Citrus Sinensis ID: 028342

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210
Protein Sequence
MSTTPSTTTQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASSSSMAMQESVSNIVPLEPESAVCSYR
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHccEEEcccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHccHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHccccccHHHHHHccEEEEccccccccccccEEEEEcccccccEEEEcccccccccHHHHHHHHHccccccHHHHHccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MSTTPSTTTQLFQDFLGKFHSRKLllqnqqpviaappsnrggessfdsNVLMVLSVLLCALICAIGLASLVKCSLRCsrleasessanssgsgscssgikqKALKTFTVVKYStelklpgldtecviclsefapgervrllpkcnhgfhvrCIDKWlrsnsscpkcrhcliescqkivgcsqassssmamqesvsnivplepesavcsyr
Flexible Loop (DISEMBL)
msttpstttqLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCSRLEAsessanssgsgscssgikqKALKTFTVVKYSTelklpgldTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASSSSMAMQEsvsnivplepesavcsyr
Low Complexity Region (SEG)
MSTTPSTTTQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVllcalicaiglaslVKCSLRCSRLEAsessanssgsgscssgIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCsqassssmamqesvsNIVPLEPESAVCSYR
Disordered region (IsUnstruct)
**********LFQDFLGKFHSRKLLL*********************SNVLMVLSVLLCALICAIGLASLVKCSLRCS***********************KALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGC******************************
Disordered Region (DISOPRED)
*********QLFQDFLGKFHSRK**************************VLMVLSVLLCALICAIGLASLVKCSLR**************************ALKTFTVVKYSTELK**GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL****************************************
Disordered Region (DISEMBL)
********TQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCS*********************KQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVG**************VSNIVPLEPESAVCSYR
Disordered Region (DISPRO)
******TTTQLFQDFLGKFHSRKLLLQN***************SSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCS******************SGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES*************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSTTPSTTTQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASSSSMAMQESVSNIVPLEPESAVCSYR
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	210	2.2.26 [Sep-21-2011]
Q6NQG7	219	RING-H2 finger protein AT	yes	no	0.961	0.922	0.556	1e-60
P0C034	251	RING-H2 finger protein AT	no	no	0.961	0.804	0.523	2e-52
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.980	0.915	0.518	4e-50
Q94BY6	226	RING-H2 finger protein AT	no	no	0.976	0.907	0.504	5e-49
Q9LS99	220	RING-H2 finger protein AT	no	no	0.952	0.909	0.460	2e-47
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.704	0.840	0.453	2e-33
Q9SG96	181	RING-H2 finger protein AT	no	no	0.704	0.817	0.465	4e-31
O22755	185	RING-H2 finger protein AT	no	no	0.685	0.778	0.445	4e-24
Q8LC69	185	RING-H2 finger protein AT	no	no	0.633	0.718	0.401	9e-24
Q9LZV8	159	RING-H2 finger protein AT	no	no	0.595	0.786	0.511	1e-23

>sp|Q6NQG7|ATL78_ARATH RING-H2 finger protein ATL78 OS=Arabidopsis thaliana GN=ATL78 PE=2 SV=1

 Score =  232 bits (592), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 114/205 (55%), Positives = 149/205 (72%), Gaps = 3/205 (1%)

Query: 9   TQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLA 68
           T++FQ+ LG  +SRKLL           PS   G+++FD+NV+MVLSVLLCAL+C++GL 
Sbjct: 15  TEIFQEILGSSYSRKLLFHTHDQSPTPAPSPYVGDNNFDANVVMVLSVLLCALVCSLGLN 74

Query: 69  SLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVIC 128
           S+++C+LRCS L  SE+  ++      ++G+K+KALK+F  V YSTEL LPGLDTEC IC
Sbjct: 75  SIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVSYSTELNLPGLDTECAIC 134

Query: 129 LSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASS--S 186
           LSEF   ERV+LLP C+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI  CSQ SS  S
Sbjct: 135 LSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCEKIADCSQTSSLNS 194

Query: 187 SMAMQESVS-NIVPLEPESAVCSYR 210
           +   Q+S+   I PLEPE  +  +R
Sbjct: 195 TQPPQDSIILQIAPLEPERWIRWFR 219

Arabidopsis thaliana (taxid: 3702)

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

 Score =  204 bits (520), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 111/212 (52%), Positives = 142/212 (66%), Gaps = 10/212 (4%)

Query: 5   PSTTTQLFQDFLGKFHSRKLLLQN------QQPVIAAPPSNRGGESSFDSNVLMVLSVLL 58
           PS+     + FLG F SRKLLL N      Q+    AP      E++   NV+M+LS+L+
Sbjct: 7   PSSAQAFQEQFLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVMMLLSILI 66

Query: 59  CALICAIGLASLVKCSLRCS-RLEASESSAN-SSGSGSCSSGIKQKALKTFTVVKYSTEL 116
           C +IC +GL  +++C+LR S R   SE   + SS  GS + GIK+KAL+ F VV YS E+
Sbjct: 67  CGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPVVSYSPEM 126

Query: 117 KLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK 176
            LPGLD ECVICLS+F  GE++RLLPKCNHGFHVRCIDKWL+ + +CPKCR+CL+E+CQK
Sbjct: 127 NLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNCLVETCQK 186

Query: 177 IVG-CSQASSSSMAMQESV-SNIVPLEPESAV 206
           I+G  SQA S +    E V   IVPLEP   V
Sbjct: 187 ILGDFSQADSVTAEPTEIVIVTIVPLEPTEIV 218

Arabidopsis thaliana (taxid: 3702)

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

 Score =  197 bits (501), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 112/216 (51%), Positives = 145/216 (67%), Gaps = 10/216 (4%)

Query: 5   PSTTTQLFQDFLGKFHSRKLLLQ-----NQQPVIAAPPSNR-GGESSFDSNVLMVLSVLL 58
           P++   L + FLG F +RKLLL      N   V A  PS     E++   NVLM+LSVL+
Sbjct: 7   PASAQSLQEQFLGSFVTRKLLLHDPFDHNSLRVFAVAPSPLITHENNLKGNVLMLLSVLI 66

Query: 59  CALICAIGLASLVKCSLR-CSRLEASES-SANSSGSGSCSSGIKQKALKTFTVVKYSTEL 116
           C +IC +GL  +++C+ R  SR   SE  S+ S+   S + GIK+KAL+ F VV YS E+
Sbjct: 67  CGIICCLGLHYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPVVSYSREM 126

Query: 117 KLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK 176
            LPG+  ECVICLS+F  GE++RLLPKCNHGFHVRCIDKWL+ + +CPKCRHCL+E+CQK
Sbjct: 127 NLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHCLVETCQK 186

Query: 177 IVG-CSQASSSSMAMQESV-SNIVPLEPESAVCSYR 210
           I+G  SQA S +    ESV   I PLEPE  V ++R
Sbjct: 187 ILGDFSQADSMASTPTESVIVRIDPLEPEGRVNTFR 222

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

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score =  194 bits (492), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 109/216 (50%), Positives = 140/216 (64%), Gaps = 11/216 (5%)

Query: 6   STTTQLFQD-FLGKFHSRKLLLQN------QQPVIAAPPSNRGGESSFDSNVLMVLSVLL 58
           S++ Q FQ+  LG F SRKLLL N      Q+    AP      E++   NVLM+LSVL+
Sbjct: 8   SSSVQAFQEQSLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVLMLLSVLI 67

Query: 59  CALICAIGLASLVKCSLR-CSRLEASESSAN-SSGSGSCSSGIKQKALKTFTVVKYSTEL 116
           C +IC +GL  +++C+ R  S    SE  A  S+  GS + GI +KAL+ F VV YS E+
Sbjct: 68  CGIICCLGLHYIIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPVVSYSPEM 127

Query: 117 KLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK 176
            LPGL  ECVICLS+F  GE++R+LPKC+HGFHVRCIDKWL+ + +CPKCRHCL+E+CQK
Sbjct: 128 NLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHCLVETCQK 187

Query: 177 IVG-CSQASSSSMAMQESV-SNIVPLEPESAVCSYR 210
           I+G  SQA   +     SV   I PLEPE  V   R
Sbjct: 188 ILGDFSQADQVAATPTASVIVRIAPLEPEGRVNILR 223

Arabidopsis thaliana (taxid: 3702)

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

 Score =  188 bits (478), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 100/217 (46%), Positives = 140/217 (64%), Gaps = 17/217 (7%)

Query: 5   PSTTTQLFQD-FLGKFHSRKLLLQ-----NQQPVIAAPPSNRGGESSFDSNVLMVLSVLL 58
           PS+++Q+FQ+ F+  F SRKLL Q     N Q       +N  G      NVLM+LS+LL
Sbjct: 7   PSSSSQVFQEHFIDSFVSRKLLQQIPFAHNAQQAHVPDKNNLSG------NVLMLLSILL 60

Query: 59  CALICAIGLASLVKCSLRCSR---LEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTE 115
           C +IC++GL  +++C+   SR   +    S  ++    S + GIK+KALK   VV YS E
Sbjct: 61  CGIICSLGLHYIIRCAFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPE 120

Query: 116 LKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ 175
           + LPG+  ECVICLS+F  GE++R+LPKCNHGFH+RCIDKWL  + +CPKCRHCL+++CQ
Sbjct: 121 INLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRHCLVDTCQ 180

Query: 176 KIV-GCSQASSSSMAMQESVS-NIVPLEPESAVCSYR 210
           K++  C  A   +    ES+   I PLEPE+ V ++R
Sbjct: 181 KVLSDCDAADQVAATATESIDIRISPLEPEARVATFR 217

Arabidopsis thaliana (taxid: 3702)

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

 Score =  142 bits (357), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 74/163 (45%), Positives = 105/163 (64%), Gaps = 15/163 (9%)

Query: 21  SRKLLLQNQQPVIAAPP----------SNRGGESSFDSNVLMVLSVLLCALICAIGLASL 70
           +R LL     P I+A            SN    +S D++++++L+ LLCALICA+G+ S+
Sbjct: 2   ARFLLATQATPTISATDANPRTLGDSVSNNKNIASMDTHMVIILAALLCALICALGINSV 61

Query: 71  VKCSLRCSR-LEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICL 129
           ++C LRC+R    +E   +++ +   + GIK++ALK   V  YS ELK+    TEC+ICL
Sbjct: 62  LRCVLRCTRRFTPNEDPVDTNAN--VAKGIKKRALKVIPVDSYSPELKMKA--TECLICL 117

Query: 130 SEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE 172
            +F  GE VR+LPKCNHGFHV+CID WL S+SSCP CR  L+E
Sbjct: 118 GDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSCPTCRQSLLE 160

Arabidopsis thaliana (taxid: 3702)

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

 Score =  134 bits (337), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 74/159 (46%), Positives = 107/159 (67%), Gaps = 11/159 (6%)

Query: 23  KLLLQNQQPVIA-APPSNRGG--ESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCSR 79
           +LLL+ Q    A A P  +GG  ++ FD+N++++L+ LLCALICA+ L S ++C LR +R
Sbjct: 3   RLLLEPQANAPANANPKPKGGINDTYFDTNMVIILAALLCALICALSLNSALRCVLRITR 62

Query: 80  LEASE------SSANSS-GSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEF 132
              S+      S+AN++ G  + ++G+K++ALK   V  Y + + +    TEC+ICL +F
Sbjct: 63  RFTSDDQVSNASNANANLGRLAAATGLKKQALKQIPVGLYGSGI-IDMKATECLICLGDF 121

Query: 133 APGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 171
             GE+VR+LPKCNHGFHVRCID WL S SSCP CR  L+
Sbjct: 122 EDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSLL 160

Arabidopsis thaliana (taxid: 3702)

>sp|O22755|ATL44_ARATH RING-H2 finger protein ATL44 OS=Arabidopsis thaliana GN=ATL44 PE=2 SV=1

 Score =  111 bits (277), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 73/164 (44%), Positives = 96/164 (58%), Gaps = 20/164 (12%)

Query: 34  AAPPSNRGGES-SFDSNVLMVLSVLLCALICAIGLASLVKCS-LRCSRLEASESSANSSG 91
           AAPP     E  + +S+++++LS LLCALIC  GLA++V+C+ LR  R  A         
Sbjct: 11  AAPPPQPSEEMIAAESDMVVILSALLCALICVAGLAAVVRCAWLR--RFTAG------GD 62

Query: 92  SGSCSSGIKQKALK-----TFTVVK-YSTELKLPGLDTECVICLSEFAPGERVRLLPKCN 145
           S S + G+K+KAL+     TFT  +  S      G  TEC ICL++FA GE +R+LP C 
Sbjct: 63  SPSPNKGLKKKALQSLPRSTFTAAESTSGAAAEEGDSTECAICLTDFADGEEIRVLPLCG 122

Query: 146 HGFHVRCIDKWLRSNSSCPKCRHCLIE-SCQKIVGCSQASSSSM 188
           H FHV CIDKWL S SSCP CR  L    C +   C  AS++ M
Sbjct: 123 HSFHVECIDKWLVSRSSCPSCRRILTPVRCDR---CGHASTAEM 163

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LC69|ATL8_ARATH RING-H2 finger protein ATL8 OS=Arabidopsis thaliana GN=ATL8 PE=2 SV=2

 Score =  110 bits (274), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 57/142 (40%), Positives = 85/142 (59%), Gaps = 9/142 (6%)

Query: 31  PVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLASLVKCS-LRCSRLEASESSANS 89
           P  A+PP        F+S+++++L+VLLCAL C IGL ++ +C+ LR           + 
Sbjct: 17  PAEASPP--------FNSDLVLILAVLLCALTCIIGLIAVSRCAWLRRIASRNRSDQTHP 68

Query: 90  SGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFH 149
               + + G+K+K L++   + YS +        EC ICL+EFA G+ +R+LP+C HGFH
Sbjct: 69  PPVAAANKGLKKKVLRSLPKLTYSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHGFH 128

Query: 150 VRCIDKWLRSNSSCPKCRHCLI 171
           V CID WL S+SSCP CR  L+
Sbjct: 129 VSCIDTWLGSHSSCPSCRQILV 150

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 67/131 (51%), Positives = 96/131 (73%), Gaps = 6/131 (4%)

Query: 43  ESSFDSNVLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQK 102
           + +FD+N++++L+ LLCALI A+GL S+++C++RC       SS+ ++G+ +  +G+K++
Sbjct: 27  DMNFDANMVIILAALLCALILALGLNSILRCAMRCG---FGLSSSAAAGTVADRAGLKKR 83

Query: 103 ALKTFTVVKY-STELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS 161
            LK F V +Y S E+K+    TEC ICL EFA GERVR+LP CNH FH+ CID WL S+S
Sbjct: 84  ELKKFPVAEYGSGEVKIAA--TECAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHS 141

Query: 162 SCPKCRHCLIE 172
           SCP CRH LIE
Sbjct: 142 SCPNCRHSLIE 152

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	210
224116596	225	predicted protein [Populus trichocarpa]	0.971	0.906	0.625	9e-73
224055977	225	predicted protein [Populus trichocarpa]	0.995	0.928	0.613	1e-72
255562369	223	RING-H2 finger protein ATL1L, putative [	0.966	0.910	0.629	3e-72
225431583	224	PREDICTED: RING-H2 finger protein ATL78	0.971	0.910	0.600	1e-66
9293902	222	unnamed protein product [Arabidopsis tha	0.966	0.914	0.569	2e-60
297830534	222	hypothetical protein ARALYDRAFT_479387 [	0.933	0.882	0.581	4e-60
15222073	219	RING-H2 finger protein ATL78 [Arabidopsi	0.961	0.922	0.556	7e-59
357464535	240	Ring-H2 zinc finger protein [Medicago tr	0.985	0.862	0.539	4e-58
388508514	228	unknown [Medicago truncatula]	0.985	0.907	0.535	1e-56
356516339	236	PREDICTED: RING-H2 finger protein ATL78-	0.961	0.855	0.532	3e-56

>gi|224116596|ref|XP_002331879.1| predicted protein [Populus trichocarpa] gi|222874628|gb|EEF11759.1| predicted protein [Populus trichocarpa]

 Score =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 137/219 (62%), Positives = 175/219 (79%), Gaps = 15/219 (6%)

Query: 6   STTTQLFQDFLGKFHSRKLLLQN---QQPVIAAPPS---------NRGGESSFDSNVLMV 53
           ++TTQLFQDFLG F+SR+LLL N   Q    A PP+         + G  SSFD+NV+MV
Sbjct: 5   TSTTQLFQDFLGDFYSRRLLLHNPLYQSTNTATPPAPGNSAPSEPSTGTGSSFDANVVMV 64

Query: 54  LSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYS 113
           LSVLLCALIC++GL S+++C+LRCS + ASES+AN S + S ++G+ ++ALK+F VV YS
Sbjct: 65  LSVLLCALICSLGLNSIIRCALRCSNIAASESAANPS-TQSANTGVNRRALKSFPVVNYS 123

Query: 114 TELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 173
           ++L LPGLDTECVICLSEF PGERVRLLPKC+HGFHV+CIDKWL S+SSCP CRHCLIE+
Sbjct: 124 SDLNLPGLDTECVICLSEFTPGERVRLLPKCHHGFHVKCIDKWLSSHSSCPTCRHCLIET 183

Query: 174 CQKIVGCSQASSS--SMAMQESVSNIVPLEPESAVCSYR 210
           CQKI+GCSQAS+S  S+ +QE++ +I+PLEPE  +  YR
Sbjct: 184 CQKIIGCSQASTSGTSLPVQETIVSILPLEPEGLIRDYR 222

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224055977|ref|XP_002298709.1| predicted protein [Populus trichocarpa] gi|222845967|gb|EEE83514.1| predicted protein [Populus trichocarpa]

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 138/225 (61%), Positives = 175/225 (77%), Gaps = 16/225 (7%)

Query: 1   MSTTPSTTTQLFQDFLGKFHSRKLLLQN---QQPVIAAPP---------SNRGGESSFDS 48
           MST+ STT QLFQ FLG F+SR+LLL     Q    A PP         +    ++SFD+
Sbjct: 1   MSTSTSTTHQLFQGFLGDFYSRRLLLHTPLYQSSNTATPPAPGNTASSETYTSTDNSFDA 60

Query: 49  NVLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFT 108
           NV+MVLS+LLCALIC++GL S+++C+LRCS L ASES+AN S   + ++G+K+KALKTF 
Sbjct: 61  NVVMVLSILLCALICSLGLNSIIRCALRCSNLVASESAANPSTQAA-NTGVKRKALKTFP 119

Query: 109 VVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
           +VKYST+L LPGLDT+CVICLSEF PGE VRLLPKCNHGFHV+CIDKWL S+SSCP CRH
Sbjct: 120 IVKYSTDLNLPGLDTQCVICLSEFTPGEHVRLLPKCNHGFHVKCIDKWLSSHSSCPTCRH 179

Query: 169 CLIESCQKIVGCSQASSS---SMAMQESVSNIVPLEPESAVCSYR 210
           CLIE+C+KI GCSQAS+S   S+ +QE++ +I+PLEPE  + +YR
Sbjct: 180 CLIETCKKIAGCSQASTSGPTSLPVQEAIVSILPLEPEGLISNYR 224

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562369|ref|XP_002522191.1| RING-H2 finger protein ATL1L, putative [Ricinus communis] gi|223538562|gb|EEF40166.1| RING-H2 finger protein ATL1L, putative [Ricinus communis]

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 141/224 (62%), Positives = 169/224 (75%), Gaps = 21/224 (9%)

Query: 3   TTPSTTTQLFQDFLGKFHSRKLLLQNQQPVI----------------AAPPSNRGGESSF 46
           TT ++T QLFQDF G F+SR+LLL    P+                 A+ P    G +SF
Sbjct: 2   TTSTSTAQLFQDFQGDFYSRRLLLHT--PLYHSPTAAAPPAPGYSQEASEPYT--GNNSF 57

Query: 47  DSNVLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKT 106
           D+NV+MVLSVLLCALIC++GL S+++C+LRCS L AS S+ NSS +G  ++G+K+KALKT
Sbjct: 58  DANVVMVLSVLLCALICSLGLNSIIRCALRCSSLVASRSADNSS-AGLANTGVKRKALKT 116

Query: 107 FTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC 166
           F  V YST+L LPGLDTEC ICLSEF PGERVRLLPKCNHGFHVRCIDKWL S+SSCP C
Sbjct: 117 FPTVNYSTDLNLPGLDTECAICLSEFTPGERVRLLPKCNHGFHVRCIDKWLSSHSSCPTC 176

Query: 167 RHCLIESCQKIVGCSQASSSSMAMQESVSNIVPLEPESAVCSYR 210
           RHCLIE+CQKIVGCSQ SSS   +QES+ NI PLEPE+ + SYR
Sbjct: 177 RHCLIETCQKIVGCSQTSSSDPPVQESIVNIAPLEPEALIRSYR 220

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431583|ref|XP_002282494.1| PREDICTED: RING-H2 finger protein ATL78 [Vitis vinifera] gi|147833208|emb|CAN75293.1| hypothetical protein VITISV_042413 [Vitis vinifera]

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/223 (60%), Positives = 166/223 (74%), Gaps = 19/223 (8%)

Query: 2   STTPSTTTQLFQDFLGKFHSRKLLLQ---NQQPVIAAPPSNRG---------GESSFDSN 49
           ST+PS   QLFQD +G F+SR+LLL    ++ P  A+PP+            G +SFD+N
Sbjct: 4   STSPSV--QLFQDLVGDFYSRRLLLHSPLHESPATASPPATGNSHDSSEPYTGSNSFDTN 61

Query: 50  VLMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTV 109
           V+MVLSVLLCALIC++GL S+++C+LRCS L AS    NS  +   ++G+K+KALKTF  
Sbjct: 62  VVMVLSVLLCALICSLGLNSIIRCALRCSSLVASP--GNSPSTRLANTGVKKKALKTFPT 119

Query: 110 VKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHC 169
           + YS  L LPGLDTECVICLS+F PGER+R+LPKCNHGFHVRCIDKWL S+SSCP CRHC
Sbjct: 120 LNYSAGLNLPGLDTECVICLSDFTPGERIRILPKCNHGFHVRCIDKWLNSHSSCPTCRHC 179

Query: 170 LIESCQKIVGCSQASSSSM--AMQESVSNIVPLEPESAVCSYR 210
           LIE+CQKI+GCSQASSS     +QES+  IVPLEPE    +YR
Sbjct: 180 LIETCQKIIGCSQASSSETPPPLQESMI-IVPLEPEGFSRNYR 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9293902|dbj|BAB01805.1| unnamed protein product [Arabidopsis thaliana]

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 123/216 (56%), Positives = 159/216 (73%), Gaps = 13/216 (6%)

Query: 2   STTPSTT-TQLFQDFLGKFHSRKLLLQN--QQPVIAAPPSNRGGESS--------FDSNV 50
           ++ P+T  T+LFQD  G F+SR+LLL    Q P  A+PP     E+S        FD+NV
Sbjct: 5   TSAPTTKPTELFQDIRGDFYSRRLLLHTAYQPPTAASPPFADAHEASHSYQSHMSFDANV 64

Query: 51  LMVLSVLLCALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVV 110
           +MVLSVLLCAL+C++GL S+++C+LR S L +SE+S   S   + ++G+KQKALK+F  V
Sbjct: 65  VMVLSVLLCALVCSLGLHSIIRCALRYSNLLSSEASDEFSVRLA-NTGVKQKALKSFQTV 123

Query: 111 KYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
            Y+ ELKLPGLDTEC ICLSEFA GERV+LLPKC+HGFHVRCIDKWL S+SSCP CRHCL
Sbjct: 124 SYTAELKLPGLDTECAICLSEFASGERVKLLPKCHHGFHVRCIDKWLSSHSSCPTCRHCL 183

Query: 171 IESCQKIVGCSQASSSSMAMQESVSNIVPLEPESAV 206
           I++C+KI G S+  SS    Q++V +I PL PES +
Sbjct: 184 IQTCKKIAGYSETESSPNQPQQNV-HISPLGPESLI 218

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830534|ref|XP_002883149.1| hypothetical protein ARALYDRAFT_479387 [Arabidopsis lyrata subsp. lyrata] gi|297328989|gb|EFH59408.1| hypothetical protein ARALYDRAFT_479387 [Arabidopsis lyrata subsp. lyrata]

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 121/208 (58%), Positives = 153/208 (73%), Gaps = 12/208 (5%)

