  Score=96.90  Aligned_cols=55  Identities=25%  Similarity=0.634  Sum_probs=46.5

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhc-CCCCCccccCCCCCCCCcCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-LNDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      ...|+||++.+.+   ++.+| |||.||..||..|+. ...+||+||..+.....-.++|
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i~v~p  387 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDP  387 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEECSCCT
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCceeEecCC
Confidence            4799999999855   56788 999999999999998 7889999999988766555544

>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=99.44  E-value=3.8e-14  Score=85.75  Aligned_cols=49  Identities=31%  Similarity=0.491  Sum_probs=42.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC-CCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND-KCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~Cr~~~~~   97 (105)
                      .+...|+||++.+.+.   +.++ |||.||..||..|+.... +||+||..+..
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            5578999999998763   5577 999999999999998755 99999998865

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

Probab=99.41  E-value=2.2e-13  Score=78.14  Aligned_cols=49  Identities=10%  Similarity=-0.029  Sum_probs=43.7

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+   .++++ |||.|+..||..|+..+.+||+|+..+..
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             chheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            457999999999977   46788 99999999999999988999999998764

>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=99.39  E-value=2.9e-13  Score=79.86  Aligned_cols=49  Identities=10%  Similarity=-0.017  Sum_probs=43.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+   .++++ |||.|+..||..|+..+.+||+|+.++..
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            457899999999977   56788 99999999999999988999999998865

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

Probab=99.38  E-value=8.9e-14  Score=77.79  Aligned_cols=49  Identities=29%  Similarity=0.688  Sum_probs=40.7

Q ss_pred             CcccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCCCCcC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPVHADY  102 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~  102 (105)
                      ++..|+||++.+.+   ++.+| |||. ||..|+..|    ..||+||..+.....-|
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~   72 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFKQKIL   72 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEEEECB
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccCcEEEe
Confidence            35799999998765   56788 9999 999999998    88999999987654433

>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=99.38  E-value=7.4e-13  Score=77.85  Aligned_cols=49  Identities=10%  Similarity=-0.033  Sum_probs=43.6

Q ss_pred             CCcccccccccccccCCceeEeCCCC-CccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECK-HCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .+...|+||++.|.+   .++++ || |.|+..||..||..+.+||+||.++..
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            457899999999977   46678 99 999999999999988999999998864

>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=99.38  E-value=1.1e-13  Score=75.16  Aligned_cols=50  Identities=20%  Similarity=0.369  Sum_probs=41.3

Q ss_pred             CCcccccccccccccCCceeEe--CCCCCc-cchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCI--PECKHC-FHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~l--p~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      .....|.||++.+.+   ...+  | |||. ||..|+..|...+..||+||.++..+
T Consensus         5 ~~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   57 (63)
T 2vje_B            5 NLLKPCSLCEKRPRD---GNIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQLV   57 (63)
T ss_dssp             GGGSBCTTTSSSBSC---EEEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCEE
T ss_pred             CcCCCCcccCCcCCC---eEEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhce
Confidence            346799999998654   2334  8 9999 99999999998889999999998654

>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=99.36  E-value=1.4e-13  Score=85.78  Aligned_cols=48  Identities=17%  Similarity=0.414  Sum_probs=40.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC-CCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND-KCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~Cr~~~~   96 (105)
                      .+...|+||++.|.+.   +.++ |||.||..||..|+.... .||+||.++.
T Consensus        29 ~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             CcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            4578999999998764   5567 999999999999998654 8999999763

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

Probab=99.34  E-value=3.2e-13  Score=71.67  Aligned_cols=47  Identities=23%  Similarity=0.514  Sum_probs=39.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      .+...|+||++.|.+   .+.++ |||.||..||..|   ...||+||..+...
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            457899999999976   36678 9999999999874   67899999987653

>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=99.33  E-value=2.5e-13  Score=82.05  Aligned_cols=45  Identities=29%  Similarity=0.704  Sum_probs=38.8

Q ss_pred             CcccccccccccccCCceeEe-CCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCI-PECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      +...|+||++.|.+.   +.+ + |||.||..||..|+.  ..||+||..+.
T Consensus        21 ~~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           21 KLLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HTTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hCCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            368999999998663   455 7 999999999999988  88999999874

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

Probab=99.31  E-value=2.8e-13  Score=94.61  Aligned_cols=60  Identities=23%  Similarity=0.533  Sum_probs=45.0

Q ss_pred             CCCcccccccccccccCCce----eEeCCCCCccchhhHHHHhcCC-----------CCCccccCCCCCCCCcCC
Q 044807           44 GPNSSACSICLSEYLSQETI----KCIPECKHCFHAECIDEWPRLN-----------DKCPVCINSATPVHADYV  103 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~----~~lp~C~H~Fh~~Ci~~wl~~~-----------~~CP~Cr~~~~~~~~~~~  103 (105)
                      +++..+|+||++.+.++..+    ...+.|+|.||..||.+||...           ++||+||.++....+..+
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf~~ll  379 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFAALL  379 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGGGGGS
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccHHHHh
Confidence            45678999999998873322    1123499999999999999642           469999999887655443

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

Probab=99.29  E-value=3.3e-12  Score=71.47  Aligned_cols=48  Identities=29%  Similarity=0.734  Sum_probs=39.1

Q ss_pred             cccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCCCCcC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPVHADY  102 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~  102 (105)
                      ...|+||++.+.+   ++.+| |||. ||..|+..    ...||+||..+.....-|
T Consensus        25 ~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~~~i~   73 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFKQKIF   73 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCCCBCC
T ss_pred             CCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCcEEEe
Confidence            5689999999765   56678 9999 99999964    378999999987755444

>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=99.25  E-value=2.1e-12  Score=82.44  Aligned_cols=50  Identities=30%  Similarity=0.454  Sum_probs=42.3

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC-CCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN-DKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~Cr~~~~~   97 (105)
                      ..+...|+||++.|.++   +.++ |||.||..||..|+... .+||+||..+..
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            35678999999998764   5577 99999999999999764 499999998865

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

Probab=99.23  E-value=9.1e-12  Score=68.55  Aligned_cols=51  Identities=24%  Similarity=0.576  Sum_probs=41.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCCCCcC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPVHADY  102 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~~~  102 (105)
                      ..+...|.||++.+.+   ++.+| |||. ||..|+..    ...||+||..+.....-|
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~~i~   63 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESFALS   63 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEECCC
T ss_pred             CCCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceEEee
Confidence            3457899999998754   67788 9999 99999984    478999999987654433

>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=99.21  E-value=9.4e-12  Score=84.23  Aligned_cols=50  Identities=16%  Similarity=0.093  Sum_probs=42.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ......|+||++.|.+   .++++ |||+||..||..|+.. ..+||+||.++..
T Consensus       205 ~~~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          205 IPDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CCSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CCcccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            4567899999999977   46788 9999999999999976 4459999998864

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=99.21  E-value=2.7e-12  Score=72.61  Aligned_cols=46  Identities=26%  Similarity=0.666  Sum_probs=38.5

Q ss_pred             cccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPVHA  100 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  100 (105)
                      ...|+||++.+.+   ++.+| |||. ||..|+..|    ..||+||..+.....
T Consensus        18 ~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~   64 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHVQH   64 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEEEE
T ss_pred             CCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCeEE
Confidence            5689999998755   67788 9999 999999877    399999999876543

>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=99.20  E-value=6.4e-12  Score=73.19  Aligned_cols=47  Identities=19%  Similarity=0.361  Sum_probs=38.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC------CCCcc--ccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN------DKCPV--CINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~------~~CP~--Cr~~   94 (105)
                      .....|+||++.|.+   .++++.|||.|+..||..||..+      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            457899999999976   45563399999999999999753      48999  9865

>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=99.17  E-value=1.2e-11  Score=71.90  Aligned_cols=49  Identities=29%  Similarity=0.706  Sum_probs=39.3

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC--------CCCCcc--ccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL--------NDKCPV--CINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~--Cr~~   94 (105)
                      .+..+|+||++++...+.+.+.+ |||.||..|+..++..        .-.||.  |+..
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            35679999999987665555556 9999999999999853        236999  9987

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

Probab=99.11  E-value=6.3e-11  Score=76.35  Aligned_cols=50  Identities=16%  Similarity=0.084  Sum_probs=42.7

