Citrus Sinensis ID: 038517

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
Protein Sequence
MAISDLFQMLSSSASSPVIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHcccccccccHHHHHcccccccccccccccHHHHccccEEEcccccccccEEcccccccccccccccccccccccccHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHccccccccccHccccccccccccccccccHHHHcccccccccccccccEEEEHHHHccccHEEEcccccccccHHHHHHHHHHcccccccccccccccc
Coil and Loop (DISEMBL)
MAISDLFQMlsssasspvidfnedyrlynntasstdgisgfslekirgfpwfdcQRNLAAICAVCLdgvhkgersrnfsicKHVFHARCIDLWLVRrltcptcrspfkmepv
Flexible Loop (DISEMBL)
maisdlfqmlsssasspvidfNEDYRLYNNTasstdgisgFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCptcrspfkmepv
Low Complexity Region (SEG)
MAISDLFQMLSSSASSPVIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV
Disordered region (IsUnstruct)
*****************VIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR********
Disordered Region (DISOPRED)
*AISDLFQML***********************************IRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF*****
Disordered Region (DISEMBL)
MAISDLFQMLSSSASSPVIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV
Disordered Region (DISPRO)
*********************NEDYRLYNN********SGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAISDLFQMLSSSASSPVIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV
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	112	2.2.26 [Sep-21-2011]
Q9ZV51	181	RING-H2 finger protein AT	yes	no	0.687	0.425	0.354	4e-09
Q9C919	178	Putative RING-H2 finger p	no	no	0.410	0.258	0.521	5e-09
Q9M0C3	176	RING-H2 finger protein AT	no	no	0.625	0.397	0.366	1e-08
Q9H6Y7	350	E3 ubiquitin-protein liga	yes	no	0.598	0.191	0.371	1e-08
P0C034	251	RING-H2 finger protein AT	no	no	0.651	0.290	0.412	1e-08
Q91XF4	347	E3 ubiquitin-protein liga	yes	no	0.598	0.193	0.371	2e-08
Q5XIL0	349	E3 ubiquitin-protein liga	yes	no	0.598	0.191	0.371	2e-08
Q9SG96	181	RING-H2 finger protein AT	no	no	0.464	0.287	0.461	2e-08
Q8LBA0	223	NEP1-interacting protein-	no	no	0.758	0.381	0.319	3e-08
Q94BY6	226	RING-H2 finger protein AT	no	no	0.580	0.287	0.4	7e-08

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

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 2/79 (2%)

Query: 33  SSTDGISGFSLEKIRGFPWFD--CQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCI 90
            S+DG+S   ++K+  F + +        + C VC DG  +G+  RN   C HVFH +C+
Sbjct: 79  ESSDGLSSRFVKKLPQFKFSEPSTYTRYESDCVVCFDGFRQGQWCRNLPGCGHVFHRKCV 138

Query: 91  DLWLVRRLTCPTCRSPFKM 109
           D WL++  TCP CR+  ++
Sbjct: 139 DTWLLKASTCPICRARVRL 157

Arabidopsis thaliana (taxid: 3702)

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

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 29/46 (63%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF 107
           CA+CL G    E  R F +C+H++HA CID WL   LTCPTCR   
Sbjct: 130 CAICLSGYVVNEECRVFPVCRHIYHALCIDAWLKNHLTCPTCRKDL 175

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M0C3|ATL14_ARATH RING-H2 finger protein ATL14 OS=Arabidopsis thaliana GN=ATL14 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 35  TDGISGFSLEKIRGFPWFDCQRNLAAI-CAVCLDGVHKGERSRNFSICKHVFHARCIDLW 93
           +DG+S   ++++  F + +         C VC+DG  +G+  R    C HVFH +C+DLW
Sbjct: 87  SDGLSPRCVKRLPQFKYCEPSSEYGGDDCVVCIDGFRQGQWCRKLPRCGHVFHRKCVDLW 146

Query: 94  LVRRLTCPTCR 104
           L++  TCP CR
Sbjct: 147 LIKVSTCPICR 157

Arabidopsis thaliana (taxid: 3702)

>sp|Q9H6Y7|RN167_HUMAN E3 ubiquitin-protein ligase RNF167 OS=Homo sapiens GN=RNF167 PE=1 SV=1

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 44  EKIRGFPWFDCQR-NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCP 101
           E+++  P  D Q+ +   +CA+CLD    G++ R    C H +H+RC+D WL + R TCP
Sbjct: 211 EQLKQIPTHDYQKGDQYDVCAICLDEYEDGDKLRVLP-CAHAYHSRCVDPWLTQTRKTCP 269

Query: 102 TCRSPFKMEP 111
            C+ P    P
Sbjct: 270 ICKQPVHRGP 279

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 43/80 (53%), Gaps = 7/80 (8%)

Query: 33  SSTDGISGFSLEK--IRGFPW--FDCQRNLAAI---CAVCLDGVHKGERSRNFSICKHVF 85
           SST G S   ++K  +R FP   +  + NL  +   C +CL     GE+ R    C H F
Sbjct: 99  SSTRGSSNKGIKKKALRMFPVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGF 158

Query: 86  HARCIDLWLVRRLTCPTCRS 105
           H RCID WL + LTCP CR+
Sbjct: 159 HVRCIDKWLQQHLTCPKCRN 178

Arabidopsis thaliana (taxid: 3702)

>sp|Q91XF4|RN167_MOUSE E3 ubiquitin-protein ligase RNF167 OS=Mus musculus GN=Rnf167 PE=2 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 44  EKIRGFPWFDCQR-NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCP 101
           E+++  P  D Q+ +   +CA+CLD    G++ R    C H +H+RC+D WL + R TCP
Sbjct: 211 EQLKQIPTHDYQKGDEYDVCAICLDEYEDGDKLRVLP-CAHAYHSRCVDPWLTQTRKTCP 269

Query: 102 TCRSPFKMEP 111
            C+ P    P
Sbjct: 270 ICKQPVHRGP 279

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5XIL0|RN167_RAT E3 ubiquitin-protein ligase RNF167 OS=Rattus norvegicus GN=Rnf167 PE=2 SV=1

 Score = 57.8 bits (138), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 44  EKIRGFPWFDCQR-NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCP 101
           E+++  P  D Q+ +   +CA+CLD    G++ R    C H +H+RC+D WL + R TCP
Sbjct: 211 EQLKQIPTHDYQKGDEYDVCAICLDEYEDGDKLRILP-CAHAYHSRCVDPWLTQTRKTCP 269

Query: 102 TCRSPFKMEP 111
            C+ P    P
Sbjct: 270 ICKQPVHRGP 279

May act as an E3 ubiquitin-protein ligase, or as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2E1, and then transfers it to substrates, such as SLC22A18. May play a role in growth regulation involved in G1/S transition.

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 29/52 (55%)

Query: 59  AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME 110
           A  C +CL     GE+ R    C H FH RCID WL+ R +CPTCR    +E
Sbjct: 111 ATECLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSLLLE 162

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LBA0|NIPL2_ARATH NEP1-interacting protein-like 2 OS=Arabidopsis thaliana GN=ATL24 PE=1 SV=2

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 9/94 (9%)

Query: 19  IDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWF----DCQRNLAAICAVCLDGVHKGER 74
           + + E   +Y    +   G+SG SL K+   P +    +  R     C +CL  +  GE 
Sbjct: 134 VSYEEREDVYGELEAR--GLSGDSLRKL---PCYIMSSEMVRRQVTHCTICLQDIKTGEI 188

Query: 75  SRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           +R+   C H FH  C+D WL+R  +CP CR   K
Sbjct: 189 TRSLPKCDHTFHLVCVDKWLIRHGSCPICRQAVK 222

May be involved in the early steps of the plant defense signaling pathway. Does not display E3 catalytic activity.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 55.8 bits (133), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 40  GFSLEKIRGFPW--FDCQRNLAAI---CAVCLDGVHKGERSRNFSICKHVFHARCIDLWL 94
           G + + +R FP   +  + NL  +   C +CL     GE+ R    C H FH RCID WL
Sbjct: 109 GINKKALRMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWL 168

Query: 95  VRRLTCPTCR 104
            + LTCP CR
Sbjct: 169 QQHLTCPKCR 178

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	112
388493108	182	unknown [Medicago truncatula]	0.446	0.274	0.58	9e-11
357479885	182	RING finger-like protein [Medicago trunc	0.446	0.274	0.58	1e-10
356542173	239	PREDICTED: E3 ubiquitin-protein ligase A	0.714	0.334	0.397	3e-09
413943909	172	putative RING zinc finger domain superfa	0.803	0.523	0.336	5e-09
50251291	202	putative RING-H2 zinc finger protein [Or	0.776	0.430	0.365	7e-09
222623015	213	hypothetical protein OsJ_07055 [Oryza sa	0.714	0.375	0.385	7e-09
125538798	673	hypothetical protein OsI_06554 [Oryza sa	0.401	0.066	0.511	8e-09
242096026	187	hypothetical protein SORBIDRAFT_10g02102	0.491	0.294	0.526	9e-09
413937169	226	putative RING zinc finger domain superfa	0.455	0.225	0.509	1e-08
242082738	200	hypothetical protein SORBIDRAFT_08g00242	0.732	0.41	0.411	1e-08

>gi|388493108|gb|AFK34620.1| unknown [Medicago truncatula]

 Score = 70.9 bits (172), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 35/50 (70%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
           CAVCLDG   G+  RN + C HVFH RCID WL++  TCPTCR+P +  P
Sbjct: 102 CAVCLDGFRNGQWRRNLAACGHVFHRRCIDTWLLKVATCPTCRTPVRSNP 151

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479885|ref|XP_003610228.1| RING finger-like protein [Medicago truncatula] gi|355511283|gb|AES92425.1| RING finger-like protein [Medicago truncatula]

 Score = 70.5 bits (171), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 35/50 (70%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
           CAVCLDG   G+  RN + C HVFH RCID WL++  TCPTCR+P +  P
Sbjct: 102 CAVCLDGFRNGQWCRNLAACGHVFHRRCIDTWLLKVATCPTCRTPVRSNP 151

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542173|ref|XP_003539544.1| PREDICTED: E3 ubiquitin-protein ligase ATL41-like [Glycine max]

 Score = 65.9 bits (159), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 35/88 (39%), Positives = 47/88 (53%), Gaps = 8/88 (9%)

Query: 28  YNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHA 87
           +NNT     G++   +  +  FP+   Q + +A CAVCL  +  GE  R    CKH FH 
Sbjct: 74  HNNT-----GLNPALITTLPTFPFKQNQHHDSAECAVCLSVLEDGEHVRLLPNCKHSFHV 128

Query: 88  RCIDLWLVRRLTCPTCRS---PFKMEPV 112
            CID WL    TCP CR+   P ++EPV
Sbjct: 129 SCIDTWLSSHSTCPICRTKAGPVQLEPV 156

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413943909|gb|AFW76558.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 65.1 bits (157), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 16  SPVIDFNEDYRLYNNTASSTDG--ISGFSLEKIRGFPWFDCQRNL------AAICAVCLD 67
           +PV           N     DG  + G  + K+ GF +              A C+VCL 
Sbjct: 56  APVTAAAAGAAAETNNPPGPDGHHVGGVDISKLPGFAYAAPSSRRRGNGGDGAQCSVCLG 115

Query: 68  GVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS 105
            V  GE  R   +CKH++H  CID+WL    TCP CRS
Sbjct: 116 AVQAGEMVRRLPLCKHLYHVECIDMWLASHATCPLCRS 153

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|50251291|dbj|BAD28071.1| putative RING-H2 zinc finger protein [Oryza sativa Japonica Group] gi|50252215|dbj|BAD28222.1| putative RING-H2 zinc finger protein [Oryza sativa Japonica Group]

 Score = 64.7 bits (156), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 23  EDYRLYNNTASSTDGISGFSLEKIRGFPW--FDCQRNLAAICAVCLDGVHKGERSRNFSI 80
           +D  L  + A+   G+     + +R  P   +      +  CA+CL  +  GER R    
Sbjct: 95  DDGELGPSAAAQAAGVR---RKALRAMPTMVYSAAGGPSPACAICLADLEPGERVRVLPK 151

Query: 81  CKHVFHARCIDLWLVRRLTCPTCRSP-FKMEPV 112
           C H FH RC+D WL+ R TCPTCR P F   PV
Sbjct: 152 CNHGFHVRCVDRWLLARSTCPTCRQPLFATPPV 184

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222623015|gb|EEE57147.1| hypothetical protein OsJ_07055 [Oryza sativa Japonica Group]

 Score = 64.7 bits (156), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 33  SSTDGISGFSLEKIRGFPW--FDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCI 90
           S+    +G   + +R  P   +      +  CA+CL  +  GER R    C H FH RC+
Sbjct: 113 SAAAQAAGVRRKALRAMPTMVYSAAGGPSPACAICLADLEPGERVRVLPKCNHGFHVRCV 172

Query: 91  DLWLVRRLTCPTCRSP-FKMEPV 112
           D WL+ R TCPTCR P F   PV
Sbjct: 173 DRWLLARSTCPTCRQPLFATPPV 195

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125538798|gb|EAY85193.1| hypothetical protein OsI_06554 [Oryza sativa Indica Group]