Query: 9   TQLFQDFLGKFHSRKLLLQN--QQPVIAAPPSNRGGESS--------FDSNVLMVLSVLL 58
           T+LFQD  G F+SR+LLL    Q P  A+ P     E+S        FD+NV+MVLSVLL
Sbjct: 13  TELFQDIRGDFYSRRLLLHTAYQPPTTASSPFADAHETSHTYASHMSFDANVVMVLSVLL 72

Query: 59  CALICAIGLASLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKL 118
           CAL+C++GL S+++C+LR S L +SE+S   S   + ++G+KQKALK+F  V Y+ ELKL
Sbjct: 73  CALVCSLGLHSIIRCALRYSNLLSSEASDELSVRLA-NTGVKQKALKSFQTVSYTAELKL 131

Query: 119 PGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIV 178
           PGLDTEC ICLSEF  GERV+LLPKC+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI 
Sbjct: 132 PGLDTECAICLSEFVSGERVKLLPKCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCKKIA 191

Query: 179 GCSQASSSSMAMQESVSNIVPLEPESAV 206
           GCS+  SS    QE+V +I PL PES +
Sbjct: 192 GCSETVSSPNQPQENV-HIAPLGPESLI 218

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15222073|ref|NP_175349.1| RING-H2 finger protein ATL78 [Arabidopsis thaliana] gi|68565178|sp|Q6NQG7.1|ATL78_ARATH RecName: Full=RING-H2 finger protein ATL78 gi|34365601|gb|AAQ65112.1| At1g49230 [Arabidopsis thaliana] gi|51970612|dbj|BAD43998.1| putative RING zinc finger protein [Arabidopsis thaliana] gi|51971166|dbj|BAD44275.1| putative RING zinc finger protein [Arabidopsis thaliana] gi|332194286|gb|AEE32407.1| RING-H2 finger protein ATL78 [Arabidopsis thaliana]

 Score =  232 bits (592), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 114/205 (55%), Positives = 149/205 (72%), Gaps = 3/205 (1%)

Query: 9   TQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVLLCALICAIGLA 68
           T++FQ+ LG  +SRKLL           PS   G+++FD+NV+MVLSVLLCAL+C++GL 
Sbjct: 15  TEIFQEILGSSYSRKLLFHTHDQSPTPAPSPYVGDNNFDANVVMVLSVLLCALVCSLGLN 74

Query: 69  SLVKCSLRCSRLEASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVIC 128
           S+++C+LRCS L  SE+  ++      ++G+K+KALK+F  V YSTEL LPGLDTEC IC
Sbjct: 75  SIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVSYSTELNLPGLDTECAIC 134

Query: 129 LSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASS--S 186
           LSEF   ERV+LLP C+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI  CSQ SS  S
Sbjct: 135 LSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCEKIADCSQTSSLNS 194

Query: 187 SMAMQESVS-NIVPLEPESAVCSYR 210
           +   Q+S+   I PLEPE  +  +R
Sbjct: 195 TQPPQDSIILQIAPLEPERWIRWFR 219

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357464535|ref|XP_003602549.1| Ring-H2 zinc finger protein [Medicago truncatula] gi|355491597|gb|AES72800.1| Ring-H2 zinc finger protein [Medicago truncatula]

 Score =  229 bits (585), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 123/228 (53%), Positives = 156/228 (68%), Gaps = 21/228 (9%)

Query: 1   MSTTPSTTTQLFQDFLGKFHSRKLLLQNQQPVIAAPP-----------SNRGGESSFDSN 49
           M  T S  + L  + +  FHSR+LLL +     A PP           S+  G+ +FD+N
Sbjct: 1   MYATTSFVSPLLHELVENFHSRRLLLHSSNS--ANPPISTSIHDSTKESSYAGDGNFDAN 58

Query: 50  VLMVLSVLLCALICAIGLASLVKCSLRCSRL--EASESSANSSGSGSCSSGIKQKALKTF 107
           V+MVLSVLLCALIC++ L S+++C+L+CS L   + + SAN+    + ++GIK+KALK F
Sbjct: 59  VVMVLSVLLCALICSLCLNSIIRCALKCSNLVVMSGDRSANNIPVRAANTGIKKKALKKF 118

Query: 108 TVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           T V YS ELKLP LD+ECVICLSEF  G++VRLLPKCNHGFHVRCIDKWL S+SSCPKCR
Sbjct: 119 TTVSYSDELKLPSLDSECVICLSEFTNGDKVRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 178

Query: 168 HCLIESCQKIVGCSQASSSS-----MAMQESVSNIVPLEPESAVCSYR 210
            CLIE+C KIVG SQ SSS        + E++  I PLEPE  V +YR
Sbjct: 179 QCLIETCNKIVG-SQGSSSQPQPMLFPVPETIVTIAPLEPEGLVRNYR 225

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508514|gb|AFK42323.1| unknown [Medicago truncatula]

 Score =  225 bits (573), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 122/228 (53%), Positives = 154/228 (67%), Gaps = 21/228 (9%)

Query: 1   MSTTPSTTTQLFQDFLGKFHSRKLLLQNQQPVIAAPP-----------SNRGGESSFDSN 49
           M  T S  + L  + +  FHSR+LLL +     A PP           S+  G+ +FD+N
Sbjct: 1   MYATTSFVSPLLHELVENFHSRRLLLHSSNS--ANPPISTSIHDSTKESSYAGDGNFDAN 58

Query: 50  VLMVLSVLLCALICAIGLASLVKCSLRCSRLEA--SESSANSSGSGSCSSGIKQKALKTF 107
           V+MVLSVLLCALIC++ L S+++C+L+CS L     + SAN+    + ++GIK+KALK F
Sbjct: 59  VVMVLSVLLCALICSLCLNSIIRCALKCSNLVVMRGDRSANNIPVRAANTGIKKKALKKF 118

Query: 108 TVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           T V YS ELKL  LD+ECVICLSEF  G++VRLLPKCNHGFHVRCIDKWL S+SSCPKCR
Sbjct: 119 TTVSYSDELKLLSLDSECVICLSEFTNGDKVRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 178

Query: 168 HCLIESCQKIVGCSQASSSS-----MAMQESVSNIVPLEPESAVCSYR 210
            CLIE+C KIVG SQ SSS        + E++  I PLEPE  V +YR
Sbjct: 179 QCLIETCNKIVG-SQGSSSQPQPMLFPVPETIVTIAPLEPEGLVRNYR 225

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516339|ref|XP_003526853.1| PREDICTED: RING-H2 finger protein ATL78-like [Glycine max]

 Score =  223 bits (569), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 122/229 (53%), Positives = 157/229 (68%), Gaps = 27/229 (11%)

Query: 6   STTTQLFQDFLGKFHSRKLLLQ----NQQPVIAAPPSNRG--------GESSFDSNVLMV 53
           S T+ L  D     +SR+LLL     NQ    A PP +          G+ +FD+NV+MV
Sbjct: 8   SLTSPLLHDLENFHYSRRLLLHSPYLNQS---AKPPRSSHDSSTETYLGDGNFDANVVMV 64

Query: 54  LSVLLCALICAIGLASLVKCSLRCSRLEASESSANSS------GSGSCSSGIKQKALKTF 107
           LSVLLCALIC++GL S+++C+LRCS    S+S A ++       +   ++G+K+KALKTF
Sbjct: 65  LSVLLCALICSLGLNSIIRCALRCSNFVVSDSVATNNNNNNPPAARVANTGVKKKALKTF 124

Query: 108 TVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           T V YS EL LP LD+ECVICLSEF  GE+VR+LPKCNHGFH+RCIDKWL S+SSCPKCR
Sbjct: 125 TTVSYSAELNLPSLDSECVICLSEFTSGEKVRILPKCNHGFHIRCIDKWLSSHSSCPKCR 184

Query: 168 HCLIESCQKIVGCSQASSSS-----MAMQESVSNIV-PLEPESAVCSYR 210
            CLIE+CQKIVGCS   +SS     +A+ E++  I+ PLEPE  V +YR
Sbjct: 185 QCLIETCQKIVGCSTQQASSSQQHVLAVPETIVTIIAPLEPEGLVRNYR 233

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	210
TAIR|locus:2028436	219	AT1G49230 [Arabidopsis thalian	0.961	0.922	0.463	1.3e-45
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.957	0.800	0.441	3.2e-41
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.980	0.915	0.430	4.8e-39
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.957	0.889	0.424	1.5e-37
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.966	0.922	0.401	6.3e-37
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.628	0.75	0.414	4.2e-24
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.595	0.786	0.404	1.4e-23
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.704	0.817	0.364	7e-22
TAIR|locus:2117622	200	RHA3B "RING-H2 finger A3B" [Ar	0.257	0.27	0.581	2.7e-18
TAIR|locus:2011686	185	ATL8 [Arabidopsis thaliana (ta	0.738	0.837	0.314	9.5e-18

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

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 95/205 (46%), Positives = 118/205 (57%)

Query:     9 TQLFQDFLGKFHSRKLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVXXXXXXXXXXXX 68
             T++FQ+ LG  +SRKLL           PS   G+++FD+NV+MVLSV            
Sbjct:    15 TEIFQEILGSSYSRKLLFHTHDQSPTPAPSPYVGDNNFDANVVMVLSVLLCALVCSLGLN 74

Query:    69 XXVKCSLRCSRLEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTELKLPGLDTECVIC 128
               ++C+LRCS L                  +K+KALK+F  V YSTEL LPGLDTEC IC
Sbjct:    75 SIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVSYSTELNLPGLDTECAIC 134

Query:   129 LSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCXXXXXXXX 188
             LSEF   ERV+LLP C+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI  C        
Sbjct:   135 LSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCEKIADCSQTSSLNS 194

Query:   189 XX---XXXXXNIVPLEPESAVCSYR 210
                        I PLEPE  +  +R
Sbjct:   195 TQPPQDSIILQIAPLEPERWIRWFR 219

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

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

 Score = 417 (151.9 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 94/213 (44%), Positives = 120/213 (56%)

Query:     5 PSTTTQLFQD-FLGKFHSRKLLLQN------QQPVIAAPPSNRGGESSFDSNVLMVLSVX 57
             PS+  Q FQ+ FLG F SRKLLL N      Q+    AP      E++   NV+M+LS+ 
Sbjct:     7 PSSA-QAFQEQFLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVMMLLSIL 65

Query:    58 XXXXXXXXXXXXXVKCSLRCSR--LEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTE 115
                          ++C+LR S   + +                IK+KAL+ F VV YS E
Sbjct:    66 ICGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPVVSYSPE 125

Query:   116 LKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ 175
             + LPGLD ECVICLS+F  GE++RLLPKCNHGFHVRCIDKWL+ + +CPKCR+CL+E+CQ
Sbjct:   126 MNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNCLVETCQ 185

Query:   176 KIVGCXXXXXXXXX--XXXXXXNIVPLEPESAV 206
             KI+G                   IVPLEP   V
Sbjct:   186 KILGDFSQADSVTAEPTEIVIVTIVPLEPTEIV 218

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

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

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 93/216 (43%), Positives = 120/216 (55%)

Query:     5 PSTTTQLFQDFLGKFHSRKLLLQ-----NQQPVIAAPPSNR-GGESSFDSNVLMVLSVXX 58
             P++   L + FLG F +RKLLL      N   V A  PS     E++   NVLM+LSV  
Sbjct:     7 PASAQSLQEQFLGSFVTRKLLLHDPFDHNSLRVFAVAPSPLITHENNLKGNVLMLLSVLI 66

Query:    59 XXXXXXXXXXXXVKCSLR-CSR-LEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTEL 116
                         ++C+ R  SR + +                IK+KAL+ F VV YS E+
Sbjct:    67 CGIICCLGLHYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPVVSYSREM 126

Query:   117 KLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK 176
              LPG+  ECVICLS+F  GE++RLLPKCNHGFHVRCIDKWL+ + +CPKCRHCL+E+CQK
Sbjct:   127 NLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHCLVETCQK 186

Query:   177 IVG--CXXXXXXXXXXXXXXXNIVPLEPESAVCSYR 210
             I+G                   I PLEPE  V ++R
Sbjct:   187 ILGDFSQADSMASTPTESVIVRIDPLEPEGRVNTFR 222

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 90/212 (42%), Positives = 116/212 (54%)

Query:     6 STTTQLFQD-FLGKFHSRKLLLQN------QQPVIAAPPSNRGGESSFDSNVLMVLSVXX 58
             S++ Q FQ+  LG F SRKLLL N      Q+    AP      E++   NVLM+LSV  
Sbjct:     8 SSSVQAFQEQSLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVLMLLSVLI 67

Query:    59 XXXXXXXXXXXXVKCSLR--CSRLEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTEL 116
                         ++C+ R   S + +                I +KAL+ F VV YS E+
Sbjct:    68 CGIICCLGLHYIIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPVVSYSPEM 127

Query:   117 KLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK 176
              LPGL  ECVICLS+F  GE++R+LPKC+HGFHVRCIDKWL+ + +CPKCRHCL+E+CQK
Sbjct:   128 NLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHCLVETCQK 187

Query:   177 IVG--CXXXXXXXXXXXXXXXNIVPLEPESAV 206
             I+G                   I PLEPE  V
Sbjct:   188 ILGDFSQADQVAATPTASVIVRIAPLEPEGRV 219

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

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

 Score = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 86/214 (40%), Positives = 121/214 (56%)

Query:     5 PSTTTQLFQD-FLGKFHSRKLLLQNQQPVIA--APPSNRGGESSFDSNVLMVLSVXXXXX 61
             PS+++Q+FQ+ F+  F SRKLL   QQ   A  A  ++   +++   NVLM+LS+     
Sbjct:     7 PSSSSQVFQEHFIDSFVSRKLL---QQIPFAHNAQQAHVPDKNNLSGNVLMLLSILLCGI 63

Query:    62 XXXXXXXXXVKCSLRCSR---LEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTELKL 118
                      ++C+   SR   +                  IK+KALK   VV YS E+ L
Sbjct:    64 ICSLGLHYIIRCAFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPEINL 123

Query:   119 PGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIV 178
             PG+  ECVICLS+F  GE++R+LPKCNHGFH+RCIDKWL  + +CPKCRHCL+++CQK++
Sbjct:   124 PGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRHCLVDTCQKVL 183

Query:   179 G-CXXXXXXXXXXXXXXX-NIVPLEPESAVCSYR 210
               C                 I PLEPE+ V ++R
Sbjct:   184 SDCDAADQVAATATESIDIRISPLEPEARVATFR 217

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

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

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 56/135 (41%), Positives = 76/135 (56%)

Query:    38 SNRGGESSFDSNVLMVLSVXXXXXXXXXXXXXXVKCSLRCSRLEAXXXXXXXXXXXXXXX 97
             SN    +S D++++++L+               ++C LRC+R                  
Sbjct:    29 SNNKNIASMDTHMVIILAALLCALICALGINSVLRCVLRCTR-RFTPNEDPVDTNANVAK 87

Query:    98 XIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL 157
              IK++ALK   V  YS ELK+    TEC+ICL +F  GE VR+LPKCNHGFHV+CID WL
Sbjct:    88 GIKKRALKVIPVDSYSPELKMKA--TECLICLGDFVEGETVRVLPKCNHGFHVKCIDTWL 145

Query:   158 RSNSSCPKCRHCLIE 172
              S+SSCP CR  L+E
Sbjct:   146 LSHSSCPTCRQSLLE 160

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

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

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 53/131 (40%), Positives = 74/131 (56%)

Query:    43 ESSFDSNVLMVLSVXXXXXXXXXXXXXXVKCSLRCSRLEAXXXXXXXXXXXXXXXXIKQK 102
             + +FD+N++++L+               ++C++RC                     +K++
Sbjct:    27 DMNFDANMVIILAALLCALILALGLNSILRCAMRCG---FGLSSSAAAGTVADRAGLKKR 83

Query:   103 ALKTFTVVKY-STELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS 161
              LK F V +Y S E+K+    TEC ICL EFA GERVR+LP CNH FH+ CID WL S+S
Sbjct:    84 ELKKFPVAEYGSGEVKIAA--TECAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHS 141

Query:   162 SCPKCRHCLIE 172
             SCP CRH LIE
Sbjct:   142 SCPNCRHSLIE 152

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

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

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 58/159 (36%), Positives = 84/159 (52%)

Query:    23 KLLLQNQQPVIA-APPSNRGG--ESSFDSNVLMVLSVXXXXXXXXXXXXXXVKCSLRCSR 79
             +LLL+ Q    A A P  +GG  ++ FD+N++++L+               ++C LR +R
Sbjct:     3 RLLLEPQANAPANANPKPKGGINDTYFDTNMVIILAALLCALICALSLNSALRCVLRITR 62

Query:    80 -------LEAXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTELKLPGLDTECVICLSEF 132
                    +                  +K++ALK   V  Y + + +    TEC+ICL +F
Sbjct:    63 RFTSDDQVSNASNANANLGRLAAATGLKKQALKQIPVGLYGSGI-IDMKATECLICLGDF 121

Query:   133 APGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 171
               GE+VR+LPKCNHGFHVRCID WL S SSCP CR  L+
Sbjct:   122 EDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSLL 160

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

TAIR|locus:2117622 RHA3B "RING-H2 finger A3B" [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 2.7e-18, Sum P(2) = 2.7e-18
 Identities = 32/55 (58%), Positives = 40/55 (72%)

Query:   123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE-SCQK 176
             TEC IC++EF+ GE +R+LP C+H FHV CIDKWL S SSCP CR  L+   C +
Sbjct:   111 TECAICITEFSEGEEIRILPLCSHAFHVACIDKWLTSRSSCPSCRRILVPVKCDR 165

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010200 "response to chitin" evidence=IEP

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0010286 "heat acclimation" evidence=RCA

GO:0015824 "proline transport" evidence=RCA

TAIR|locus:2011686 ATL8 [Arabidopsis thaliana (taxid:3702)]

 Score = 216 (81.1 bits), Expect = 9.5e-18, P = 9.5e-18
 Identities = 50/159 (31%), Positives = 77/159 (48%)

Query:    23 KLLLQNQQPVIAAPPSNRGGESSFDSNVLMVLSVXXXXXXXXXXXXXXVKCS-LRCSRLE 81
             +LL +  Q   +  P+       F+S+++++L+V               +C+ LR     
Sbjct:     3 RLLFRLLQEANSTSPAE--ASPPFNSDLVLILAVLLCALTCIIGLIAVSRCAWLRRIASR 60

Query:    82 AXXXXXXXXXXXXXXXXIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLL 141
                              +K+K L++   + YS +        EC ICL+EFA G+ +R+L
Sbjct:    61 NRSDQTHPPPVAAANKGLKKKVLRSLPKLTYSPDSPPAEKLVECAICLTEFAAGDELRVL 120

Query:   142 PKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES-CQKIVG 179
             P+C HGFHV CID WL S+SSCP CR  L+ + C K  G
Sbjct:   121 PQCGHGFHVSCIDTWLGSHSSCPSCRQILVVTRCHKCGG 159

GO:0005634 "nucleus" evidence=ISM

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

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6NQG7	ATL78_ARATH	No assigned EC number	0.5560	0.9619	0.9223	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.01850007 hypothetical protein (225 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	210
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	6e-13
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	5e-11
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-09
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	9e-09
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	9e-08
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	1e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	6e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-05
smart00184	40	smart00184, RING, Ring finger	3e-04
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	6e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.001
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.001
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	0.003

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

 Score = 60.5 bits (147), Expect = 6e-13
 Identities = 28/45 (62%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
           EC ICL EF PGE V +LP C H FH  C+DKWLRS+++CP CR 
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 60.8 bits (147), Expect = 5e-11
 Identities = 25/45 (55%), Positives = 31/45 (68%), Gaps = 2/45 (4%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCR 167
           EC IC+S F   +R+R+LP C+H FHV C+DKWL   S  CP CR
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 51.7 bits (124), Expect = 2e-09
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 9/55 (16%)

Query: 122 DTECVICLSEFA--------PGERVRL-LPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           D  C IC + F         PG+   +   +C H FH+ CI +WL++ ++CP CR
Sbjct: 19  DDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

 Score = 49.4 bits (118), Expect = 9e-09
 Identities = 22/48 (45%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL 170
           EC ICL EF       +L  C H F   CIDKWL+S  ++CP CR  +
Sbjct: 1   ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 50.5 bits (121), Expect = 9e-08
 Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 21/83 (25%)

Query: 100 KQKALKTFT-----VVKYSTELKLPGLDTECVICLSEFAPGERVR----------LLPKC 144
           K K  K F      V+    +L     D EC IC+      E+V           +L  C
Sbjct: 147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICM------EKVYDKEIKNMYFGILSNC 200

Query: 145 NHGFHVRCIDKWLRSNSSCPKCR 167
           NH F + CID W +  ++CP CR
Sbjct: 201 NHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 48.1 bits (114), Expect = 1e-06
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 97   SGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERV---RLLPKCNHGFHVRCI 153
                   +    + K + + K  G + EC IC S     +R    +    C + FH RC+
Sbjct: 1445 IKKNGSFMDLLGLWKKNIDEKFSGHE-ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCL 1503

Query: 154  DKWLRS--NSSCPKCR 167
             KW  S   S+CP CR
Sbjct: 1504 YKWFASSARSNCPLCR 1519

Length = 1525

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

 Score = 42.9 bits (101), Expect = 6e-06
 Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 125 CVICLSEFAPGERVRLL-PKCNHGFHVRCIDKWLRSNSSCPKCR 167
           C  C     PG+   ++   CNH FH  CI +WL +   CP  R
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 39.0 bits (91), Expect = 6e-05
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
           + EC ICL      + V L P C H F   CI ++L+  S CP CR 
Sbjct: 2   ELECPICLDLLR--DPVVLTP-CGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKC 166
           C ICL E+   +   +LP C H F   CI KWL S N++CP C
Sbjct: 1   CPICLEEYL--KDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 7/70 (10%)

Query: 124 ECVICLSEFAPGERVRLL----PKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVG 179
           EC IC +    G  +  +    PKC   FH+ C+ +WLR+     +  +    +C     
Sbjct: 4   ECGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPY--- 60

Query: 180 CSQASSSSMA 189
           C    S   +
Sbjct: 61  CKAKISVKFS 70

This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. Length = 70

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 23/58 (39%), Positives = 27/58 (46%), Gaps = 12/58 (20%)

Query: 122 DTECVICLSEF--------APGERVRL-LPKCNHGFHVRCIDKWLRSNSS---CPKCR 167
           D  C IC   F         PG+   L   KC H FH+ CI KWL + +S   CP CR
Sbjct: 21  DDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 78

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

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

 Score = 38.8 bits (90), Expect = 0.001
 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 9/67 (13%)

Query: 114 TELKLPGLDTECVICLSE-FAPGER-----VRLLPK---CNHGFHVRCIDKWLRSNSSCP 164
           TE +L   D  C IC+ E F P        + + PK   C H  H+ C+  WL    +CP
Sbjct: 279 TEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCP 338

Query: 165 KCRHCLI 171
            CR  +I
Sbjct: 339 ICRRPVI 345

Length = 491

>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 37.4 bits (86), Expect = 0.003
 Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 118 LPGLDT--ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           L GLD+   C IC         +     C H F   CI + L +   CP CR
Sbjct: 19  LKGLDSMLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.83
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.65
PHA02929	238	N1R/p28-like protein; Provisional	99.45
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.42
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.37
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.34
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.23
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.13
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.13
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.13
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.11
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.11
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.06
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.98
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.94
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.92
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.92
PHA02926	242	zinc finger-like protein; Provisional	98.9
PF14634	44	zf-RING_5: zinc-RING finger domain	98.9
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.84
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.84
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.79
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.79
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.7
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.7
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.62
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.56
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.47
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.43
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.41
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.26
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.24
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.18
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.08
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.07
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.07
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.05
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.0
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.98
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.84
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.74
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.72
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.7
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.61
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.57
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.47
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.46
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.3
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.24
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.22
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.18
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.15
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.15
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.06
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.04
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.91
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.88
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.65
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.56
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.45
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.38
PHA02862	156	5L protein; Provisional	96.26
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.11
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.02
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.95
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.92
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.9
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.87
PHA03096	284	p28-like protein; Provisional	95.86
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.84
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.76
KOG2660	331	consensus Locus-specific chromosome binding protei	95.75
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.64
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.3
COG5152	259	Uncharacterized conserved protein, contains RING a	95.12
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.07
KOG4739	233	consensus Uncharacterized protein involved in syna	94.94
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.72
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	94.44
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.32
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	94.27
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.16
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.02
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	92.94
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	92.75
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.55
KOG1001	674	consensus Helicase-like transcription factor HLTF/	92.41
PF04641	260	Rtf2: Rtf2 RING-finger	92.38
KOG1940	276	consensus Zn-finger protein [General function pred	91.75
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	91.53
COG5175	480	MOT2 Transcriptional repressor [Transcription]	91.49
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	90.95
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	90.72
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	90.56
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	90.14
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	89.15
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	88.65
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	88.43
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	87.58
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	87.57
KOG1609	323	consensus Protein involved in mRNA turnover and st	86.87
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	86.52
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	84.67
KOG3053	293	consensus Uncharacterized conserved protein [Funct	84.5
KOG0269	839	consensus WD40 repeat-containing protein [Function	83.98
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	82.86
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	82.84
PF15050	133	SCIMP: SCIMP protein	82.83
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	82.74
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	82.73
KOG3899	381	consensus Uncharacterized conserved protein [Funct	81.62
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	81.37
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	81.03
KOG1829	580	consensus Uncharacterized conserved protein, conta	80.46
KOG3002	299	consensus Zn finger protein [General function pred	80.39