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ..+...|+||++.|.+   .++++ |||.|+..||..|+.. +.+||+|+.++..
T Consensus       103 ip~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          103 IPDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CCGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcHhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            4678999999999977   46678 9999999999999976 3479999998764

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

Probab=99.08  E-value=8.5e-11  Score=63.12  Aligned_cols=48  Identities=23%  Similarity=0.548  Sum_probs=37.4

Q ss_pred             CCcccccccccccccCCceeEeCCCC--C---ccchhhHHHHhcC--CCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECK--H---CFHAECIDEWPRL--NDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~--H---~Fh~~Ci~~wl~~--~~~CP~Cr~~~~   96 (105)
                      .+...|.||+++..  +.. ++| |.  +   .||..||.+|+..  +.+||+|+.++.
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            46789999999742  333 467 75  3   8999999999964  678999999865

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

Probab=99.02  E-value=6e-11  Score=83.37  Aligned_cols=46  Identities=28%  Similarity=0.730  Sum_probs=39.4

Q ss_pred             CcccccccccccccCCceeEeCCCCCc-cchhhHHHHhcCCCCCccccCCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHC-FHAECIDEWPRLNDKCPVCINSATPVH   99 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~   99 (105)
                      ++..|+||++.+.+   ++.+| |||. ||..|+..|    ..||+||..+....
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~~  340 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKGTV  340 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCEEE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccCeE
Confidence            35799999999865   56778 9999 999999988    78999999987643

>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=98.99  E-value=1.4e-10  Score=78.43  Aligned_cols=50  Identities=20%  Similarity=0.454  Sum_probs=40.4

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC--CCCcc--ccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN--DKCPV--CINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~--Cr~~~~~   97 (105)
                      .....|+||++.|.++  |..+. |||.|++.||..|+..+  .+||+  |+..+..
T Consensus       179 ~~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          179 KIELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             BCCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             ceeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            4568999999999764  44446 99999999999999764  46999  9987643

>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=98.88  E-value=7.2e-10  Score=59.64  Aligned_cols=48  Identities=8%  Similarity=0.102  Sum_probs=40.9

Q ss_pred             cccccccccccccCCceeEe-CCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCI-PECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ...|+|+++.+.+.   +++ + +||.|.+.||.+||..+.+||+.+.++...
T Consensus         3 ~~~CpIs~~~m~dP---V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRRP---VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSSE---EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCCC---EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            46899999999763   556 6 999999999999999888999999988653

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

Probab=98.71  E-value=8.8e-09  Score=59.97  Aligned_cols=48  Identities=25%  Similarity=0.524  Sum_probs=37.9

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhc-CCCCCccccCCCCCCC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-LNDKCPVCINSATPVH   99 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~Cr~~~~~~~   99 (105)
                      .|.+|--.+..  ..+.+| |+|.||.+|+..|.+ ..++||.|+.++..++
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe   51 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIE   51 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeE
Confidence            46777666533  356788 999999999999985 4788999999987654

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

Probab=98.56  E-value=1e-07  Score=63.87  Aligned_cols=55  Identities=22%  Similarity=0.497  Sum_probs=42.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC--CCCccccCCCCCCCCcC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN--DKCPVCINSATPVHADY  102 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~Cr~~~~~~~~~~  102 (105)
                      +....|.||.+.+..+  ..... |+|.||..|+..|++.+  ..||.|+........+.
T Consensus       178 ~~i~~C~iC~~iv~~g--~~C~~-C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~~~  234 (238)
T 3nw0_A          178 DAVKICNICHSLLIQG--QSCET-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKV  234 (238)
T ss_dssp             TTCCBCTTTCSBCSSC--EECSS-SCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCCCC
T ss_pred             CCCCcCcchhhHHhCC--cccCc-cChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCC
Confidence            3578999999988765  44444 99999999999999764  48999999876544433

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

Probab=97.34  E-value=0.00012  Score=42.32  Aligned_cols=36  Identities=19%  Similarity=0.657  Sum_probs=27.0

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHH-Hh
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDE-WP   82 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~-wl   82 (105)
                      ++..|.||++.+........+. |+|.||..|+.. |.
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATHP   38 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHSC
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHhc
Confidence            3578999998653333344477 999999999998 53

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

Probab=96.75  E-value=0.0023  Score=34.45  Aligned_cols=49  Identities=22%  Similarity=0.624  Sum_probs=35.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC----CCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND----KCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~----~CP~Cr~~~~~   97 (105)
                      .....|.||.+.   ++.+..- .|...||..|+...|....    .||.|......
T Consensus        10 ~~~~~C~vC~~~---~~ll~Cd-~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~p   62 (66)
T 2lri_C           10 APGARCGVCGDG---TDVLRCT-HCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTP   62 (66)
T ss_dssp             CTTCCCTTTSCC---TTCEECS-SSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCCC
T ss_pred             CCCCCcCCCCCC---CeEEECC-CCCCceecccCCCccCcCCCCCEECccccCCCcc
Confidence            346789999753   3334444 4999999999998886532    59999876544

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=94.73  E-value=0.018  Score=28.95  Aligned_cols=44  Identities=27%  Similarity=0.620  Sum_probs=28.6

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~   93 (105)
                      .|.||...-..++.+..- .|...||..|+.+=+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd-~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCD-ECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECT-TTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECC-CCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588888654333334444 49999999999764433    224888864

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

Probab=94.55  E-value=0.025  Score=29.71  Aligned_cols=47  Identities=26%  Similarity=0.609  Sum_probs=32.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINS   94 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~   94 (105)
                      ...+..|.||...   ++.+..- .|.-.||..|+..-+..    .-.||.|...
T Consensus         8 ~~~~~~C~vC~~~---g~ll~CD-~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---GEIILCD-TCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC---SSEEECS-SSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC---CcEEECC-CCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            3557889999873   3334434 48899999999875543    2359999653

>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=94.51  E-value=0.01  Score=31.40  Aligned_cols=50  Identities=32%  Similarity=0.700  Sum_probs=33.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhc-----CCCCCccccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-----LNDKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-----~~~~CP~Cr~~   94 (105)
                      .+...|+||...+.+...++.-..|..-||..|+.--..     ....||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            456789999988754444443334888999999864321     34569999754

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=93.74  E-value=0.026  Score=33.07  Aligned_cols=38  Identities=21%  Similarity=0.507  Sum_probs=27.3

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhc
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR   83 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~   83 (105)
                      ..+..|.||.+.-...+.+.... |+..||..|+...+.
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C~~-C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFCTT-CGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEECSS-SCCEECTTTTTCCCC
T ss_pred             CCCCCCcCCCCCCCCcCCeECCC-CCCCcChHHhCCccc
Confidence            45789999987643223355444 999999999987764

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=93.71  E-value=0.021  Score=30.02  Aligned_cols=47  Identities=23%  Similarity=0.556  Sum_probs=32.2

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~~   95 (105)
                      ..+..|.||.+.   ++.+..-. |...||..|+..-+..    .-.||.|+...
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~-C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GELLCCDT-CPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSS-SCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC---CCEEEcCC-CCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            456789999863   33344444 8999999999865543    22599997653

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=93.64  E-value=0.071  Score=30.19  Aligned_cols=48  Identities=21%  Similarity=0.592  Sum_probs=33.6

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccccCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVCINSA   95 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~~~   95 (105)
                      ...+..|.+|...   ++.+..- .|.-.||..|+.+=+...    -.||.|+...
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD-~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCN-QCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECT-TSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCcCcCcCCC---CCEEECC-CCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            4567899999974   3334433 488999999998766542    2599998653

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=93.62  E-value=0.022  Score=36.25  Aligned_cols=46  Identities=24%  Similarity=0.507  Sum_probs=32.6

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccccCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVCINSA   95 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~~~   95 (105)
                      .+..|.+|.+.   ++.+..- .|.-.||..|+.+-+...    -.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd-~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCE-KCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECS-SSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---CeeeecC-CCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            46789999854   4434444 499999999998766542    3599998754

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=92.76  E-value=0.21  Score=27.82  Aligned_cols=40  Identities=20%  Similarity=0.388  Sum_probs=30.4

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      .....|.+|.+.+++..-|..-..=+|.||..|-...+++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            4568999999999876656422223799999999998864

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.71  E-value=0.014  Score=30.04  Aligned_cols=45  Identities=24%  Similarity=0.660  Sum_probs=30.4