 Score = 64.3 bits (155), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 23/45 (51%), Positives = 30/45 (66%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C+VCL  + +GE ++   +C HVFH  CID+WL    TCP CRSP
Sbjct: 144 CSVCLGEMRQGEAAKRLPVCLHVFHEECIDMWLGSHATCPICRSP 188

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242096026|ref|XP_002438503.1| hypothetical protein SORBIDRAFT_10g021020 [Sorghum bicolor] gi|241916726|gb|EER89870.1| hypothetical protein SORBIDRAFT_10g021020 [Sorghum bicolor]

 Score = 64.3 bits (155), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 49  FPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS 105
           FP+ D     AA CAVCL+G+  GE +R    C H FHA CID+WL    TCP CRS
Sbjct: 102 FPYKD--DAAAAQCAVCLEGMKDGEAARRLPACSHAFHAGCIDMWLDSHATCPVCRS 156

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413937169|gb|AFW71720.1| putative RING zinc finger domain superfamily protein [Zea mays]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 31/51 (60%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
           +CA+CL  +  GER R    C H FH RC+D WL+ R TCPTCR P    P
Sbjct: 140 VCAICLAELEPGERVRVLPKCNHGFHVRCVDRWLLARSTCPTCRQPLFGAP 190

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242082738|ref|XP_002441794.1| hypothetical protein SORBIDRAFT_08g002420 [Sorghum bicolor] gi|241942487|gb|EES15632.1| hypothetical protein SORBIDRAFT_08g002420 [Sorghum bicolor]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/85 (41%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 29  NNTASSTDGISGFSLEKIRGFPWFD-CQRNLAAICAVCLDGVHKGERSRNFSICKHVFHA 87
           N   SS  G+S   +E     P F+ C++  A  CAVC++ V  GE  R    C H FHA
Sbjct: 106 NCGGSSASGLSQAEVEG--AIPVFEYCRKAAAEQCAVCINVVRDGEAVRRLPACAHTFHA 163

Query: 88  RCIDLWLVRRLTCPTCRSPFKMEPV 112
            CID WL    TCP CR+  K+  V
Sbjct: 164 PCIDGWLRAHATCPMCRADVKVAAV 188

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	112
UNIPROTKB|F1Q390	359	RNF167 "Uncharacterized protei	0.642	0.200	0.4	7.1e-13
TAIR|locus:2053994	181	AT2G18670 [Arabidopsis thalian	0.75	0.464	0.348	5e-12
UNIPROTKB|F1RFY0	350	RNF167 "Uncharacterized protei	0.598	0.191	0.385	3.5e-11
TAIR|locus:2011491	178	AT1G53010 [Arabidopsis thalian	0.383	0.241	0.558	4.5e-11
GENEDB_PFALCIPARUM|PF10_0276	274	PF10_0276 "hypothetical protei	0.651	0.266	0.355	5.2e-11
UNIPROTKB|Q8IJC2	274	PF10_0276 "Zinc finger, C3HC4	0.651	0.266	0.355	5.2e-11
TAIR|locus:2118651	176	AT4G30370 [Arabidopsis thalian	0.625	0.397	0.366	7.4e-11
TAIR|locus:2081907	334	ATL4 "TOXICOS EN LEVADURA 4" [	0.875	0.293	0.343	2.8e-10
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.651	0.290	0.412	4e-10
TAIR|locus:4010713762	223	AT3G20395 [Arabidopsis thalian	0.776	0.390	0.325	5.2e-10

UNIPROTKB|F1Q390 RNF167 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 155 (59.6 bits), Expect = 7.1e-13, Sum P(2) = 7.1e-13
 Identities = 30/75 (40%), Positives = 41/75 (54%)

Query:    39 SGFSLEKIRGFPWFDCQRNLAA-ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR- 96
             S  + E++   P  D QR     +CA+CLD    GER R    C H +H+RC+D WL + 
Sbjct:   210 SRLTREQLERIPTRDYQRGAPDDVCAICLDAYEVGERLRVLP-CAHAYHSRCVDPWLTQT 268

Query:    97 RLTCPTCRSPFKMEP 111
             R TCP C+ P +  P
Sbjct:   269 RRTCPVCKQPVRRSP 283

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 30/86 (34%), Positives = 47/86 (54%)

Query:    26 RLYNNTASSTDGISGFSLEKIRGFPWFD--CQRNLAAICAVCLDGVHKGERSRNFSICKH 83
             R  N    S+DG+S   ++K+  F + +        + C VC DG  +G+  RN   C H
Sbjct:    72 RRRNRRQESSDGLSSRFVKKLPQFKFSEPSTYTRYESDCVVCFDGFRQGQWCRNLPGCGH 131

Query:    84 VFHARCIDLWLVRRLTCPTCRSPFKM 109
             VFH +C+D WL++  TCP CR+  ++
Sbjct:   132 VFHRKCVDTWLLKASTCPICRARVRL 157

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|F1RFY0 RNF167 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 144 (55.7 bits), Expect = 3.5e-11, Sum P(2) = 3.5e-11
 Identities = 27/70 (38%), Positives = 40/70 (57%)

Query:    44 EKIRGFPWFDCQR-NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCP 101
             E+++  P  D Q+ +   +CA+CLD    G+R R    C H +H+RC+D WL + R TCP
Sbjct:   211 EQLKQIPTHDYQKGDQYDVCAICLDEYEDGDRLRVLP-CAHAYHSRCVDPWLTQTRKTCP 269

Query:   102 TCRSPFKMEP 111
              C+ P    P
Sbjct:   270 ICKQPVHRGP 279

GO:0045786 "negative regulation of cell cycle" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0000209 "protein polyubiquitination" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2011491 AT1G53010 [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 24/43 (55%), Positives = 29/43 (67%)

Query:    62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR 104
             CA+CL G    E  R F +C+H++HA CID WL   LTCPTCR
Sbjct:   130 CAICLSGYVVNEECRVFPVCRHIYHALCIDAWLKNHLTCPTCR 172

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

GENEDB_PFALCIPARUM|PF10_0276 PF10_0276 "hypothetical protein" [Plasmodium falciparum (taxid:5833)]

 Score = 155 (59.6 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query:    39 SGFSLEKIRGFPWFDCQRNLA--AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR 96
             +G  L++I   P++   +N++  + C++CL+     E  R   +C H FH  CIDLWL+R
Sbjct:   196 NGLRLKQIENLPFYYI-KNISNESKCSICLNDFQIDECVRTLLLCNHTFHKSCIDLWLIR 254

Query:    97 RLTCPTCRSPFKMEPV 112
               TCP C+SP   + +
Sbjct:   255 SATCPNCKSPIASQGI 270

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q8IJC2 PF10_0276 "Zinc finger, C3HC4 type, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 155 (59.6 bits), Expect = 5.2e-11, P = 5.2e-11
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query:    39 SGFSLEKIRGFPWFDCQRNLA--AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR 96
             +G  L++I   P++   +N++  + C++CL+     E  R   +C H FH  CIDLWL+R
Sbjct:   196 NGLRLKQIENLPFYYI-KNISNESKCSICLNDFQIDECVRTLLLCNHTFHKSCIDLWLIR 254

Query:    97 RLTCPTCRSPFKMEPV 112
               TCP C+SP   + +
Sbjct:   255 SATCPNCKSPIASQGI 270

GO:0008150 "biological_process" evidence=ND

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

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 26/71 (36%), Positives = 41/71 (57%)

Query:    35 TDGISGFSLEKIRGFPWFDCQRNLAAI-CAVCLDGVHKGERSRNFSICKHVFHARCIDLW 93
             +DG+S   ++++  F + +         C VC+DG  +G+  R    C HVFH +C+DLW
Sbjct:    87 SDGLSPRCVKRLPQFKYCEPSSEYGGDDCVVCIDGFRQGQWCRKLPRCGHVFHRKCVDLW 146

Query:    94 LVRRLTCPTCR 104
             L++  TCP CR
Sbjct:   147 LIKVSTCPICR 157

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2081907 ATL4 "TOXICOS EN LEVADURA 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 2.8e-10, P = 2.8e-10
 Identities = 35/102 (34%), Positives = 50/102 (49%)

Query:     9 MLSSSASSPVIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWFDCQRNLAAI----CAV 64
             +L  S+SS V     D R ++    S +      L+ +  F +    R  +++    CAV
Sbjct:    60 VLPLSSSSSVATVTSDSRRFSGHRVSPETERSSVLDSLPIFKFSSVTRRSSSMNSGDCAV 119

Query:    65 CLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
             CL      ++ R   +C H FHA CID+WLV   TCP CRSP
Sbjct:   120 CLSKFEPEDQLRLLPLCCHAFHADCIDIWLVSNQTCPLCRSP 161

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 146 (56.5 bits), Expect = 4.0e-10, P = 4.0e-10
 Identities = 33/80 (41%), Positives = 43/80 (53%)

Query:    33 SSTDGISGFSLEK--IRGFPW--FDCQRNLAAI---CAVCLDGVHKGERSRNFSICKHVF 85
             SST G S   ++K  +R FP   +  + NL  +   C +CL     GE+ R    C H F
Sbjct:    99 SSTRGSSNKGIKKKALRMFPVVSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGF 158

Query:    86 HARCIDLWLVRRLTCPTCRS 105
             H RCID WL + LTCP CR+
Sbjct:   159 HVRCIDKWLQQHLTCPKCRN 178

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

TAIR|locus:4010713762 AT3G20395 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 29/89 (32%), Positives = 41/89 (46%)

Query:    18 VIDFNEDYRLYNNTASSTDGISGFSLEKIRGFPWF--DCQRNLAAICAVCLDGVHKGERS 75
             +I  +  Y   +N         G S   I+  P F    +    + C++CL    +GE  
Sbjct:   125 IIALDTSYMESSNLYDFNHEKKGLSKSSIQNIPMFYNRSEHQTKSSCSICLQDWEEGEVG 184

Query:    76 RNFSICKHVFHARCIDLWLVRRLTCPTCR 104
             R  + C H FH  CID WL+R+ TCP CR
Sbjct:   185 RKLARCGHTFHMNCIDEWLLRQETCPICR 213

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	OsJ_07055	RING-H2 finger protein, putative, expressed (202 aa)
		(Oryza sativa Japonica)
Predicted Functional Partners:
	OsI_14159	ATCHX, putative, expressed (780 aa)							•		0.746
	LOC_Os10g13440.1	monosaccharide-sensing protein 2, putative (136 aa)							•		0.663
	4341492	elongation factor, putative, expressed (997 aa)							•		0.500
	OsJ_16426	oryzain alpha chain precursor, putative, expressed (262 aa)							•		0.500
	4332840	nucleolar protein NOP5-1, putative (568 aa)							•		0.500
	4329604	elongation factor Tu family protein, putative, expressed (1005 aa)							•		0.500
	4326544	elongation factor, putative, expressed (826 aa)							•		0.500
	OsJ_03302	elongation factor, putative, expressed (853 aa)							•		0.500
	4340558	aquaporin protein, putative, expressed; Aquaporins facilitate the transport of water and small [...] (298 aa)							•		0.491
	LIR1	light-induced protein 1-like, putative, expressed (128 aa)							•		0.486

---

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	112
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	7e-10
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-09
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-08
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	4e-07
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	1e-06
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	8e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	1e-04
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	9e-04
PHA02926	242	PHA02926, PHA02926, zinc finger-like protein; Prov	0.002

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

 Score = 50.1 bits (120), Expect = 7e-10
 Identities = 21/45 (46%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C +CLD    GE       C HVFH  C+D WL    TCP CR+P
Sbjct: 3   CPICLDEFEPGEEVV-VLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 52.7 bits (126), Expect = 3e-09
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSP 106
           CA+C+    K +R R    C H FH  C+D WL+     CP CR+ 
Sbjct: 326 CAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTA 370

Length = 374

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 22/50 (44%), Positives = 31/50 (62%), Gaps = 4/50 (8%)

Query: 62  CAVCLDGVH-KGERSRNFSI---CKHVFHARCIDLWLVRRLTCPTCRSPF 107
           CA+C++ V+ K  ++  F I   C HVF   CID+W   + TCP CR+PF
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226

Length = 238

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

 Score = 42.8 bits (101), Expect = 4e-07
 Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPF 107
           C +CL+   +         C HVF   CID WL     TCP CR+P 
Sbjct: 2   CPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 9/55 (16%)

Query: 61  ICAVCLDG-VHKGERS--RNFSI------CKHVFHARCIDLWLVRRLTCPTCRSP 106
            C +C+D   H       R   +      C H+ H  C+  WL R+ TCP CR P
Sbjct: 289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRP 343

Length = 491

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

 Score = 41.6 bits (98), Expect = 2e-06
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 78  FSICKHVFHARCIDLWLVRRLTCPTCR 104
           +  C H FH  CI  WL  R TCP CR
Sbjct: 47  WGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 42.7 bits (100), Expect = 8e-06
 Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 60   AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPF 107
            AIC   LD V +   S+  + CK+ FH RC+  W     R  CP CRS  
Sbjct: 1473 AICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

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 = 37.9 bits (88), Expect = 1e-04
 Identities = 11/28 (39%), Positives = 14/28 (50%)