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

Probab=99.83  E-value=1.4e-20  Score=164.83  Aligned_cols=78  Identities=31%  Similarity=0.778  Sum_probs=67.2

Q ss_pred             CCccHhhhhhcceeeeccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCcccccccccccc
Q 028342           97 SGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIESCQ  175 (210)
Q Consensus        97 ~gl~~~~i~~lp~~~y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~~~~  175 (210)
                      ..+.++.++++|...|......... ..|+||||+|++||++|.|| |+|.||..|||.||..++ .||+|++++....+
T Consensus       205 ~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  205 NRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             hhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            3567889999999999887655444 69999999999999999999 999999999999997765 59999998886654


Q ss_pred             c
Q 028342          176 K  176 (210)
Q Consensus       176 ~  176 (210)
                      .
T Consensus       283 ~  283 (348)
T KOG4628|consen  283 S  283 (348)
T ss_pred             C
Confidence            3

>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=99.65  E-value=4.9e-17  Score=102.52  Aligned_cols=44  Identities=59%  Similarity=1.290  Sum_probs=40.6

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      ++|+||+++|.+++.+..++ |+|.||.+||..|++.+.+||+||
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            47999999999999999998 999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.45  E-value=6e-14  Score=118.10  Aligned_cols=75  Identities=35%  Similarity=0.631  Sum_probs=56.5

Q ss_pred             CCccHhhhhhcceeeecccc-CCCCCCCccccccCcccCCCc----eEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342           97 SGIKQKALKTFTVVKYSTEL-KLPGLDTECVICLSEFAPGER----VRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus        97 ~gl~~~~i~~lp~~~y~~~~-~~~~~~~~CaICLeef~~~~~----vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      .+..++.++.+|.+...... .....+.+|+||++++.+.+.    +.+++.|+|.||.+||..|++.+.+||+||..+.
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            34567788888888755321 122345899999999876542    2345459999999999999999999999999876

>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=99.42  E-value=1.1e-13  Score=96.50  Aligned_cols=46  Identities=39%  Similarity=0.949  Sum_probs=35.6

Q ss_pred             CCccccccCcccCC---------CceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          122 DTECVICLSEFAPG---------ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       122 ~~~CaICLeef~~~---------~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      ++.|+||+++|.+.         +....+..|||.||.+||.+||+.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45699999999422         23333434999999999999999999999998

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

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

Probab=99.37  E-value=2.7e-13  Score=115.87  Aligned_cols=51  Identities=47%  Similarity=1.136  Sum_probs=46.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-cCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~  172 (210)
                      .+-+|+|||+.|-++|.++++| |+|.||..|+++|+. -+..||+||..+.+
T Consensus       322 ~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            3479999999999999999999 999999999999998 45679999998864

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

Probab=99.34  E-value=1.1e-12  Score=114.92  Aligned_cols=54  Identities=37%  Similarity=0.938  Sum_probs=45.1

Q ss_pred             CCCCCccccccCc-ccCC---------CceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          119 PGLDTECVICLSE-FAPG---------ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       119 ~~~~~~CaICLee-f~~~---------~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ...|..|+||+|+ |+.+         .+...+| |||+||-+|++.|++++++||+||.++.-.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~ifd  347 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIFD  347 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccccc
Confidence            3457899999999 5544         2456788 999999999999999999999999996533

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

Probab=99.23  E-value=7.7e-12  Score=88.87  Aligned_cols=52  Identities=40%  Similarity=0.881  Sum_probs=41.2

Q ss_pred             CCccccccCccc--------CCC-ceEEcCCCCCccchHHHHHHHhc---CCCCcccccccccc
Q 028342          122 DTECVICLSEFA--------PGE-RVRLLPKCNHGFHVRCIDKWLRS---NSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~--------~~~-~vr~lp~C~H~FH~~CI~~Wl~~---~~~CPlCR~~l~~~  173 (210)
                      ++.|.||...|+        .|+ ...++..|+|.||.+||.+|+..   +..||+||+.+.-+
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            689999999997        222 23455579999999999999975   46899999987643

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

Probab=99.13  E-value=6.8e-11  Score=100.72  Aligned_cols=50  Identities=30%  Similarity=0.739  Sum_probs=43.7

Q ss_pred             CCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          119 PGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       119 ~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+....|.+||+..++   ...+| |||+||+.||..|...+..||+||.....
T Consensus       236 ~~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~p  285 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQP  285 (293)
T ss_pred             CCCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCC
Confidence            3455899999999876   56788 99999999999999999999999998764

>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=99.13  E-value=5.3e-11  Score=73.61  Aligned_cols=44  Identities=59%  Similarity=1.231  Sum_probs=36.9

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL  170 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l  170 (210)
                      +|+||++.+  .+.+...+ |+|.||.+|++.|++. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  34455565 9999999999999987 77899999764

>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=99.13  E-value=4.1e-11  Score=77.36  Aligned_cols=46  Identities=39%  Similarity=0.872  Sum_probs=39.7

Q ss_pred             CCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      +..|.||++...+   +..+| |||. |+..|+..|++.+..||+||+.+.
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999998765   77888 9999 999999999999999999999875

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.11  E-value=1e-10  Score=95.14  Aligned_cols=48  Identities=33%  Similarity=0.718  Sum_probs=39.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc----------------CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS----------------NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~----------------~~~CPlCR~~l~~  172 (210)
                      ++.+|+||++.+++   ..+++ |||.||..||..|+..                +..||+||..+..
T Consensus        17 ~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            35799999999875   34566 9999999999999852                3479999998864

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

Probab=99.11  E-value=3.9e-11  Score=83.48  Aligned_cols=52  Identities=31%  Similarity=0.659  Sum_probs=41.7

Q ss_pred             CccccccCccc------------CCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          123 TECVICLSEFA------------PGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       123 ~~CaICLeef~------------~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      +.|+||...|.            .++.......|+|.||.+||.+||..+..||++|+..+-..
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~   84 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLAD   84 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEec
Confidence            67888877764            23344555679999999999999999999999999887543

>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=99.06  E-value=1.2e-10  Score=71.29  Aligned_cols=39  Identities=46%  Similarity=1.097  Sum_probs=32.8

Q ss_pred             cccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccc
Q 028342          125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlC  166 (210)
                      |+||++.+.+  .+..++ |||.|+.+||.+|++.+..||+|
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            8999999886  445676 99999999999999998899998

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

Probab=98.98  E-value=1.9e-10  Score=107.83  Aligned_cols=54  Identities=37%  Similarity=0.929  Sum_probs=46.7

Q ss_pred             CCCccccccCcccCCCc--eEEcCCCCCccchHHHHHHHhcCCCCcccccccccccc
Q 028342          121 LDTECVICLSEFAPGER--VRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~--vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      .++.|+||+|++..++.  ...++ |+|+||..|+..|++++.+||.||..+.....
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~  345 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDYVL  345 (543)
T ss_pred             cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcccc
Confidence            46899999999998765  67788 99999999999999999999999995554444

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

Probab=98.94  E-value=8.9e-10  Score=91.41  Aligned_cols=50  Identities=30%  Similarity=0.656  Sum_probs=39.1

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC---CCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~---~CPlCR~~l~~~  173 (210)
                      +...+|.|||+.-++  .| ++. |||.|++-||-+||..+.   .||+|+..+..+
T Consensus        45 ~~~FdCNICLd~akd--PV-vTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKD--PV-VTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             CCceeeeeeccccCC--CE-Eee-cccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            345799999998553  44 444 999999999999997654   589999987743

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

Probab=98.92  E-value=6.1e-10  Score=88.93  Aligned_cols=60  Identities=27%  Similarity=0.548  Sum_probs=45.9

Q ss_pred             eccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          112 YSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       112 y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +..+...++.-..|+|||+.+.+...+. . +|||+|+.+||+.-++....||+||..|..+
T Consensus       121 k~v~~~~~~~~~~CPiCl~~~sek~~vs-T-kCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  121 KDVDPLRKEGTYKCPICLDSVSEKVPVS-T-KCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             ccccccccccccCCCceecchhhccccc-c-ccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            3333333344478999999998744432 3 5999999999999999999999999877654

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

Probab=98.92  E-value=1.5e-10  Score=79.96  Aligned_cols=51  Identities=35%  Similarity=0.758  Sum_probs=40.4

Q ss_pred             CCccccccCccc---------CCCceEEcCCCCCccchHHHHHHHhc---CCCCccccccccc
Q 028342          122 DTECVICLSEFA---------PGERVRLLPKCNHGFHVRCIDKWLRS---NSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~---------~~~~vr~lp~C~H~FH~~CI~~Wl~~---~~~CPlCR~~l~~  172 (210)
                      ++.|.||.-+|.         .+|...++..|.|.||.+||.+|+..   +..||+||+.+.-
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            358999999987         33444556679999999999999965   4579999998763

>PHA02926 zinc finger-like protein; Provisional

Probab=98.90  E-value=9.4e-10  Score=90.89  Aligned_cols=51  Identities=35%  Similarity=0.800  Sum_probs=38.6

Q ss_pred             CCCccccccCcccCC----C-ceEEcCCCCCccchHHHHHHHhcC------CCCcccccccc
Q 028342          121 LDTECVICLSEFAPG----E-RVRLLPKCNHGFHVRCIDKWLRSN------SSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~----~-~vr~lp~C~H~FH~~CI~~Wl~~~------~~CPlCR~~l~  171 (210)
                      .+.+|+||+|..-+.    + .--+|+.|+|.||..||..|.+.+      .+||+||..+.
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            458999999986432    1 123566699999999999999753      35999998754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.90  E-value=1.3e-09  Score=68.51  Aligned_cols=44  Identities=34%  Similarity=0.853  Sum_probs=38.6

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH  168 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~  168 (210)
                      +|.||+++|.+....++++ |||+|+..|++.+......||+||+
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            5999999996667788887 9999999999999866678999984

>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=98.84  E-value=1.8e-09  Score=66.50  Aligned_cols=39  Identities=46%  Similarity=1.121  Sum_probs=32.9

Q ss_pred             cccccCcccCCCceEEcCCCCCccchHHHHHHHh--cCCCCccc
Q 028342          125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR--SNSSCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~--~~~~CPlC  166 (210)
                      |+||++.+.+..  +.++ |||.|+.+||..|++  ....||+|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999987633  5777 999999999999998  44579998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....

>smart00184 RING Ring finger

Probab=98.84  E-value=2.9e-09  Score=63.42  Aligned_cols=38  Identities=50%  Similarity=1.228  Sum_probs=32.1

Q ss_pred             cccccCcccCCCceEEcCCCCCccchHHHHHHHh-cCCCCccc
Q 028342          125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlC  166 (210)
                      |+||++..   .....++ |+|.||..|++.|++ .+..||+|
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            78999883   3467777 999999999999998 56679987

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

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

Probab=98.79  E-value=2.6e-09  Score=77.90  Aligned_cols=50  Identities=30%  Similarity=0.721  Sum_probs=40.8

Q ss_pred             CccccccCccc-------------CCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          123 TECVICLSEFA-------------PGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       123 ~~CaICLeef~-------------~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      +.|+||...+.             .++.......|+|.||.+||.+||+.+..||+|.++++-
T Consensus        47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~  109 (114)
T KOG2930|consen   47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVF  109 (114)
T ss_pred             chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeE
Confidence            67999877653             334455566799999999999999999999999888764

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

Probab=98.79  E-value=4.9e-09  Score=65.34  Aligned_cols=38  Identities=39%  Similarity=0.980  Sum_probs=29.6

Q ss_pred             cccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCccc
Q 028342          125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlC  166 (210)
                      |+||++.|.+   ...++ |||.|+..||..|++..    ..||.|
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            8999999997   67787 99999999999999654    369988

>smart00504 Ubox Modified RING finger domain

Probab=98.70  E-value=1.5e-08  Score=67.86  Aligned_cols=45  Identities=29%  Similarity=0.485  Sum_probs=39.1

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      -.|+||++.+.+   ..+++ |||+|..+||..|++.+.+||+|+..+.
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKD---PVILP-SGQTYERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCC---CEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence            369999999886   34566 9999999999999998889999998774

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

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

Probab=98.70  E-value=2.6e-08  Score=90.38  Aligned_cols=50  Identities=36%  Similarity=0.873  Sum_probs=39.3

Q ss_pred             CCccccccCccc---CCC-------c----eEEcCCCCCccchHHHHHHHh-cCCCCccccccccc
Q 028342          122 DTECVICLSEFA---PGE-------R----VRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~---~~~-------~----vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~  172 (210)
                      ...|+||+.++.   .+.       .    -+++| |+|+||..|+.+|+. .+..||+||+.|..
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            368999999875   111       1    23467 999999999999998 45599999998864

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

Probab=98.62  E-value=2.6e-08  Score=84.40  Aligned_cols=50  Identities=30%  Similarity=0.697  Sum_probs=40.7

Q ss_pred             CCCCccccccCcccCCC-------ceEEcCCCCCccchHHHHHHH--hcCCCCccccccc
Q 028342          120 GLDTECVICLSEFAPGE-------RVRLLPKCNHGFHVRCIDKWL--RSNSSCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~-------~vr~lp~C~H~FH~~CI~~Wl--~~~~~CPlCR~~l  170 (210)
                      .++..|+||-..+....       ..-.|. |+|+||+.||.-|-  .++++||.|+..+
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekV  280 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKV  280 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHh
Confidence            35689999999887554       456777 99999999999995  5678999997654

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.56  E-value=4.1e-08  Score=88.42  Aligned_cols=48  Identities=33%  Similarity=0.637  Sum_probs=41.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      ....|+||++.|.+   ..+++ |+|.||..||..|+..+..||+||..+..
T Consensus        25 ~~l~C~IC~d~~~~---Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        25 TSLRCHICKDFFDV---PVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccCCCcCchhhhC---ccCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            35799999999875   34577 99999999999999988899999997654

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

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

Probab=98.47  E-value=1.4e-07  Score=60.76  Aligned_cols=42  Identities=26%  Similarity=0.808  Sum_probs=32.5

Q ss_pred             ccccccCcccCCCceEEcCCCC-----CccchHHHHHHHhcC--CCCcccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCN-----HGFHVRCIDKWLRSN--SSCPKCR  167 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~-----H~FH~~CI~~Wl~~~--~~CPlCR  167 (210)
                      .|.||++. .+++...+.| |.     |.+|..|++.|+..+  .+||+|+
T Consensus         1 ~CrIC~~~-~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDE-GDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCC-CCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48999993 4444555778 75     899999999999654  4799995

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

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

Probab=98.43  E-value=5.1e-08  Score=67.37  Aligned_cols=52  Identities=31%  Similarity=0.668  Sum_probs=25.6

Q ss_pred             CCccccccCcccCCC-c-eEEcC--CCCCccchHHHHHHHhc----C-------CCCcccccccccc
Q 028342          122 DTECVICLSEFAPGE-R-VRLLP--KCNHGFHVRCIDKWLRS----N-------SSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~-~-vr~lp--~C~H~FH~~CI~~Wl~~----~-------~~CPlCR~~l~~~  173 (210)
                      +.+|.||.+.+.+++ . ..+.+  .|++.||..|+.+||+.    +       .+||.|+..|.-+
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            368999999876333 2 23333  79999999999999953    1       2599999988644

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

Probab=98.41  E-value=1.4e-07  Score=79.86  Aligned_cols=51  Identities=29%  Similarity=0.658  Sum_probs=41.3

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHH-HHhcCCC-Cccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDK-WLRSNSS-CPKCRHCLIESC  174 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~-Wl~~~~~-CPlCR~~l~~~~  174 (210)
                      ..+..|+||++....   ...++ |||+|+..||-. |-+.+.- ||+||+....+.
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            346899999998665   55566 999999999999 9777665 999999877543

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

Probab=98.26  E-value=2.2e-07  Score=89.85  Aligned_cols=52  Identities=35%  Similarity=0.784  Sum_probs=39.4

Q ss_pred             CCCCccccccCcccCCC---ceEEcCCCCCccchHHHHHHHhcC--CCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGE---RVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~---~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~  171 (210)
                      +..++||||......-|   .-..++.|+|-||..|+-+|+++.  .+||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            45689999987765211   113455799999999999999874  47999998764

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

Probab=98.24  E-value=9e-07  Score=55.36  Aligned_cols=38  Identities=37%  Similarity=0.853  Sum_probs=22.4

Q ss_pred             cccccCcccCCC-ceEEcCCCCCccchHHHHHHHhcC----CCCc
Q 028342          125 CVICLSEFAPGE-RVRLLPKCNHGFHVRCIDKWLRSN----SSCP  164 (210)
Q Consensus       125 CaICLeef~~~~-~vr~lp~C~H~FH~~CI~~Wl~~~----~~CP  164 (210)
                      |+||.+ |.+.+ ...+|+ |||+|..+||+.++++.    -.||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 457898 99999999999999753    2576

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

Probab=98.18  E-value=5.4e-07  Score=78.69  Aligned_cols=48  Identities=35%  Similarity=0.742  Sum_probs=42.9

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      -.|.||.+-|..   ..++| |+|.||.-||..+|..+..||.|+..+.+..
T Consensus        24 LRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~   71 (442)
T KOG0287|consen   24 LRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESD   71 (442)
T ss_pred             HHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccchhh
Confidence            579999999986   56778 9999999999999999999999999877653

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

Probab=98.18  E-value=9.7e-07  Score=80.74  Aligned_cols=48  Identities=31%  Similarity=0.616  Sum_probs=37.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-----CCCcccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-----SSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-----~~CPlCR~~l~~~  173 (210)
                      +..|+|||++...   ...+ .|||+||..||-.++...     ..||+||..+..+
T Consensus       186 ~~~CPICL~~~~~---p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~k  238 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLK  238 (513)
T ss_pred             CCcCCcccCCCCc---cccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhcccc
Confidence            5789999998653   2233 399999999999988543     4799999988763

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

Probab=98.08  E-value=3e-06  Score=58.85  Aligned_cols=47  Identities=28%  Similarity=0.449  Sum_probs=36.5

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCcccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  173 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~  173 (210)
                      -.|+|+.+-|.+   ..+++ +||.|...||..|++. +.+||+|+..+...
T Consensus         5 f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    5 FLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            579999999987   56677 9999999999999988 78999999887653

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

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

Probab=98.07  E-value=1.6e-06  Score=76.85  Aligned_cols=45  Identities=31%  Similarity=0.900  Sum_probs=35.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc---CCCCcccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS---NSSCPKCR  167 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~---~~~CPlCR  167 (210)
                      .+|.||-+-+.....+.-...|||+||..|+.+|+..   ..+||.||
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~   52 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQ   52 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCcee
Confidence            5899995444454556556579999999999999965   35799999

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.07  E-value=3.3e-06  Score=73.63  Aligned_cols=51  Identities=24%  Similarity=0.599  Sum_probs=37.3

Q ss_pred             CCccccccCc-ccCCC-ceEEcCCCCCccchHHHHHHHh-cCCCCcccccccccc
Q 028342          122 DTECVICLSE-FAPGE-RVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLee-f~~~~-~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~~  173 (210)
                      +..|++|..+ +-..+ .+.+-+ |||.||..||+..+. ....||.|+..+...
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~   56 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKN   56 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence            4689999996 33333 233334 999999999999664 455899999887754

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).

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

Probab=98.05  E-value=1.6e-06  Score=78.06  Aligned_cols=48  Identities=38%  Similarity=0.897  Sum_probs=38.9

Q ss_pred             CCCccccccCcccCCC-ceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGE-RVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~-~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      +-..|+||||-+.... .++... |.|.||..|+..|  ...+||+||-...
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            3479999999988654 344455 9999999999999  5568999998766

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

Probab=98.00  E-value=3.9e-06  Score=74.90  Aligned_cols=50  Identities=34%  Similarity=0.802  Sum_probs=39.1

Q ss_pred             CCCccccccCccc-CCCceEEcCCCCCccchHHHHHHHhc--CCCCccccccc
Q 028342          121 LDTECVICLSEFA-PGERVRLLPKCNHGFHVRCIDKWLRS--NSSCPKCRHCL  170 (210)
Q Consensus       121 ~~~~CaICLeef~-~~~~vr~lp~C~H~FH~~CI~~Wl~~--~~~CPlCR~~l  170 (210)
                      .+..|+|||+++. .++..++.++|||.|-.+||+.||..  +..||.|...-
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            3579999999986 45555566679999999999999952  33699996543

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

Probab=97.98  E-value=3.5e-06  Score=72.32  Aligned_cols=48  Identities=31%  Similarity=0.572  Sum_probs=40.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      ..|-||-+-|..   ...++ |||.|+.-||...|..+..||+||.+.-+..
T Consensus        26 lrC~IC~~~i~i---p~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~esr   73 (391)
T COG5432          26 LRCRICDCRISI---PCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCESR   73 (391)
T ss_pred             HHhhhhhheeec---ceecc-cccchhHHHHHHHhcCCCCCccccccHHhhh
Confidence            689999887764   33455 9999999999999999999999999776543

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

Probab=97.97  E-value=2.8e-06  Score=71.43  Aligned_cols=43  Identities=40%  Similarity=0.861  Sum_probs=38.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      +.-.|+||++.|.+.   .+++ |+|.|+..|+..++.....||.||
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             ccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            457999999999986   7788 999999999999988556799999

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

Probab=97.94  E-value=7.8e-06  Score=71.97  Aligned_cols=54  Identities=33%  Similarity=0.617  Sum_probs=43.6

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCcccccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCQKI  177 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~~  177 (210)
                      +.+.+|.|||.+-++   ..+|| |.|. .|..|-+.-.-.+.+||+||+.+.+.-.-+
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~i~  342 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEELLEIY  342 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHhhheec
Confidence            335799999999776   77899 9995 788898887666778999999988765543

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

Probab=97.84  E-value=8.8e-06  Score=67.60  Aligned_cols=62  Identities=26%  Similarity=0.649  Sum_probs=49.8

Q ss_pred             eccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc--------CCCCcccccccccccc
Q 028342          112 YSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS--------NSSCPKCRHCLIESCQ  175 (210)
Q Consensus       112 y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~--------~~~CPlCR~~l~~~~~  175 (210)
                      |-++.+..++..-|..|-..+..||.+|+.  |-|+||.+|+++|-.+        ...||.|..+|+..-.
T Consensus        40 YLqWL~DsDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~N  109 (299)
T KOG3970|consen   40 YLQWLQDSDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPIN  109 (299)
T ss_pred             HHHHHhhcCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCcc
Confidence            334444455678999999999999999986  9999999999999743        2379999998886544

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

Probab=97.74  E-value=8.2e-06  Score=70.34  Aligned_cols=53  Identities=30%  Similarity=0.758  Sum_probs=45.1

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-----------------------CCCCcccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-----------------------NSSCPKCRHCLIESCQ  175 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-----------------------~~~CPlCR~~l~~~~~  175 (210)
                      ...|.|||--|.+++...+++ |.|.||..|+.++|..                       +..||+||..|.....
T Consensus       115 ~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~  190 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEEN  190 (368)
T ss_pred             CCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccccc
Confidence            368999999999999999998 9999999999988722                       2369999999886655

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

Probab=97.72  E-value=5.8e-06  Score=78.88  Aligned_cols=49  Identities=22%  Similarity=0.442  Sum_probs=42.2

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ...|++|+..+.++......+ |+|.||.+||+.|-+.-.+||+||...-
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~  171 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFG  171 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhh
Confidence            468999999988876666665 9999999999999999999999998654

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

Probab=97.70  E-value=8.2e-06  Score=54.97  Aligned_cols=49  Identities=27%  Similarity=0.520  Sum_probs=23.9

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK  176 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~  176 (210)
                      -.|++|.+-+++   ...+..|.|+|+..||..-+..  .||+|+.+...++-+
T Consensus         8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS--
T ss_pred             cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHH
Confidence            479999988775   3233459999999999886553  499999887765543

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

Probab=97.61  E-value=6.2e-06  Score=72.47  Aligned_cols=52  Identities=37%  Similarity=0.685  Sum_probs=43.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCcccccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIESCQ  175 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~~~~  175 (210)
                      .+-.|+|||+-++.   -+..+.|.|.|+.+||..-++.. ..||.||..+..+..
T Consensus        42 ~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   42 IQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             hhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            35689999998876   45566799999999999999764 579999999986654

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

Probab=97.57  E-value=3.9e-05  Score=68.12  Aligned_cols=49  Identities=41%  Similarity=0.956  Sum_probs=37.6

Q ss_pred             CCCccccccCcccCCC----ceEEcCCCCCccchHHHHHHHh--c-----CCCCcccccc
Q 028342          121 LDTECVICLSEFAPGE----RVRLLPKCNHGFHVRCIDKWLR--S-----NSSCPKCRHC  169 (210)
Q Consensus       121 ~~~~CaICLeef~~~~----~vr~lp~C~H~FH~~CI~~Wl~--~-----~~~CPlCR~~  169 (210)
                      .+.+|.||++...+..    ....+|.|.|.|+..||..|-.  .     .+.||.||..
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~  219 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVP  219 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCc
Confidence            4679999999866433    1234578999999999999973  2     3579999984

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

Probab=97.47  E-value=2.9e-05  Score=50.56  Aligned_cols=48  Identities=25%  Similarity=0.558  Sum_probs=33.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCc-cchHH-HHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHG-FHVRC-IDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~-FH~~C-I~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+++|.||+|.-.+  .  ++-.|||. .+.+| +..|-..+..||+||+++.+
T Consensus         6 ~~dECTICye~pvd--s--VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    6 WSDECTICYEHPVD--S--VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             cccceeeeccCcch--H--HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            34899999987443  2  23349997 45556 44554578899999998764

>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=97.46  E-value=5e-05  Score=58.54  Aligned_cols=38  Identities=24%  Similarity=0.572  Sum_probs=31.6

Q ss_pred             CCccccccCcccCCCceEEcCCCC------CccchHHHHHHHhcC
Q 028342          122 DTECVICLSEFAPGERVRLLPKCN------HGFHVRCIDKWLRSN  160 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~------H~FH~~CI~~Wl~~~  160 (210)
                      .-||+||++.+.+++.++.++ ||      |.||.+|+++|-+.+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~~~   69 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRRER   69 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHhhc
Confidence            479999999999977777776 76      999999999995433

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.