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccccC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~   93 (105)
                      ..+..|.||...   ++.+..- .|...||..|+.+-+...    -.||.|..
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd-~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLMCD-TCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEECS-SSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEEcC-CCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            456789999874   3334444 499999999998655432    24877753

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=92.63  E-value=0.11  Score=27.68  Aligned_cols=35  Identities=23%  Similarity=0.505  Sum_probs=24.9

Q ss_pred             CCcccccccccccccCCceeEeC-CCCCccchhhHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIP-ECKHCFHAECID   79 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp-~C~H~Fh~~Ci~   79 (105)
                      .....|++|...+.+...++.-. .|.--||..|+.
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            45679999999887665555444 588889999974

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=92.52  E-value=0.13  Score=40.68  Aligned_cols=50  Identities=8%  Similarity=-0.019  Sum_probs=42.9

Q ss_pred             CCCcccccccccccccCCceeEeCCCC-CccchhhHHHHhcCCCCCccccCCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECK-HCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+...|+|=++.+.+   .+++| -| +.|-+..|.+||..+.+||+=|.++..
T Consensus       888 iP~~F~cPIs~~lM~D---PVilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKD---PVILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             SCGGGBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CcHHhCCcchhhHHhC---CeEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            4567899999999877   46777 77 689999999999999999999988864

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=92.44  E-value=0.049  Score=29.60  Aligned_cols=51  Identities=18%  Similarity=0.367  Sum_probs=34.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~~~   96 (105)
                      .+...|.||.... +++.++.-..|.--||..|+..-+..    .-.||.|+..+.
T Consensus        16 ~~~~~C~~C~~~~-~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           16 NQIWICPGCNKPD-DGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             CEEECBTTTTBCC-SSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCcCCCCCCCCC-CCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            4456799998765 34334433349999999999765432    345999976543

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=92.01  E-value=0.034  Score=29.61  Aligned_cols=46  Identities=28%  Similarity=0.694  Sum_probs=31.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~   94 (105)
                      ..+..|.||.+.   ++.+..- .|.-.||..|+.+-+..    .-.||.|...
T Consensus         6 ~~~~~C~vC~~~---g~ll~CD-~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---GELICCD-GCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---SSCEECS-SCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---CCEEEcC-CCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            457899999864   3444444 48999999999865543    2249999653

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=91.86  E-value=0.078  Score=33.96  Aligned_cols=50  Identities=16%  Similarity=0.408  Sum_probs=34.3

Q ss_pred             cccccccccccccCCc---eeEeCCCCCccchhhHHHH------hc-----CCCCCccccCCCC
Q 044807           47 SSACSICLSEYLSQET---IKCIPECKHCFHAECIDEW------PR-----LNDKCPVCINSAT   96 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~---~~~lp~C~H~Fh~~Ci~~w------l~-----~~~~CP~Cr~~~~   96 (105)
                      ...|+||...+.+++.   ++.-..|..-||..|+.--      +.     ..-.||.|+..-.
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            3469999998877652   4444459999999996421      11     1568999987543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=91.85  E-value=0.031  Score=29.17  Aligned_cols=45  Identities=24%  Similarity=0.677  Sum_probs=31.1

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINS   94 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~   94 (105)
                      .+..|.||...   ++.+..- .|.-.||..|+.+-+..    .-.||.|...
T Consensus         4 ~~~~C~vC~~~---g~ll~Cd-~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   52 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLMCD-TCSRVYHLDCLDPPLKTIPKGMWICPRCQDQ   52 (60)
T ss_dssp             CCSSCTTTCCC---SSCEECS-SSSCEECGGGSSSCCSSCCCSCCCCHHHHHH
T ss_pred             CCCCCcCCCCC---CcEEEcC-CCCcCEECCcCCCCcCCCCCCceEChhccCh
Confidence            46789999874   3444444 49999999999865543    2248888654

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=91.81  E-value=0.054  Score=35.12  Aligned_cols=47  Identities=23%  Similarity=0.554  Sum_probs=32.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~~~   95 (105)
                      ..+..|.+|...   ++ +..-..|...||..|+.+-+...    -.||.|+..-
T Consensus         5 ~~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG---GD-LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC---EE-EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC---Cc-eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            456789999854   23 33334489999999998776542    3599998753

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.78  E-value=0.29  Score=28.62  Aligned_cols=33  Identities=30%  Similarity=0.673  Sum_probs=22.6

Q ss_pred             Ccccccccccccc-----cC-CceeEeCCCCCccchhhHH
Q 044807           46 NSSACSICLSEYL-----SQ-ETIKCIPECKHCFHAECID   79 (105)
Q Consensus        46 ~~~~C~ICl~~~~-----~~-~~~~~lp~C~H~Fh~~Ci~   79 (105)
                      ....|.+|+..-.     .+ +.+.... |+..||..||.
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~-C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCAD-CGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTT-TCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhhh-cCCCCCCchhc
Confidence            4678999987521     12 3344444 99999999995

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.54  E-value=0.072  Score=31.26  Aligned_cols=47  Identities=23%  Similarity=0.458  Sum_probs=30.0

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCIN   93 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~   93 (105)
                      -..|.||.+.-.+.+.+..-..|...||..|+.+-|..    .=.||.|+.
T Consensus        61 C~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           61 CKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             TCCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CCccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            34688887643232333333349999999999765544    235888874

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=91.53  E-value=0.078  Score=30.46  Aligned_cols=47  Identities=21%  Similarity=0.370  Sum_probs=31.4

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcC---CCCCccccCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL---NDKCPVCINS   94 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~Cr~~   94 (105)
                      +...| ||-.....+..|..-. |.--||..|+..=+..   .-.||.|+..
T Consensus        27 d~vrC-iC~~~~~~~~mi~Cd~-C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDGYMICCDK-CSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CBCCC-TTSCCSCSSCEEEBTT-TCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CCEEe-ECCCccCCCcEEEcCC-CCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            34567 8977665555555444 9999999998653322   3469999753

>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=91.41  E-value=0.03  Score=31.87  Aligned_cols=48  Identities=23%  Similarity=0.451  Sum_probs=32.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~   93 (105)
                      .+...|.||...-.....+..- .|...||..|+.+=|..    .=.||.|..
T Consensus        14 ~~~~~C~vC~~~~~~~~ll~CD-~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           14 IDSYICQVCSRGDEDDKLLFCD-GCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCCCSSSCCSGGGGGCEECT-TTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             cCCCCCccCCCcCCCCCEEEcC-CCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            4567899998764333334444 49999999999754433    224999965

>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=91.11  E-value=0.23  Score=27.82  Aligned_cols=35  Identities=23%  Similarity=0.623  Sum_probs=22.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      ..+..|.||-..- ..+....- .|+-.||..|+.+-
T Consensus        13 ~~D~~C~VC~~~t-~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEVWT-AESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCCCC-SSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCCcccCcccccc-ccceeccc-cccccccHhhcccc
Confidence            4578999986322 22211111 28999999999996

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=90.95  E-value=0.058  Score=30.43  Aligned_cols=53  Identities=23%  Similarity=0.387  Sum_probs=33.7

Q ss_pred             CCccccccccccc-ccCCceeEeCCCCCccchhhHHHHhc--CCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEY-LSQETIKCIPECKHCFHAECIDEWPR--LNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~-~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~Cr~~~~~   97 (105)
                      .++..|.||...- .+.+.++.-..|.-.||..|+..-+.  ..-.||.|......
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~   78 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR   78 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTS
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccch
Confidence            4578999998753 12223444345888999999975331  13359999765443

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=90.36  E-value=0.15  Score=31.07  Aligned_cols=35  Identities=20%  Similarity=0.477  Sum_probs=25.5

Q ss_pred             CCCcccccccccccc-c-CCceeEeCCCCCccchhhHH
Q 044807           44 GPNSSACSICLSEYL-S-QETIKCIPECKHCFHAECID   79 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~-~-~~~~~~lp~C~H~Fh~~Ci~   79 (105)
                      ..++..|.+|...|. . +....... |.|.+|..|-.
T Consensus        52 ~~~~~~C~~C~~~~g~l~~~g~~C~~-C~~~VC~~C~~   88 (134)
T 1zbd_B           52 GDGVNRCILCGEQLGMLGSASVVCED-CKKNVCTKCGV   88 (134)
T ss_dssp             SCSSSBCSSSCCBCSTTSCCEEECTT-TCCEEETTSEE
T ss_pred             cCCCccccccCCCcccccCCCCCCCC-CCcccccccCC
Confidence            356889999999883 2 33344555 99999999844