Query: 80  ICKHVFHARCIDLWLVRRLTCPTCRSPF 107
           +C H FH  CI  WL  +  CP  R  +
Sbjct: 53  VCNHAFHDHCIYRWLDTKGVCPLDRQTW 80

Length = 88

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

 Score = 34.4 bits (79), Expect = 9e-04
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 3/45 (6%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS 105
            C +CLD +         + C HVF   CI  +L ++  CP CR+
Sbjct: 4   ECPICLDLL---RDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 11/58 (18%)

Query: 62  CAVCLDGVH--KGERSRNFSI---CKHVFHARCIDLW-LVRRLT-----CPTCRSPFK 108
           C +C + V+  + E  R F +   C H+F   CI++W   RR T     CP CR+ F+
Sbjct: 173 CGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230

Length = 242

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	112
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.82
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.76
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.58
PHA02929	238	N1R/p28-like protein; Provisional	99.57
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.51
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.48
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.47
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.44
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.41
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.39
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.34
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.33
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.33
PHA02926	242	zinc finger-like protein; Provisional	99.27
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.27
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.27
PF14634	44	zf-RING_5: zinc-RING finger domain	99.27
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.22
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.21
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.19
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	99.18
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.15
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.1
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.07
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.99
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.89
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.89
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.87
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.86
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.85
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.77
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.76
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.75
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.73
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.7
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.68
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.59
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.57
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.55
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.5
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.46
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.31
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.28
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.26
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.13
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.11
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.02
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.0
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.94
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.86
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.75
PHA02862	156	5L protein; Provisional	97.75
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.74
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.68
COG5152	259	Uncharacterized conserved protein, contains RING a	97.65
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.64
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.61
KOG2660	331	consensus Locus-specific chromosome binding protei	97.61
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.4
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.34
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.34
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.34
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.26
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.18
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.17
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.11
PHA03096	284	p28-like protein; Provisional	97.1
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.03
PF04641	260	Rtf2: Rtf2 RING-finger	96.99
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.94
KOG4739	233	consensus Uncharacterized protein involved in syna	96.88
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.82
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.78
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.75
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.74
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.74
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.72
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.6
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.5
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	96.45
KOG1940	276	consensus Zn-finger protein [General function pred	96.36
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.22
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	95.84
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.77
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.75
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	95.74
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.57
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	95.54
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.5
KOG3053	293	consensus Uncharacterized conserved protein [Funct	95.37
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.0
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.97
KOG3899	381	consensus Uncharacterized conserved protein [Funct	94.94
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.63
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.59
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.56
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	94.39
KOG3002	299	consensus Zn finger protein [General function pred	94.12
KOG1609	323	consensus Protein involved in mRNA turnover and st	94.1
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	93.76
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	93.29
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.39
COG5109	396	Uncharacterized conserved protein, contains RING Z	89.8
KOG3113	293	consensus Uncharacterized conserved protein [Funct	89.72
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	89.26
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	89.18
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	89.17
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	89.1
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	88.96
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.9
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	88.43
KOG4367	699	consensus Predicted Zn-finger protein [Function un	88.38
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.34
KOG0269	839	consensus WD40 repeat-containing protein [Function	87.94
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	86.36
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	86.26
KOG1829	580	consensus Uncharacterized conserved protein, conta	85.91
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	85.26
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	85.26
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	84.93
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	84.41
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	83.02
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	82.8
KOG2068	327	consensus MOT2 transcription factor [Transcription	81.75

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

Probab=99.82  E-value=7.3e-21  Score=135.03  Aligned_cols=74  Identities=27%  Similarity=0.666  Sum_probs=64.1

Q ss_pred             CCCCCCCHHHHcCCCceecCCCCcc----ccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-CCCccccCCCCCC
Q 038517           36 DGISGFSLEKIRGFPWFDCQRNLAA----ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPFKME  110 (112)
Q Consensus        36 ~~~~~~~~~~~~~l~~~~~~~~~~~----~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~~  110 (112)
                      .+..++.++.+.++|...+....++    .|+||+|+|+.|++++.|| |+|.||..||++|+.+. ..||+|++++...
T Consensus       202 ~~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  202 LRRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            4666677799999999999887443    8999999999999999999 99999999999999876 5599999977543

>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=99.76  E-value=2.6e-19  Score=93.03  Aligned_cols=44  Identities=43%  Similarity=1.089  Sum_probs=40.2

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcccc
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR  104 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr  104 (112)
                      +.|+||++++..++.++.++ |+|.||.+||.+|++++.+||+||
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            36999999999889999999 999999999999999999999997

...

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

Probab=99.58  E-value=1.6e-15  Score=86.74  Aligned_cols=47  Identities=36%  Similarity=0.847  Sum_probs=35.9

Q ss_pred             CccccccccccccCC---------CceeecCCCcCcccHHhHHHHHhCCCCCcccc
Q 038517           58 LAAICAVCLDGVHKG---------ERSRNFSICKHVFHARCIDLWLVRRLTCPTCR  104 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~---------~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr  104 (112)
                      .++.|+||++.+...         +....+..|||.||..||.+|++.+.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            355699999999422         23334434999999999999999999999998

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.57  E-value=2.3e-15  Score=102.91  Aligned_cols=66  Identities=33%  Similarity=0.704  Sum_probs=49.1

Q ss_pred             HHHHcCCCceecCC------CCccccccccccccCCC----ceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           43 LEKIRGFPWFDCQR------NLAAICAVCLDGVHKGE----RSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        43 ~~~~~~l~~~~~~~------~~~~~C~IC~~~~~~~~----~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ...++.+|....+.      ..+.+|+||++.+..++    ....++.|+|.||..||.+|++.+.+||+||.++.
T Consensus       152 ~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        152 KKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             HHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            35556666554332      25689999999876543    12345459999999999999999999999999764

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

Probab=99.51  E-value=1e-14  Score=101.47  Aligned_cols=51  Identities=35%  Similarity=0.888  Sum_probs=47.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~  109 (112)
                      .+-+|+||++.|-.+++++.+| |+|.||..|+..|+.. +..||+||+++++
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            5678999999999999999999 9999999999999984 7889999999875

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

Probab=99.48  E-value=2.2e-14  Score=102.27  Aligned_cols=51  Identities=33%  Similarity=0.933  Sum_probs=44.5

Q ss_pred             Ccccccccccc-ccCC---------CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDG-VHKG---------ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~-~~~~---------~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|.||+++ +..+         ..+..+| |||.||..|++.|++++++||+||.++-.
T Consensus       286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~if  346 (491)
T COG5243         286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIF  346 (491)
T ss_pred             CCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcccc
Confidence            78899999999 5544         2568899 99999999999999999999999999643

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

Probab=99.47  E-value=4.5e-14  Score=97.60  Aligned_cols=51  Identities=29%  Similarity=0.733  Sum_probs=44.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~~  112 (112)
                      ....|.+|++..+   .+.-+| |||+||..||.+|...+..||+||..+.+.+|
T Consensus       238 a~~kC~LCLe~~~---~pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  238 ATRKCSLCLENRS---NPSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCceEEEecCCC---CCCcCc-CcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            5678999999764   467777 99999999999999999999999999988764

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

Probab=99.44  E-value=7.7e-14  Score=80.87  Aligned_cols=53  Identities=30%  Similarity=0.769  Sum_probs=41.9

Q ss_pred             CccccccccccccC---------CCceeecCCCcCcccHHhHHHHHhC---CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHK---------GERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~---------~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~~~~~~  110 (112)
                      .++.|.||...|+.         ++.+.....|+|.||..||.+|+..   +..||+||+++..+
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            57889999988861         1334445559999999999999975   57899999988764

>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=99.41  E-value=2.1e-13  Score=72.44  Aligned_cols=46  Identities=28%  Similarity=0.801  Sum_probs=39.2

Q ss_pred             ccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      +..|.||++...   .+..+| |||. |+..|+.+|++++..||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            568999999864   377788 9999 999999999999999999999875

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.39  E-value=4e-13  Score=88.87  Aligned_cols=50  Identities=30%  Similarity=0.624  Sum_probs=41.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----------------CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----------------RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----------------~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   +++++ |||.||..||.+|+..                ...||+||.++...+
T Consensus        17 ~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            57889999998753   56667 9999999999999842                347999999987654

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

Probab=99.34  E-value=6.2e-13  Score=89.53  Aligned_cols=52  Identities=27%  Similarity=0.617  Sum_probs=43.3

Q ss_pred             CCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC---CCCCccccCCCCCCCC
Q 038517           57 NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRSPFKMEPV  112 (112)
Q Consensus        57 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~~~~~~~~  112 (112)
                      ....+|.|||+.-+   .++++. |||.||..||.+|+..   ++.||+|+..|..++|
T Consensus        45 ~~~FdCNICLd~ak---dPVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v   99 (230)
T KOG0823|consen   45 GGFFDCNICLDLAK---DPVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV   99 (230)
T ss_pred             CCceeeeeeccccC---CCEEee-cccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence            36789999999764   366666 9999999999999974   4679999999988764

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

Probab=99.33  E-value=1.5e-12  Score=66.82  Aligned_cols=44  Identities=43%  Similarity=1.020  Sum_probs=36.0

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPF  107 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~  107 (112)
                      .|+||++.+.  +.....+ |+|.||..|+..|++. +..||.||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4999999882  3344455 9999999999999987 77899999764

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=99.33  E-value=1.2e-12  Score=66.04  Aligned_cols=39  Identities=33%  Similarity=0.889  Sum_probs=31.8

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~C  103 (112)
                      |+||++.+.+  .++.++ |||.|+..|+.+|++++.+||+|
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            7999998854  335566 99999999999999999999987

>PHA02926 zinc finger-like protein; Provisional

Probab=99.27  E-value=2.7e-12  Score=86.17  Aligned_cols=51  Identities=29%  Similarity=0.761  Sum_probs=39.5

Q ss_pred             CccccccccccccCC-----CceeecCCCcCcccHHhHHHHHhCC------CCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKG-----ERSRNFSICKHVFHARCIDLWLVRR------LTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~-----~~~~~~~~C~H~fh~~Ci~~w~~~~------~~CP~Cr~~~~  108 (112)
                      .+.+|+||+|..-+.     .....+++|+|.||..||..|.+.+      .+||+||..+.
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            578999999976321     2345666699999999999999742      45999998654

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

Probab=99.27  E-value=1.9e-12  Score=84.12  Aligned_cols=51  Identities=33%  Similarity=0.670  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      ....|+|||+.+.+ ..+.... |||+||..||+..++....||+||+.+..+
T Consensus       130 ~~~~CPiCl~~~se-k~~vsTk-CGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSE-KVPVSTK-CGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhh-ccccccc-cchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            45789999999864 2223344 999999999999999999999999987655

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

Probab=99.27  E-value=1.5e-12  Score=98.73  Aligned_cols=49  Identities=37%  Similarity=1.070  Sum_probs=44.1

Q ss_pred             CccccccccccccCCCc--eeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGER--SRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~--~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      .+..|+||+|.+..+..  +.+++ |+|+||..|++.|++++++||+||..+
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhh
Confidence            58899999999987655  78888 999999999999999999999999844

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.27  E-value=5.1e-12  Score=65.39  Aligned_cols=44  Identities=30%  Similarity=0.812  Sum_probs=37.9

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS  105 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~  105 (112)
                      .|+||++.|.......+++ |||+|+..|+..+......||+||+
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            4899999995555677777 9999999999999867789999985

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

Probab=99.22  E-value=1.2e-11  Score=63.26  Aligned_cols=38  Identities=29%  Similarity=0.869  Sum_probs=29.2

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHhCC----CCCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR----LTCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~----~~CP~C  103 (112)
                      |+||++.|..   ++.++ |||.|+..||.+|.++.    ..||.|
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            8999999964   88898 99999999999999753    369987

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

Probab=99.21  E-value=6.7e-12  Score=71.32  Aligned_cols=51  Identities=31%  Similarity=0.799  Sum_probs=38.2

Q ss_pred             ccccccccccc-----------CC-CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           60 AICAVCLDGVH-----------KG-ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        60 ~~C~IC~~~~~-----------~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      +.|+||...+-           .+ +.+..-..|+|.||..||.+||..++.||++|+++...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            55777665542           22 34444444999999999999999999999999987543

>smart00504 Ubox Modified RING finger domain

Probab=99.19  E-value=2.6e-11  Score=67.06  Aligned_cols=48  Identities=21%  Similarity=0.469  Sum_probs=41.6

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ..|+||.+.+..   ++.++ |||+|++.||.+|++++.+||+|+.++..+.
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~   49 (63)
T smart00504        2 FLCPISLEVMKD---PVILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHED   49 (63)
T ss_pred             cCCcCCCCcCCC---CEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhh
Confidence            469999999865   56677 9999999999999998899999999886554

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

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

Probab=99.18  E-value=3.5e-12  Score=71.88  Aligned_cols=53  Identities=28%  Similarity=0.708  Sum_probs=41.7