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

Probab=97.30  E-value=0.00011  Score=63.59  Aligned_cols=47  Identities=28%  Similarity=0.530  Sum_probs=37.4

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~  172 (210)
                      ..+|+||+....-   ...++ |+|.|+..||+--.++ +.+|++||.++..
T Consensus         7 ~~eC~IC~nt~n~---Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    7 KKECLICYNTGNC---PVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             CCcceeeeccCCc---Ccccc-ccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            4799999887543   34566 9999999999988766 4579999998763

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

Probab=97.24  E-value=0.00012  Score=65.50  Aligned_cols=52  Identities=29%  Similarity=0.692  Sum_probs=40.8

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc--CCCCccccccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS--NSSCPKCRHCLIESCQKIV  178 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~--~~~CPlCR~~l~~~~~~~~  178 (210)
                      ..|-||-|.-   ..|++-| |||..+..|+..|-..  ..+||.||..|......++
T Consensus       370 eLCKICaend---KdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vii  423 (563)
T KOG1785|consen  370 ELCKICAEND---KDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVII  423 (563)
T ss_pred             HHHHHhhccC---CCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccceee
Confidence            4699997653   4488888 9999999999999744  4689999998876554433

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

Probab=97.22  E-value=9.6e-05  Score=70.67  Aligned_cols=45  Identities=27%  Similarity=0.755  Sum_probs=34.7

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~  171 (210)
                      -.|++|-+-..+  .+  +++|+|+||.+||..-+.. +..||.|...+-
T Consensus       644 LkCs~Cn~R~Kd--~v--I~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg  689 (698)
T KOG0978|consen  644 LKCSVCNTRWKD--AV--ITKCGHVFCEECVQTRYETRQRKCPKCNAAFG  689 (698)
T ss_pred             eeCCCccCchhh--HH--HHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            579999865554  33  3359999999999999965 568999976553

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

Probab=97.18  E-value=0.00027  Score=71.57  Aligned_cols=66  Identities=24%  Similarity=0.560  Sum_probs=48.5

Q ss_pred             hhcceeeeccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----------CCCcccccccc
Q 028342          105 KTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----------SSCPKCRHCLI  171 (210)
Q Consensus       105 ~~lp~~~y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----------~~CPlCR~~l~  171 (210)
                      .-+|...-++.....+.++.|-||+.|--.....+.|. |+|+||-+|...-|.++          -+||+|...+-
T Consensus      3469 ~CLPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3469 HCLPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hcccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            33455554443334456789999999977777788887 99999999998766553          16999988654

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

Probab=97.15  E-value=0.00018  Score=64.22  Aligned_cols=45  Identities=42%  Similarity=1.009  Sum_probs=37.0

Q ss_pred             CCccccccCccc-CCCceEEcCCCCCccchHHHHHHHhcCC--CCcccc
Q 028342          122 DTECVICLSEFA-PGERVRLLPKCNHGFHVRCIDKWLRSNS--SCPKCR  167 (210)
Q Consensus       122 ~~~CaICLeef~-~~~~vr~lp~C~H~FH~~CI~~Wl~~~~--~CPlCR  167 (210)
                      +-.|..|-+.+- .++.+..+| |.|+||..|+.+.|.++.  +||.||
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            467999988764 445677899 999999999999996654  799998

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

Probab=97.15  E-value=0.00014  Score=57.70  Aligned_cols=30  Identities=37%  Similarity=0.798  Sum_probs=27.3

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccch
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHV  150 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~  150 (210)
                      +...||.||||++..++.+..|| |-.+||+
T Consensus       175 ddkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  175 DDKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             ccCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            34579999999999999999999 9999996

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

Probab=97.06  E-value=0.00036  Score=46.23  Aligned_cols=41  Identities=29%  Similarity=0.636  Sum_probs=28.0

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPK  165 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPl  165 (210)
                      +..|+|.+..|++  .++... |+|+|-.+.|.+|++++  ..||+
T Consensus        11 ~~~CPiT~~~~~~--PV~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFED--PVKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SS--EEEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhC--CcCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            4789999999884  455554 99999999999999443  36998

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

Probab=97.04  E-value=0.0012  Score=57.69  Aligned_cols=45  Identities=18%  Similarity=0.349  Sum_probs=36.6

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      .....|+||+...++.-.+.+   -|-+||..||-..+++++.||+=-
T Consensus       298 ~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT~  342 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVTG  342 (357)
T ss_pred             CccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCccC
Confidence            345799999998776444433   689999999999999999999853

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

Probab=96.91  E-value=0.0006  Score=61.83  Aligned_cols=53  Identities=26%  Similarity=0.592  Sum_probs=42.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      +.+..|++|...+.+.-..  . .|||.|+..|+..|+..+..||.||..+.....
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             cccccCccccccccCCCCC--C-CCCCcccccccchhhccCcCCcccccccchhhc
Confidence            4557999999988863222  3 499999999999999999999999887775433

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

Probab=96.88  E-value=0.00058  Score=66.10  Aligned_cols=52  Identities=35%  Similarity=0.762  Sum_probs=41.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-------CCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-------SCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-------~CPlCR~~l~  171 (210)
                      ....+|.||.+.+...+.+-....|.|+||..||..|-++..       .||.|.....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence            345799999999998777766667999999999999986521       5999985444

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

Probab=96.65  E-value=0.00098  Score=60.42  Aligned_cols=48  Identities=35%  Similarity=0.901  Sum_probs=40.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+.+|.||..-+..   ...+| |||.|+..||+.-+.....||.||..+.+
T Consensus        83 sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   83 SEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             chhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            45799999888776   66778 99999999999977767789999999885

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

Probab=96.56  E-value=0.0014  Score=41.56  Aligned_cols=41  Identities=34%  Similarity=0.959  Sum_probs=26.2

Q ss_pred             cccccCcccCCCceEEcC-CCC---CccchHHHHHHHhc--CCCCccc
Q 028342          125 CVICLSEFAPGERVRLLP-KCN---HGFHVRCIDKWLRS--NSSCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp-~C~---H~FH~~CI~~Wl~~--~~~CPlC  166 (210)
                      |-||+++-.+++.+ +.| .|.   ...|.+|+..|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            67999987766533 345 243   37899999999964  4569887

>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=96.45  E-value=0.0013  Score=48.17  Aligned_cols=32  Identities=28%  Similarity=0.692  Sum_probs=26.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHH
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCID  154 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~  154 (210)
                      .+..|++|-..+.. ....+.| |||+||..|++
T Consensus        77 ~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            34789999999877 5666778 99999999975

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

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.38  E-value=0.0037  Score=49.56  Aligned_cols=51  Identities=24%  Similarity=0.600  Sum_probs=35.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCC---ccchHHHHHHHhcC--CCCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNH---GFHVRCIDKWLRSN--SSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H---~FH~~CI~~Wl~~~--~~CPlCR~~l~~~  173 (210)
                      ..+..|-||.++-.  +...-. +|..   .-|.+|+..|+..+  ..|++|+....-.
T Consensus         6 ~~~~~CRIC~~~~~--~~~~PC-~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYD--VVTNYC-NCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCC--CccCCc-ccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            34589999998843  333322 2555   56999999999654  4699998876543

>PHA02862 5L protein; Provisional

Probab=96.26  E-value=0.0039  Score=48.67  Aligned_cols=48  Identities=23%  Similarity=0.589  Sum_probs=34.1

Q ss_pred             CCccccccCcccCCCceEEcCCC---CCccchHHHHHHHhc--CCCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKC---NHGFHVRCIDKWLRS--NSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C---~H~FH~~CI~~Wl~~--~~~CPlCR~~l~~  172 (210)
                      ++.|=||+++-+  +.+.-.. |   ...-|.+|+.+|++.  +..|++|+.+..-
T Consensus         2 ~diCWIC~~~~~--e~~~PC~-C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCD--ERNNFCG-CNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCC--CCccccc-ccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            468999999843  3332222 4   367899999999965  3479999987653

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.11  E-value=0.0069  Score=51.28  Aligned_cols=64  Identities=13%  Similarity=0.138  Sum_probs=51.6

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccccccccCCCCCCC
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIVGCSQASS  185 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~~~~~~~~~~  185 (210)
                      ...|+||.+.+.+.-.+.+|..|||+|..+|++..++.-..||+|-..+.+.+=.-.-.++|+=
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~LqrGGTGf  284 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQRGGTGF  284 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeeecccccc
Confidence            3679999999998888877777999999999999999999999998888765443333355543

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

Probab=96.02  E-value=0.0058  Score=38.96  Aligned_cols=44  Identities=23%  Similarity=0.553  Sum_probs=22.0

Q ss_pred             cccccCcccCCC-ceEEcCCCCCccchHHHHHHHhc-CCCCcccccc
Q 028342          125 CVICLSEFAPGE-RVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHC  169 (210)
Q Consensus       125 CaICLeef~~~~-~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~  169 (210)
                      |++|.+++...+ ...-.+ |++.++..|...-+++ ...||-||.+
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence            789999984433 334444 8899989998887763 6689999975

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

Probab=95.95  E-value=0.0033  Score=55.73  Aligned_cols=46  Identities=28%  Similarity=0.553  Sum_probs=34.6

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      .+.|.||+++..+   ...+| |||+=+  |...-.. -.+||+||+.+.-..
T Consensus       305 p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs~~-l~~CPvCR~rI~~~~  350 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCSKH-LPQCPVCRQRIRLVR  350 (355)
T ss_pred             CCceEEecCCccc---eeeec-CCcEEE--chHHHhh-CCCCchhHHHHHHHH
Confidence            4789999999887   66788 999955  7666432 234999999886543

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

Probab=95.92  E-value=0.004  Score=57.85  Aligned_cols=48  Identities=29%  Similarity=0.594  Sum_probs=36.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-----CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-----NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-----~~~CPlCR~~l~~  172 (210)
                      +.-+|.+|.++-++   .+... |.|.||.-||.+++..     .-+||+|...|.-
T Consensus       535 ~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi  587 (791)
T KOG1002|consen  535 GEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI  587 (791)
T ss_pred             CceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence            34799999887554   44554 9999999999998743     4589999876653

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

Probab=95.90  E-value=0.0041  Score=56.01  Aligned_cols=45  Identities=27%  Similarity=0.718  Sum_probs=37.5

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--------CCCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--------SSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--------~~CPlCR~  168 (210)
                      ..|.||+++....+....+| |+|+|+..|...++..+        -+||-+..
T Consensus       185 f~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             ccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            68999999988878889999 99999999999998442        25876643

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

Probab=95.87  E-value=0.00041  Score=61.89  Aligned_cols=49  Identities=24%  Similarity=0.598  Sum_probs=43.4

Q ss_pred             CCccccccCcccCC-CceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPG-ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~-~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ...|+||.+.++.. +.+..+. |||++|.+|+..||..+..||.||+.|.
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~  245 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELP  245 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence            36899999999877 6677776 9999999999999999999999999775

>PHA03096 p28-like protein; Provisional

Probab=95.86  E-value=0.0039  Score=54.18  Aligned_cols=46  Identities=26%  Similarity=0.606  Sum_probs=32.9

Q ss_pred             CccccccCcccCCC----ceEEcCCCCCccchHHHHHHHhcC---CCCccccc
Q 028342          123 TECVICLSEFAPGE----RVRLLPKCNHGFHVRCIDKWLRSN---SSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~----~vr~lp~C~H~FH~~CI~~Wl~~~---~~CPlCR~  168 (210)
                      .+|.||++......    .--.|+.|.|.|+..||..|...+   ..||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            58999999876432    223577899999999999998542   24555443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.84  E-value=0.013  Score=38.20  Aligned_cols=35  Identities=26%  Similarity=0.745  Sum_probs=31.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHH
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDK  155 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~  155 (210)
                      ....|.+|-+.|.+++.+.+.|.|+-.+|.+|-+.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            34789999999998899999999999999999654

>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=95.76  E-value=0.0046  Score=38.51  Aligned_cols=41  Identities=34%  Similarity=0.831  Sum_probs=23.2

Q ss_pred             cccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC--CCccc
Q 028342          125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS--SCPKC  166 (210)
Q Consensus       125 CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~--~CPlC  166 (210)
                      |.+|-+-.-.|...... .|+=.+|..|++.+++.+.  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            66776665555444333 4888999999999998766  69988

; PDB: 3NW0_A 2CT0_A.

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

Probab=95.75  E-value=0.0021  Score=56.31  Aligned_cols=50  Identities=24%  Similarity=0.611  Sum_probs=42.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ....|.+|-+-|.+...+.   .|-|-||..||-..|....+||.|...+-..
T Consensus        14 ~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             cceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            3579999999988755543   4999999999999999999999998877644

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

Probab=95.64  E-value=0.017  Score=51.21  Aligned_cols=67  Identities=21%  Similarity=0.367  Sum_probs=46.6

Q ss_pred             HhhhhhcceeeeccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHH--HhcCCCCcccccccc
Q 028342          101 QKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKW--LRSNSSCPKCRHCLI  171 (210)
Q Consensus       101 ~~~i~~lp~~~y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~W--l~~~~~CPlCR~~l~  171 (210)
                      +..+..-|...-.......++...|.||-+...-   ..++| |+|..+.-|--.-  |-.++.||+||...-
T Consensus        40 KNnlsaEPnlttsSaddtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          40 KNNLSAEPNLTTSSADDTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccccccCCccccccccccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3345555665554444444556789999877554   56788 9999999986543  456789999998654

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

Probab=95.30  E-value=0.012  Score=47.61  Aligned_cols=32  Identities=31%  Similarity=0.880  Sum_probs=26.0

Q ss_pred             CCCCccchHHHHHHHhc----C-------CCCccccccccccc
Q 028342          143 KCNHGFHVRCIDKWLRS----N-------SSCPKCRHCLIESC  174 (210)
Q Consensus       143 ~C~H~FH~~CI~~Wl~~----~-------~~CPlCR~~l~~~~  174 (210)
                      .||.-||.-|+..||+.    +       ..||.|-.++.-+.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            49999999999999964    1       26999988877554

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

Probab=95.12  E-value=0.0079  Score=49.40  Aligned_cols=44  Identities=20%  Similarity=0.525  Sum_probs=36.9

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL  170 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l  170 (210)
                      ..|.||-.+|+.   ..+.. |||.|+..|...-++....|-+|-...
T Consensus       197 F~C~iCKkdy~s---pvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYES---PVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccc---hhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            479999999986   44454 999999999999888888999996543

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

Probab=95.07  E-value=0.024  Score=48.67  Aligned_cols=49  Identities=27%  Similarity=0.484  Sum_probs=34.1

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~  171 (210)
                      ..+.+|++|-+.-..   ..+..+|+|+||.-||..=+...  -+||.|-.+..
T Consensus       237 t~~~~C~~Cg~~Pti---P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTI---PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCC---CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            456899999665221   22222499999999999876543  48999955544

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

Probab=94.94  E-value=0.0093  Score=50.23  Aligned_cols=43  Identities=26%  Similarity=0.701  Sum_probs=32.4

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCcccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLI  171 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~  171 (210)
                      .|-.|.- +..++...++. |+|+||..|...-   .. .||+||.++-
T Consensus         5 hCn~C~~-~~~~~~f~LTa-C~HvfC~~C~k~~---~~~~C~lCkk~ir   48 (233)
T KOG4739|consen    5 HCNKCFR-FPSQDPFFLTA-CRHVFCEPCLKAS---SPDVCPLCKKSIR   48 (233)
T ss_pred             Eeccccc-cCCCCceeeee-chhhhhhhhcccC---Cccccccccceee
Confidence            4666654 34478888886 9999999997763   33 8999999843

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

Probab=94.72  E-value=0.024  Score=49.38  Aligned_cols=43  Identities=30%  Similarity=0.660  Sum_probs=33.2

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHh-cCCCCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~  168 (210)
                      -.|+.|..-..+   ...++-|+|.|+.+||..-|. .-..||.|.+
T Consensus       275 LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            689999776654   233466999999999998875 4568999954

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

Probab=94.44  E-value=0.03  Score=49.83  Aligned_cols=49  Identities=27%  Similarity=0.565  Sum_probs=40.3

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+++.|+||...   .......| |+|.=+..||.+-+.+.+.|=.|+..+.+
T Consensus       420 sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            467899999754   22244567 99999999999999999999999998774

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

Probab=94.32  E-value=0.0088  Score=51.79  Aligned_cols=44  Identities=25%  Similarity=0.680  Sum_probs=31.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCcc-chHHHHHHHhcCCCCcccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGF-HVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~F-H~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ...|+||++.-.+   +..|+ |||.. +.+|-+.    -..||+||+-++..
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~rv  344 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKR----MNECPICRQYIVRV  344 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhccc----cccCchHHHHHHHH
Confidence            5689999988665   77888 99973 3444222    23799999987643

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

Probab=94.27  E-value=0.024  Score=54.81  Aligned_cols=24  Identities=33%  Similarity=0.935  Sum_probs=22.0

Q ss_pred             CCCCCccchHHHHHHHhcCCCCcc
Q 028342          142 PKCNHGFHVRCIDKWLRSNSSCPK  165 (210)
Q Consensus       142 p~C~H~FH~~CI~~Wl~~~~~CPl  165 (210)
                      ..|+|+.|..|..+|+++...||.
T Consensus      1046 g~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1046 GTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccccHHHHHHHHhcCCcCCC
Confidence            359999999999999999999985

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

Probab=93.16  E-value=0.043  Score=53.82  Aligned_cols=36  Identities=22%  Similarity=0.533  Sum_probs=28.6

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHH
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL  157 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl  157 (210)
                      +-++.|.+|.-.+... .-.+.| |||.||.+||..-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            3468999998887753 445667 99999999998875

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

Probab=93.02  E-value=0.043  Score=53.60  Aligned_cols=42  Identities=26%  Similarity=0.699  Sum_probs=30.6

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL  170 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l  170 (210)
                      ..|..|-...+-   ..+--.|||.||.+|++   .....||-|+.++
T Consensus       841 skCs~C~~~Ldl---P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDL---PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCcccc---ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            589999776553   22222399999999999   4556799998833

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

Probab=92.94  E-value=0.051  Score=47.18  Aligned_cols=45  Identities=27%  Similarity=0.455  Sum_probs=37.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ..|-||...|..   ..+. .|+|-|+..|-..=++....|.+|-+...
T Consensus       242 f~c~icr~~f~~---pVvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYR---PVVT-KCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             cccccccccccc---chhh-cCCceeehhhhccccccCCcceecccccc
Confidence            469999999986   3344 49999999999988888899999977654

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

Probab=92.75  E-value=0.085  Score=45.71  Aligned_cols=47  Identities=32%  Similarity=0.755  Sum_probs=38.4

Q ss_pred             CccccccCcccCCCc---eEEcCCCCCccchHHHHHHHhcCC-CCccccccc
Q 028342          123 TECVICLSEFAPGER---VRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCL  170 (210)
Q Consensus       123 ~~CaICLeef~~~~~---vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l  170 (210)
                      .+|-||-++|..++.   .|.+. |||.|+..|+..-+.+.. .||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            589999999987643   35665 999999999998876644 699999985

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

Probab=92.55  E-value=0.039  Score=56.12  Aligned_cols=45  Identities=31%  Similarity=0.699  Sum_probs=37.9

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHC  169 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~  169 (210)
                      ...|.||++.+.....+..   |||.++..|+..|+..+..||.|...
T Consensus      1153 ~~~c~ic~dil~~~~~I~~---cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGIAG---CGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             ccchHHHHHHHHhcCCeee---echhHhhhHHHHHHHHhccCcchhhh
Confidence            3589999999886444442   99999999999999999999999743

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

Probab=92.41  E-value=0.049  Score=52.77  Aligned_cols=48  Identities=31%  Similarity=0.692  Sum_probs=36.9

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIESCQ  175 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~~~~~  175 (210)
                      ..|.||++    .+.....+ |+|.|+.+|+..-+...  ..||+||..+.++.-
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL  504 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence            68999999    23445555 99999999999887543  369999998875543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=92.38  E-value=0.15  Score=43.73  Aligned_cols=50  Identities=18%  Similarity=0.398  Sum_probs=38.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ....|+|...+|........+-.|||+|-..+|++- +....||+|-.++.
T Consensus       112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~  161 (260)
T PF04641_consen  112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFT  161 (260)
T ss_pred             ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccc
Confidence            347899999999655444444339999999999997 33457999977766

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

Probab=91.75  E-value=0.095  Score=45.35  Aligned_cols=45  Identities=27%  Similarity=0.648  Sum_probs=37.0

Q ss_pred             CccccccCcccCCC-ceEEcCCCCCccchHHHHHHHhcCCCCccccc
Q 028342          123 TECVICLSEFAPGE-RVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~-~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~  168 (210)
                      ..|+||.+.+-... .+..++ |||.-|..|+......+-+||+|..
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            45999999865544 445666 9999999999999887899999977

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=91.53  E-value=0.093  Score=34.34  Aligned_cols=42  Identities=29%  Similarity=0.602  Sum_probs=29.7

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      .|-.|...   +..-.++| |+|+....|++-|  +-.-||.|-..+.
T Consensus         9 ~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~   50 (55)
T PF14447_consen    9 PCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFE   50 (55)
T ss_pred             eEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCccc
Confidence            45555433   23345677 9999999998875  5556999977665

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=91.49  E-value=0.15  Score=45.19  Aligned_cols=59  Identities=19%  Similarity=0.424  Sum_probs=39.4

Q ss_pred             CCCCccccccCcccCCCce-EEcCCCCCccchHHHHHHHh-cCCCCcccccccccccccccC
Q 028342          120 GLDTECVICLSEFAPGERV-RLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIESCQKIVG  179 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~v-r~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~~~~~~~~  179 (210)
                      ++++-|+.|++++.-.|+- .-+| ||-..+.-|...--+ -+..||-||+...+..-+++.
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~   72 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVT   72 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccccceeEEe
Confidence            4456799999999876654 3456 887766666444322 256899999877655444443

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

Probab=90.95  E-value=0.18  Score=45.33  Aligned_cols=27  Identities=33%  Similarity=1.010  Sum_probs=19.7

Q ss_pred             CCCccchHHHHHHHhc-------------CCCCccccccc
Q 028342          144 CNHGFHVRCIDKWLRS-------------NSSCPKCRHCL  170 (210)
Q Consensus       144 C~H~FH~~CI~~Wl~~-------------~~~CPlCR~~l  170 (210)
                      |.-..+.+|+.+|+..             +..||+||+..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F  350 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF  350 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence            3345578999999944             33699999864

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

>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=90.72  E-value=0.3  Score=38.82  Aligned_cols=36  Identities=25%  Similarity=0.616  Sum_probs=22.3

Q ss_pred             CCccccccCcccCCCce---------EEcCCCCCc-cchHHHHHHHh
Q 028342          122 DTECVICLSEFAPGERV---------RLLPKCNHG-FHVRCIDKWLR  158 (210)
Q Consensus       122 ~~~CaICLeef~~~~~v---------r~lp~C~H~-FH~~CI~~Wl~  158 (210)
                      +..|+||||--.+.-.+         |--- |+-. =|..|++++-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpym-c~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYM-CDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccc-cCCccchhHHHHHHHH
Confidence            46899999876543222         1111 5533 37889999864

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.