>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=90.04  E-value=0.14  Score=26.93  Aligned_cols=50  Identities=22%  Similarity=0.491  Sum_probs=32.8

Q ss_pred             CCccccccccccccc-CCceeEeCCCCCccchhhHHHHhc-------CCCCCccccCC
Q 044807           45 PNSSACSICLSEYLS-QETIKCIPECKHCFHAECIDEWPR-------LNDKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~-~~~~~~lp~C~H~Fh~~Ci~~wl~-------~~~~CP~Cr~~   94 (105)
                      .++..|.||...... ...++.-..|.-.||..|+..-+.       ..-.||.|...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~   61 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFA   61 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCc
Confidence            457899999976432 233444345999999999876432       23358888654

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=89.27  E-value=0.36  Score=26.64  Aligned_cols=37  Identities=19%  Similarity=0.442  Sum_probs=26.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      .+...|.+|...|.....-..--.||.+||..|....
T Consensus        17 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   53 (82)
T 2yw8_A           17 DEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNE   53 (82)
T ss_dssp             CCCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEE
T ss_pred             ccCCcccCcCCcccCccccccCCCCCCEEChHHhCCe
Confidence            4567899999998754322222249999999997654

>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=89.19  E-value=0.44  Score=26.01  Aligned_cols=50  Identities=20%  Similarity=0.361  Sum_probs=31.7

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHh-----cCCCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP-----RLNDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~Cr~~~   95 (105)
                      ....-| ||...+.....++.-..|..-||..|+.--.     .....||.|+...
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            344566 8988765333333333488889999985321     1355799998754

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=89.04  E-value=0.44  Score=26.41  Aligned_cols=38  Identities=13%  Similarity=0.337  Sum_probs=26.7

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      ..+...|.+|...|.....-..--.||.+||..|....
T Consensus        18 d~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           18 DEDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             TTTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCCCCcCcCCccccchhcccccCCCcEEChHHhCCe
Confidence            34567999999998764432222249999999997654

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=88.56  E-value=1.4  Score=24.94  Aligned_cols=51  Identities=20%  Similarity=0.419  Sum_probs=36.0

Q ss_pred             CCcccccccccccccC---Cc-eeEeCCCCCccchhhHHHHh-cCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQ---ET-IKCIPECKHCFHAECIDEWP-RLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~---~~-~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~Cr~~~~   96 (105)
                      .....|.||-+++-..   +. +... .|+--.|..|++-=. +.+..||.|++.+.
T Consensus        14 ~~~qiCqiCGD~VG~~~~Ge~FVAC~-eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           14 LDGQFCEICGDQIGLTVEGDLFVACN-ECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCS-SSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             cCCCccccccCccccCCCCCEEEeee-ccCChhhHHHHHHHHhccCccccccCCccc
Confidence            4568999999986432   22 2223 377779999987544 45788999999875

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=88.31  E-value=0.27  Score=25.66  Aligned_cols=43  Identities=23%  Similarity=0.455  Sum_probs=29.3

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      ..|--|...|.+.. ...-+.|++.||.+|=.---+.-..||.|
T Consensus        16 ~~C~~C~~~~~~~~-~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQH-VYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSE-EECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCCc-cEECCccCcCcccchhHHHHhhccCCcCC
Confidence            46999999885432 23345699999999954333445679987

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=88.16  E-value=0.38  Score=27.08  Aligned_cols=37  Identities=14%  Similarity=0.345  Sum_probs=26.1

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHh
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP   82 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl   82 (105)
                      +...|.+|...|.....-..-..||.+||..|...+.
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~   55 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKC   55 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEE
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCee
Confidence            4568999999987543322233499999999976553

>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=88.12  E-value=0.35  Score=28.91  Aligned_cols=37  Identities=19%  Similarity=0.364  Sum_probs=25.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      .+...|.+|...|.....-..--.||++||..|....
T Consensus        67 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           67 NEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GGCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            3456899999998754332222249999999996543

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=88.12  E-value=0.081  Score=29.13  Aligned_cols=44  Identities=30%  Similarity=0.557  Sum_probs=26.9

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcC----C-CCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----N-DKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~-~~CP~Cr~   93 (105)
                      .|.||...-.. +.++.-..|...||..|+.+-|..    . =.||.|+.
T Consensus        28 ~C~vC~~~~d~-~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQDP-DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCSCG-GGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCCCC-cceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            46666554322 233333348899999999876543    1 35888865

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=87.90  E-value=0.5  Score=26.13  Aligned_cols=36  Identities=17%  Similarity=0.439  Sum_probs=24.9

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDE   80 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~   80 (105)
                      .+...|.+|...|..-..-..--.||.+||..|...
T Consensus        12 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           12 NNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            456789999999865432222223999999999654

>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=87.72  E-value=0.21  Score=25.15  Aligned_cols=44  Identities=20%  Similarity=0.381  Sum_probs=28.2

Q ss_pred             cccccccccccCCceeEeC-CCCCccchhhHHHHh----cCCCCCcccc
Q 044807           49 ACSICLSEYLSQETIKCIP-ECKHCFHAECIDEWP----RLNDKCPVCI   92 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp-~C~H~Fh~~Ci~~wl----~~~~~CP~Cr   92 (105)
                      .|.||...+.++..++.-. .|.--||..|+.--.    .....||.|+
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            5778888775555444433 488889999965321    2456788875

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=87.43  E-value=0.17  Score=32.40  Aligned_cols=45  Identities=22%  Similarity=0.638  Sum_probs=30.8

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINSA   95 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~~   95 (105)
                      +..|.+|.+.   ++.+.... |.-.||..|+.+=+..    .-.||.|+...
T Consensus         2 ~~~C~~C~~~---g~ll~Cd~-C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GDLVMCNQ-CEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SSCCCCTT-TCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---CceeECCC-CCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            4679999864   33344444 8899999999765543    22599998653

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.20  E-value=0.82  Score=28.05  Aligned_cols=47  Identities=21%  Similarity=0.394  Sum_probs=32.8

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhc-----------CCCCCccccCC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR-----------LNDKCPVCINS   94 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~-----------~~~~CP~Cr~~   94 (105)
                      ...+..|.||.+.   ++-+..- .|.-.||..||.+-+.           ..=.||+|+..
T Consensus        60 Dg~~d~C~vC~~G---G~LlcCD-~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GNLICCD-FCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC---SSEEECS-SSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC---CcEEeCC-CCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            3457899999874   2333333 4999999999997653           13359999753

>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=86.99  E-value=0.56  Score=25.22  Aligned_cols=46  Identities=24%  Similarity=0.543  Sum_probs=28.4

Q ss_pred             CCcccccccccccccCCceeEeCC--CC-CccchhhHHHHhcC----CCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPE--CK-HCFHAECIDEWPRL----NDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~--C~-H~Fh~~Ci~~wl~~----~~~CP~Cr~~~   95 (105)
                      .+..-| ||-... .++.+ .-..  |. .-||..|+.  |..    .-.||.|+...
T Consensus        14 ~~~~~C-~C~~~~-~g~MI-~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           14 NEPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             TSCCCS-TTCCCS-CSSEE-CCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCCEE-ECCCCC-CCCEe-EeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            445667 898754 24333 2233  44 589999997  433    33599997653

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.63  E-value=0.16  Score=27.94  Aligned_cols=45  Identities=20%  Similarity=0.482  Sum_probs=28.6

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCIN   93 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~   93 (105)
                      ..|.||...-..++.+. -..|...||..|+.+=|..     .=.||.|..
T Consensus        27 c~C~vC~~~~~~~~ll~-CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKHEPNMQLL-CDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCCCSTTEEE-CSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcCCCCCEEE-cCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            47888886432333343 3349999999999864433     224888854

>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=86.53  E-value=0.61  Score=26.13  Aligned_cols=37  Identities=16%  Similarity=0.273  Sum_probs=25.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      .+...|.+|...|..-..-..--.||.+||..|....
T Consensus         7 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~   43 (88)
T 1wfk_A            7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFS   43 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEE
T ss_pred             CcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCc
Confidence            4567899999998754332222239999999997653

>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=86.32  E-value=0.7  Score=24.84  Aligned_cols=34  Identities=24%  Similarity=0.410  Sum_probs=23.6