Q ss_pred             Ccccccccccccc---------CCCceeecCCCcCcccHHhHHHHHhC---CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVH---------KGERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~---------~~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~~~~~~  110 (112)
                      .+++|.||.-.|.         .++.+.++..|.|.||..||.+|+..   +..||+||+++..+
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~~   83 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQFK   83 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEec
Confidence            4668999998886         33455555559999999999999964   56799999988654

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.15  E-value=2.3e-11  Score=61.84  Aligned_cols=39  Identities=31%  Similarity=0.905  Sum_probs=32.4

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHh--CCCCCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV--RRLTCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~--~~~~CP~C  103 (112)
                      |+||++.+..  ....++ |||.|+..|+.+|++  ....||.|
T Consensus         1 C~iC~~~~~~--~~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED--PVILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS--EEEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC--CCEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            7899999864  224666 999999999999998  56789987

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=99.10  E-value=1e-10  Score=57.96  Aligned_cols=38  Identities=37%  Similarity=0.993  Sum_probs=32.2

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHh-CCCCCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-RRLTCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~C  103 (112)
                      |+||++..   ..+..++ |+|.||..|+..|++ .+..||+|
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   4577777 999999999999998 66789987

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.07  E-value=1.1e-10  Score=85.08  Aligned_cols=50  Identities=28%  Similarity=0.528  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.|..   +++++ |||.||..||..|+.....||+||.++...+
T Consensus        25 ~~l~C~IC~d~~~~---Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~   74 (397)
T TIGR00599        25 TSLRCHICKDFFDV---PVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESK   74 (397)
T ss_pred             cccCCCcCchhhhC---ccCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccccc
Confidence            46789999999854   55677 9999999999999998889999999876543

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

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

Probab=98.99  E-value=2e-10  Score=79.16  Aligned_cols=52  Identities=33%  Similarity=0.842  Sum_probs=42.5

Q ss_pred             CccccccccccccCCC-------ceeecCCCcCcccHHhHHHHHh--CCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGE-------RSRNFSICKHVFHARCIDLWLV--RRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~-------~~~~~~~C~H~fh~~Ci~~w~~--~~~~CP~Cr~~~~~~  110 (112)
                      ++..|+||-..+....       +...+. |+|+||..||+.|-.  ++++||+|+..+..+
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            5778999988775433       566787 999999999999984  688999999877654

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

Probab=98.89  E-value=7.1e-10  Score=76.16  Aligned_cols=51  Identities=25%  Similarity=0.667  Sum_probs=42.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHH-HHhCCCC-CccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDL-WLVRRLT-CPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~-w~~~~~~-CP~Cr~~~~~~~~  112 (112)
                      .+..|+||++...   .+..++ |||+||..||.. |-+++.- ||+||+-+.+++|
T Consensus       214 ~d~kC~lC~e~~~---~ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPE---VPSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccC---Cccccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            4778999999864   466677 999999999999 9877655 9999998887763

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

Probab=98.89  E-value=1.3e-09  Score=55.89  Aligned_cols=38  Identities=24%  Similarity=0.721  Sum_probs=22.6

Q ss_pred             cccccccccC-CCceeecCCCcCcccHHhHHHHHhCC----CCCc
Q 038517           62 CAVCLDGVHK-GERSRNFSICKHVFHARCIDLWLVRR----LTCP  101 (112)
Q Consensus        62 C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~w~~~~----~~CP  101 (112)
                      |+||.+ +.. .+.++.|+ |||+|+++||.++++++    .+||
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 644 44578898 99999999999999843    3576

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

Probab=98.87  E-value=2.1e-09  Score=56.69  Aligned_cols=42  Identities=26%  Similarity=0.766  Sum_probs=32.9

Q ss_pred             ccccccccccCCCceeecCCCc-----CcccHHhHHHHHhC--CCCCcccc
Q 038517           61 ICAVCLDGVHKGERSRNFSICK-----HVFHARCIDLWLVR--RLTCPTCR  104 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~--~~~CP~Cr  104 (112)
                      .|.||++ ..+++.+...| |.     |.+|..|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899998 33445566777 86     88999999999964  45899995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

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

Probab=98.86  E-value=9.5e-10  Score=81.22  Aligned_cols=51  Identities=27%  Similarity=0.784  Sum_probs=39.1

Q ss_pred             CccccccccccccCCC--------------ceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGE--------------RSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~--------------~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~  109 (112)
                      ....|+||+.+..--.              .....| |+|+||..|+.+|+.. +-.||+||.+++.
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3457999998775111              123346 9999999999999985 5599999998864

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

Probab=98.85  E-value=1.3e-09  Score=80.74  Aligned_cols=49  Identities=27%  Similarity=0.659  Sum_probs=39.0

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~~~~~~  111 (112)
                      +..|||||+....   ...+. |||+||..||.+++..     ...||+||..+..+.
T Consensus       186 ~~~CPICL~~~~~---p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCc---ccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            7789999998643   44455 9999999999998853     357999999887654

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

Probab=98.77  E-value=6.7e-09  Score=59.22  Aligned_cols=49  Identities=18%  Similarity=0.361  Sum_probs=38.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      +..|+|+.+.+..   ++.++ +||.|.+.+|.+|+++ +.+||.++.++..+.
T Consensus         4 ~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~   53 (73)
T PF04564_consen    4 EFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESD   53 (73)
T ss_dssp             GGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred             ccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence            5789999999965   88888 9999999999999998 899999999887654

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 ....

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

Probab=98.76  E-value=4e-09  Score=62.86  Aligned_cols=54  Identities=28%  Similarity=0.716  Sum_probs=41.3

Q ss_pred             Cccccccccccc-------------cCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGV-------------HKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~-------------~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ..+.|+||..-+             ..++..+.-..|+|.||.-||.+|++.++.||+|.+++.+.+
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~qr  111 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQR  111 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEee
Confidence            567899987432             122344444459999999999999999999999999887653

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

Probab=98.75  E-value=1.9e-09  Score=84.72  Aligned_cols=52  Identities=33%  Similarity=0.779  Sum_probs=39.8

Q ss_pred             CccccccccccccCCC---ceeecCCCcCcccHHhHHHHHhC--CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGE---RSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~---~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~~~  109 (112)
                      +.++|+||...+..-+   .-.+.+.|.|.||..|+..|+++  +++||+||.+++.
T Consensus      1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219        1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred             CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccccc
Confidence            6789999998765111   11233449999999999999986  5789999998864

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

Probab=98.73  E-value=1e-09  Score=62.13  Aligned_cols=51  Identities=29%  Similarity=0.697  Sum_probs=23.8

Q ss_pred             cccccccccccc-CCCceee-c--CCCcCcccHHhHHHHHhC----C-------CCCccccCCCCC
Q 038517           59 AAICAVCLDGVH-KGERSRN-F--SICKHVFHARCIDLWLVR----R-------LTCPTCRSPFKM  109 (112)
Q Consensus        59 ~~~C~IC~~~~~-~~~~~~~-~--~~C~H~fh~~Ci~~w~~~----~-------~~CP~Cr~~~~~  109 (112)
                      +..|.||+.... .++.+.. -  +.|+..||..||.+||..    +       ..||.|++++..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            467999999865 3333222 2  359999999999999962    1       149999998753

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.70  E-value=1.6e-08  Score=71.52  Aligned_cols=51  Identities=24%  Similarity=0.578  Sum_probs=36.8

Q ss_pred             ccccccccccc-cCCC-ceeecCCCcCcccHHhHHHHHh-CCCCCccccCCCCCC
Q 038517           59 AAICAVCLDGV-HKGE-RSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~-~~~~-~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~~~~  110 (112)
                      +..||+|..+- ...+ ...+.+ |||.||..|+...+. ....||.|+.++...
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            56799999952 2222 223335 999999999999664 456899999877654

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

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

Probab=98.68  E-value=6.4e-09  Score=73.93  Aligned_cols=48  Identities=25%  Similarity=0.589  Sum_probs=41.9

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      -..|.||++.|..   +...| |+|.||.-||...|..+..||.|+.++...
T Consensus        23 lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   23 LLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             HHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            4569999999953   67777 999999999999999999999999987653

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

Probab=98.59  E-value=2.8e-08  Score=69.44  Aligned_cols=46  Identities=26%  Similarity=0.516  Sum_probs=39.2

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      -..|.||-+.+..   +..++ |||.||.-||...|..+..||+||.+..
T Consensus        25 ~lrC~IC~~~i~i---p~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          25 MLRCRICDCRISI---PCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             HHHhhhhhheeec---ceecc-cccchhHHHHHHHhcCCCCCccccccHH
Confidence            4569999998853   55566 9999999999999999999999998653

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

Probab=98.57  E-value=1.3e-08  Score=55.95  Aligned_cols=47  Identities=26%  Similarity=0.694  Sum_probs=23.5

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ..|++|.+.+.+   ++.+..|.|+|+..||.+-+.  ..||+|+.+...++
T Consensus         8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS
T ss_pred             cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHH
Confidence            359999998854   655545999999999988554  34999999886655

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

Probab=98.55  E-value=3.2e-08  Score=71.42  Aligned_cols=48  Identities=29%  Similarity=0.825  Sum_probs=35.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC---CCCCccccCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRSP  106 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~~  106 (112)
                      -..|.||-+-+.....+.-...|||+||..|+.+|+..   +..||.|+-.
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik   54 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIK   54 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeec
Confidence            35699995554444455545459999999999999985   3689999833

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

Probab=98.50  E-value=4.2e-08  Score=71.88  Aligned_cols=48  Identities=29%  Similarity=0.724  Sum_probs=37.8

Q ss_pred             CccccccccccccCCC-ceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGE-RSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      +-.+|++|||.+.... -+.... |.|.||..|+..|  ...+||+||.-..
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            4567999999986543 234445 9999999999999  4678999998555

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

Probab=98.46  E-value=7e-08  Score=66.96  Aligned_cols=43  Identities=28%  Similarity=0.667  Sum_probs=37.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcccc
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR  104 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr  104 (112)
                      +...|+||++.|...   ..++ |+|.||..|+..+......||.||
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            577899999999764   7777 999999999999988557899999

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

Probab=98.31  E-value=3.5e-07  Score=65.90  Aligned_cols=50  Identities=28%  Similarity=0.741  Sum_probs=38.6

Q ss_pred             CccccccccccccCCC----ceeecCCCcCcccHHhHHHHHh--C-----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGE----RSRNFSICKHVFHARCIDLWLV--R-----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~----~~~~~~~C~H~fh~~Ci~~w~~--~-----~~~CP~Cr~~~  107 (112)
                      .+.+|.||++......    ....+|+|.|.||..||..|-.  +     .+.||.||...
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            5889999999764322    1344577999999999999983  3     47899999754

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

Probab=98.28  E-value=3.9e-07  Score=63.94  Aligned_cols=48  Identities=27%  Similarity=0.533  Sum_probs=39.5

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~  110 (112)
                      ..+|+||+...   ..++.++ |+|.||.-||+.-.+. ..+|++||.+++..
T Consensus         7 ~~eC~IC~nt~---n~Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTG---NCPVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccC---CcCcccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            56799999864   5567788 9999999999987765 46699999998754

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

Probab=98.26  E-value=6.3e-07  Score=64.15  Aligned_cols=47  Identities=23%  Similarity=0.684  Sum_probs=40.3

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      .+.+|.||+.+...   ..+|| |-|. .|..|-+...-.++.||+||+++.
T Consensus       289 ~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  289 SGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             CCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchH
Confidence            47789999998644   77899 9999 999999887767899999999874

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

Probab=98.22  E-value=1.3e-07  Score=67.60  Aligned_cols=49  Identities=33%  Similarity=0.617  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~  109 (112)
                      .+..|+||++-++.   .+..+.|.|.||.+||..-+.. ++.||.||+.+..
T Consensus        42 ~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   42 IQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            57789999998853   5555569999999999887764 7899999997643

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

Probab=98.20  E-value=2.8e-07  Score=48.96  Aligned_cols=46  Identities=26%  Similarity=0.585  Sum_probs=33.0

Q ss_pred             ccccccccccccCCCceeecCCCcCc-ccHHhHHH-HHhCCCCCccccCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHV-FHARCIDL-WLVRRLTCPTCRSPFK  108 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~-w~~~~~~CP~Cr~~~~  108 (112)
                      .++|.||+|.--  + -+... |||. .+..|-.+ |-..+..||+||+++.
T Consensus         7 ~dECTICye~pv--d-sVlYt-CGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPV--D-SVLYT-CGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcc--h-HHHHH-cchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            367999998632  1 22334 9998 88999555 4446899999999763

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

Probab=98.13  E-value=8.4e-07  Score=68.66  Aligned_cols=49  Identities=27%  Similarity=0.599  Sum_probs=38.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHh-CCCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~~~~~  111 (112)
                      -..|+.|-..++.   .+.. .|+|.||..|+...+. ++..||.|.+.+..-+
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             ceeCCCccCchhh---HHHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            4569999977643   3333 4999999999999986 6889999999886544

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

Probab=98.11  E-value=5.8e-07  Score=70.00  Aligned_cols=50  Identities=24%  Similarity=0.525  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ....|++|+..+..+.....-+ |+|.||..||..|...-++||+||.++.
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~  171 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFG  171 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhh
Confidence            4567888887775544444455 9999999999999999999999998764