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=90.56  E-value=0.22  Score=41.11  Aligned_cols=41  Identities=39%  Similarity=0.815  Sum_probs=31.0

Q ss_pred             CCCccccccCc-----ccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          121 LDTECVICLSE-----FAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       121 ~~~~CaICLee-----f~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      .+..|.+|-++     |+. +.+...++|+-+||.+|..     +..||-|-
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            35789999753     333 4667788899999999976     36799993

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

Probab=90.14  E-value=0.14  Score=48.40  Aligned_cols=49  Identities=33%  Similarity=0.798  Sum_probs=40.8

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK  176 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~  176 (210)
                      +..+.|+||++++    ..+..+ |.   |.-|+..|+..+..||+|+..+......
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~  525 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFL  525 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccccc
Confidence            4468999999998    456666 88   9999999999999999999988765553

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

Probab=89.15  E-value=0.11  Score=49.55  Aligned_cols=42  Identities=29%  Similarity=0.585  Sum_probs=31.5

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      -.|.||+..|......-+...|||..+.+|+..-  -+.+|| |.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~   53 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TK   53 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CC
Confidence            4799999998765544333459999999999874  466788 53

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

Probab=88.65  E-value=1.2  Score=26.83  Aligned_cols=30  Identities=17%  Similarity=0.369  Sum_probs=14.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Q 028342           49 NVLMVLSVLLCALICAIGLASLVKCSLRCSR   79 (210)
Q Consensus        49 ~~iiil~il~~~li~~l~l~~i~~~~~r~~~   79 (210)
                      .+.++.++++.+.++++.+. .+-|++|+.+
T Consensus         5 ~IaIIv~V~vg~~iiii~~~-~YaCcykk~~   34 (38)
T PF02439_consen    5 TIAIIVAVVVGMAIIIICMF-YYACCYKKHR   34 (38)
T ss_pred             hhhHHHHHHHHHHHHHHHHH-HHHHHHcccc
Confidence            34555555555444444443 4445555443

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

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

Probab=88.43  E-value=0.19  Score=45.65  Aligned_cols=38  Identities=26%  Similarity=0.624  Sum_probs=28.6

Q ss_pred             CCccccccCcccCC-CceEEcCCCCCccchHHHHHHHhcC
Q 028342          122 DTECVICLSEFAPG-ERVRLLPKCNHGFHVRCIDKWLRSN  160 (210)
Q Consensus       122 ~~~CaICLeef~~~-~~vr~lp~C~H~FH~~CI~~Wl~~~  160 (210)
                      ..+|.||..+...+ +... ..+|+|.|+.+|+.+.+..+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~-~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFS-VLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHH-HhcccchhhhHHhHHHhhhh
Confidence            47899999555544 4444 44599999999999998644

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

Probab=87.58  E-value=0.23  Score=43.55  Aligned_cols=44  Identities=30%  Similarity=0.620  Sum_probs=28.1

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ..|--|--.+.  .--|..| |+|+||.+|-..  ..-+.||.|-..+.
T Consensus        91 HfCd~Cd~PI~--IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcce--eeecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            35766633322  2236788 999999999654  23457999965443

>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=87.57  E-value=0.23  Score=42.08  Aligned_cols=48  Identities=27%  Similarity=0.740  Sum_probs=35.6

Q ss_pred             CCCccccccCcc-c-CCCceEEcCCCCCccchHHHHHHHhc-CCCCc--cccc
Q 028342          121 LDTECVICLSEF-A-PGERVRLLPKCNHGFHVRCIDKWLRS-NSSCP--KCRH  168 (210)
Q Consensus       121 ~~~~CaICLeef-~-~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CP--lCR~  168 (210)
                      .+..|+||-.+. - .+-.+-+-|.|-|..|..|++.-+.. ...||  -|-.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            346899998873 3 33344455789999999999999965 45899  7743

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

Probab=86.87  E-value=0.41  Score=41.41  Aligned_cols=51  Identities=27%  Similarity=0.686  Sum_probs=35.9

Q ss_pred             CCccccccCcccCCCc-eEEcCCCC-----CccchHHHHHHHhc--CCCCcccccccccc
Q 028342          122 DTECVICLSEFAPGER-VRLLPKCN-----HGFHVRCIDKWLRS--NSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~-vr~lp~C~-----H~FH~~CI~~Wl~~--~~~CPlCR~~l~~~  173 (210)
                      +..|-||.++...... ....| |.     +..|..|++.|+..  ...|.+|.......
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4789999998664332 23444 54     67799999999974  44699997755433

>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=86.52  E-value=0.62  Score=40.47  Aligned_cols=46  Identities=22%  Similarity=0.640  Sum_probs=33.1

Q ss_pred             ccccccCc-ccCCCce-EEcCCCCCccchHHHHHHHh-cCCCCccccccc
Q 028342          124 ECVICLSE-FAPGERV-RLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCL  170 (210)
Q Consensus       124 ~CaICLee-f~~~~~v-r~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l  170 (210)
                      .|++|-.. |-+.+.. .+-+ |+|..+..|++.-+. ....||-|-..|
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~-C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINE-CGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeecc-ccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            58888766 3333433 3335 999999999999985 456899996544

>smart00249 PHD PHD zinc finger

Probab=84.67  E-value=0.79  Score=27.47  Aligned_cols=31  Identities=19%  Similarity=0.504  Sum_probs=23.0

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHH
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDK  155 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~  155 (210)
                      .|.+|.... +++.++....|+..||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            378887766 4455666667999999999754

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

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.50  E-value=0.48  Score=40.54  Aligned_cols=52  Identities=27%  Similarity=0.742  Sum_probs=34.7

Q ss_pred             CCCCccccccCcccCCCce-EEcC-CCC---CccchHHHHHHHhcC--------CCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERV-RLLP-KCN---HGFHVRCIDKWLRSN--------SSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~v-r~lp-~C~---H~FH~~CI~~Wl~~~--------~~CPlCR~~l~  171 (210)
                      +.+..|=||+..=+++..- -+-| .|.   |=-|..|+..|+..+        -.||-|+..-.
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            3457899999875544322 1233 143   889999999999332        15999988654

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

Probab=83.98  E-value=0.96  Score=44.09  Aligned_cols=41  Identities=24%  Similarity=0.508  Sum_probs=31.1

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPK  165 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPl  165 (210)
                      ..|.+|-..+..  .....+.|+|.-|.+|+..|+.....||.
T Consensus       780 ~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            478999665443  22245579999999999999988887766

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

Probab=82.86  E-value=2.4  Score=32.39  Aligned_cols=17  Identities=6%  Similarity=0.124  Sum_probs=7.9

Q ss_pred             hHHHHHHHHHHHHHHHH
Q 028342           49 NVLMVLSVLLCALICAI   65 (210)
Q Consensus        49 ~~iiil~il~~~li~~l   65 (210)
                      ..+|++++++.++.++|
T Consensus        66 i~~Ii~gv~aGvIg~Il   82 (122)
T PF01102_consen   66 IIGIIFGVMAGVIGIIL   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             eeehhHHHHHHHHHHHH
Confidence            34455555544444333

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

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

Probab=82.84  E-value=1.1  Score=40.60  Aligned_cols=45  Identities=18%  Similarity=0.409  Sum_probs=37.2

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC---CCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS---SCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~---~CPlCR~  168 (210)
                      -.|||=-++=.++.....|. |||+...+-+.+--++..   .||.|=.
T Consensus       335 F~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  335 FICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             eecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            57999888877777778887 999999999999877654   6999943

>PF15050 SCIMP: SCIMP protein

Probab=82.83  E-value=2.8  Score=31.85  Aligned_cols=32  Identities=22%  Similarity=0.399  Sum_probs=15.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHH--HHHHHhccCcc
Q 028342           49 NVLMVLSVLLCALICAIGLAS--LVKCSLRCSRL   80 (210)
Q Consensus        49 ~~iiil~il~~~li~~l~l~~--i~~~~~r~~~~   80 (210)
                      +.||||++.++++.+.|++++  ++|+.+|..+.
T Consensus         7 nFWiiLAVaII~vS~~lglIlyCvcR~~lRqGkk   40 (133)
T PF15050_consen    7 NFWIILAVAIILVSVVLGLILYCVCRWQLRQGKK   40 (133)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            456666665444444444333  34444444433

>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=82.74  E-value=0.69  Score=29.06  Aligned_cols=43  Identities=23%  Similarity=0.563  Sum_probs=30.3

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHh------cCCCCcccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR------SNSSCPKCR  167 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~------~~~~CPlCR  167 (210)
                      .|.||.. ..+++.+.....|+..||..|+..=..      ..-.||.|+
T Consensus         1 ~C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            3889988 444556666777999999999876542      123688775

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 ....

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

Probab=82.73  E-value=1.1  Score=44.03  Aligned_cols=52  Identities=23%  Similarity=0.545  Sum_probs=38.5

Q ss_pred             CCCCCccccccCcccCCCceEEcC-CCC---CccchHHHHHHHhcC--CCCcccccccc
Q 028342          119 PGLDTECVICLSEFAPGERVRLLP-KCN---HGFHVRCIDKWLRSN--SSCPKCRHCLI  171 (210)
Q Consensus       119 ~~~~~~CaICLeef~~~~~vr~lp-~C~---H~FH~~CI~~Wl~~~--~~CPlCR~~l~  171 (210)
                      ++++..|-||..+=-.++.+-. | +|.   .-.|.+|+-+|+.-.  ..|-+|+.+..
T Consensus         9 N~d~~~CRICr~e~~~d~pLfh-PCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLFH-PCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             CccchhceeecCCCCCCCcCcc-cccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            4456899999998666666533 3 243   568999999999754  46999988765

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.62  E-value=0.82  Score=39.89  Aligned_cols=36  Identities=19%  Similarity=0.490  Sum_probs=25.9

Q ss_pred             CCCccchHHHHHHHhc-------------CCCCcccccccccccccccC
Q 028342          144 CNHGFHVRCIDKWLRS-------------NSSCPKCRHCLIESCQKIVG  179 (210)
Q Consensus       144 C~H~FH~~CI~~Wl~~-------------~~~CPlCR~~l~~~~~~~~~  179 (210)
                      |.-..+.+|+.+|+..             +.+||+||...--.+-.+++
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~  373 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVD  373 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEE
Confidence            6677889999999833             44799999977655444433

>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=81.37  E-value=1.1  Score=28.54  Aligned_cols=44  Identities=23%  Similarity=0.521  Sum_probs=25.1

Q ss_pred             ccccccCcccCCCceEEcCCCC-CccchHHHHHHHhcCCCCcccccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCN-HGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~-H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      -|--|+-+.+.   ++.   |+ |-.+-.|+..-+.....||+|..+|.++
T Consensus         4 nCKsCWf~~k~---Li~---C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFANKG---LIK---CSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S--SS---EEE----SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcCCC---eee---ecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            35556644332   333   76 9999999999999999999999888754

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.

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

Probab=81.03  E-value=1.3  Score=28.60  Aligned_cols=42  Identities=31%  Similarity=0.812  Sum_probs=22.3

Q ss_pred             cccccCcccCCC------ceEEcCCCCCccchHHHHHHHhc-CCCCcccc
Q 028342          125 CVICLSEFAPGE------RVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCR  167 (210)
Q Consensus       125 CaICLeef~~~~------~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR  167 (210)
                      |--|+..|..+.      ..-..|+|++.|+.+| |..+-. =.+||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC-DVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHH-HHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCc-ChhhhccccCCcCCC
Confidence            556777777652      4566788999999998 333322 23799883

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=80.46  E-value=0.58  Score=44.54  Aligned_cols=41  Identities=27%  Similarity=0.771  Sum_probs=27.4

Q ss_pred             CCccccccC-----cccCCCceEEcCCCCCccchHHHHHHHhcCCCCccc
Q 028342          122 DTECVICLS-----EFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC  166 (210)
Q Consensus       122 ~~~CaICLe-----ef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlC  166 (210)
                      ...|.+|-.     .|+ .+.++.+-.|+++||..|+..   ....||.|
T Consensus       511 gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  511 GFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             eeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence            467888822     133 344555556999999999655   34459999

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

Probab=80.39  E-value=1.4  Score=38.79  Aligned_cols=44  Identities=20%  Similarity=0.538  Sum_probs=31.7

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      -+|+||.+.+...  +.+.+ =||.-+..|-.   +....||.||.++..
T Consensus        49 leCPvC~~~l~~P--i~QC~-nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   49 LDCPVCFNPLSPP--IFQCD-NGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             ccCchhhccCccc--ceecC-CCcEehhhhhh---hhcccCCcccccccc
Confidence            5899999998752  23322 35888888854   346689999998873

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	210
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-11
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		7e-09
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		3e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		6e-07
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		9e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		1e-04

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 25/44 (56%), Positives = 31/44 (70%)
Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           EC +CL+E   GE  R LP+C HGFH  C+D WL S+S+CP CR
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 34/45 (75%), Gaps = 1/45 (2%)
Query: 123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           T CV+C+ +F   + +R+LP CNH FH +C+DKWL++N +CP CR
Sbjct: 24  TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
           G   EC +C  ++A GE VR LP CNH FH  CI  WL  + SCP CR  L
Sbjct: 13  GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           +C ICLS    GE VR LP C H FH  C+D+WL +N  CP CR
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           G +  C IC SE+  G+    LP C+H FH  C+  WL+ + +CP CR
Sbjct: 38  GQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 113 STELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKC 166
           S ++K   L   C +CL +F P + + + P C H FH +C+ KWL     CP C
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	210
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-27
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-25
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	4e-25
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	9e-22
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-21
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-21
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-16
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	3e-12
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	8e-12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-09
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-09
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	8e-09
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	9e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-08
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-06
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	6e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-06
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	3e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	8e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-04

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

 Score = 97.3 bits (243), Expect = 3e-27
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 171
             EC +CL+E   GE  R LP+C HGFH  C+D WL S+S+CP CR  ++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

 Score = 93.2 bits (232), Expect = 3e-25
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 100 KQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS 159
            ++++     +  + +    G +  C IC SE+  G+    LP C+H FH  C+  WL+ 
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQK 76

Query: 160 NSSCPKCRHCL 170
           + +CP CR   
Sbjct: 77  SGTCPVCRCMF 87

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

 Score = 92.4 bits (230), Expect = 4e-25
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 101 QKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN 160
             +       +++         T CV+C+ +F   + +R+LP CNH FH +C+DKWL++N
Sbjct: 3   SGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN 60

Query: 161 SSCPKCRHCLIES 173
            +CP CR     S
Sbjct: 61  RTCPICRADSGPS 73

>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 = 83.6 bits (207), Expect = 9e-22
 Identities = 24/50 (48%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 119 PGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
              + +C ICLS    GE VR LP C H FH  C+D+WL +N  CP CR 
Sbjct: 11  EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRV 59

>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 = 83.2 bits (206), Expect = 2e-21
 Identities = 25/49 (51%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
             EC +C  ++A GE VR LP CNH FH  CI  WL  + SCP CR  L
Sbjct: 15  GLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

 Score = 82.1 bits (203), Expect = 4e-21
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 113 STELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE 172
           S ++K   L   C +CL +F P + + + P C H FH +C+ KWL     CP C   +++
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ 64

Query: 173 SCQKIVGCS 181
             Q     S
Sbjct: 65  LAQLSGPSS 73

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

 Score = 70.3 bits (172), Expect = 2e-16
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           +   C+ C +E    + V +  +CNH FH  C+  W++ N+ CP C+
Sbjct: 25  VMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

>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 = 68.8 bits (169), Expect = 3e-16
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
            + C ICL +      V  +  C H  H  C ++ L+    CP C 
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 62.4 bits (152), Expect = 1e-13
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 173
           + EC IC+   A      +LP C H F  +CIDKW   + +CP CR  +  +
Sbjct: 15  EEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA 61

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

 Score = 59.0 bits (143), Expect = 3e-12
 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 118 LPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
           +  +   C ICL +         LP C H F   CI +W+R N +CP C+ 
Sbjct: 1   MATVAERCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKV 48

>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 = 58.7 bits (141), Expect = 8e-12
 Identities = 19/96 (19%), Positives = 31/96 (32%), Gaps = 17/96 (17%)

Query: 86  SANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVIC--------------LSE 131
             ++    +  +G K+  +K +  V          +   C IC               + 
Sbjct: 4   DVDTPSGTNSGAGKKRFEVKKWNAVALW---AWDIVVDNCAICRNHIMDLCIECQANQAS 60

Query: 132 FAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
               E       CNH FH  CI +WL++   CP   
Sbjct: 61  ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 57.6 bits (138), Expect = 3e-11
 Identities = 20/101 (19%), Positives = 31/101 (30%), Gaps = 17/101 (16%)

Query: 81  EASESSANSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVIC------------ 128
           E +          +  +G K+  +K +  V          +   C IC            
Sbjct: 10  EENLYFQGGGRGTNSGAGKKRFEVKKWNAVALW---AWDIVVDNCAICRNHIMDLCIECQ 66

Query: 129 --LSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
              +     E       CNH FH  CI +WL++   CP   
Sbjct: 67  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 120 GLDTECVICLSEF---APGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
           G    C IC+  +       R+ +  +C H F  +C+   L++ ++CP CR 
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52

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

 Score = 51.1 bits (122), Expect = 2e-09
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 119 PGLDTECVICLSEFAPGERVRLLP---KCNHGFHVRCIDKWLRSNSSCPKCRH 168
           P     C IC+  ++   +   L    +C H F  +C+   L++ ++CP CR 
Sbjct: 12  PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64

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

 Score = 51.8 bits (123), Expect = 3e-09
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 20/82 (24%)

Query: 107 FTVVKYSTELKLPGLDTECVICLSEFAPG--------------ERVRLLPKCNHGFHVRC 152
             + KY+ ELK+   + +C+IC+ + A                  V  L KC+H FH+ C
Sbjct: 11  QVIRKYTEELKVA-PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLC 69

Query: 153 IDKWLRSNS-----SCPKCRHC 169
           +     + +      CP C+  
Sbjct: 70  LLAMYCNGNKDGSLQCPSCKTI 91

>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 = 50.2 bits (120), Expect = 5e-09
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 119 PGLDTECVICLSEFAPGERVRLLP---KCNHGFHVRCIDKWLRSNSSCPKCRH 168
           P     C IC+  ++   +   L    +C H F  +C+   L++ ++CP CR 
Sbjct: 7   PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59

>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 = 49.9 bits (119), Expect = 8e-09
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 5/46 (10%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS--NSSCPKCR 167
            C IC S    G+       C    H+ C+ K+ +S     CP C 
Sbjct: 17  ICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCN 59

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

 Score = 53.3 bits (127), Expect = 9e-09
 Identities = 16/72 (22%), Positives = 25/72 (34%), Gaps = 7/72 (9%)

Query: 122 DTECVICLSEFAPGERVRLL----PKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKI 177
           +  C IC +    G  V L+     KC    H  C+++W ++              C   
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQC--- 364

Query: 178 VGCSQASSSSMA 189
             C    S+S A
Sbjct: 365 PFCKAKLSTSFA 376

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 49.1 bits (117), Expect = 2e-08
 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 4/51 (7%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL-RSNSSCPKCRHCLIES 173
            C IC+ +       RL P C+      CI +WL    + CP CR  L   
Sbjct: 24  RCFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 71

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

 Score = 48.2 bits (114), Expect = 4e-07
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 5/52 (9%)

Query: 119 PGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS--NSSCPKCRH 168
           P     C IC S    G+       C    H+ C+ K+ +S     CP C  
Sbjct: 177 PDAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

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

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 173
            C IC            + +C H F   CI +    ++ CPKC   + ++
Sbjct: 17  LCSICKGYL---IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQT 63

>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 = 46.3 bits (109), Expect = 2e-06
 Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 6/69 (8%)

Query: 111 KYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHC 169
           +Y    ++      C IC         V++ P C H     C+  W  S    CP CR C
Sbjct: 321 QYELYCEMGSTFQLCKICAENDK---DVKIEP-CGHLMCTSCLTSWQESEGQGCPFCR-C 375

Query: 170 LIESCQKIV 178
            I+  + IV
Sbjct: 376 EIKGTEPIV 384

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 10/94 (10%)

Query: 113 STELKLPGLDTE--CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
           +T +K+  L+    CV+C   F        + +C H F   CI ++L ++  CP C   +
Sbjct: 4   TTRIKITELNPHLMCVLCGGYF---IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

Query: 171 IESCQKIVGCSQASSSSMAMQESVSNIVPLEPES 204
            ++            S   +Q+ V  +VP   ++
Sbjct: 61  HKT-----RPLLNIRSDKTLQDIVYKLVPGLFKN 89

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

 Score = 42.1 bits (99), Expect = 6e-06
 Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 4/47 (8%)

Query: 121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
           +   C IC   F     V    KC H F   C  +  R+   C  C 
Sbjct: 14  IPFRCFICRQAFQ--NPVVT--KCRHYFCESCALEHFRATPRCYICD 56

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

 Score = 42.8 bits (100), Expect = 8e-06
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 3/89 (3%)

Query: 122 DTECVICLSEFAPGERVRLLP---KCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQKIV 178
              C IC+  ++   +   L    +C H F  +C+   L++ ++CP CR  +       +
Sbjct: 7   TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 66

Query: 179 GCSQASSSSMAMQESVSNIVPLEPESAVC 207
                + S     +  S IV         
Sbjct: 67  YIGSGTVSCPICMDGYSEIVQNGRLIVST 95

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

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 4/49 (8%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
             EC ICL        V L   C H F   C+         C  CR  +
Sbjct: 15  VPECAICLQTCV--HPVSL--PCKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 40.4 bits (94), Expect = 8e-05
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 170
           + +C+IC   F       +   C H F   CI++W++    CP CR  +
Sbjct: 64  ELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 173
           C IC   F       ++P+C+H +   CI K+L   + CP C   + E 
Sbjct: 25  CGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP 70

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

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 10/48 (20%), Positives = 15/48 (31%), Gaps = 1/48 (2%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRH 168
             EC +C+      +       C +     C  +     N  CP CR 
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.8
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.72
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.66
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.64
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.62
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.62
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.61
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.55
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.51
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.5
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.5
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.5
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.49
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.47
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.46
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.44
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.42
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.42
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.42
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.4
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.38
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.34
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.34
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.33
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.3
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.29
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.26
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.25
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.24
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.23
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.23
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.23
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.22
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.21
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.21
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.2
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.18
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.18
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.15
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.14
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.14
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.11
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.06
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.06
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.03
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.0
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.0
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.99
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.95
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.93
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.92
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.89
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.87
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.86
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.84
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.81
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.8
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.74
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.7
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.69
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.64
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.64
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.63
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.45
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.43
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.39
3nw0_A	238	Non-structural maintenance of chromosomes element	98.26
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.26
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.95
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.75
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.67
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	94.43
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	93.85
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	93.84
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	93.8
1we9_A	64	PHD finger family protein; structural genomics, PH	93.33
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	92.73
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	92.63
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	92.62
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	92.49
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	91.95
2l8s_A	54	Integrin alpha-1; transmembrane region, detergent	91.09
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	90.53
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	89.84
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	89.55
2knc_A	54	Integrin alpha-IIB; transmembrane signaling, prote	89.23
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	88.88
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	88.88
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	88.25
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	88.01
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.88
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	87.85
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	87.79
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	86.9
2yt5_A	66	Metal-response element-binding transcription facto	86.6
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	86.3
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	86.14
2k1a_A	42	Integrin alpha-IIB; single-PASS transmembrane segm	86.07
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	85.91
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	85.53
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	84.67
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	84.59
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	84.58
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	83.3
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	82.96
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	82.63
1wem_A	76	Death associated transcription factor 1; structura	80.79
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	80.64
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	80.51