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHH
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDE   80 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~   80 (105)
                      +..|.+|...|..-..-..--.||.+||..|...
T Consensus        11 ~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A           11 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CCcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            3589999999865432222224999999999653

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=86.21  E-value=0.9  Score=24.41  Aligned_cols=50  Identities=22%  Similarity=0.372  Sum_probs=31.6

Q ss_pred             CCCccccccccccc-ccCCceeEeCCCCCccchhhHHHHhc--CCCCCccccC
Q 044807           44 GPNSSACSICLSEY-LSQETIKCIPECKHCFHAECIDEWPR--LNDKCPVCIN   93 (105)
Q Consensus        44 ~~~~~~C~ICl~~~-~~~~~~~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~Cr~   93 (105)
                      ...+..|.||.+.- .+.+.++.-..|.-.||..|+..-..  ..=.||.|+.
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            35678999998753 22333444445999999999875321  1224777754

>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=86.01  E-value=0.18  Score=27.07  Aligned_cols=44  Identities=30%  Similarity=0.533  Sum_probs=27.2

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~   93 (105)
                      .|.||...-..+ .++.-..|...||..|+.+=|..     .=.||.|+.
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            566777532222 33333448999999999865433     225888865

>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=85.86  E-value=0.53  Score=27.25  Aligned_cols=49  Identities=22%  Similarity=0.477  Sum_probs=32.1

Q ss_pred             cccccccccccccCCceeEeC-CCCCccchhhHHHHh----------cCCCCCccccCCC
Q 044807           47 SSACSICLSEYLSQETIKCIP-ECKHCFHAECIDEWP----------RLNDKCPVCINSA   95 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp-~C~H~Fh~~Ci~~wl----------~~~~~CP~Cr~~~   95 (105)
                      ...|.||...+.+....+.-. .|.--||..|+.--.          .....||.|+...
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            468999999875544443332 488889999974211          0244699997643

>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=85.80  E-value=0.69  Score=26.21  Aligned_cols=46  Identities=26%  Similarity=0.641  Sum_probs=28.5

Q ss_pred             CCcccccccccccccCCceeEeCC--CC-CccchhhHHHHhcC----CCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPE--CK-HCFHAECIDEWPRL----NDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~--C~-H~Fh~~Ci~~wl~~----~~~CP~Cr~~~   95 (105)
                      .+..-| ||-... .++.|.. ..  |. .-||..|+.  |..    .-.||.|+...
T Consensus        34 ~e~~yC-iC~~~~-~g~MI~C-D~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~   86 (91)
T 1weu_A           34 NEPTYC-LCHQVS-YGEMIGC-DNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   86 (91)
T ss_dssp             CCCBCS-TTCCBC-CSCCCCC-SCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCC
T ss_pred             CCCcEE-ECCCCC-CCCEeEe-cCCCCCCCCEecccCC--cCcCCCCCEECcCccCcC
Confidence            345667 998864 2443332 23  44 579999987  332    34699997653

>2d8v_A Zinc finger FYVE domain-containing protein 19; zfyve19, ZF- B_BOX, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.43.1.1

Probab=85.46  E-value=0.64  Score=24.77  Aligned_cols=33  Identities=27%  Similarity=0.684  Sum_probs=26.1

Q ss_pred             CCCcccccccccccccCCceeEeCCC-CCccchhhHHHH
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPEC-KHCFHAECIDEW   81 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C-~H~Fh~~Ci~~w   81 (105)
                      +.+..-|.||.++    ..++.+. | +-.||..|..+-
T Consensus         5 ~ee~pWC~ICneD----AtlrC~g-CdgDLYC~rC~rE~   38 (67)
T 2d8v_A            5 SSGLPWCCICNED----ATLRCAG-CDGDLYCARCFREG   38 (67)
T ss_dssp             CCCCSSCTTTCSC----CCEEETT-TTSEEECSSHHHHH
T ss_pred             CcCCCeeEEeCCC----CeEEecC-CCCceehHHHHHHH
Confidence            3556789999998    2367776 9 889999998775

>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=85.19  E-value=0.48  Score=29.60  Aligned_cols=48  Identities=19%  Similarity=0.434  Sum_probs=31.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHh-----cCCCCCccccC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP-----RLNDKCPVCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~Cr~   93 (105)
                      .+...| ||......+..++.-..|.--||..|+.--.     ...-.||.|+.
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~   58 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS   58 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcc
Confidence            456778 9988764444344333489999999985321     23556999975

>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=84.26  E-value=0.21  Score=26.69  Aligned_cols=48  Identities=21%  Similarity=0.513  Sum_probs=30.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHHhc---CCCCCccccC
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPR---LNDKCPVCIN   93 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~Cr~   93 (105)
                      ..+...| ||-........|..- .|.--||..|+.--..   ....||.|+.
T Consensus        16 ~~~~~~C-iC~~~~~~~~MIqCd-~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           16 FQGLVTC-FCMKPFAGRPMIECN-ECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TTTCCCS-TTCCCCTTCCEEECT-TTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCCceEe-ECCCcCCCCCEEECC-CCCccccccccCcCcccCCCcEECCCCCC
Confidence            3456678 998766432344444 4888999999864221   2345888864

>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=82.65  E-value=0.16  Score=30.36  Aligned_cols=48  Identities=17%  Similarity=0.401  Sum_probs=28.2

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      .....|..|-..|..-..-..--.||.+||..|..........|-.|-
T Consensus        17 ~~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~   64 (120)
T 1y02_A           17 GLEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   64 (120)
T ss_dssp             ---CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             cccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHH
Confidence            345689999998865332222234999999999765544455565553

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}

Probab=82.29  E-value=0.31  Score=22.57  Aligned_cols=15  Identities=20%  Similarity=0.443  Sum_probs=11.2

Q ss_pred             CcccccccccccccC
Q 044807           46 NSSACSICLSEYLSQ   60 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~   60 (105)
                      +...|+||+.++...
T Consensus         4 EGFiCP~C~~~l~s~   18 (34)
T 3mjh_B            4 EGFICPQCMKSLGSA   18 (34)
T ss_dssp             EEEECTTTCCEESSH
T ss_pred             cccCCcHHHHHcCCH
Confidence            457899999887653

>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=82.00  E-value=0.2  Score=29.15  Aligned_cols=44  Identities=18%  Similarity=0.406  Sum_probs=27.7

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~   93 (105)
                      .|.||...-.. ..+..-..|...||..|+.+=+..    .-.||.|+.
T Consensus        56 ~C~~C~~~~~~-~~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~  103 (111)
T 2ysm_A           56 VCQNCKQSGED-SKMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRI  103 (111)
T ss_dssp             CCTTTCCCSCC-TTEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHC
T ss_pred             cccccCccCCC-CCeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcC
Confidence            56677665332 234443459999999999865543    234888854

>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=81.61  E-value=1.5  Score=25.47  Aligned_cols=47  Identities=19%  Similarity=0.439  Sum_probs=29.2

Q ss_pred             CCcccccccccccccCCceeEeC-CCCCccchhhHHHHhcCC----CCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIP-ECKHCFHAECIDEWPRLN----DKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp-~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~~~~   96 (105)
                      ..+..|.+|.+.   ++.+..-. .|...||..|+.  |...    -.||.|...+.
T Consensus        13 ~~~~~C~~C~~~---G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C   64 (107)
T 4gne_A           13 MHEDYCFQCGDG---GELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDEC   64 (107)
T ss_dssp             SSCSSCTTTCCC---SEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTT
T ss_pred             CCCCCCCcCCCC---CcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcC
Confidence            456789999842   33333330 388899999987  4432    24887765443

>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=81.57  E-value=0.43  Score=31.56  Aligned_cols=45  Identities=31%  Similarity=0.647  Sum_probs=26.1

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----CCCCccccC
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCIN   93 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~   93 (105)
                      ..|.+|...-..+..+..- .|...||..|+.+=|..     .=.||.|+.
T Consensus       175 c~C~vC~~~~~~~~lL~CD-~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~  224 (226)
T 3ask_A          175 CACHLCGGRQDPDKQLMCD-ECDMAFHIYCLDPPLSSVPSEDEWYCPECRN  224 (226)
T ss_dssp             TSCSSSCCCCC--CCEECS-SSCCEECSCC--CCCCSCCSSSCCCCGGGC-
T ss_pred             CCCcCCCCCCCCCCeEEcC-CCCcceeCccCCCCcccCCCCCCCCCcCCcC
Confidence            3688887643233334434 49999999999865543     225999965