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

Probab=98.02  E-value=4.1e-06  Score=61.08  Aligned_cols=48  Identities=31%  Similarity=0.915  Sum_probs=36.7

Q ss_pred             ccccccccccccCC--CceeecCCCcCcccHHhHHHHHhC--CCCCccccCCC
Q 038517           59 AAICAVCLDGVHKG--ERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~--~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~  107 (112)
                      +..|+||++++...  ..+..+. |||.|..+||.+|+.+  ...||.|...-
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~-cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQ-CGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeec-ccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            56799999988643  2444454 9999999999999963  35699997643

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

Probab=98.00  E-value=1.9e-06  Score=62.87  Aligned_cols=45  Identities=27%  Similarity=0.757  Sum_probs=36.8

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhC--CCCCccccCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPFK  108 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~~  108 (112)
                      +.|.||-|.=   ..+..-| |||..|..|+..|-.+  .++||.||.++.
T Consensus       370 eLCKICaend---KdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  370 ELCKICAEND---KDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             HHHHHhhccC---CCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            5799999852   3466667 9999999999999854  689999999874

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

Probab=97.94  E-value=1.1e-06  Score=66.07  Aligned_cols=49  Identities=27%  Similarity=0.630  Sum_probs=39.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~~~~~  110 (112)
                      ++..|.+|-++-+.   .+... |.|.||+.||++++..     +-+||+|...+..+
T Consensus       535 ~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  535 GEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             CceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            67889999997543   44555 9999999999998852     56899999887654

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

Probab=97.86  E-value=1.3e-05  Score=43.47  Aligned_cols=42  Identities=21%  Similarity=0.502  Sum_probs=26.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--CCCCcc
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPT  102 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~  102 (112)
                      ....|+|.+..|++   ++....|+|+|-+..|.+|+++  ...||+
T Consensus        10 ~~~~CPiT~~~~~~---PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED---PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS---EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC---CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            45679999999864   5444349999999999999943  457998

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

Probab=97.75  E-value=2e-05  Score=41.05  Aligned_cols=40  Identities=28%  Similarity=0.859  Sum_probs=26.7

Q ss_pred             cccccccccCCCceeecCCCc-----CcccHHhHHHHHh--CCCCCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICK-----HVFHARCIDLWLV--RRLTCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~--~~~~CP~C  103 (112)
                      |-||++.-.+++ ....| |+     -..|..|+.+|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999876545 33445 65     3689999999997  45679887

>PHA02862 5L protein; Provisional

Probab=97.75  E-value=1.8e-05  Score=50.20  Aligned_cols=47  Identities=28%  Similarity=0.801  Sum_probs=35.1

Q ss_pred             ccccccccccccCCCceeecCCCc-----CcccHHhHHHHHhC--CCCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICK-----HVFHARCIDLWLVR--RLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~--~~~CP~Cr~~~~~~  110 (112)
                      ++.|-||+++-++.    ..| |.     ...|.+|+.+|++.  +..|+.|+.+...+
T Consensus         2 ~diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            46799999985332    234 65     56899999999974  56899999876543

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

Probab=97.74  E-value=9.3e-06  Score=57.24  Aligned_cols=52  Identities=29%  Similarity=0.695  Sum_probs=42.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----------------------CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----------------------RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----------------------~~~CP~Cr~~~~~~  110 (112)
                      ....|.|||--|..++...+++ |-|.||..|+.+++..                       ...||+||..+..+
T Consensus       114 p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            5577999999999988888888 9999999999987731                       12599999987654

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

Probab=97.73  E-value=3.6e-05  Score=52.40  Aligned_cols=53  Identities=23%  Similarity=0.606  Sum_probs=43.8

Q ss_pred             CCCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--------CCCCccccCCCCCC
Q 038517           56 RNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--------RLTCPTCRSPFKME  110 (112)
Q Consensus        56 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--------~~~CP~Cr~~~~~~  110 (112)
                      ++....|..|-..+..|+.++..  |-|.||.+|+++|...        ...||-|..++.+.
T Consensus        47 sDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   47 SDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             cCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            33566799999999998888755  9999999999999863        34799999988654

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

Probab=97.71  E-value=2.3e-05  Score=57.67  Aligned_cols=48  Identities=27%  Similarity=0.549  Sum_probs=41.4

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      .+..|.||..-+..   ++.+| |||.|+..||.+-+.....||.||.++..
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            67899999988754   77777 99999999999988888899999988763

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

Probab=97.68  E-value=2e-05  Score=58.00  Aligned_cols=49  Identities=24%  Similarity=0.611  Sum_probs=40.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ....|++|...+..   +.....|||.||..|+..|+..+..||.|+.++..
T Consensus        20 ~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~   68 (391)
T KOG0297|consen   20 ENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQ   68 (391)
T ss_pred             ccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCcccccccch
Confidence            46789999998865   33322399999999999999999999999987654

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

Probab=97.65  E-value=3.3e-05  Score=51.63  Aligned_cols=46  Identities=17%  Similarity=0.423  Sum_probs=39.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      ....|.||-++|+.   ++... |||.||..|...-+++...|-+|.+..
T Consensus       195 IPF~C~iCKkdy~s---pvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         195 IPFLCGICKKDYES---PVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             Cceeehhchhhccc---hhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            45689999999964   66666 999999999888888899999998753

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

Probab=97.64  E-value=1.6e-05  Score=57.89  Aligned_cols=47  Identities=30%  Similarity=0.795  Sum_probs=38.0

Q ss_pred             CccccccccccccCCC-ceeecCCCcCcccHHhHHHHHhCC--CCCccccC
Q 038517           58 LAAICAVCLDGVHKGE-RSRNFSICKHVFHARCIDLWLVRR--LTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~--~~CP~Cr~  105 (112)
                      .+..|..|=+.+-..+ ..--+| |.|+||..|+.+.+.++  .+||-||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            5678999998875443 455678 99999999999999764  68999994

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

Probab=97.61  E-value=6.7e-05  Score=39.11  Aligned_cols=45  Identities=22%  Similarity=0.561  Sum_probs=22.9

Q ss_pred             cccccccccCCC-ceeecCCCcCcccHHhHHHHHh-CCCCCccccCCC
Q 038517           62 CAVCLDGVHKGE-RSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPF  107 (112)
Q Consensus        62 C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~  107 (112)
                      |++|.+++...+ ...--+ |++.++..|...-++ ....||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999985433 333344 899999999988876 478999999875

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

Probab=97.61  E-value=1.2e-05  Score=57.14  Aligned_cols=48  Identities=25%  Similarity=0.535  Sum_probs=38.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ....|.+|-..+-.  .. +.+.|-|.||++||...+...++||.|...+-
T Consensus        14 ~~itC~LC~GYliD--AT-TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen   14 PHITCRLCGGYLID--AT-TITECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             cceehhhccceeec--ch-hHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            45679999998753  22 22349999999999999999999999987653

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

Probab=97.43  E-value=4.6e-05  Score=49.36  Aligned_cols=29  Identities=21%  Similarity=0.684  Sum_probs=27.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHA   87 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~   87 (112)
                      ...+|.||+|+++.++.+..+| |-.+||+
T Consensus       176 dkGECvICLEdL~~GdtIARLP-CLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLP-CLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccc-eEEEeec
Confidence            6679999999999999999999 9999996

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

Probab=97.40  E-value=0.0001  Score=46.41  Aligned_cols=36  Identities=19%  Similarity=0.509  Sum_probs=29.3

Q ss_pred             ccccccccccccCCCceeecCCCc------CcccHHhHHHHHh
Q 038517           59 AAICAVCLDGVHKGERSRNFSICK------HVFHARCIDLWLV   95 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~------H~fh~~Ci~~w~~   95 (112)
                      ..+|+||++.+...+.++.++ ||      |.||.+|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            567999999998755666666 66      9999999999943

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

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

Probab=97.34  E-value=0.00026  Score=49.49  Aligned_cols=48  Identities=23%  Similarity=0.514  Sum_probs=36.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--CCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~~  108 (112)
                      .+.+|++|-+.-..   +.+..+|+|+||..||..-+..  ..+||.|..++.
T Consensus       238 ~~~~C~~Cg~~Pti---P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  238 SDTECPVCGEPPTI---PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             CCceeeccCCCCCC---CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            67899999987432   3333339999999999876653  468999998775

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.34  E-value=0.00021  Score=46.15  Aligned_cols=47  Identities=21%  Similarity=0.733  Sum_probs=34.6

Q ss_pred             CccccccccccccCCCceeecCCCcC-----cccHHhHHHHHhC--CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKH-----VFHARCIDLWLVR--RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H-----~fh~~Ci~~w~~~--~~~CP~Cr~~~~~  109 (112)
                      .+..|-||.++..  +.  ..| |..     ..|.+|+.+|+..  ..+|+.|+++...
T Consensus         7 ~~~~CRIC~~~~~--~~--~~P-C~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          7 MDKCCWICKDEYD--VV--TNY-CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCeeEecCCCCC--Cc--cCC-cccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            5678999998843  22  234 654     5699999999974  5679999987643

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

Probab=97.34  E-value=0.00017  Score=60.14  Aligned_cols=50  Identities=24%  Similarity=0.751  Sum_probs=39.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC----------CCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR----------LTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~----------~~CP~Cr~~~~  108 (112)
                      .++.|.||+.+-......+.+. |+|+||..|...-+.++          -+||+|+.++.
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            6788999998776656667788 99999999998766542          26999998764

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

Probab=97.31  E-value=0.00016  Score=53.00  Aligned_cols=47  Identities=21%  Similarity=0.532  Sum_probs=37.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--------CCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--------RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--------~~~CP~Cr~  105 (112)
                      .-..|.||+++....+....+| |+|+||+.|++.++..        .-.||-+..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            4568999999986657888898 9999999999999952        235877654

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=97.26  E-value=0.00013  Score=44.00  Aligned_cols=32  Identities=31%  Similarity=0.606  Sum_probs=26.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCID   91 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~   91 (112)
                      .+..|++|-..+.. ......| |||+||..|++
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            67889999999865 5566677 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 [].

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.18  E-value=0.00049  Score=47.54  Aligned_cols=55  Identities=18%  Similarity=0.346  Sum_probs=46.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~~  112 (112)
                      ....|++|.+.+.+......|.+|||+|...|+...+.....||+|-.++..++|
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdi  274 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDI  274 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccce
Confidence            4467999999998777666665699999999999998889999999999887654

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

Probab=97.17  E-value=0.00015  Score=51.08  Aligned_cols=46  Identities=20%  Similarity=0.337  Sum_probs=38.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      ..+.|-||.+.|..   +++.. |+|.||..|-..-+++...|++|.++.
T Consensus       240 ~Pf~c~icr~~f~~---pVvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  240 LPFKCFICRKYFYR---PVVTK-CGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             CCcccccccccccc---chhhc-CCceeehhhhccccccCCcceeccccc
Confidence            45679999999964   66666 999999999888888889999998865

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

Probab=97.11  E-value=0.00031  Score=55.60  Aligned_cols=49  Identities=29%  Similarity=0.722  Sum_probs=37.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-------CCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-------LTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-------~~CP~Cr~~  106 (112)
                      ...+|.||.+.+...+.+-.-..|=|+||..||..|..+.       -.||.|...
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            6679999999987666554444477999999999999642       259999843

>PHA03096 p28-like protein; Provisional

Probab=97.10  E-value=0.00029  Score=49.89  Aligned_cols=46  Identities=30%  Similarity=0.659  Sum_probs=33.2

Q ss_pred             cccccccccccCC----CceeecCCCcCcccHHhHHHHHhC---CCCCccccC
Q 038517           60 AICAVCLDGVHKG----ERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRS  105 (112)
Q Consensus        60 ~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~  105 (112)
                      ..|.||++.....    ..-..++.|.|.|+..|+..|-..   ..+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5799999976532    244567779999999999999864   234555543

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.03  E-value=0.00038  Score=37.18  Aligned_cols=36  Identities=25%  Similarity=0.681  Sum_probs=28.3

Q ss_pred             CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           73 ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        73 ~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ..-.++| |+|..+..|..-  .+-+-||.|.+++...+
T Consensus        18 ~~~~~~p-CgH~I~~~~f~~--~rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen   18 TKGTVLP-CGHLICDNCFPG--ERYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ccccccc-ccceeeccccCh--hhccCCCCCCCcccCCC
Confidence            4456677 999999999764  35678999999987664

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.99  E-value=0.00096  Score=46.67  Aligned_cols=53  Identities=23%  Similarity=0.431  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ....|||...++......+.+-+|||+|-..+|.+. .....||+|-.++..++
T Consensus       112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccCC
Confidence            667899999999554444444339999999999987 34668999999987665

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.94  E-value=0.00074  Score=48.72  Aligned_cols=56  Identities=16%  Similarity=0.383  Sum_probs=40.7

Q ss_pred             CCCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           56 RNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        56 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      .++++.|+.|+|++...++-..--+||-..|.-|...--+. +..||-||+....+.
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            33567799999999876654443239998888887654333 678999999877664

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

Probab=96.88  E-value=0.00036  Score=47.89  Aligned_cols=45  Identities=22%  Similarity=0.566  Sum_probs=31.7