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

Probab=99.80  E-value=1.1e-19  Score=130.77  Aligned_cols=84  Identities=24%  Similarity=0.584  Sum_probs=73.8

Q ss_pred             CCCCCCCCCCCccHhhhhhcceeeeccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccc
Q 028342           88 NSSGSGSCSSGIKQKALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR  167 (210)
Q Consensus        88 ~~~~~~~~~~gl~~~~i~~lp~~~y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR  167 (210)
                      ..........|++++.++.+|.+.+.......+.+..|+||+++|..++.++.++ |+|.||..||+.|++.+.+||+||
T Consensus         6 ~~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr   84 (91)
T 2l0b_A            6 HHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR   84 (91)
T ss_dssp             CCSCCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTC
T ss_pred             ccCCCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcC
Confidence            3455667788999999999999999876655566789999999999999999999 999999999999999999999999


Q ss_pred             ccccc
Q 028342          168 HCLIE  172 (210)
Q Consensus       168 ~~l~~  172 (210)
                      ..+..
T Consensus        85 ~~~~~   89 (91)
T 2l0b_A           85 CMFPP   89 (91)
T ss_dssp             CBSSC
T ss_pred             ccCCC
Confidence            98764

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

Probab=99.72  E-value=2.2e-18  Score=119.19  Aligned_cols=70  Identities=34%  Similarity=0.824  Sum_probs=59.6

Q ss_pred             hhhhhcceeeeccccCCCCCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          102 KALKTFTVVKYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       102 ~~i~~lp~~~y~~~~~~~~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +.++.+|..+|..... ..++.+|+||+++|..++.++.++ |+|.||.+||+.|++.+.+||+||..+...
T Consensus         4 ~~i~~lp~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            4 GSSGQLPSYRFNPNNH-QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCCSSCCCEEBCSSSC-SSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hhHhhCCcEEecCccc-cCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            4567788888876432 345679999999999999999998 999999999999999999999999988754

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

Probab=99.66  E-value=4.5e-17  Score=105.72  Aligned_cols=51  Identities=49%  Similarity=1.198  Sum_probs=46.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ++.+|+||+++|.+++.+..++.|+|.||.+||..|++.+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            457999999999999988888779999999999999999999999998874

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

Probab=99.64  E-value=2.2e-16  Score=108.63  Aligned_cols=55  Identities=35%  Similarity=0.945  Sum_probs=49.1

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      ..+.+|+||+++|.+++.++.++ |+|.||.+||..|++.+.+||+||..+.....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCS
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccccc
Confidence            34579999999999999999998 99999999999999999999999999875433

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

Probab=99.62  E-value=3.8e-16  Score=108.43  Aligned_cols=55  Identities=47%  Similarity=0.982  Sum_probs=49.2

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      ..+.+|+||+++|.+++.++.++ |+|.||.+||..|++.+.+||+||..+.....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            34579999999999989999998 99999999999999999999999999886543

>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=99.62  E-value=4.5e-16  Score=105.61  Aligned_cols=53  Identities=45%  Similarity=0.960  Sum_probs=48.2

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +.+..|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||..+...
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            44579999999999888899998 999999999999999999999999988754

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

Probab=99.61  E-value=2.6e-16  Score=110.73  Aligned_cols=52  Identities=29%  Similarity=0.754  Sum_probs=43.2

Q ss_pred             CCccccccCcccC-----------CCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          122 DTECVICLSEFAP-----------GERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~-----------~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ++.|+||+++|.+           ++.++.++.|+|.||.+||++||+.+.+||+||+++...
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            4678888888853           455666767999999999999999999999999998744

>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=99.55  E-value=3.4e-15  Score=96.66  Aligned_cols=50  Identities=28%  Similarity=0.653  Sum_probs=43.3

Q ss_pred             CCCccccccCcccCC-CceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPG-ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~-~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      .+.+|+||+++|.++ +.++.++ |+|.||.+||..|++.+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            357999999999654 4567777 9999999999999999999999998764

>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=99.51  E-value=8.6e-15  Score=108.65  Aligned_cols=51  Identities=29%  Similarity=0.740  Sum_probs=42.2

Q ss_pred             CCccccccCcccCCC---------------ceEEcCCCCCccchHHHHHHHh-----cCCCCcccccccccc
Q 028342          122 DTECVICLSEFAPGE---------------RVRLLPKCNHGFHVRCIDKWLR-----SNSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~---------------~vr~lp~C~H~FH~~CI~~Wl~-----~~~~CPlCR~~l~~~  173 (210)
                      +.+|+||+++|.++.               .++.++ |+|+||.+||+.|+.     .+.+||+||..+..+
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            469999999997643               345677 999999999999994     466899999988755

>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=99.50  E-value=1.1e-14  Score=107.55  Aligned_cols=49  Identities=31%  Similarity=0.657  Sum_probs=42.2

Q ss_pred             CCccccccCcccCC---------------CceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPG---------------ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~---------------~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ++.|+||+++|.+.               ..++.++ |+|.||.+||+.||+.+.+||+||+.+.
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            57899999999854               1356676 9999999999999999999999999864

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

Probab=99.50  E-value=1.6e-14  Score=101.57  Aligned_cols=54  Identities=28%  Similarity=0.695  Sum_probs=45.2

Q ss_pred             CCCCCccccccCcccCCCceEEcCCCC-----CccchHHHHHHHhcC--CCCccccccccccc
Q 028342          119 PGLDTECVICLSEFAPGERVRLLPKCN-----HGFHVRCIDKWLRSN--SSCPKCRHCLIESC  174 (210)
Q Consensus       119 ~~~~~~CaICLeef~~~~~vr~lp~C~-----H~FH~~CI~~Wl~~~--~~CPlCR~~l~~~~  174 (210)
                      ..++..|.||+++|.+++.+ ++| |+     |.||.+||++||+.+  .+||+||..+....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            34567999999999887776 588 96     999999999999765  48999999987543

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

Probab=99.50  E-value=1.4e-14  Score=97.70  Aligned_cols=52  Identities=23%  Similarity=0.614  Sum_probs=44.1

Q ss_pred             CCCCccccccCcccCC----CceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          120 GLDTECVICLSEFAPG----ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       120 ~~~~~CaICLeef~~~----~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      ..+.+|+||++.|.+.    ..+..++ |||.||.+||+.|++.+.+||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3457999999999753    4456777 99999999999999999999999998753

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

Probab=99.49  E-value=9.4e-15  Score=99.27  Aligned_cols=53  Identities=25%  Similarity=0.673  Sum_probs=45.1

Q ss_pred             CCCCccccccCcccC----CCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          120 GLDTECVICLSEFAP----GERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~----~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +++.+|+||++.|.+    ++.+..++ |||.||.+||+.|++.+.+||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            345799999999875    35557777 999999999999999999999999988743

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

Probab=99.47  E-value=1.3e-14  Score=96.48  Aligned_cols=52  Identities=23%  Similarity=0.614  Sum_probs=44.4

Q ss_pred             CCCccccccCcccCC----CceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPG----ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~----~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ++.+|+||++.+.+.    +.+..++ |||.||.+||..|++.+.+||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            357999999999753    4556777 999999999999999999999999988754

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

Probab=99.46  E-value=1.9e-14  Score=97.70  Aligned_cols=52  Identities=37%  Similarity=0.859  Sum_probs=44.6

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQK  176 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~  176 (210)
                      ..+..|+||++.+.+    ..++ |+|.||.+||..|++.+.+||+||..+......
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   64 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANES   64 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCcc
Confidence            345799999999886    5677 999999999999999999999999998865443

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

Probab=99.44  E-value=1.1e-13  Score=93.42  Aligned_cols=50  Identities=34%  Similarity=0.826  Sum_probs=43.3

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      .+.+|+||++.+.+  .+..++ |||.||.+||..|++.+.+||+||..+...
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            45799999999874  346787 999999999999999999999999988743

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

Probab=99.42  E-value=8e-14  Score=95.09  Aligned_cols=50  Identities=30%  Similarity=0.540  Sum_probs=43.2

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ..+..|+||++.+.+   ...++ |+|.||.+||..|++.+.+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            345789999999876   45677 999999999999999999999999998753

>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=99.42  E-value=1.3e-14  Score=108.93  Aligned_cols=50  Identities=30%  Similarity=0.671  Sum_probs=0.5

Q ss_pred             CCccccccCcccCC-------------Cc-eEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPG-------------ER-VRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~-------------~~-vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ++.|+||+++|.+.             +. .+++..|+|.||.+||+.||+.+.+||+||.++.
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             C---------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            47999999999752             22 2232349999999999999999999999999864

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

Probab=99.42  E-value=1.3e-13  Score=95.37  Aligned_cols=53  Identities=26%  Similarity=0.637  Sum_probs=44.3

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIESCQ  175 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~~~~~  175 (210)
                      +...+|+||.+.|..++...   .|+|.||.+||.+||+.+  .+||+||.++.....
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCC
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCC
Confidence            34589999999998765443   599999999999999887  789999998875544

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

Probab=99.40  E-value=2.9e-13  Score=92.51  Aligned_cols=50  Identities=24%  Similarity=0.535  Sum_probs=42.3

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      .+..|+||++.|.+  .+.+++ |||.||..||..|++.+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           14 PYILCSICKGYLID--ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             GGGSCTTTSSCCSS--CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             CCCCCCCCChHHHC--cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            34789999999986  333346 999999999999999999999999988754

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

Probab=99.38  E-value=4.2e-13  Score=94.61  Aligned_cols=53  Identities=30%  Similarity=0.630  Sum_probs=45.1

Q ss_pred             CCCCccccccCcccCCCc-eEEcCCCCCccchHHHHHHHhcC---CCCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGER-VRLLPKCNHGFHVRCIDKWLRSN---SSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~-vr~lp~C~H~FH~~CI~~Wl~~~---~~CPlCR~~l~~~  173 (210)
                      .+..+|+||++.|.+++. .+.++ |||.||.+||..|++.+   ..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            345799999999998775 67787 99999999999999876   6899999987643

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

Probab=99.34  E-value=8.8e-13  Score=90.71  Aligned_cols=51  Identities=22%  Similarity=0.563  Sum_probs=41.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCccccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIESC  174 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~~~~  174 (210)
                      .+..|+||++.|.+   ...++.|||.||..||..|++.+  .+||+||..+....
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           14 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             GGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            34789999999986   34566699999999999999865  58999999765443

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

Probab=99.34  E-value=1.1e-12  Score=91.64  Aligned_cols=47  Identities=23%  Similarity=0.499  Sum_probs=41.5

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ....|+||++.|.+   ..+++ |||.||..||..|++...+||+||..+.
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            45789999999976   44677 9999999999999999999999999875

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

Probab=99.33  E-value=1.4e-12  Score=89.00  Aligned_cols=49  Identities=24%  Similarity=0.607  Sum_probs=41.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh---cCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR---SNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~---~~~~CPlCR~~l~~~  173 (210)
                      .+..|+||++.|.+   ...++ |||.||.+||..|++   .+..||+||..+...
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            45799999999885   55667 999999999999996   455899999988643

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

Probab=99.30  E-value=1.3e-12  Score=87.63  Aligned_cols=49  Identities=20%  Similarity=0.560  Sum_probs=40.4

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-cCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~~  173 (210)
                      ++..|+||++.+.+.   ..++ |||.||..||..|++ .+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           14 DKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            457899999999863   2366 999999999999994 567899999988643

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

Probab=99.29  E-value=1.2e-12  Score=100.63  Aligned_cols=47  Identities=32%  Similarity=0.859  Sum_probs=41.8

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ..|+||++.|.+   ...++ |||.||..||..|++.+.+||+||..+...
T Consensus        54 ~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           54 LQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             SBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             CCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            579999999976   56677 999999999999999999999999988644

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

Probab=99.26  E-value=1.5e-12  Score=97.99  Aligned_cols=54  Identities=22%  Similarity=0.566  Sum_probs=45.9

Q ss_pred             CCCccccccCcccCC----CceEEcCCCCCccchHHHHHHHhcCCCCcccccccccccc
Q 028342          121 LDTECVICLSEFAPG----ERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       121 ~~~~CaICLeef~~~----~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      ++.+|+||++.|.+.    +.+..++ |||.||.+||+.|++.+.+||+||..+....-
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            457899999999753    5557777 99999999999999999999999999875544

>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=99.25  E-value=3.4e-12  Score=92.85  Aligned_cols=47  Identities=32%  Similarity=0.769  Sum_probs=40.7

Q ss_pred             CCccccccCcccCCCceEE-cCCCCCccchHHHHHHHhcC-CCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRL-LPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~-lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~  172 (210)
                      +..|+||++.|.+   ... ++ |||.||..||..|++.+ .+||+||..+..
T Consensus        22 ~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           22 VFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            3689999999975   445 76 99999999999999887 699999999864

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

Probab=99.24  E-value=7.3e-12  Score=86.55  Aligned_cols=48  Identities=23%  Similarity=0.513  Sum_probs=41.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ...++ |||.||..||..|++. +.+||+||..+..
T Consensus         7 ~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            7 EYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             ccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            35799999999976   45567 9999999999999987 7789999998764

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

Probab=99.23  E-value=9e-12  Score=86.86  Aligned_cols=48  Identities=31%  Similarity=0.563  Sum_probs=41.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc------CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS------NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~------~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ...++ |+|.||..||..|++.      ...||+||..+..
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           18 EEVTCPICLELLKE---PVSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             TTTSCTTTCSCCSS---CEECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             cCCCCcCCChhhCc---ceeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            45799999999876   34677 9999999999999987      6689999998764

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

Probab=99.23  E-value=9.6e-12  Score=82.55  Aligned_cols=43  Identities=28%  Similarity=0.653  Sum_probs=36.2

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh---cCCCCccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR---SNSSCPKC  166 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~---~~~~CPlC  166 (210)
                      +++..|+||++.|.+   ...++ |||.||.+||..|++   .+.+||+|
T Consensus        18 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            345799999999986   45567 999999999999998   45689998

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

Probab=99.23  E-value=3.2e-12  Score=96.21  Aligned_cols=53  Identities=25%  Similarity=0.673  Sum_probs=44.7

Q ss_pred             CCCCccccccCcccC----CCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          120 GLDTECVICLSEFAP----GERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~----~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +....|+||++.|.+    +.....++ |||.||..||+.|++.+.+||+||..+...
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            345789999999875    23446676 999999999999999999999999998754

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

Probab=99.22  E-value=8.7e-12  Score=86.93  Aligned_cols=48  Identities=31%  Similarity=0.650  Sum_probs=41.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc------CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS------NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~------~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ...++ |||.||.+||..|++.      ...||+||..+..
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           18 EEVTCPICLELLTQ---PLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCTTTCSCCSS---CBCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             CCCCCCCCCcccCC---ceeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            45799999999976   34567 9999999999999987      6789999998874

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

Probab=99.21  E-value=8.4e-12  Score=90.25  Aligned_cols=47  Identities=30%  Similarity=0.729  Sum_probs=40.9

Q ss_pred             CCccccccCcccCCCceEEc-CCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLL-PKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~l-p~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      +..|+||++.|.+   ...+ + |||.||..||..|+..+.+||+||..+..
T Consensus        22 ~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNI---AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCC---cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            3689999999986   4444 6 99999999999999998999999998874

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

Probab=99.21  E-value=2.8e-12  Score=88.63  Aligned_cols=48  Identities=29%  Similarity=0.541  Sum_probs=40.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-------CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-------NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-------~~~CPlCR~~l~~  172 (210)
                      ++..|+||++.|.+   ...++ |||.||.+||..|++.       ...||+||..+..
T Consensus        11 ~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           11 EEVTCPICLELLTE---PLSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCEETTTTEECSS---CCCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cCCCCcCCCcccCC---eeECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            45799999999976   34577 9999999999999976       5689999998874

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

Probab=99.20  E-value=8.5e-12  Score=83.40  Aligned_cols=51  Identities=24%  Similarity=0.537  Sum_probs=40.7

Q ss_pred             CCccccccC-cccCCCce-EEcCCCCCccchHHHHHHHhc-CCCCcccccccccc
Q 028342          122 DTECVICLS-EFAPGERV-RLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLe-ef~~~~~v-r~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~  173 (210)
                      +..|+||++ .|.+.... ..++ |||.||..||+.|+.. +..||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            468999999 77765543 3466 9999999999999765 46799999988643

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

Probab=99.18  E-value=1.5e-11  Score=79.91  Aligned_cols=42  Identities=29%  Similarity=0.926  Sum_probs=35.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh---cCCCCccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR---SNSSCPKC  166 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~---~~~~CPlC  166 (210)
                      .+..|+||++.+.+.   ..++ |||.||.+||..|++   .+.+||+|
T Consensus        14 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            457999999999863   4477 999999999999954   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=99.18  E-value=1.1e-11  Score=91.14  Aligned_cols=49  Identities=27%  Similarity=0.671  Sum_probs=41.8

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      +..|+||++.|.+  .+..++ |||.||..||..|++.+.+||+||..+...
T Consensus        15 ~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           15 HLMCVLCGGYFID--ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GTBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCCccCChHHhC--cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            4789999999975  344447 999999999999999999999999988753

>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=99.15  E-value=2.3e-11  Score=91.52  Aligned_cols=47  Identities=28%  Similarity=0.578  Sum_probs=40.5

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~  172 (210)
                      +..|+||++.|.+   ...++ |||.||..||..|+..+. .||+||..+..
T Consensus        52 ~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            3689999999985   55677 999999999999998655 89999998865

>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=99.14  E-value=2.6e-11  Score=95.57  Aligned_cols=47  Identities=38%  Similarity=0.745  Sum_probs=40.2

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  172 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~  172 (210)
                      ..|+||++.|.+  .+..++ |||.||..||..|++. +..||+||..+..
T Consensus        55 ~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           55 LMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            589999999986  344447 9999999999999987 7789999998854

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

Probab=99.14  E-value=3.7e-11  Score=85.54  Aligned_cols=49  Identities=22%  Similarity=0.592  Sum_probs=40.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~~l~  171 (210)
                      .++..|+||++.|.+   ...++.|||.||..||..|+..+  ..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            345799999999985   44565599999999999999754  58999999874

>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=99.11  E-value=3.4e-11  Score=88.52  Aligned_cols=46  Identities=30%  Similarity=0.637  Sum_probs=39.2

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC---CCccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLIE  172 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~---~CPlCR~~l~~  172 (210)
                      ..|+||++.|.+   ...++ |||.||..||..|+..+.   .||+||..+..
T Consensus        22 ~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (112)
T 1jm7_A           22 LECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (112)
T ss_dssp             TSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCCcccChhhcC---eEECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCH
Confidence            689999999976   33467 999999999999998754   89999998774

>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=99.06  E-value=7e-11  Score=79.14  Aligned_cols=49  Identities=24%  Similarity=0.426  Sum_probs=41.0

Q ss_pred             CCCccccccCcccCCCceEEc--CCCCCc-cchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLL--PKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~l--p~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ++.+|.||++.+.+   ...+  | |||. |+.+|+..|.+.+..||+||+.+...
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   58 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQMI   58 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCEE
T ss_pred             CcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhce
Confidence            34789999998775   3333  8 9999 79999999999888999999988644

>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=99.06  E-value=7.9e-11  Score=87.91  Aligned_cols=48  Identities=35%  Similarity=0.666  Sum_probs=41.1

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ...++ |||.||..||..|++.+. +||+||..+..
T Consensus        17 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           17 SKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCcCChhhcC---eEECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            34799999999986   45577 999999999999998765 99999998875

>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=99.06  E-value=9.7e-11  Score=86.97  Aligned_cols=48  Identities=31%  Similarity=0.566  Sum_probs=41.0

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCcccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~  173 (210)
                      +..|+||++.|.+   ...++ |||.||..||..|++. +.+||+||..+...
T Consensus        23 ~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            3689999999975   44577 9999999999999987 67899999988753

>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=99.06  E-value=9.7e-11  Score=91.31  Aligned_cols=48  Identities=27%  Similarity=0.569  Sum_probs=41.2

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCcccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~~  173 (210)
                      ...|+||++.|.+   ...++ |||.||..||..|+.... .||+||..+...
T Consensus        78 ~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            3689999999976   45577 999999999999998765 899999998754

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

Probab=99.05  E-value=2.1e-10  Score=79.94  Aligned_cols=55  Identities=20%  Similarity=0.367  Sum_probs=41.8

Q ss_pred             CCCCccccccCcccCCCce-EEcCCCCCccchHHHHHHHhc-CCCCcccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERV-RLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIESCQ  175 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~v-r~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~~~  175 (210)
                      +++.+|+||++.+...+.. .-++ |||.||..|+..|+.. ...||+||..+....-
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            3457999999998654332 2244 9999999999999854 5689999998875443

>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=99.03  E-value=4.4e-11  Score=88.72  Aligned_cols=47  Identities=28%  Similarity=0.682  Sum_probs=40.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~  172 (210)
                      +..|+||++.|.+   ...++ |||.||..||..|+.. +..||+||..+..
T Consensus        15 ~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            4689999999875   45667 9999999999999976 5689999998864

>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=99.00  E-value=2.4e-10  Score=101.52  Aligned_cols=49  Identities=27%  Similarity=0.642  Sum_probs=42.7

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-cCCCCccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIESC  174 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-~~~~CPlCR~~l~~~~  174 (210)
                      ..+|+||++.+.+   ...+| |||.||..|+..|+. .+.+||+||..+....
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            4699999999865   66788 999999999999998 6789999999887643

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

Probab=99.00  E-value=6.3e-11  Score=77.16  Aligned_cols=48  Identities=25%  Similarity=0.464  Sum_probs=39.6

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      .++..|+||++.|.+   .+.++ |||.||..||..|   ...||+||..+....
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            345789999999986   46688 9999999999885   678999999877543

>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=98.99  E-value=1.5e-10  Score=77.23  Aligned_cols=51  Identities=20%  Similarity=0.392  Sum_probs=40.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      .+.+|.||++.+.+. .+..+| |||. |+.+|+..|.+.+..||+||..+...
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   57 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQLV   57 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCEE
T ss_pred             cCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhce
Confidence            347999999987651 122348 9998 99999999998888999999998644

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

Probab=98.95  E-value=1.7e-10  Score=100.40  Aligned_cols=54  Identities=28%  Similarity=0.625  Sum_probs=42.2

Q ss_pred             CCCCccccccCcccCCCceE----EcCCCCCccchHHHHHHHhcC-----------CCCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVR----LLPKCNHGFHVRCIDKWLRSN-----------SSCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr----~lp~C~H~FH~~CI~~Wl~~~-----------~~CPlCR~~l~~~  173 (210)
                      +...+|+||++.+.+++.+-    ..++|+|.||..|+.+||++.           .+||+||.++..+
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            45689999999998844332    123699999999999999752           4699999988754

>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=98.93  E-value=2.4e-10  Score=88.17  Aligned_cols=48  Identities=23%  Similarity=0.434  Sum_probs=40.4

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ...++ |||.||..||..|++... +||+||.++..
T Consensus        30 ~~~~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           30 AKYLCSACRNVLRR---PFQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCcCCCCCChhhcC---cEECC-CCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            45789999999986   34576 999999999999998665 89999998643

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

Probab=98.92  E-value=1.2e-09  Score=77.13  Aligned_cols=48  Identities=17%  Similarity=0.071  Sum_probs=42.6

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ..+++ |||.|...||..|+..+.+||+||..+..
T Consensus        13 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             hheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            35789999999987   66787 99999999999999988999999988764

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

Probab=98.89  E-value=6.6e-10  Score=76.33  Aligned_cols=46  Identities=22%  Similarity=0.604  Sum_probs=39.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCcccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCQ  175 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~~  175 (210)
                      +..|+||++.+.+   ...+| |||. |+..|+..|    ..||+||..+.....
T Consensus        24 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~   70 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFKQK   70 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEEEE
T ss_pred             CCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccCcEE
Confidence            3689999999876   66778 9999 999999999    889999998876543