>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1

Probab=81.56  E-value=0.88  Score=29.57  Aligned_cols=35  Identities=17%  Similarity=0.453  Sum_probs=24.8

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      +..|.+|...|.....-..--.||++||..|....
T Consensus       161 ~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~~  195 (220)
T 1dvp_A          161 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ  195 (220)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccCCCCCccCCcccccccCCcCCEEChHHhCCe
Confidence            57999999998654332222349999999996543

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=81.27  E-value=0.93  Score=29.70  Aligned_cols=36  Identities=14%  Similarity=0.458  Sum_probs=25.6

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      ++..|.+|...|..-..-..-..||.+||..|....
T Consensus       163 ~~~~C~~C~~~F~~~~RrhHCR~CG~v~C~~Cs~~~  198 (226)
T 3zyq_A          163 DAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSKY  198 (226)
T ss_dssp             CCSBCTTTCCBCBTTBCCEECTTTCCEECTTTCCEE
T ss_pred             cCCCCcCcCCCCCccccccccCCCcCEeChhhcCCc
Confidence            356999999998754332223349999999997654

>2a20_A Regulating synaptic membrane exocytosis protein 2; zinc-finger domain, metal binding protein; NMR {Rattus norvegicus} PDB: 2cjs_C

Probab=80.69  E-value=1.1  Score=23.32  Aligned_cols=37  Identities=22%  Similarity=0.507  Sum_probs=25.3

Q ss_pred             CCCccccccccc-ccccCCceeEeCCCCCccchhhHHHH
Q 044807           44 GPNSSACSICLS-EYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        44 ~~~~~~C~ICl~-~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      .++...|.||+. .|.++-.-.... |.-.||..|-..|
T Consensus         6 ~~d~~~C~iC~KTKFADG~Gh~C~y-Ck~r~CaRCGg~v   43 (62)
T 2a20_A            6 KGDAPTCGICHKTKFADGCGHNCSY-CQTKFCARCGGRV   43 (62)
T ss_dssp             SSCCCCCSSSSCSCCCSSCCEEBTT-TCCEECTTSEEEE
T ss_pred             cCCcchhhhhccceeccCCCccccc-cCCeeecccCCEe
Confidence            356789999997 576664444444 6667777776555

---

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	105
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	4e-07
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-06
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	4e-04
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	5e-04
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	8e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	0.001

>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 = 52.9 bits (127), Expect = 1e-11
 Identities = 18/42 (42%), Positives = 26/42 (61%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C++CL+E    E  + +P C H FHAEC+D W   +  CP+C
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLC 49

>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 = 41.5 bits (97), Expect = 4e-07
 Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 3/42 (7%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C ICL +  +         C H F   CI  W R N  CP+C
Sbjct: 8  CPICLEDPSNYSMALP---CLHAFCYVCITRWIRQNPTCPLC 46

>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 = 40.1 bits (93), Expect = 3e-06
 Identities = 12/42 (28%), Positives = 16/42 (38%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC 91
          C    +   S+E       C H FH  CI  W +    CP+ 
Sbjct: 38 CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLD 79

>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 = 34.2 bits (78), Expect = 4e-04
 Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 5/69 (7%)

Query: 38  ESKCLPGPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND-KCPVCINSAT 96
           E  C  G     C IC       + +K  P C H     C+  W       CP C     
Sbjct: 14  ELYCEMGSTFQLCKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIK 69

Query: 97  PVHADYVNP 105
                 V+P
Sbjct: 70  GTEPIVVDP 78

>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 = 33.6 bits (76), Expect = 5e-04
 Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 2/44 (4%)

Query: 50 CSICLSEYLSQETIKCIP-ECKHCFHAECIDEWPRLN-DKCPVC 91
          C  C +      ++K +   C H     C+D         CP C
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPEC 49

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (74), Expect = 8e-04
 Identities = 4/40 (10%), Positives = 9/40 (22%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCP 89
          C +C+      +       C +     C        +   
Sbjct: 3  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLC 42

>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 = 33.5 bits (75), Expect = 0.001
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 50 CSICLSEYLSQETIKCIPECKHCFHAECIDEW-----PRLNDKCPVC 91
            +  S+ L    +  + +C H FH  C+           + +CP C
Sbjct: 42 SDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSC 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	105
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.87
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.76
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.74
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.71
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.71
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.69
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.68
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.6
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.52
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.52
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.5
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.45
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.4
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.4
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.25
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.09
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.44
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	95.23
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.72
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	94.31
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	94.14
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	93.08
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	92.42
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	92.1
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	90.73
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	90.32
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	89.72
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	88.99
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	88.88
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	88.47
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	87.34
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	86.88
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	86.67
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	85.79
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	84.26
d2dasa1	49	Zinc finger MYM-type protein 5 {Human (Homo sapien	83.31
d2co8a2	36	Nedd9 interacting protein with calponin homology,	83.08
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	82.78
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	81.47

>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=99.87  E-value=6.3e-23  Score=108.06  Aligned_cols=52  Identities=35%  Similarity=0.889  Sum_probs=47.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSAT   96 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   96 (105)
                      +++.+|+|||++|..++.+..++.|+|.||..||.+|++.+.+||+||.+|.
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            4567899999999998888877669999999999999999999999999875

>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=99.76  E-value=1.3e-19  Score=98.98  Aligned_cols=50  Identities=34%  Similarity=0.786  Sum_probs=42.9

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      ...+|+||++.|.+  .++.++ |||.||..||..|+..+.+||+||.++..+
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~~   53 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHhh
Confidence            45789999999864  356677 999999999999999999999999988653

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1.1e-18  Score=97.80  Aligned_cols=55  Identities=25%  Similarity=0.639  Sum_probs=47.3

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCCCcCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVHADYVNP  105 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~~~~~~~  105 (105)
                      ...|+||++.+.+   +++++ |||.||..||..||.. +.+||+||..|.....-.++|
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i~i~~   78 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDP   78 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCSSCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCceeecCC
Confidence            4579999998865   56788 9999999999999974 578999999999888777776

>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=99.71  E-value=1.6e-18  Score=90.00  Aligned_cols=49  Identities=16%  Similarity=0.336  Sum_probs=40.4

Q ss_pred             ccccccccccccCCce-eEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           48 SACSICLSEYLSQETI-KCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      .+|+||+++|..++.. ..++ |||.||..||..|+.. +.+||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            3799999999776554 4456 9999999999999986 5579999998753

>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=99.71  E-value=5.5e-18  Score=96.75  Aligned_cols=52  Identities=25%  Similarity=0.542  Sum_probs=42.5

Q ss_pred             CCcccccccccccccCC---------------ceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQE---------------TIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~---------------~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ..+..|+||++.+....               .+..++ |||.||..||.+||+.+.+||+||.++..
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            34567999998875432               255677 99999999999999999999999998753

>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=99.69  E-value=1.5e-17  Score=98.90  Aligned_cols=53  Identities=21%  Similarity=0.424  Sum_probs=40.8

Q ss_pred             CCcccccccccccccC---------------CceeEeCCCCCccchhhHHHHhcC-----CCCCccccCCCCCC
Q 044807           45 PNSSACSICLSEYLSQ---------------ETIKCIPECKHCFHAECIDEWPRL-----NDKCPVCINSATPV   98 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~---------------~~~~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~Cr~~~~~~   98 (105)
                      ..+..|+||++.|...               ..+.+++ |+|.||..||..||..     +.+||+||+.+...
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            3467899999988542               2345566 9999999999999964     34799999877543

>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=99.68  E-value=1.8e-17  Score=89.64  Aligned_cols=51  Identities=18%  Similarity=0.433  Sum_probs=40.4

Q ss_pred             CcccccccccccccC-Cc-eeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           46 NSSACSICLSEYLSQ-ET-IKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~-~~-~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      ++..|+||++.+..+ +. +.+++ |||.||..||..|+.. +.+||+||..+..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            468999999986443 33 34456 9999999999999965 5679999998854

>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=99.60  E-value=1.2e-16  Score=83.88  Aligned_cols=49  Identities=10%  Similarity=0.156  Sum_probs=41.5

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCCCC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPVHA  100 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~~~  100 (105)
                      .|+||++.+.+   .+.++.|||.||.+||.+||..+++||+||.++...+.
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            69999999866   34554499999999999999999999999998876443