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      .|.-|...-. ++...++. |+|+||..|...-  ....||.|++++..
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~   49 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRI   49 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceeee
Confidence            4667776544 45555565 9999999997642  23389999998654

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

Probab=96.82  E-value=0.00093  Score=47.32  Aligned_cols=47  Identities=26%  Similarity=0.637  Sum_probs=38.3

Q ss_pred             cccccccccccCCC---ceeecCCCcCcccHHhHHHHHhC-CCCCccccCCC
Q 038517           60 AICAVCLDGVHKGE---RSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPF  107 (112)
Q Consensus        60 ~~C~IC~~~~~~~~---~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~  107 (112)
                      ..|-||-++|+.++   .++.+. |||.|+..|+...+.. ...||.||.+.
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            46999999998663   456676 9999999999887764 46799999874

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

Probab=96.78  E-value=0.00065  Score=48.60  Aligned_cols=48  Identities=25%  Similarity=0.472  Sum_probs=37.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      +...|++|+....+   +..+.--|-+||..|+...+.+.+.||+=..+..
T Consensus       299 ~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  299 DREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             ccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            67899999998754   2222226899999999999999999998666554

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

Probab=96.75  E-value=0.001  Score=33.96  Aligned_cols=41  Identities=32%  Similarity=0.836  Sum_probs=22.1

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHhCCC--CCccc
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRL--TCPTC  103 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~--~CP~C  103 (112)
                      |.+|.+..-.|+.-.... |+=.+|..|+..++..+.  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            566777655444333333 888999999999998644  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.74  E-value=0.001  Score=43.90  Aligned_cols=30  Identities=37%  Similarity=0.960  Sum_probs=24.7

Q ss_pred             CcCcccHHhHHHHHhC----C-------CCCccccCCCCCC
Q 038517           81 CKHVFHARCIDLWLVR----R-------LTCPTCRSPFKME  110 (112)
Q Consensus        81 C~H~fh~~Ci~~w~~~----~-------~~CP~Cr~~~~~~  110 (112)
                      ||.-||.-|+..|+..    +       ..||+|..++..+
T Consensus       190 CgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  190 CGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             cCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            9999999999999963    1       1499999988654

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

Probab=96.74  E-value=0.001  Score=48.26  Aligned_cols=47  Identities=21%  Similarity=0.456  Sum_probs=39.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ++..|+||.-.-   ...+..| |+|.=|+.||.+-+.+.+.|=.|++.+.
T Consensus       421 Ed~lCpICyA~p---i~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  421 EDNLCPICYAGP---INAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             ccccCcceeccc---chhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            778999998642   2244566 9999999999999999999999998765

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

Probab=96.72  E-value=5.5e-05  Score=55.08  Aligned_cols=51  Identities=20%  Similarity=0.644  Sum_probs=42.7

Q ss_pred             CccccccccccccCC-CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKG-ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ....|+||.++++.. +++..+- |||.+|..||.+|+.+...||.|+++++.
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            466799999998764 4455555 99999999999999999999999998753

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

Probab=96.60  E-value=0.0019  Score=47.26  Aligned_cols=49  Identities=18%  Similarity=0.362  Sum_probs=41.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC---CCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR---LTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~---~~CP~Cr~~~  107 (112)
                      ....|||=.+.-.+.+.+..+. |||+..++-+++..++.   ..||+|=.+.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            5688999888887778889998 99999999999998764   4799995543

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

Probab=96.50  E-value=0.0028  Score=45.92  Aligned_cols=47  Identities=21%  Similarity=0.492  Sum_probs=36.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHH--hCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL--VRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~--~~~~~CP~Cr~~~~  108 (112)
                      +...|.||-+...   ...++| |+|..|--|-.+.-  -.++.||+||+++.
T Consensus        60 en~~C~ICA~~~T---Ys~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          60 ENMNCQICAGSTT---YSARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccceeEEecCCce---EEEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            6678999998763   366778 99999999965533  36889999999763

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

Probab=96.45  E-value=0.0021  Score=46.91  Aligned_cols=31  Identities=32%  Similarity=0.956  Sum_probs=24.2

Q ss_pred             CcCcccHHhHHHHHhCCC-------------CCccccCCCCCCC
Q 038517           81 CKHVFHARCIDLWLVRRL-------------TCPTCRSPFKMEP  111 (112)
Q Consensus        81 C~H~fh~~Ci~~w~~~~~-------------~CP~Cr~~~~~~~  111 (112)
                      |...+|.+|+-+||..++             .||+||+.+...+
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            557889999999996422             5999999876543

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

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

Probab=96.36  E-value=0.0025  Score=44.93  Aligned_cols=47  Identities=23%  Similarity=0.617  Sum_probs=38.4

Q ss_pred             CccccccccccccCCCc-eeecCCCcCcccHHhHHHHHhCCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGER-SRNFSICKHVFHARCIDLWLVRRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~  105 (112)
                      ....|+||.+.+-.... +..++ |||.-|..|+.+....+.+||+|.+
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            55669999997765554 45566 9999999999998887899999987

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

Probab=96.22  E-value=0.00093  Score=47.22  Aligned_cols=41  Identities=27%  Similarity=0.690  Sum_probs=30.8

Q ss_pred             ccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      ...|+||++...   ....|+ |||. -|.+|.++    -+.||+||+-+
T Consensus       300 ~~LC~ICmDaP~---DCvfLe-CGHmVtCt~CGkr----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLE-CGHMVTCTKCGKR----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCc---ceEEee-cCcEEeehhhccc----cccCchHHHHH
Confidence            568999999743   356787 9997 57777654    34899999854

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

Probab=95.84  E-value=0.0052  Score=48.59  Aligned_cols=40  Identities=33%  Similarity=0.708  Sum_probs=29.4

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcc
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPT  102 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~  102 (112)
                      .|+||--.. .|....... |+|+.|.+|..+|+.....||.
T Consensus      1030 ~C~~C~l~V-~gss~~Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAV-RGSSNFCGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEe-eccchhhcc-ccccccHHHHHHHHhcCCcCCC
Confidence            466665544 233344455 9999999999999999999985

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

Probab=95.77  E-value=0.0063  Score=43.36  Aligned_cols=44  Identities=25%  Similarity=0.638  Sum_probs=34.1

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHh-CCCCCccccC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-RRLTCPTCRS  105 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~  105 (112)
                      ...|+.|-..+..   ....+.|+|.||..||..-|. ....||.|.+
T Consensus       274 ~LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            3679998877643   444566999999999987665 5688999976

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

Probab=95.75  E-value=0.0055  Score=44.41  Aligned_cols=43  Identities=30%  Similarity=0.636  Sum_probs=31.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      ....|.||+++..+   ...+| |||+-+  |..- .+...+||+||+.+
T Consensus       304 ~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~c-s~~l~~CPvCR~rI  346 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLC-SKHLPQCPVCRQRI  346 (355)
T ss_pred             CCCceEEecCCccc---eeeec-CCcEEE--chHH-HhhCCCCchhHHHH
Confidence            56789999998754   66777 999855  5433 23455699999865

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

Probab=95.74  E-value=0.0066  Score=48.40  Aligned_cols=53  Identities=19%  Similarity=0.528  Sum_probs=40.3

Q ss_pred             CccccccccccccCCCceeecCCCc-----CcccHHhHHHHHhC--CCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICK-----HVFHARCIDLWLVR--RLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~--~~~CP~Cr~~~~~~~~  112 (112)
                      ++..|.||..+=.+++.. ..| |+     -..|.+|+.+|+.-  ...|-.|+.++..++|
T Consensus        11 d~~~CRICr~e~~~d~pL-fhP-CKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I   70 (1175)
T COG5183          11 DKRSCRICRTEDIRDDPL-FHP-CKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI   70 (1175)
T ss_pred             cchhceeecCCCCCCCcC-ccc-ccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence            568899999876554433 445 66     45899999999974  5679999999887764

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

Probab=95.57  E-value=0.0042  Score=32.12  Aligned_cols=29  Identities=34%  Similarity=0.855  Sum_probs=21.9

Q ss_pred             Cc-CcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           81 CK-HVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        81 C~-H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      |+ |..+..|+...+.++..||+|..+++.
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            66 999999999999999999999988764

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.

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

Probab=95.54  E-value=0.0063  Score=48.69  Aligned_cols=35  Identities=23%  Similarity=0.442  Sum_probs=28.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL   94 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~   94 (112)
                      .++.|.+|...+.. ..-.+.| |||.||++||.+-.
T Consensus       816 p~d~C~~C~~~ll~-~pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  816 PQDSCDHCGRPLLI-KPFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             CccchHHhcchhhc-Ccceeee-ccchHHHHHHHHHH
Confidence            68899999998865 3455667 99999999998755

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.50  E-value=0.021  Score=30.47  Aligned_cols=44  Identities=20%  Similarity=0.483  Sum_probs=33.6

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcc--ccCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPT--CRSP  106 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~--Cr~~  106 (112)
                      ...|++|-+.|..++.+++-|.|+-.+|+.|...    ...|-.  |..+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~   50 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTG   50 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCC
Confidence            4579999999987788888888999999999643    444544  5443

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.37  E-value=0.0063  Score=42.34  Aligned_cols=49  Identities=20%  Similarity=0.740  Sum_probs=33.6

Q ss_pred             CccccccccccccCCCc-eeecCCCc-----CcccHHhHHHHHhCC--------CCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGER-SRNFSICK-----HVFHARCIDLWLVRR--------LTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~-~~~~~~C~-----H~fh~~Ci~~w~~~~--------~~CP~Cr~~~  107 (112)
                      .+..|-||+..=++.-. .-+.| |-     |..|.+|+..|+.++        -+||.|+++.
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            56779999986432211 12234 54     889999999999532        2599999865

>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=95.00  E-value=0.029  Score=36.38  Aligned_cols=35  Identities=20%  Similarity=0.596  Sum_probs=22.1

Q ss_pred             CccccccccccccCCCceeecC-----------CCc-CcccHHhHHHHHh
Q 038517           58 LAAICAVCLDGVHKGERSRNFS-----------ICK-HVFHARCIDLWLV   95 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~-----------~C~-H~fh~~Ci~~w~~   95 (112)
                      ++..|+||||--.+   .++|-           -|+ -.-|..|++++-+
T Consensus         1 ed~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            36789999997543   22222           044 3468999998754

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.

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

Probab=94.97  E-value=0.0056  Score=48.21  Aligned_cols=45  Identities=27%  Similarity=0.640  Sum_probs=34.8

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhC--CCCCccccCCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPFKM  109 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~~~  109 (112)
                      ..|.||++ .   +.....+ |+|.|+..|+..-+..  ...||.||..+..
T Consensus       455 ~~c~ic~~-~---~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~  501 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKE  501 (674)
T ss_pred             cccccccc-c---ccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHH
Confidence            78999999 2   3455566 9999999999887764  3469999986644

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.94  E-value=0.01  Score=42.16  Aligned_cols=30  Identities=27%  Similarity=0.820  Sum_probs=23.9

Q ss_pred             CcCcccHHhHHHHHhC-------------CCCCccccCCCCCC
Q 038517           81 CKHVFHARCIDLWLVR-------------RLTCPTCRSPFKME  110 (112)
Q Consensus        81 C~H~fh~~Ci~~w~~~-------------~~~CP~Cr~~~~~~  110 (112)
                      |...+|.+|+-+|+..             +-+||+||+.+...
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~  367 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR  367 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence            6788999999999953             23699999987544

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

Probab=94.63  E-value=0.036  Score=46.26  Aligned_cols=45  Identities=33%  Similarity=0.744  Sum_probs=36.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~  105 (112)
                      .-..|.||++.+..-.-+  .. |||.++..|...|+..+..||.|..
T Consensus      1152 ~~~~c~ic~dil~~~~~I--~~-cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGI--AG-CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHhcCCe--ee-echhHhhhHHHHHHHHhccCcchhh
Confidence            456899999988631222  22 9999999999999999999999974

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

Probab=94.59  E-value=0.018  Score=46.01  Aligned_cols=43  Identities=21%  Similarity=0.632  Sum_probs=32.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~  106 (112)
                      ....|..|-..++-   +.+.=.|||.||..|+.   .+...||-|+.+
T Consensus       839 q~skCs~C~~~Ldl---P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  839 QVSKCSACEGTLDL---PFVHFLCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eeeeecccCCcccc---ceeeeecccHHHHHhhc---cCcccCCccchh
Confidence            44589999888743   33332399999999997   456789999864

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

Probab=94.56  E-value=0.036  Score=34.95  Aligned_cols=53  Identities=17%  Similarity=0.359  Sum_probs=36.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh---CCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV---RRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~---~~~~CP~Cr~~~~~~  110 (112)
                      .-.+|.||.|...+..-+.--..||-..|..|.....+   -...||+|++.+...
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            35679999998654333322223999999999665444   367899999987654

>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=94.39  E-value=0.043  Score=38.87  Aligned_cols=47  Identities=19%  Similarity=0.458  Sum_probs=33.0

Q ss_pred             cccccccc-ccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCC
Q 038517           61 ICAVCLDG-VHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPF  107 (112)
Q Consensus        61 ~C~IC~~~-~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~  107 (112)
                      .|++|-.. |...+-......|+|..|.+|+...+.. ...||.|...+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            48888763 3333322223349999999999999865 57899997654