>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=98.87  E-value=1.2e-09  Score=79.50  Aligned_cols=48  Identities=17%  Similarity=0.065  Sum_probs=42.5

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ..+++ |||.|+..||..|+..+.+||+||..+..
T Consensus        28 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           28 DEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             TTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             HhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            35799999999987   66677 99999999999999988899999998764

>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=98.86  E-value=1.8e-09  Score=78.36  Aligned_cols=48  Identities=19%  Similarity=0.077  Sum_probs=42.3

Q ss_pred             CCCccccccCcccCCCceEEcCCCC-CccchHHHHHHHhcCCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCN-HGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~-H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      .+..|+||++.|.+   ..+++ || |.|+..||..|+..+.+||+||..+..
T Consensus        21 ~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           21 DEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             HhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            34789999999987   56677 99 999999999999988899999998764

>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=98.84  E-value=5.6e-10  Score=83.10  Aligned_cols=44  Identities=23%  Similarity=0.512  Sum_probs=38.0

Q ss_pred             CCccccccCcccCCCceEEc-CCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          122 DTECVICLSEFAPGERVRLL-PKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~l-p~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ...|+||++.|.+   ...+ + |||.||..||..|+.  ..||+||..+.
T Consensus        22 ~~~C~IC~~~~~~---pv~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           22 LLRCSRCTNILRE---PVCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             TTSCSSSCSCCSS---CBCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             CCCCCCCChHhhC---ccEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            4789999999975   3445 6 999999999999988  78999999874

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

Probab=98.81  E-value=4.5e-09  Score=71.12  Aligned_cols=49  Identities=31%  Similarity=0.648  Sum_probs=40.5

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCcccccccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCQKI  177 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~~  177 (210)
                      ++..|.||++.+.+   +..+| |||. |+..|+..    ...||+||..+.....-+
T Consensus        14 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~~i~   63 (68)
T 2ea5_A           14 NSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESFALS   63 (68)
T ss_dssp             CSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEECCC
T ss_pred             CCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceEEee
Confidence            45799999998765   77888 9999 99999984    578999999988755443

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

Probab=98.80  E-value=3.2e-09  Score=70.28  Aligned_cols=48  Identities=27%  Similarity=0.632  Sum_probs=37.0

Q ss_pred             CCCCccccccCcccCCCceEEcCCCC--C---ccchHHHHHHHhc--CCCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCN--H---GFHVRCIDKWLRS--NSSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~--H---~FH~~CI~~Wl~~--~~~CPlCR~~l~  171 (210)
                      +++..|.||+++.  ++.+ ++| |.  |   .||.+|++.|+..  +.+||+||..+.
T Consensus         4 ~~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            3457999999983  3344 577 65  4   9999999999965  568999998765

>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=98.74  E-value=4.6e-09  Score=82.84  Aligned_cols=49  Identities=35%  Similarity=0.659  Sum_probs=41.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC-CCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~~  173 (210)
                      +...|+||++.|.+   ...++ |||.|+..||..|++.+. +||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           17 SKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCChhhcC---cEECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            34799999999986   45577 999999999999997654 899999988653

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

Probab=98.70  E-value=7.3e-09  Score=71.10  Aligned_cols=44  Identities=23%  Similarity=0.603  Sum_probs=36.6

Q ss_pred             CccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      ..|+||++.+.+   ...+| |||. |+.+|+..    ...||+||..+....
T Consensus        26 ~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~~   70 (75)
T 2ecg_A           26 KLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFKQ   70 (75)
T ss_dssp             HSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCCC
T ss_pred             CCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCcE
Confidence            589999999876   55678 9999 99999964    478999999887543

>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=98.69  E-value=1e-08  Score=73.57  Aligned_cols=46  Identities=24%  Similarity=0.477  Sum_probs=37.5

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC------CCCcc--cccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN------SSCPK--CRHC  169 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~------~~CPl--CR~~  169 (210)
                      .+..|+||++.|.+   ..+++.|||.|+..||..|+..+      .+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            34789999999986   44553499999999999999754      48999  9855

>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=98.64  E-value=1.9e-08  Score=84.31  Aligned_cols=48  Identities=15%  Similarity=0.084  Sum_probs=40.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~  172 (210)
                      ....|+||++.|.+   ..+++ |||.|+..||..|+..+ .+||+||..+..
T Consensus       207 ~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            35789999999987   66788 99999999999999764 459999998853

>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=98.64  E-value=1.2e-08  Score=70.97  Aligned_cols=48  Identities=25%  Similarity=0.570  Sum_probs=40.4

Q ss_pred             CccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCccccccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCQKIV  178 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~~~~~  178 (210)
                      ..|.||++.+.+   +..+| |||. |+..|+..|    ..||+||..+.....-+.
T Consensus        19 ~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~~i~~   67 (79)
T 2yho_A           19 MLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHVQHVYL   67 (79)
T ss_dssp             TBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEEEECBC
T ss_pred             CEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCeEEEEe
Confidence            689999998776   67788 9999 999999987    399999999887655443

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

Probab=98.63  E-value=1.2e-08  Score=72.92  Aligned_cols=47  Identities=23%  Similarity=0.663  Sum_probs=39.6

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--------CCCcc--cccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--------SSCPK--CRHC  169 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--------~~CPl--CR~~  169 (210)
                      ..+|+||++++...+.+.+.+ |||.|+.+|+..++..+        ..||.  ||..
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            468999999998777776666 99999999999999641        36999  9987

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

Probab=98.45  E-value=1.3e-07  Score=75.71  Aligned_cols=48  Identities=15%  Similarity=0.074  Sum_probs=40.6

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~  172 (210)
                      ....|+||++.|.+   ..+++ |||.|...||..|+..+ .+||+||..+..
T Consensus       105 ~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          105 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             HhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            45789999999986   55677 99999999999999764 469999988754

>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=98.43  E-value=1e-07  Score=63.07  Aligned_cols=48  Identities=19%  Similarity=0.228  Sum_probs=40.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ..|+||++.|.+  .+ +++.|||+|..+||.+|++.+.+||+++..|...
T Consensus         4 ~~CpIs~~~m~d--PV-~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            4 MLCAISGKVPRR--PV-LSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             CCCTTTCSCCSS--EE-EETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             EEecCCCCCCCC--CE-EeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            579999999985  34 4423999999999999999888999999988643

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

Probab=98.39  E-value=7.8e-08  Score=84.35  Aligned_cols=45  Identities=24%  Similarity=0.699  Sum_probs=39.0

Q ss_pred             CCccccccCcccCCCceEEcCCCCCc-cchHHHHHHHhcCCCCccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~-FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      +..|+||++.+.+   ...+| |||. ||..|+..|    ..||+||..+....
T Consensus       295 ~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~~  340 (345)
T 3t6p_A          295 ERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKGTV  340 (345)
T ss_dssp             TCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCEEE
T ss_pred             CCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccCeE
Confidence            4789999999876   66778 9999 999999998    78999999987553

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

Probab=98.26  E-value=9e-07  Score=73.81  Aligned_cols=51  Identities=27%  Similarity=0.638  Sum_probs=41.8

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC--CCccccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS--SCPKCRHCLIESC  174 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~--~CPlCR~~l~~~~  174 (210)
                      .-.+|+||.+-.-.|   ..++.|+|.||.+|+..|++.+.  +||.|+..+....
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~  231 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI  231 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCC
Confidence            457999999988765   34556999999999999998765  8999999887543

>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=98.26  E-value=4.5e-07  Score=76.37  Aligned_cols=47  Identities=23%  Similarity=0.571  Sum_probs=38.7

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--CCCcc--cccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPK--CRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPl--CR~~l~  171 (210)
                      +-.|+||++.|.+  .|+... |||.|+..||..|++.+  ..||+  ||..+.
T Consensus       181 el~CPIcl~~f~D--PVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~  231 (267)
T 3htk_C          181 ELTCPITCKPYEA--PLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS  231 (267)
T ss_dssp             CSBCTTTSSBCSS--EEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEEC
T ss_pred             eeECcCccCcccC--CeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCc
Confidence            4689999999974  455455 99999999999999764  36999  998765

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

Probab=97.95  E-value=5.6e-06  Score=59.66  Aligned_cols=49  Identities=24%  Similarity=0.461  Sum_probs=39.2

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCcccccccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIESCQ  175 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~~~  175 (210)
                      .|.+|--.+.  .-.|..| |+|+|+.+|+..|.+. .++||.||..+..-+.
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe~   52 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQ   52 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEEE
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeEE
Confidence            4778865554  4568899 9999999999999865 5689999998876554

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

Probab=96.67  E-value=0.0017  Score=43.32  Aligned_cols=47  Identities=26%  Similarity=0.472  Sum_probs=35.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l  170 (210)
                      ..+..|.||.+    +..+.....|...||..|++..|....    .||.|+...
T Consensus        10 ~~~~~C~vC~~----~~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGD----GTDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSC----CTTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCC----CCeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            34578999964    344666777999999999998886543    699996543

>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=94.43  E-value=0.034  Score=38.61  Aligned_cols=35  Identities=20%  Similarity=0.436  Sum_probs=24.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHH
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKW  156 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~W  156 (210)
                      ..++.|.||- .+..++... ..-|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceec-cccccccccHhhcccc
Confidence            3568999994 444444332 2239999999999996

>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=93.85  E-value=0.028  Score=44.38  Aligned_cols=47  Identities=23%  Similarity=0.449  Sum_probs=35.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l~  171 (210)
                      +++.|.+|.+.    ..+..+..|.-.||..|++.-+....    .||.|+..-.
T Consensus         3 ~~~~C~~C~~~----g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG----GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC----SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC----CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            45789999743    44667778999999999987765422    6999986543

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

Probab=93.84  E-value=0.041  Score=38.77  Aligned_cols=34  Identities=15%  Similarity=0.365  Sum_probs=25.9

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHH
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKW  156 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~W  156 (210)
                      +..|.||++.+.......-+. |+|.|+..|+..+
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            468999998754434444465 9999999999983

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

Probab=93.80  E-value=0.049  Score=35.33  Aligned_cols=45  Identities=27%  Similarity=0.724  Sum_probs=33.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKCRH  168 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlCR~  168 (210)
                      ..+..|.||.+    +..+.....|...||..|++.-+...    -.||.|+.
T Consensus         9 ~~~~~C~vC~~----~g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQ----GGEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSC----CSSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCC----CCcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            34578999976    24566677799999999999865332    26999964

>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=93.33  E-value=0.026  Score=36.82  Aligned_cols=49  Identities=24%  Similarity=0.510  Sum_probs=37.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-----cCCCCccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-----SNSSCPKCRH  168 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-----~~~~CPlCR~  168 (210)
                      +++..|+||...+.++...+....|..=||..|+..-..     .+-.||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            345789999998876677777778999999999876432     2346999965

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=92.73  E-value=0.015  Score=37.56  Aligned_cols=50  Identities=20%  Similarity=0.626  Sum_probs=35.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCccccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKCRHCLIESC  174 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlCR~~l~~~~  174 (210)
                      ++..|.||...    ..+.....|.-.||..|++.=+...    -.||.|+.....+.
T Consensus         4 ~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~~   57 (60)
T 2puy_A            4 HEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKE   57 (60)
T ss_dssp             CCSSCTTTCCC----SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHTT
T ss_pred             CCCCCcCCCCC----CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhchh
Confidence            45789999763    3455666799999999999655432    25999977655443

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=92.63  E-value=0.052  Score=43.13  Aligned_cols=48  Identities=19%  Similarity=0.439  Sum_probs=37.1

Q ss_pred             CCccccccCcccCCCc---eEEcCCCCCccchHHHHHH------Hh-----cCCCCcccccc
Q 028342          122 DTECVICLSEFAPGER---VRLLPKCNHGFHVRCIDKW------LR-----SNSSCPKCRHC  169 (210)
Q Consensus       122 ~~~CaICLeef~~~~~---vr~lp~C~H~FH~~CI~~W------l~-----~~~~CPlCR~~  169 (210)
                      +..|+||...|.+++.   ++.+..|..=||..|+..=      +.     ..-.||.|+..
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~   63 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTER   63 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCC
Confidence            3579999999998774   7788889999999997532      11     15689999874

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=92.62  E-value=0.032  Score=44.90  Aligned_cols=47  Identities=28%  Similarity=0.482  Sum_probs=35.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l  170 (210)
                      .+++.|.+|.+    +..+..+..|...||..|++..+....    .||.|+..-
T Consensus         5 ~~~~~C~~C~~----~g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQN----GGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCC----CEEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCC----CCceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            34578999973    345777788999999999988765432    699997643

>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=92.49  E-value=0.03  Score=36.37  Aligned_cols=47  Identities=21%  Similarity=0.548  Sum_probs=33.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l  170 (210)
                      .++..|.||.+    +..+.....|...||..|+..-+....    .||.|+...
T Consensus         7 ~~~~~C~vC~~----~g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKD----GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCC----CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCC----CCCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            34578999975    234556667999999999986554322    599997643

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=91.95  E-value=0.047  Score=36.69  Aligned_cols=50  Identities=20%  Similarity=0.337  Sum_probs=36.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc----CCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS----NSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~----~~~CPlCR~~l~  171 (210)
                      +...|.||.... +++.++....|.--||..|+..-...    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~-~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPD-DGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCC-SSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCC-CCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            345799997764 35566777789999999999876532    236999977654

>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}

Probab=91.09  E-value=0.78  Score=28.99  Aligned_cols=34  Identities=15%  Similarity=0.034  Sum_probs=24.1

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Q 028342           46 FDSNVLMVLSVLLCALICAIGLASLVKCSLRCSR   79 (210)
Q Consensus        46 ~~~~~iiil~il~~~li~~l~l~~i~~~~~r~~~   79 (210)
                      ..+.+++++++++..+++++++.++.+|-+.+++
T Consensus         6 ~vp~WiIi~svl~GLLLL~Lii~~LwK~GFFKR~   39 (54)
T 2l8s_A            6 RVPLWVILLSAFAGLLLLMLLILALWKIGFFKRP   39 (54)
T ss_dssp             CCCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHHHcCcccCC
Confidence            4457888888888888888777777766554433

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=90.53  E-value=0.051  Score=35.76  Aligned_cols=45  Identities=24%  Similarity=0.623  Sum_probs=32.8

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRH  168 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~  168 (210)
                      .++..|.||.+.    ..+.....|...||..|+..-+....    .||.|+.
T Consensus         6 ~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            6 KNEDECAVCRDG----GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             SCCCSBSSSSCC----SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCccCCCC----CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccC
Confidence            356899999853    34566667999999999986553322    5999954

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.84  E-value=0.15  Score=35.70  Aligned_cols=47  Identities=26%  Similarity=0.540  Sum_probs=34.4

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l  170 (210)
                      +++..|.+|.+.   + .+.....|.-.||..|++.=+....    .||.|+...
T Consensus        23 ~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           23 DSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            456799999853   3 4556667999999999977664422    699997643

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.55  E-value=0.053  Score=34.43  Aligned_cols=45  Identities=24%  Similarity=0.760  Sum_probs=32.0

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRH  168 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~  168 (210)
                      .++..|.||.+.    ..+.....|...||..|++.-+....    .||.|+.
T Consensus         7 ~~~~~C~vC~~~----g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS----SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC----CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            345789999863    34556667999999999986554322    5888853

>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=89.23  E-value=1.7  Score=27.39  Aligned_cols=33  Identities=15%  Similarity=0.033  Sum_probs=23.0

Q ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHHHhccCc
Q 028342           47 DSNVLMVLSVLLCALICAIGLASLVKCSLRCSR   79 (210)
Q Consensus        47 ~~~~iiil~il~~~li~~l~l~~i~~~~~r~~~   79 (210)
                      .+.+++++++++.++++++++.++.+|-+.+++
T Consensus        10 vp~wiIi~svl~GLllL~li~~~LwK~GFFkR~   42 (54)
T 2knc_A           10 IPIWWVLVGVLGGLLLLTILVLAMWKVGFFKRN   42 (54)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHcCcccCC
Confidence            456777888888877777777777766554433

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=88.88  E-value=0.18  Score=33.77  Aligned_cols=49  Identities=20%  Similarity=0.417  Sum_probs=34.5

Q ss_pred             CCCCccccccCcc-cCCCceEEcCCCCCccchHHHHHHHhcC--CCCccccc
Q 028342          120 GLDTECVICLSEF-APGERVRLLPKCNHGFHVRCIDKWLRSN--SSCPKCRH  168 (210)
Q Consensus       120 ~~~~~CaICLeef-~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--~~CPlCR~  168 (210)
                      .++..|.||.+.- .+++.+.....|.-.||..|+..-..-.  =.||.|+.
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            3457999998653 3455677777899999999998543211  25888854

>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=88.88  E-value=0.39  Score=32.49  Aligned_cols=49  Identities=18%  Similarity=0.449  Sum_probs=35.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-----cCCCCccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-----SNSSCPKCRHCL  170 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-----~~~~CPlCR~~l  170 (210)
                      ....| ||...+.++...+....|..=||..|+..--.     ..-.||.|+..-
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            34567 99988875666777778999999999864321     234799998654

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=88.25  E-value=0.42  Score=31.33  Aligned_cols=34  Identities=26%  Similarity=0.481  Sum_probs=29.1

Q ss_pred             CCccccccCcccCCCceEEcC-CCCCccchHHHHH
Q 028342          122 DTECVICLSEFAPGERVRLLP-KCNHGFHVRCIDK  155 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp-~C~H~FH~~CI~~  155 (210)
                      ...|.+|...+.+++..+... .|.-=||..|+..
T Consensus         8 ~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvgl   42 (65)
T 2vpb_A            8 VYPCGICTNEVNDDQDAILCEASCQKWFHRICTGM   42 (65)
T ss_dssp             -CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTC
T ss_pred             cCcCccCCCccCCCCCeEecccCccccCchhccCC
Confidence            468999999998888888887 8999999999754

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.01  E-value=0.3  Score=30.03  Aligned_cols=44  Identities=27%  Similarity=0.726  Sum_probs=30.6

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRH  168 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~  168 (210)
                      .|.||...-. ++.+.....|...||..|++.=+....    .||.|+.
T Consensus         2 ~C~vC~~~~~-~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGE-DDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSC-CSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCC-CCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            5888976533 345566677999999999976443322    5999964

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.88  E-value=0.67  Score=35.21  Aligned_cols=46  Identities=26%  Similarity=0.559  Sum_probs=34.5

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh---------c--CCCCcccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR---------S--NSSCPKCRHC  169 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~---------~--~~~CPlCR~~  169 (210)
                      +.++.|.||-+    |..+.....|-.+||..||+.=+.         .  .=.||.|+..
T Consensus        61 g~~d~C~vC~~----GG~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           61 GMDEQCRWCAE----GGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             SCBCSCSSSCC----CSSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCeecccCC----CCcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            45689999964    455667777999999999997652         1  2269999754

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=87.85  E-value=0.16  Score=35.32  Aligned_cols=50  Identities=20%  Similarity=0.408  Sum_probs=35.1

Q ss_pred             CCCCccccccCcc-cCCCceEEcCCCCCccchHHHHHHHhc--CCCCcccccc
Q 028342          120 GLDTECVICLSEF-APGERVRLLPKCNHGFHVRCIDKWLRS--NSSCPKCRHC  169 (210)
Q Consensus       120 ~~~~~CaICLeef-~~~~~vr~lp~C~H~FH~~CI~~Wl~~--~~~CPlCR~~  169 (210)
                      +++..|.||.+.- .+++.+.....|.-.||..|+..-+.-  .-.||.|+..
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~   75 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCc
Confidence            4567999998653 344467777789999999999864322  2259999654

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=87.79  E-value=0.17  Score=36.75  Aligned_cols=46  Identities=26%  Similarity=0.598  Sum_probs=33.0

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlCR~  168 (210)
                      ..|.||.+.-.+++.+.....|...||..|++.-|..-    =.||.||.
T Consensus        62 ~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           62 KTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            36889986533445566777799999999998765442    26999974

>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=86.90  E-value=0.16  Score=39.43  Aligned_cols=48  Identities=21%  Similarity=0.492  Sum_probs=35.7

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHh-----cCCCCcccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-----SNSSCPKCRHC  169 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~-----~~~~CPlCR~~  169 (210)
                      +...| +|.....++...+.+..|.--||..|+..--.     ..-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            34689 99988776666777878999999999964321     23479999753

>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=86.60  E-value=0.36  Score=31.30  Aligned_cols=51  Identities=25%  Similarity=0.625  Sum_probs=35.8

Q ss_pred             CCCCccccccCcc-cCCCceEEcCCCCCccchHHHHHHHhc-------CCCCccccccc
Q 028342          120 GLDTECVICLSEF-APGERVRLLPKCNHGFHVRCIDKWLRS-------NSSCPKCRHCL  170 (210)
Q Consensus       120 ~~~~~CaICLeef-~~~~~vr~lp~C~H~FH~~CI~~Wl~~-------~~~CPlCR~~l  170 (210)
                      +++..|.||.... .++..+.....|.-.||..|+..=+..       .-.|+.|+...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            4567999998764 334566677789999999998864421       22699886543

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=86.30  E-value=0.94  Score=33.80  Aligned_cols=48  Identities=25%  Similarity=0.531  Sum_probs=34.8

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHH------hc-----CCCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL------RS-----NSSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl------~~-----~~~CPlCR~~l~  171 (210)
                      ++++.|.||-+    |.++.....|-.+||.+||+.-+      +.     .=.|++|+....
T Consensus        55 g~~~~C~vC~d----GG~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~pl  113 (129)
T 3ql9_A           55 GMDEQCRWCAE----GGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPL  113 (129)
T ss_dssp             SCBSSCTTTCC----CSEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCGGG
T ss_pred             CCCCcCeecCC----CCeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCHHH
Confidence            45678999974    45566777899999999999752      21     127999976543

>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=86.14  E-value=0.32  Score=30.28  Aligned_cols=44  Identities=16%  Similarity=0.284  Sum_probs=32.8

Q ss_pred             ccccccCcccCCCceEEcC-CCCCccchHHHHHHH----hcCCCCcccc
Q 028342          124 ECVICLSEFAPGERVRLLP-KCNHGFHVRCIDKWL----RSNSSCPKCR  167 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp-~C~H~FH~~CI~~Wl----~~~~~CPlCR  167 (210)
                      .|.+|...+.+++..+... .|.-=||..|+..-.    ..+-.||.|+
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            5789999887777777777 699999999976432    2455799885

>2k1a_A Integrin alpha-IIB; single-PASS transmembrane segment, alternative splicing, calcium, cell adhesion, cleavage on PAIR of basic residues; NMR {Homo sapiens} PDB: 2k9j_A

Probab=86.07  E-value=2  Score=25.65  Aligned_cols=31  Identities=16%  Similarity=0.039  Sum_probs=21.8

Q ss_pred             CChhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028342           46 FDSNVLMVLSVLLCALICAIGLASLVKCSLR   76 (210)
Q Consensus        46 ~~~~~iiil~il~~~li~~l~l~~i~~~~~r   76 (210)
                      -.+.++++++++...++++++...+.+|-+.
T Consensus         7 ~vp~wiIi~s~l~GLllL~li~~~LwK~GFF   37 (42)
T 2k1a_A            7 AIPIWWVLVGVLGGLLLLTILVLAMWKVGFF   37 (42)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence            3457777888888877777777777766443

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=85.91  E-value=0.16  Score=35.37  Aligned_cols=51  Identities=18%  Similarity=0.479  Sum_probs=36.6

Q ss_pred             CCccccccCcccC-CCceEEcCCCCCccchHHHHHHHhc--------CCCCccccccccc
Q 028342          122 DTECVICLSEFAP-GERVRLLPKCNHGFHVRCIDKWLRS--------NSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~-~~~vr~lp~C~H~FH~~CI~~Wl~~--------~~~CPlCR~~l~~  172 (210)
                      +..|.||...-.. +..+.....|...||..|++.=|..        .=.|+.|+.....
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~~   75 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKR   75 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHCC
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhhh
Confidence            4689999875332 3567777789999999999876531        1269999765543

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=85.53  E-value=0.19  Score=39.82  Aligned_cols=45  Identities=27%  Similarity=0.551  Sum_probs=32.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKCRHCL  170 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlCR~~l  170 (210)
                      ++.|.+|.+.   | .+..+..|...||..|++.=+...    -.||.|+..-
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---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---S-SCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---C-ceeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            4689999743   3 455566799999999997655332    2699998663