>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=4.8e-16  Score=88.06  Aligned_cols=49  Identities=29%  Similarity=0.550  Sum_probs=41.2

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATPVH   99 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~~~   99 (105)
                      ...|+||++.+.+   .++++ |||.||..||..|++. +..||+||.++...+
T Consensus        23 ~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          23 SISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            4689999999866   56778 9999999999999974 568999999876543

>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=99.52  E-value=2.8e-15  Score=87.49  Aligned_cols=47  Identities=28%  Similarity=0.589  Sum_probs=39.4

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCC---CCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN---DKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~Cr~~~~~   97 (105)
                      ...|+||++.|.++   +.++ |||.||..||..|+...   ..||+||.++..
T Consensus        21 ~l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CcCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            46899999998663   5577 99999999999999664   479999998854

>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=99.52  E-value=1.1e-15  Score=80.08  Aligned_cols=46  Identities=24%  Similarity=0.553  Sum_probs=38.2

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATPV   98 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   98 (105)
                      +..+|+||++.|.+   .+.++ |||.||..||..|   +.+||+||.++...
T Consensus         5 ~~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            35699999999876   45678 9999999999765   67899999998653

>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=99.50  E-value=5.8e-15  Score=78.31  Aligned_cols=53  Identities=19%  Similarity=0.372  Sum_probs=38.8

Q ss_pred             CCCcccccccccccccCCcee-EeCCCCCccchhhHHHHhc--CCCCCccccCCCC
Q 044807           44 GPNSSACSICLSEYLSQETIK-CIPECKHCFHAECIDEWPR--LNDKCPVCINSAT   96 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~-~lp~C~H~Fh~~Ci~~wl~--~~~~CP~Cr~~~~   96 (105)
                      +++...|.||++.+....... ...+|+|.||..||..|+.  ++.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            356789999999876532211 1112569999999999995  4668999999864

>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=99.45  E-value=1.8e-14  Score=83.12  Aligned_cols=46  Identities=26%  Similarity=0.532  Sum_probs=37.7

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      ...|+||++.|.++  +...+ |||.||..||..|+.  ..||+||.++..
T Consensus        22 ~l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          22 LLRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TTSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             cCCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCch
Confidence            56899999999764  43446 999999999999984  459999987754

>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=99.40  E-value=1.1e-13  Score=77.24  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=41.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      .++..|+||++.|.+.   ++++ |||.|+..||..|+.. +.+||+|+.++..
T Consensus         5 P~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            4678999999999774   5677 9999999999999975 5679999998754

>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=99.40  E-value=1.6e-13  Score=76.10  Aligned_cols=49  Identities=16%  Similarity=0.384  Sum_probs=42.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-CCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-NDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~Cr~~~~~   97 (105)
                      .++..|+||++.|.+.   ++++ |||.|+..||..|+.. ...||.|+.++..
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            4678999999999774   5678 9999999999999976 4679999998765

>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=99.25  E-value=5.7e-12  Score=72.60  Aligned_cols=50  Identities=10%  Similarity=-0.013  Sum_probs=42.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccccCCCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCINSATP   97 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   97 (105)
                      .++..|+||++.|.+   .++++.|+|.|++.||..||..+.+||+|+.++..
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            457999999999987   46777234689999999999999999999998764

>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=99.09  E-value=2.6e-11  Score=69.08  Aligned_cols=48  Identities=27%  Similarity=0.618  Sum_probs=37.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC-----C---CCCccccC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL-----N---DKCPVCIN   93 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~-----~---~~CP~Cr~   93 (105)
                      .+..+|+||++++...+.+..++ |+|.||..|+..|++.     .   -.||.|..
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            45789999999986655566556 9999999999999852     1   25998654

>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=96.44  E-value=0.00072  Score=33.14  Aligned_cols=44  Identities=27%  Similarity=0.620  Sum_probs=29.7

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcCC----CCCccccC
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLN----DKCPVCIN   93 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~Cr~   93 (105)
                      .|.||-..-..+..+.. ..|...||..|+..-+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~C-d~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILC-DECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEEC-TTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEc-CCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            58888765433333443 3499999999998876542    24998864

>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=95.23  E-value=0.0063  Score=31.61  Aligned_cols=47  Identities=21%  Similarity=0.641  Sum_probs=31.8

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCC----CCccccCCCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLND----KCPVCINSAT   96 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~----~CP~Cr~~~~   96 (105)
                      ....|.||.+.   ++.+..- .|...||..|+.+.+....    .||.|+....
T Consensus         6 ~c~~C~~C~~~---~~ll~Cd-~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           6 SATICRVCQKP---GDLVMCN-QCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSCCSSSCSS---SCCEECT-TSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCCc---CEEEECC-CCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            45567777643   4444444 4999999999998775432    4999976543

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.72  E-value=0.0095  Score=30.22  Aligned_cols=50  Identities=32%  Similarity=0.707  Sum_probs=34.6

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHh---c--CCCCCccccCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWP---R--LNDKCPVCINS   94 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl---~--~~~~CP~Cr~~   94 (105)
                      .....|.||.....+++.++.-..|+..||..|+..-.   .  ....||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            35679999998776665544334499999999985321   1  24569999754

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.31  E-value=0.0068  Score=30.59  Aligned_cols=47  Identities=23%  Similarity=0.556  Sum_probs=32.1

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC----CCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL----NDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~Cr~~~   95 (105)
                      ..+..|.||.+.   ++.+..-. |.-.||..|+...+..    .-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~lv~Cd~-C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELLCCDT-CPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSS-SCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEEEeCC-CCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            345679999753   44454444 9999999999766543    33599997653

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.14  E-value=0.027  Score=30.14  Aligned_cols=36  Identities=22%  Similarity=0.678  Sum_probs=25.0

Q ss_pred             CCCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           44 GPNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      ...+..|.|| +.|......-.- .|+-.||..|+.+-
T Consensus        12 v~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            3567899999 666443322111 27899999999997

>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=93.08  E-value=0.031  Score=27.96  Aligned_cols=45  Identities=22%  Similarity=0.434  Sum_probs=30.7

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCccc
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVC   91 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C   91 (105)
                      ....|--|...+.+. .+..-+.|++.||.+|=.--=+.-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            356799999887543 334445599999999954332345679987

>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=92.42  E-value=0.31  Score=25.32  Aligned_cols=50  Identities=18%  Similarity=0.327  Sum_probs=31.7

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHH--H-hc--CCCCCccccCCCC
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDE--W-PR--LNDKCPVCINSAT   96 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~--w-l~--~~~~CP~Cr~~~~   96 (105)
                      ...+-||...+.....++.-..|.--||..|+..  . +.  ....||.|+....
T Consensus        11 ~pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          11 VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CCeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            3455599876654444443334899999999842  2 12  2467999987543

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.10  E-value=0.13  Score=26.60  Aligned_cols=40  Identities=20%  Similarity=0.388  Sum_probs=29.8

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHHhcC
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRL   84 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~   84 (105)
                      .....|.+|.+.+++..-+..-..=+|.||..|-...+++
T Consensus         6 ~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           6 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            3457899999999876655422223799999999998854

>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=90.73  E-value=0.013  Score=28.62  Aligned_cols=44  Identities=18%  Similarity=0.468  Sum_probs=26.9

Q ss_pred             cccccccccccCCceeEeCCCCCccchhhHHHHhcCCCCCcccc
Q 044807           49 ACSICLSEYLSQETIKCIPECKHCFHAECIDEWPRLNDKCPVCI   92 (105)
Q Consensus        49 ~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~wl~~~~~CP~Cr   92 (105)
                      .|.+|...|.....-..--.||.+|+..|..........|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            58888888865443222234999999999755433445566664

>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=90.32  E-value=0.17  Score=25.97  Aligned_cols=47  Identities=28%  Similarity=0.596  Sum_probs=29.5

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchhhHH----H--H---hcCCCCCccccCC
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAECID----E--W---PRLNDKCPVCINS   94 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~----~--w---l~~~~~CP~Cr~~   94 (105)
                      ....| ||-.....+..|..-. |.--||..|+.    .  .   ......||.|+..
T Consensus        15 ~~~~C-iC~~~~~~~~mi~Cd~-C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          15 NALYC-ICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TCCCS-TTCCCCCSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CcCEE-ECCCccCCCeEEEECC-CCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            34557 8877654444444444 88899999982    1  1   1235689999654