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

Probab=94.12  E-value=0.042  Score=39.35  Aligned_cols=45  Identities=24%  Similarity=0.419  Sum_probs=32.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      +-.+||||.+.+..   ++..-.=||..|.+|-.   +..+.||.||.++.
T Consensus        47 ~lleCPvC~~~l~~---Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSP---PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hhccCchhhccCcc---cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            55789999999864   33221136999999864   45788999999876

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

Probab=94.10  E-value=0.026  Score=40.06  Aligned_cols=50  Identities=24%  Similarity=0.636  Sum_probs=35.9

Q ss_pred             CccccccccccccCCCc-eeecCCCc-----CcccHHhHHHHHh--CCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGER-SRNFSICK-----HVFHARCIDLWLV--RRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~-~~~~~~C~-----H~fh~~Ci~~w~~--~~~~CP~Cr~~~~  108 (112)
                      .+..|.||.++...... ....| |.     ...|+.|+..|+.  ....|..|.....
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            34789999997654322 33444 55     6689999999997  4677999987543

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

Probab=93.76  E-value=0.024  Score=40.60  Aligned_cols=43  Identities=28%  Similarity=0.565  Sum_probs=27.5

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      ..|--|=-.+.  ..-+..| |+|+||.+|-.  +...+.||.|-..|
T Consensus        91 HfCd~Cd~PI~--IYGRmIP-CkHvFCl~CAr--~~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIP-CKHVFCLECAR--SDSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcce--eeecccc-cchhhhhhhhh--cCccccCcCcccHH
Confidence            45655544332  1224456 99999999964  24467899997544

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

Probab=93.29  E-value=0.052  Score=36.88  Aligned_cols=38  Identities=29%  Similarity=0.679  Sum_probs=28.1

Q ss_pred             cccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCC
Q 038517           62 CAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      |-.|.+.-   ..+..+| |.|. +|..|-..    -..||+|+.+.
T Consensus       161 Cr~C~~~~---~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGERE---ATVLLLP-CRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             ceecCcCC---ceEEeec-ccceEeccccccc----CccCCCCcChh
Confidence            88888753   4577888 9987 88888432    45699998754

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

Probab=92.39  E-value=0.055  Score=40.05  Aligned_cols=37  Identities=16%  Similarity=0.434  Sum_probs=27.1

Q ss_pred             CccccccccccccCC-CceeecCCCcCcccHHhHHHHHh
Q 038517           58 LAAICAVCLDGVHKG-ERSRNFSICKHVFHARCIDLWLV   95 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~-~~~~~~~~C~H~fh~~Ci~~w~~   95 (112)
                      ....|.||+.+.... +...... |+|.||.+|+++.+.
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIE  182 (384)
T ss_pred             ccccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhh
Confidence            467899999444333 3333344 999999999999886

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

Probab=89.80  E-value=0.26  Score=35.60  Aligned_cols=47  Identities=19%  Similarity=0.414  Sum_probs=35.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC---CCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~  105 (112)
                      .-..||+--+.-.+.+.+..+. |||+.-+.-+.+..++   ...||+|--
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYCP~  384 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYCPE  384 (396)
T ss_pred             ceeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCCCc
Confidence            4567888666665556677777 9999999999987765   356999943

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.72  E-value=0.36  Score=33.81  Aligned_cols=52  Identities=19%  Similarity=0.357  Sum_probs=37.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ....|+|---++.....-..+-.|||+|-..-+++-  +..+|++|...+..++
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD  161 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence            456788877666544443333339999999888773  4788999999887765

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

Probab=89.26  E-value=1.1  Score=23.99  Aligned_cols=48  Identities=23%  Similarity=0.551  Sum_probs=33.7

Q ss_pred             ccccccccccCCCceeecCCCc--CcccHHhHHHHHhCCCCCccccCCCCCCCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICK--HVFHARCIDLWLVRRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~--H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~~  112 (112)
                      .|-.|-.++..+......  |.  ..|+.+|....|  +..||.|.-++...|+
T Consensus         7 nCE~C~~dLp~~s~~A~I--CSfECTFC~~C~e~~l--~~~CPNCgGelv~RP~   56 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI--CSFECTFCADCAETML--NGVCPNCGGELVRRPR   56 (57)
T ss_pred             CccccCCCCCCCCCcceE--EeEeCcccHHHHHHHh--cCcCcCCCCccccCCC
Confidence            466777777654422111  55  569999998866  7889999988877664

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

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

Probab=89.18  E-value=0.098  Score=41.23  Aligned_cols=47  Identities=23%  Similarity=0.636  Sum_probs=36.2

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC---CCCCccccCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR---RLTCPTCRSPFKM  109 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~---~~~CP~Cr~~~~~  109 (112)
                      ..+|+||+..+.+.   ..+. |.|.|+..|+..-|..   ...||+|+..+..
T Consensus        21 ~lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   21 ILECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            56799999988653   4555 9999999998876654   4569999976543

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

Probab=89.17  E-value=0.43  Score=29.26  Aligned_cols=30  Identities=23%  Similarity=0.535  Sum_probs=21.1

Q ss_pred             eecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           76 RNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        76 ~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      +..|+|++.      ...+.+...|+.|++++..++
T Consensus        70 V~CP~C~K~------TKmLGr~D~CM~C~~pLTLd~   99 (114)
T PF11023_consen   70 VECPNCGKQ------TKMLGRVDACMHCKEPLTLDP   99 (114)
T ss_pred             eECCCCCCh------HhhhchhhccCcCCCcCccCc
Confidence            345568773      334566678999999998774

; GO: 0005887 integral to plasma membrane

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=89.10  E-value=0.32  Score=32.88  Aligned_cols=42  Identities=29%  Similarity=0.772  Sum_probs=29.5

Q ss_pred             Ccccccccccc-----ccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccC
Q 038517           58 LAAICAVCLDG-----VHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~-----~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~  105 (112)
                      .+..|.+|-.+     |+. +.+..-+.|+-+||+.|..     +..||-|.+
T Consensus       151 kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R  197 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCAR  197 (202)
T ss_pred             CCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence            56778888752     222 3455566699999999975     267999954

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

Probab=88.96  E-value=0.25  Score=37.21  Aligned_cols=37  Identities=19%  Similarity=0.475  Sum_probs=29.8

Q ss_pred             CCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC
Q 038517           57 NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR   96 (112)
Q Consensus        57 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~   96 (112)
                      .....|.||.+.+..  ....+. |+|.|+..|+...+.+
T Consensus        68 ~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             CccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            356789999999854  455566 9999999999988863

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

Probab=88.90  E-value=0.41  Score=25.02  Aligned_cols=43  Identities=21%  Similarity=0.539  Sum_probs=18.4

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSP  106 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~  106 (112)
                      ..|+|....+..   ++....|.|.-+.+ +..|+..     .-.||+|.++
T Consensus         3 L~CPls~~~i~~---P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI---PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS---EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe---CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            357887776643   44444499984433 4455542     2369999864

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

>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=88.43  E-value=0.25  Score=34.42  Aligned_cols=48  Identities=23%  Similarity=0.477  Sum_probs=34.4

Q ss_pred             Cccccccccccc-cCCC-ceeecCCCcCcccHHhHHHHHhC-CCCCc--cccC
Q 038517           58 LAAICAVCLDGV-HKGE-RSRNFSICKHVFHARCIDLWLVR-RLTCP--TCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~-~~~~-~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP--~Cr~  105 (112)
                      .+..||+|..+- ...+ ++..-|.|=|..|.+|+.+-|.. ...||  -|.+
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~k   61 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGK   61 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHH
Confidence            456899999743 3333 33444569999999999999975 56899  5643

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

Probab=88.38  E-value=0.22  Score=37.50  Aligned_cols=34  Identities=24%  Similarity=0.375  Sum_probs=27.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV   95 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~   95 (112)
                      ++..|+||-.-|++   ++.+| |+|..|..|-..-+.
T Consensus         3 eelkc~vc~~f~~e---piil~-c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYRE---PIILP-CSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccC---ceEee-cccHHHHHHHHhhcc
Confidence            35679999998864   88898 999999999765543

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

Probab=88.34  E-value=0.3  Score=37.74  Aligned_cols=45  Identities=31%  Similarity=0.805  Sum_probs=35.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      ....|.||+++.    ..+..+ |.   |..|+..|+..+..||.|+..+..+
T Consensus       478 ~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~  522 (543)
T KOG0802|consen  478 PNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKED  522 (543)
T ss_pred             ccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcc
Confidence            567899999987    234444 77   8999999999999999998866544

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

Probab=87.94  E-value=0.45  Score=38.06  Aligned_cols=43  Identities=21%  Similarity=0.449  Sum_probs=30.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcc
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPT  102 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~  102 (112)
                      ....|.+|-..+.. ..+- .+-|+|.-|.+|+++|+.+...||.
T Consensus       778 a~~~CtVC~~vi~G-~~~~-c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  778 ASAKCTVCDLVIRG-VDVW-CQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hhcCceeecceeee-eEee-cccccccccHHHHHHHHhcCCCCcc
Confidence            34467777766532 2121 2339999999999999998887766

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

Probab=86.36  E-value=0.31  Score=25.64  Aligned_cols=39  Identities=23%  Similarity=0.542  Sum_probs=22.4

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      |+-|-+.+..++.+. .. -+..||..|+.        |-.|++++...
T Consensus         1 C~~C~~~I~~~~~~~-~~-~~~~~H~~Cf~--------C~~C~~~l~~~   39 (58)
T PF00412_consen    1 CARCGKPIYGTEIVI-KA-MGKFWHPECFK--------CSKCGKPLNDG   39 (58)
T ss_dssp             BTTTSSBESSSSEEE-EE-TTEEEETTTSB--------ETTTTCBTTTS
T ss_pred             CCCCCCCccCcEEEE-Ee-CCcEEEccccc--------cCCCCCccCCC
Confidence            555666665433332 22 56677777753        77777766543

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

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

Probab=86.26  E-value=0.46  Score=26.32  Aligned_cols=12  Identities=25%  Similarity=0.750  Sum_probs=8.8

Q ss_pred             cccHHhHHHHHh
Q 038517           84 VFHARCIDLWLV   95 (112)
Q Consensus        84 ~fh~~Ci~~w~~   95 (112)
                      -||+.|+..|..
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999985

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

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

Probab=85.91  E-value=0.28  Score=38.17  Aligned_cols=44  Identities=30%  Similarity=0.749  Sum_probs=27.8

Q ss_pred             Cccccccccc-----cccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccC
Q 038517           58 LAAICAVCLD-----GVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~-----~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~  105 (112)
                      .+..|.+|..     .|+ .+.++....|+++||+.|+.+   ++..||.|-+
T Consensus       510 ~gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r---~s~~CPrC~R  558 (580)
T KOG1829|consen  510 KGFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR---KSPCCPRCER  558 (580)
T ss_pred             CeeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc---cCCCCCchHH
Confidence            6677888832     121 223333334999999999754   4555999954

>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=85.26  E-value=0.84  Score=24.05  Aligned_cols=43  Identities=23%  Similarity=0.479  Sum_probs=20.1

Q ss_pred             cccccccccCCC------ceeecCCCcCcccHHhHHHHHhCCCCCcccc
Q 038517           62 CAVCLDGVHKGE------RSRNFSICKHVFHARCIDLWLVRRLTCPTCR  104 (112)
Q Consensus        62 C~IC~~~~~~~~------~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr  104 (112)
                      |--|+..+..+.      ....-+.|++.|+.+|=.--=..--.||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            445666665431      3445567999999999321112345799884

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.

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

Probab=85.26  E-value=0.6  Score=22.08  Aligned_cols=37  Identities=30%  Similarity=0.732  Sum_probs=23.8

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      |..|-+.+..++.... . =+..||..|+.        |..|+.++.
T Consensus         2 C~~C~~~i~~~~~~~~-~-~~~~~H~~Cf~--------C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLR-A-LGKVWHPECFK--------CSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEE-e-CCccccccCCC--------CcccCCcCc
Confidence            6777777655422222 2 46789988864        888887663

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

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

Probab=84.93  E-value=0.75  Score=31.42  Aligned_cols=47  Identities=32%  Similarity=0.590  Sum_probs=35.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~  107 (112)
                      .-..|.+|..-.-.  .++.-. |+-.+|..|+...+++...||.|.--+
T Consensus       180 nlk~Cn~Ch~LvIq--g~rCg~-c~i~~h~~c~qty~q~~~~cphc~d~w  226 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQ--GIRCGS-CNIQYHRGCIQTYLQRRDICPHCGDLW  226 (235)
T ss_pred             HHHHHhHhHHHhhe--eeccCc-ccchhhhHHHHHHhcccCcCCchhccc
Confidence            34579999886532  233233 888899999999999999999995433

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

Probab=84.41  E-value=0.37  Score=37.98  Aligned_cols=40  Identities=23%  Similarity=0.678  Sum_probs=28.9

Q ss_pred             ccccccccccccCCC-ceeecCCCcCcccHHhHHHHHhCCCCCc
Q 038517           59 AAICAVCLDGVHKGE-RSRNFSICKHVFHARCIDLWLVRRLTCP  101 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~CP  101 (112)
                      -..|.||+..|-... .++.+. |||+.|+.|+....  +.+||
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~-cghtic~~c~~~ly--n~scp   51 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQ-CGHTICGHCVQLLY--NASCP   51 (861)
T ss_pred             HhhchHHHHHHHHHhcCccccc-ccchHHHHHHHhHh--hccCC
Confidence            356999987775433 455565 99999999987643  56677

>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=83.02  E-value=0.87  Score=23.36  Aligned_cols=43  Identities=23%  Similarity=0.549  Sum_probs=27.9

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHh------CCCCCcccc
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV------RRLTCPTCR  104 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~------~~~~CP~Cr  104 (112)
                      .|.||...- .++..+.-..|+..||..|+..=..      ..-.||.|+
T Consensus         1 ~C~vC~~~~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQSD-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTSSC-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCCcC-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            378888843 3344444445999999999765432      134688775

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 ....