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=84.67  E-value=0.39  Score=34.49  Aligned_cols=47  Identities=21%  Similarity=0.524  Sum_probs=31.9

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc----CCCCcccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS----NSSCPKCR  167 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~----~~~CPlCR  167 (210)
                      .+++.|.||.+.=+. +.+.....|+..||..|++..+..    .-.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~-~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDL-LDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCT-TTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCC-cCCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            456899999765322 223455679999999999988642    22477664

>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=84.59  E-value=0.9  Score=32.78  Aligned_cols=48  Identities=21%  Similarity=0.497  Sum_probs=33.1

Q ss_pred             CCCCccccccCcccCCCceEEcC--CCCCccchHHHHHHHhcCC----CCcccccccccc
Q 028342          120 GLDTECVICLSEFAPGERVRLLP--KCNHGFHVRCIDKWLRSNS----SCPKCRHCLIES  173 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp--~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l~~~  173 (210)
                      .+++.|.+|.+    +..+....  .|...||..|+.  |....    .||.|+..+-.+
T Consensus        13 ~~~~~C~~C~~----~G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C~k   66 (107)
T 4gne_A           13 MHEDYCFQCGD----GGELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDECSS   66 (107)
T ss_dssp             SSCSSCTTTCC----CSEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTTCS
T ss_pred             CCCCCCCcCCC----CCcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcCCC
Confidence            45688999973    34566665  599999999998  54422    588876554433

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=84.58  E-value=1  Score=32.39  Aligned_cols=46  Identities=20%  Similarity=0.459  Sum_probs=31.0

Q ss_pred             CCccccccCcc-----cCCCceEEcCCCCCccchHHHHHH------Hhc-CCCCcccc
Q 028342          122 DTECVICLSEF-----APGERVRLLPKCNHGFHVRCIDKW------LRS-NSSCPKCR  167 (210)
Q Consensus       122 ~~~CaICLeef-----~~~~~vr~lp~C~H~FH~~CI~~W------l~~-~~~CPlCR  167 (210)
                      ...|.+|+..=     .+++.+.....|+..||..|++.+      +.. .=.||.|+
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            46899998753     133456677779999999999642      222 22577775

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.30  E-value=0.3  Score=33.18  Aligned_cols=45  Identities=24%  Similarity=0.628  Sum_probs=31.6

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-----CCCCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-----NSSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-----~~~CPlCR~  168 (210)
                      ..|.||...- +++.+.....|...||..|++.=|..     .=.||.|+.
T Consensus        27 c~C~vC~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKH-EPNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCC-CSTTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcC-CCCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            4788997642 34556677789999999999854432     125888864

>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=82.96  E-value=0.36  Score=32.09  Aligned_cols=44  Identities=30%  Similarity=0.766  Sum_probs=30.2

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-----CCCCccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-----NSSCPKCRH  168 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-----~~~CPlCR~  168 (210)
                      .|.||... .+++.+.....|...||..|++.=|..     .=.||.|+.
T Consensus        20 ~C~~C~~~-~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGR-QDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCC-SCGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCc-CCCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            56777654 234556677789999999999854432     126888864

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=82.63  E-value=0.46  Score=34.45  Aligned_cols=34  Identities=21%  Similarity=0.384  Sum_probs=25.4

Q ss_pred             CccccccCccc------CCCceEEcCCCCCccchHHHHHH
Q 028342          123 TECVICLSEFA------PGERVRLLPKCNHGFHVRCIDKW  156 (210)
Q Consensus       123 ~~CaICLeef~------~~~~vr~lp~C~H~FH~~CI~~W  156 (210)
                      +.|.||++.-.      +++.++....|+..||..|++.+
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh
Confidence            57999987541      23456666679999999999865

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=80.79  E-value=0.93  Score=30.25  Aligned_cols=46  Identities=22%  Similarity=0.475  Sum_probs=32.4

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHH---------hcCCCCcccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL---------RSNSSCPKCRHC  169 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl---------~~~~~CPlCR~~  169 (210)
                      ...| ||...+. ++..+....|..=||..|+..-.         ..+-.||.|+..
T Consensus        16 ~~~C-~C~~~~~-~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           16 ALYC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCEE-ECCCccC-CCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            3567 8988765 44566666799999999985322         235679999653

>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=80.64  E-value=0.27  Score=34.48  Aligned_cols=52  Identities=19%  Similarity=0.457  Sum_probs=35.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l~~~  173 (210)
                      ++..|.||...-. .+.+.....|...||..|++.=|....    .||.|+..-..+
T Consensus        15 ~~~~C~vC~~~~~-~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~~~~~   70 (92)
T 2e6r_A           15 DSYICQVCSRGDE-DDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAECKQ   70 (92)
T ss_dssp             CCCCCSSSCCSGG-GGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHHHHSC
T ss_pred             CCCCCccCCCcCC-CCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCccccC
Confidence            4568999987643 345667778999999999985443322    599997654333

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=80.51  E-value=0.37  Score=32.75  Aligned_cols=45  Identities=29%  Similarity=0.685  Sum_probs=30.0

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-----CCCcccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-----SSCPKCRHC  169 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-----~~CPlCR~~  169 (210)
                      .|.||...- +++.+.....|...||..|++.-|...     =.||.|+.+
T Consensus        28 ~C~vC~~~~-d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~d   77 (77)
T 3shb_A           28 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   77 (77)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC--
T ss_pred             cCCccCCCC-CCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCcccc
Confidence            566775543 335566677799999999999765432     269998753

---

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	210
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	2e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	9e-08
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-06
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-05
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-05
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.001
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.002
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	0.002

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 71.4 bits (175), Expect = 1e-17
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 171
             EC +CL+E   GE  R LP+C HGFH  C+D WL S+S+CP CR  ++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 53.0 bits (127), Expect = 2e-10
 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 3/45 (6%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
            C ICL +         LP C H F   CI +W+R N +CP C+ 
Sbjct: 7   RCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKV 48

>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 = 49.3 bits (117), Expect = 2e-09
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 1/46 (2%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLR-SNSSCPKCRH 168
           EC +C+      +       C +     C  +     N  CP CR 
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 47

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 2e-08
 Identities = 14/60 (23%), Positives = 18/60 (30%), Gaps = 14/60 (23%)

Query: 122 DTECVICLSEFAPGE--------------RVRLLPKCNHGFHVRCIDKWLRSNSSCPKCR 167
              C IC +                           CNH FH  CI +WL++   CP   
Sbjct: 21  VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 9e-08
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 122 DTECVICLSEFAPGERVRLLP-KCNHGFHVRCIDKWLRSNS-SCPKCRHCLIESCQKI 177
           D  C  C +       ++L+   C H     C+D      + +CP+C   L +S  ++
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV 60

>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 = 45.4 bits (107), Expect = 1e-07
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 111 KYSTELKLPGLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSS-CPKCRHC 169
           +Y    ++      C IC       + V++ P C H     C+  W  S    CP CR  
Sbjct: 12  QYELYCEMGSTFQLCKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCE 67

Query: 170 L 170
           +
Sbjct: 68  I 68

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (96), Expect = 6e-06
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 20/79 (25%)

Query: 108 TVVKYSTELKLPGLDTECVICL--------------SEFAPGERVRLLPKCNHGFHVRCI 153
            + KY+ ELK+   + +C+IC+              S+      V  L KC+H FH+ C+
Sbjct: 12  VIRKYTEELKVAP-EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCL 70

Query: 154 DKWLRS-----NSSCPKCR 167
                +     +  CP C+
Sbjct: 71  LAMYCNGNKDGSLQCPSCK 89

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (92), Expect = 1e-05
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 7/45 (15%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRH 168
            C  C +E    +  +LLP C H     C++        CP C+ 
Sbjct: 8   RCQQCQAEA---KCPKLLP-CLHTLCSGCLEAS---GMQCPICQA 45

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 39.8 bits (92), Expect = 1e-05
 Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 3/48 (6%)

Query: 125 CVICLSEFAPGERVRLLPK-CNHGFHVRCIDKWLRSN--SSCPKCRHC 169
           C IC  E                  H  C+  WL  +  ++C  C   
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 6e-04
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 7/50 (14%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS---SCPKCRHCL 170
           EC ICL      +       C+H F   C+ K L        CP C++ +
Sbjct: 23  ECPICLELI---KEPVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 0.001
 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 9/54 (16%)

Query: 122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS--------NSSCPKCR 167
            + C +CL E+   +   +   C   F   C+ +++            SCP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.002
 Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 5/50 (10%)

Query: 124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 173
            C  C +          L  C H F   C+   +   + CP C       
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQ 68

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 125 CVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL 170
           C IC           +   C H F   CI + L+   S CP CR+  
Sbjct: 26  CQICEHIL----ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	210
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.78
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.6
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.54
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.54
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.53
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.46
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.36
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.24
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.24
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.19
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.18
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.99
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.92
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.91
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.69
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.65
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	94.01
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.96
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.58
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	93.49
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.95
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.69
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	89.6
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	87.38
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	87.24
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	86.69
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	83.57
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	82.68

>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=99.78  E-value=4e-20  Score=119.74  Aligned_cols=51  Identities=49%  Similarity=1.198  Sum_probs=47.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      ++.+|+||+++|.+++.++.++.|+|.||.+||+.|++++.+||+||.+|+
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            456899999999999999888779999999999999999999999999875

>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=99.60  E-value=3e-16  Score=105.34  Aligned_cols=50  Identities=34%  Similarity=0.826  Sum_probs=43.2

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      ..++|+||++.|.+  .++.++ |||.||.+||..|++.+.+||+||.++...
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            35789999999964  456787 999999999999999999999999987643

>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=99.54  E-value=4.7e-15  Score=108.75  Aligned_cols=51  Identities=29%  Similarity=0.700  Sum_probs=40.9

Q ss_pred             CCccccccCcccC---------------CCceEEcCCCCCccchHHHHHHHhcC-----CCCcccccccccc
Q 028342          122 DTECVICLSEFAP---------------GERVRLLPKCNHGFHVRCIDKWLRSN-----SSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~---------------~~~vr~lp~C~H~FH~~CI~~Wl~~~-----~~CPlCR~~l~~~  173 (210)
                      +++|+||+++|.+               ...+++++ |+|+||.+||+.||+.+     .+||+||+.+.++
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            4689999999853               23456777 99999999999999754     3799999887554

>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=99.54  E-value=1.6e-15  Score=106.68  Aligned_cols=50  Identities=30%  Similarity=0.618  Sum_probs=42.3

Q ss_pred             CCccccccCcccCCC---------------ceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          122 DTECVICLSEFAPGE---------------RVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~---------------~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      +++|+||++++.+..               .+..++ |||+||.+||+.||+.+.+||+||+.+.-
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            467999999887532               356676 99999999999999999999999998763

>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=99.53  E-value=8.8e-16  Score=97.79  Aligned_cols=48  Identities=21%  Similarity=0.461  Sum_probs=40.4

Q ss_pred             ccccccCcccCCCce-EEcCCCCCccchHHHHHHHhcCC-CCccccccccc
Q 028342          124 ECVICLSEFAPGERV-RLLPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  172 (210)
Q Consensus       124 ~CaICLeef~~~~~v-r~lp~C~H~FH~~CI~~Wl~~~~-~CPlCR~~l~~  172 (210)
                      +|+||+++|..++.. +.++ |||.||.+||+.|++.+. +||+||.++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            799999999877654 4456 999999999999998654 69999998754

>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=99.47  E-value=2.4e-14  Score=98.69  Aligned_cols=50  Identities=28%  Similarity=0.644  Sum_probs=42.3

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCcccccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIESCQ  175 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~~~~  175 (210)
                      ...|+||++.+.+   .++++ |||.||.+||..||+.+ .+||+||..|.....
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            3579999999876   77888 99999999999999854 679999999975443

>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=99.46  E-value=2.1e-14  Score=95.37  Aligned_cols=51  Identities=24%  Similarity=0.531  Sum_probs=40.2

Q ss_pred             CCccccccCcccCC-C-ceEEcCCCCCccchHHHHHHHhc-CCCCcccccccccc
Q 028342          122 DTECVICLSEFAPG-E-RVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  173 (210)
Q Consensus       122 ~~~CaICLeef~~~-~-~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~~  173 (210)
                      +..|+||++++..+ + .+.+++ |||.||.+||..|+.. +.+||+||..+...
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            57999999986432 3 345566 9999999999999965 45799999988643

>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=99.36  E-value=1.3e-13  Score=88.74  Aligned_cols=47  Identities=17%  Similarity=0.193  Sum_probs=40.6

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  173 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~  173 (210)
                      .|+||++.|++   ...++.|||+|+.+||.+||+.+.+||+||..+..+
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            59999999975   444555999999999999999999999999988754

>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=99.24  E-value=2.3e-12  Score=89.94  Aligned_cols=47  Identities=32%  Similarity=0.557  Sum_probs=40.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCcccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIES  173 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~~  173 (210)
                      -.|+||++.|.+   ..+++ |||.|+..||..|++.+ .+||+||.++.+.
T Consensus        24 l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          24 ISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             TBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            579999999976   66787 99999999999999765 5799999987643

>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=99.24  E-value=6e-13  Score=85.67  Aligned_cols=45  Identities=27%  Similarity=0.578  Sum_probs=38.4

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  174 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~~~  174 (210)
                      -+|+||++.|.+   .+++| |||.||..||+.|   +.+||+||..+....
T Consensus         7 l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           7 LRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             SSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            589999999986   46788 9999999999876   668999999987443

>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=99.19  E-value=3.8e-12  Score=82.77  Aligned_cols=52  Identities=21%  Similarity=0.356  Sum_probs=37.7

Q ss_pred             CCCCccccccCcccCCCceE-EcCCCCCccchHHHHHHHhc--CCCCcccccccc
Q 028342          120 GLDTECVICLSEFAPGERVR-LLPKCNHGFHVRCIDKWLRS--NSSCPKCRHCLI  171 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr-~lp~C~H~FH~~CI~~Wl~~--~~~CPlCR~~l~  171 (210)
                      ++...|.||++++.+..... ...+|+|.||..||..|++.  +.+||+||+.+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            34579999999887533221 11235699999999999954  458999998764

>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=99.18  E-value=4.6e-12  Score=90.97  Aligned_cols=45  Identities=31%  Similarity=0.642  Sum_probs=38.4

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC---CCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~---~CPlCR~~l~  171 (210)
                      -.|+||++.|.+   ...++ |||.||..||..|++.+.   .||+||..+.
T Consensus        22 l~CpIC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   69 (103)
T d1jm7a_          22 LECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT   69 (103)
T ss_dssp             TSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCC
T ss_pred             cCCCccCchhCC---eEEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCC
Confidence            579999999976   34577 999999999999997653   7999999875

>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=98.99  E-value=3.5e-11  Score=85.32  Aligned_cols=44  Identities=25%  Similarity=0.546  Sum_probs=36.1

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCcccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  171 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~  171 (210)
                      -.|+||++.|.+.  +...+ |||.||.+||..|+..  .||.||..+.
T Consensus        23 l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~~--~CP~Cr~~~~   66 (97)
T d1jm7b_          23 LRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIGT--GCPVCYTPAW   66 (97)
T ss_dssp             TSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTTT--BCSSSCCBCS
T ss_pred             CCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHhc--cccccCCcCc
Confidence            5899999999753  33345 9999999999999853  5999998765

>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=98.92  E-value=5.5e-10  Score=75.84  Aligned_cols=48  Identities=23%  Similarity=0.508  Sum_probs=40.6

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC-CCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~-~~CPlCR~~l~~  172 (210)
                      ++-.|+||++.|.+   ..+++ |||.|+..||..|++.+ ..||.||..+..
T Consensus         7 ~~l~CpIc~~~m~d---PV~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           7 EYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             ccCCCcCcCchhhC---ceEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            45789999999987   45677 99999999999999765 579999987753

>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=98.91  E-value=5.1e-10  Score=76.41  Aligned_cols=48  Identities=15%  Similarity=0.102  Sum_probs=40.6

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhc-CCCCccccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  172 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~-~~~CPlCR~~l~~  172 (210)
                      ++-.|+||++-|.+   ..+++ |||.|+..||..|+.. +.+||.||..+..
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             ccccCcCcCchhhh---hcccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            35789999999987   45677 9999999999999975 5579999998753

>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=98.69  E-value=6.5e-09  Score=73.64  Aligned_cols=48  Identities=19%  Similarity=0.101  Sum_probs=41.6

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCCCCccccccccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  172 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~~CPlCR~~l~~  172 (210)
                      +..|+||++-|.+   ..+++.|||.|...||..||+.+.+||+||..|..
T Consensus        22 ~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          22 EFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             TTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             HhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            5799999999997   66777455789999999999999999999998763

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=4.1e-09  Score=73.69  Aligned_cols=45  Identities=22%  Similarity=0.627  Sum_probs=37.0

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC--------CCCcccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN--------SSCPKCR  167 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~--------~~CPlCR  167 (210)
                      ..+|+||++++..++.++.++ |+|.||.+|+..|++.+        -+||.|+
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            479999999998877777776 99999999999999532        1599864

>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=94.01  E-value=0.014  Score=34.90  Aligned_cols=44  Identities=27%  Similarity=0.726  Sum_probs=32.8

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRH  168 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~  168 (210)
                      .|.||...-. ++.+.....|...||..|++.-+....    .||.||.
T Consensus         2 ~C~vC~~~~~-~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGE-DDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSC-CSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCC-CCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            5889976543 345667778999999999998765432    5999975

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.96  E-value=0.0061  Score=38.08  Aligned_cols=47  Identities=21%  Similarity=0.552  Sum_probs=34.0

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHHhcC----CCCcccccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSN----SSCPKCRHCLI  171 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~----~~CPlCR~~l~  171 (210)
                      .++.|.+|.+    +..+.....|.-.||..|++..+...    -.||.|+....
T Consensus         8 ~~~~C~~C~~----~g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~~   58 (61)
T d1mm2a_           8 HMEFCRVCKD----GGELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             SCSSCTTTCC----CSSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CcCCCcCCCC----CCeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCccc
Confidence            4468999974    34456666799999999998766432    26999976543

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.58  E-value=0.015  Score=37.29  Aligned_cols=44  Identities=30%  Similarity=0.655  Sum_probs=31.4

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHHHHHhcCC----CCccccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  170 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl~~~~----~CPlCR~~l  170 (210)
                      ..|.||.+   .+ .+.....|...||..|+...+....    .||.|+..-
T Consensus         8 ~~C~~C~~---~~-~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           8 TICRVCQK---PG-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SCCSSSCS---SS-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCC---cC-EEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            46777753   33 4666778999999999998875433    599996433

>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=93.49  E-value=0.017  Score=36.10  Aligned_cols=48  Identities=23%  Similarity=0.481  Sum_probs=36.9

Q ss_pred             CCCccccccCcccCCCceEEcCCCCCccchHHHHHHH---h--cCCCCccccc
Q 028342          121 LDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL---R--SNSSCPKCRH  168 (210)
Q Consensus       121 ~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl---~--~~~~CPlCR~  168 (210)
                      .+..|.||.....+++.++....|+.-||..|+..=.   .  .+-.||.|+.
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            4578999998888877777788899999999986421   1  2347999964

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.95  E-value=0.21  Score=32.20  Aligned_cols=48  Identities=17%  Similarity=0.336  Sum_probs=34.6

Q ss_pred             ccccccCcccCCCceEEcCCCCCccchHHHHH--H-Hhc--CCCCcccccccc
Q 028342          124 ECVICLSEFAPGERVRLLPKCNHGFHVRCIDK--W-LRS--NSSCPKCRHCLI  171 (210)
Q Consensus       124 ~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~--W-l~~--~~~CPlCR~~l~  171 (210)
                      .+-||...+..++..+....|+--||..|+..  . ...  +-.||.|+...-
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            33499988777777778888999999999852  2 122  347999986543

>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=90.69  E-value=0.087  Score=34.69  Aligned_cols=35  Identities=20%  Similarity=0.451  Sum_probs=26.2

Q ss_pred             CCCCccccccCcccCCCceEEcCCCCCccchHHHHHH
Q 028342          120 GLDTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKW  156 (210)
Q Consensus       120 ~~~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~W  156 (210)
                      .++..|.|| +.|..++.. -..-|+-+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            457899999 666655543 23348999999999986

>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=89.60  E-value=0.052  Score=35.88  Aligned_cols=50  Identities=18%  Similarity=0.489  Sum_probs=34.5

Q ss_pred             CCccccccCcccC-CCceEEcCCCCCccchHHHHHHH-----hc---CCCCcccccccc
Q 028342          122 DTECVICLSEFAP-GERVRLLPKCNHGFHVRCIDKWL-----RS---NSSCPKCRHCLI  171 (210)
Q Consensus       122 ~~~CaICLeef~~-~~~vr~lp~C~H~FH~~CI~~Wl-----~~---~~~CPlCR~~l~  171 (210)
                      ...|.||...... +..+.....|+..||..|+...+     +.   .-.||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            3579999875443 34566677899999999987543     11   236999965433

>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=87.38  E-value=0.22  Score=30.55  Aligned_cols=43  Identities=33%  Similarity=0.708  Sum_probs=31.8

Q ss_pred             CCccccccCcccCCCceEEcCCCCCccchHHHHHHH-hcCCCCccc
Q 028342          122 DTECVICLSEFAPGERVRLLPKCNHGFHVRCIDKWL-RSNSSCPKC  166 (210)
Q Consensus       122 ~~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~~Wl-~~~~~CPlC  166 (210)
                      ...|--|..++.+ ..+...++|++.|+.+| |.++ ..-.+||-|
T Consensus        15 ~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dC-D~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKD-QHVYVCAVCQNVFCVDC-DVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTT-SEEECCTTTTCCBCHHH-HHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCC-CceEECcCCCCcccccc-chhhhhhhcCCCCC
Confidence            4689999988864 45567889999999999 3333 233479988

>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=87.24  E-value=0.096  Score=28.01  Aligned_cols=29  Identities=21%  Similarity=0.481  Sum_probs=25.1

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHH
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCI  153 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI  153 (210)
                      ..|+-|...+...|.|+.-  =+++||-+|+
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            4799999999999999875  4799999994

>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=86.69  E-value=0.12  Score=33.01  Aligned_cols=42  Identities=36%  Similarity=0.707  Sum_probs=25.2

Q ss_pred             CccccccCcccCCCceEE-cCCCCC-ccchHHHHHHHhcC----CCCccccc
Q 028342          123 TECVICLSEFAPGERVRL-LPKCNH-GFHVRCIDKWLRSN----SSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~-lp~C~H-~FH~~CI~~Wl~~~----~~CPlCR~  168 (210)
                      .-| ||.... +++.+.. ...|.+ -||..|+.  |...    -.||.|+.
T Consensus        17 ~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~   64 (71)
T d1wesa_          17 TYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRG   64 (71)
T ss_dssp             CCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSS
T ss_pred             CEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCcc
Confidence            456 998753 3343333 223544 59999985  3332    26999965

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.57  E-value=0.069  Score=29.35  Aligned_cols=27  Identities=22%  Similarity=0.641  Sum_probs=20.8

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHH
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCI  153 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI  153 (210)
                      +.|.+|-..+.+    +++.+.|-.||..|+
T Consensus         9 EkC~~C~~~I~d----riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           9 EKCATCSQPILD----RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CBCTTTCCBCCS----CCEEETTEEECTTTC
T ss_pred             HHHHHhchHHHH----HHHHHhCCCCCCCCC
Confidence            689999888775    344458899998884

>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=82.68  E-value=0.59  Score=29.41  Aligned_cols=44  Identities=25%  Similarity=0.593  Sum_probs=30.3

Q ss_pred             CccccccCcccCCCceEEcCCCCCccchHHHH----HH--H---hcCCCCccccc
Q 028342          123 TECVICLSEFAPGERVRLLPKCNHGFHVRCID----KW--L---RSNSSCPKCRH  168 (210)
Q Consensus       123 ~~CaICLeef~~~~~vr~lp~C~H~FH~~CI~----~W--l---~~~~~CPlCR~  168 (210)
                      ..| ||..... ++.++....|.--||..|+.    ..  .   ...-.||.|+.
T Consensus        17 ~~C-iC~~~~~-~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          17 LYC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             CCS-TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CEE-ECCCccC-CCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            468 8976654 44567777899999999983    11  1   22458999953