>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=89.72  E-value=0.083  Score=30.11  Aligned_cols=34  Identities=21%  Similarity=0.516  Sum_probs=24.4

Q ss_pred             CCCccccccccccccc-CC-ceeEeCCCCCccchhhH
Q 044807           44 GPNSSACSICLSEYLS-QE-TIKCIPECKHCFHAECI   78 (105)
Q Consensus        44 ~~~~~~C~ICl~~~~~-~~-~~~~lp~C~H~Fh~~Ci   78 (105)
                      ..+...|.+|...|.. .. ...... ||+.||..|-
T Consensus        45 ~~~~~~C~~C~~~f~~~~~~~~~C~~-C~~~~C~~C~   80 (124)
T d1zbdb_          45 GDGVNRCILCGEQLGMLGSASVVCED-CKKNVCTKCG   80 (124)
T ss_dssp             SCSSSBCSSSCCBCSTTSCCEEECTT-TCCEEETTSE
T ss_pred             ccCCCcCcccCCcccCCCCCCCcCcc-CCcccccCCC
Confidence            4556889999998763 22 233444 9999999994

>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=88.99  E-value=0.16  Score=25.54  Aligned_cols=37  Identities=19%  Similarity=0.364  Sum_probs=25.5

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      .+...|.+|-..|..-..-..--.||.+||..|....
T Consensus         6 ~~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           6 NEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             GGCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             ccCCcCcCcCCcccCCccccchhhhCCeecccccCCc
Confidence            3456899999988654332222349999999997654

>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=88.88  E-value=0.21  Score=25.96  Aligned_cols=50  Identities=20%  Similarity=0.474  Sum_probs=31.0

Q ss_pred             CCcccccccccccccCCceeEe-CCCCCccchhhHHH----Hhc-----CCCCCccccCCC
Q 044807           45 PNSSACSICLSEYLSQETIKCI-PECKHCFHAECIDE----WPR-----LNDKCPVCINSA   95 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~l-p~C~H~Fh~~Ci~~----wl~-----~~~~CP~Cr~~~   95 (105)
                      .+...| ||-.....+..+... ..|..-||..|+.-    +..     ....||.|+..-
T Consensus        14 ~~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          14 EIKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            334567 898876554444432 13888999999842    101     135699997643

>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=88.47  E-value=0.25  Score=25.36  Aligned_cols=35  Identities=17%  Similarity=0.453  Sum_probs=24.9

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      +..|.+|-..|..-..-..-..||++||..|....
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            46799999998764433223349999999997544

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.34  E-value=1.1  Score=23.83  Aligned_cols=55  Identities=16%  Similarity=0.300  Sum_probs=37.3

Q ss_pred             CCCCcccccccccccccC---CceeEeCCCCCccchhhHHHHh-cCCCCCccccCCCCC
Q 044807           43 PGPNSSACSICLSEYLSQ---ETIKCIPECKHCFHAECIDEWP-RLNDKCPVCINSATP   97 (105)
Q Consensus        43 ~~~~~~~C~ICl~~~~~~---~~~~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~Cr~~~~~   97 (105)
                      .......|-||-+.+...   +..+--..|+--.|+.|++-=. +.+..||.|++.+..
T Consensus        12 ~~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          12 KNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             hhcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            345678999999986542   2222122377778999976543 457789999987654

>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=86.88  E-value=0.3  Score=24.63  Aligned_cols=35  Identities=23%  Similarity=0.367  Sum_probs=24.3

Q ss_pred             cccccccccccccCCceeEeCCCCCccchhhHHHH
Q 044807           47 SSACSICLSEYLSQETIKCIPECKHCFHAECIDEW   81 (105)
Q Consensus        47 ~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci~~w   81 (105)
                      +..|.+|-..|..-..-..--.||.+||..|...+
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCCc
Confidence            35799999988654332222249999999997544

>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=86.67  E-value=0.21  Score=25.64  Aligned_cols=43  Identities=28%  Similarity=0.640  Sum_probs=25.0

Q ss_pred             ccccccccccccCCceeEe-CCCCC-ccchhhHHHHhcC----CCCCccccCC
Q 044807           48 SACSICLSEYLSQETIKCI-PECKH-CFHAECIDEWPRL----NDKCPVCINS   94 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~l-p~C~H-~Fh~~Ci~~wl~~----~~~CP~Cr~~   94 (105)
                      .-| ||.... .++.+... ..|-. -||..|+.  |..    .-.||.|+..
T Consensus        17 ~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            445 998753 33333321 12444 59999984  332    3469999764

>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=85.79  E-value=0.26  Score=21.19  Aligned_cols=29  Identities=24%  Similarity=0.504  Sum_probs=23.0

Q ss_pred             ccccccccccccCCceeEeCCCCCccchhhH
Q 044807           48 SACSICLSEYLSQETIKCIPECKHCFHAECI   78 (105)
Q Consensus        48 ~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci   78 (105)
                      ..|+-|...+...+.|...  =+++||..|+
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            4689999999888877654  4788999884

>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=84.26  E-value=0.23  Score=26.27  Aligned_cols=48  Identities=19%  Similarity=0.427  Sum_probs=30.7

Q ss_pred             ccccccccccccc-CCceeEeCCCCCccchhhHHHHh-----cC---CCCCccccCC
Q 044807           47 SSACSICLSEYLS-QETIKCIPECKHCFHAECIDEWP-----RL---NDKCPVCINS   94 (105)
Q Consensus        47 ~~~C~ICl~~~~~-~~~~~~lp~C~H~Fh~~Ci~~wl-----~~---~~~CP~Cr~~   94 (105)
                      ...|.||...... ...++.-..|...||..|+...+     ..   .-.||.|...
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~   72 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCch
Confidence            4679999865433 22343333499999999986433     11   3469999654

>d2dasa1 g.39.1.17 (A:8-56) Zinc finger MYM-type protein 5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: TRASH domain
domain: Zinc finger MYM-type protein 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.31  E-value=0.78  Score=21.53  Aligned_cols=36  Identities=17%  Similarity=0.367  Sum_probs=29.8

Q ss_pred             CcccccccccccccCCceeEeCCCCCccchh-hHHHH
Q 044807           46 NSSACSICLSEYLSQETIKCIPECKHCFHAE-CIDEW   81 (105)
Q Consensus        46 ~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~-Ci~~w   81 (105)
                      ....|.-|-..+..++....-.+..|.||.. ||..+
T Consensus        12 ~~v~Ca~Ckk~lqKGQTAyqrkGs~~LFCSt~Cl~~~   48 (49)
T d2dasa1          12 AKITCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSF   48 (49)
T ss_dssp             SSCBCTTTCCBCCTTSCCEECTTCCCEESSHHHHHHH
T ss_pred             eEeEecccchHHhccchHHhhCCCcceeEcchhhccc
Confidence            4678999999999999887766799999986 77653

>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=83.08  E-value=0.42  Score=21.24  Aligned_cols=31  Identities=23%  Similarity=0.509  Sum_probs=22.0

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhhH
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAECI   78 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~Ci   78 (105)
                      .....|.+|-.....-+.+.  - =|+.||+.|+
T Consensus         6 g~~~~C~~C~K~VY~~Erl~--a-~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLC--V-NGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCC--B-TTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEE--e-cCcEeccccC
Confidence            45689999988765655443  1 4788999883

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=82.78  E-value=0.24  Score=25.83  Aligned_cols=11  Identities=36%  Similarity=1.135  Sum_probs=10.1

Q ss_pred             cchhhHHHHhc
Q 044807           73 FHAECIDEWPR   83 (105)
Q Consensus        73 Fh~~Ci~~wl~   83 (105)
                      ||+.|+..|+.
T Consensus        40 FCRNCLskWy~   50 (79)
T d2o35a1          40 FCRNCLSNWYR   50 (79)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999983

>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=81.47  E-value=0.52  Score=20.53  Aligned_cols=31  Identities=23%  Similarity=0.500  Sum_probs=24.4

Q ss_pred             CCcccccccccccccCCceeEeCCCCCccchhh
Q 044807           45 PNSSACSICLSEYLSQETIKCIPECKHCFHAEC   77 (105)
Q Consensus        45 ~~~~~C~ICl~~~~~~~~~~~lp~C~H~Fh~~C   77 (105)
                      -....|.-|-+.|.+.++++-.  =|-.||..|
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            3467899999999998888755  467788766