>smart00249 PHD PHD zinc finger

Probab=82.80  E-value=0.86  Score=22.36  Aligned_cols=30  Identities=20%  Similarity=0.472  Sum_probs=20.2

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHHH
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCIDL   92 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~   92 (112)
                      |.+|...... ...+.-..|...||..|+..
T Consensus         2 C~~C~~~~~~-~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        2 CSVCGKPDDG-GELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             cccCCCcCCC-CCEEECCCCCchhhhhhCCC
Confidence            7778776533 33444334999999999754

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

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=81.75  E-value=1.4  Score=31.90  Aligned_cols=51  Identities=18%  Similarity=0.447  Sum_probs=36.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ....|+||-+.....+...+--+|++..|..|+..-...+.+||.||++..
T Consensus       248 v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~  298 (327)
T KOG2068|consen  248 VPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE  298 (327)
T ss_pred             cCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence            347899999987544444332228888777777776677889999998654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	112
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		3e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		9e-05
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-04
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		8e-04

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 26/43 (60%)
Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR 104
           CAVCL  +  GE +R    C H FHA C+D+WL    TCP CR
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR 104
           C +CL  + +GE  R    C H+FH  C+D WL+    CP CR
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 55  QRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF 107
           + NL  +CAVCL+   K         CKH FH +C+  WL  R  CP C  P 
Sbjct: 11  ELNLHELCAVCLEDF-KPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 42  SLEKIRGFPWFDCQRNLAAI-----CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR 96
           S E I   P      +  A+     C +C     KG+ +     C H FH  C+ +WL +
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQK 76
Query: 97  RLTCPTCRSPF 107
             TCP CR  F
Sbjct: 77  SGTCPVCRCMF 87

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 60  AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRS 105
            +C VC+      +  R    C H FHA+C+D WL    TCP CR+
Sbjct: 24  TLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRA 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	112
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-16
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-14
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	4e-14
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	8e-14
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-13
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-13
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	6e-13
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	8e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-10
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-10
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	4e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	6e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	8e-09
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-06
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	9e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-05
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	2e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-05
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-04
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-04

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

 Score = 66.5 bits (163), Expect = 2e-16
 Identities = 22/45 (48%), Positives = 26/45 (57%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           CAVCL  +  GE +R    C H FHA C+D+WL    TCP CR  
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLT 52

>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 = 61.3 bits (149), Expect = 3e-14
 Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR 104
           C VC +    GE  R    C H+FH  CI  WL +  +CP CR
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCR 59

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

 Score = 61.6 bits (150), Expect = 4e-14
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR 104
           C +C     KG+ +     C H FH  C+ +WL +  TCP CR
Sbjct: 43  CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

>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 = 59.6 bits (145), Expect = 8e-14
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF 107
           C +CL+ +H      +   C H+ H  C +  L     CP C  P 
Sbjct: 8   CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

>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 = 60.1 bits (146), Expect = 1e-13
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C +CL  + +GE  R    C H+FH  C+D WL+    CP CR  
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVD 60

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

 Score = 59.5 bits (144), Expect = 2e-13
 Identities = 13/55 (23%), Positives = 23/55 (41%)

Query: 54  CQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           C+  +   C  C     + +    +  C H FH  C+ LW+ +   CP C+  + 
Sbjct: 21  CRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV 75

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

 Score = 58.1 bits (141), Expect = 6e-13
 Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C VC+      +  R    C H FHA+C+D WL    TCP CR+ 
Sbjct: 26  CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRAD 69

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

 Score = 57.9 bits (140), Expect = 8e-13
 Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 55  QRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           + NL  +CAVCL+     +       CKH FH +C+  WL  R  CP C  P
Sbjct: 11  ELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMP 61

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

 Score = 52.0 bits (125), Expect = 1e-10
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           C +CL+       +     C H F   CI  W+ +  TCP C+ P +
Sbjct: 8   CPICLEDPSNYSMALP---CLHAFCYVCITRWIRQNPTCPLCKVPVE 51

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

 Score = 50.9 bits (122), Expect = 3e-10
 Identities = 16/45 (35%), Positives = 19/45 (42%), Gaps = 5/45 (11%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C +C+DG            C H F  +CID W  R   CP CR  
Sbjct: 18  CCICMDGRADLI-----LPCAHSFCQKCIDKWSDRHRNCPICRLQ 57

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

 Score = 50.3 bits (120), Expect = 7e-10
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 62  CAVCLDGVHKGERSRNFSI---CKHVFHARCIDLWLVRRLTCPTCRSPFKME 110
           C +C+DG  +  ++    +   C HVF ++C+   L    TCPTCR     +
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

>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 = 50.6 bits (120), Expect = 1e-09
 Identities = 22/100 (22%), Positives = 33/100 (33%), Gaps = 13/100 (13%)

Query: 22  NEDYRLYNNTASSTDGISGFSLEKIRGF-PWF-DCQRNLAAIC-----------AVCLDG 68
           N  ++      +S  G   F ++K      W  D   +  AIC                 
Sbjct: 12  NLYFQGGGRGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS 71

Query: 69  VHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
               E +  + +C H FH  CI  WL  R  CP     ++
Sbjct: 72  ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE 111

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

 Score = 48.2 bits (115), Expect = 3e-09
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 62  CAVCLDGVHKGERSRNFSI---CKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV 112
           C +C+DG  +  ++    +   C HVF ++C+   L    TCPTCR     +  
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 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 = 48.4 bits (115), Expect = 4e-09
 Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 5/48 (10%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR--LTCPTCRSPF 107
           C +C   + +G+       C    H  C+  +        CP C   +
Sbjct: 18  CNICHSLLIQGQSCET---CGIRMHLPCVAKYFQSNAEPRCPHCNDYW 62

>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 = 47.9 bits (114), Expect = 6e-09
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 62  CAVCLDGVHKGERSRNFSI---CKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV 112
           C +C+DG  +  ++    +   C HVF ++C+   L    TCPTCR     +  
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY 66

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

 Score = 48.3 bits (114), Expect = 8e-09
 Identities = 13/47 (27%), Positives = 18/47 (38%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           C          E +  + +C H FH  CI  WL  R  CP     ++
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE 100

>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-08
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 5/59 (8%)

Query: 51  WFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR--LTCPTCRSPF 107
             +   +   IC +C   + +G+       C    H  C+  +        CP C   +
Sbjct: 172 IRETYPDAVKICNICHSLLIQGQSCET---CGIRMHLPCVAKYFQSNAEPRCPHCNDYW 227

>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 = 42.2 bits (99), Expect = 2e-06
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEPV 112
           C +C++ +     +R    C  +    CI  WL   R  CP CR+P ++  +
Sbjct: 25  CFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL 73

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

 Score = 44.1 bits (103), Expect = 2e-06
 Identities = 19/87 (21%), Positives = 29/87 (33%), Gaps = 15/87 (17%)

Query: 37  GISGFSLEKIRGFPWFDCQRNLAAICAVC----LDGVHKGERSRNFSICKHVFHARCIDL 92
            +  F +      P  D + N    C +C    LDG      S + + C    HA C++ 
Sbjct: 286 DLCYFPMPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEE 345

Query: 93  WL-----------VRRLTCPTCRSPFK 108
           W            V    CP C++   
Sbjct: 346 WFKTLMDGKTFLEVSFGQCPFCKAKLS 372

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

 Score = 40.2 bits (94), Expect = 5e-06
 Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 4/51 (7%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV 112
           CA+CL              CKHVF   C+         C  CR     + +
Sbjct: 18  CAICLQTCVHPVSLP----CKHVFCYLCVKGASWLGKRCALCRQEIPEDFL 64

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

 Score = 39.8 bits (93), Expect = 9e-06
 Identities = 9/45 (20%), Positives = 13/45 (28%), Gaps = 4/45 (8%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           C +C         ++    C+H F   C          C  C  P
Sbjct: 18  CFICRQAFQNPVVTK----CRHYFCESCALEHFRATPRCYICDQP 58

>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 = 39.8 bits (92), Expect = 2e-05
 Identities = 11/65 (16%), Positives = 20/65 (30%), Gaps = 19/65 (29%)

Query: 62  CAVCLD--------------GVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPT 102
           C +C++                         + C H FH  C+            L CP+
Sbjct: 28  CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 103 CRSPF 107
           C++ +
Sbjct: 88  CKTIY 92

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

 Score = 39.0 bits (91), Expect = 2e-05
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 3/46 (6%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           +C++C   +     +   + C H F   CI         CP C   
Sbjct: 17  LCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIV 59

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

 Score = 38.6 bits (90), Expect = 5e-05
 Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 3/47 (6%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPF 107
           +C +C         +     C H F   CI  +L     CP C    
Sbjct: 17  MCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

>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 = 39.7 bits (92), Expect = 5e-05
 Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 9/54 (16%)

Query: 62  CAVCLDGVHKGERSRNFSI--CKHVFHARCIDLWLVRR-LTCPTCRSPFKMEPV 112
           C +C       E  ++  I  C H+    C+  W       CP CR   K    
Sbjct: 335 CKICA------ENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP 382

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

 Score = 38.6 bits (89), Expect = 6e-05
 Identities = 16/67 (23%), Positives = 24/67 (35%)

Query: 44  EKIRGFPWFDCQRNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTC 103
            K     +         IC      + +  R    + C HVF ++C+   L    TCPTC
Sbjct: 60  HKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 119

Query: 104 RSPFKME 110
           R     +
Sbjct: 120 RKKINHK 126

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

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 62  CAVCLDGVHKGERSRNF---SICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
           C +C+DG  +  ++      + C HVF ++C+   L    TCPTCR     + 
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 62

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

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 6/51 (11%)

Query: 62  CAVCLDGVHKGERSRNFSI-CKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
           C +C +   +       ++ C H F + CI+ W+ R++ CP CR   K + 
Sbjct: 67  CIICSEYFIEA-----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT 112

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	112
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.83
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.8
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.76
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.73
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.73
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.73
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.72
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.68
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.67
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.67
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.66
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.65
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.65
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.62
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.61
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.61
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.61
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.6
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.59
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.59
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.59
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.59
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.57
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.56
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.55
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.54
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.54
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.53
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.53
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.52
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.52
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.5
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.5
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.49
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.48
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.47
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.46
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.46
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.45
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.43
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.42
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.41
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.41
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.41
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.39
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.38
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.38
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.37
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.36
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.36
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.34
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.32
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.3
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.29
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.27
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.27
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.23
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.21
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.17
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.17
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.16
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.11
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.08
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.06
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.01
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.0
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.0
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.92
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.86
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.84
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.64
3nw0_A	238	Non-structural maintenance of chromosomes element	98.52
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.71
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.5
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.46
1we9_A	64	PHD finger family protein; structural genomics, PH	95.42
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	95.01
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.2
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	94.02
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	93.74
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	93.3
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	92.82
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	92.7
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	91.85
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	91.81
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	90.41
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	90.07
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	89.78
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	89.21
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	88.94
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	88.92
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	88.67
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	88.5
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	88.41
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	88.24
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	87.91
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	87.51
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.42
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	87.3
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	87.2
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	87.04
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	86.68
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.89
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	85.86
1wem_A	76	Death associated transcription factor 1; structura	85.75
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	85.43
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	84.38
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	83.69
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	82.96
2yt5_A	66	Metal-response element-binding transcription facto	82.71
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	82.57
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	82.33
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	82.29
2o35_A	105	Hypothetical protein DUF1244; helix bundle, struct	82.01
3fyb_A	104	Protein of unknown function (DUF1244); hydrocar de	81.96
1weu_A	91	Inhibitor of growth family, member 4; structural g	81.87
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	81.58
2co8_A	82	NEDD9 interacting protein with calponin homology a	81.07
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	80.89
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	80.8
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	80.14
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	80.06

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

Probab=99.83  E-value=1.8e-20  Score=110.55  Aligned_cols=74  Identities=28%  Similarity=0.619  Sum_probs=64.4

Q ss_pred             CCCCCCCCHHHHcCCCceecCCC-----CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           35 TDGISGFSLEKIRGFPWFDCQRN-----LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        35 ~~~~~~~~~~~~~~l~~~~~~~~-----~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      .....+++++.++.+|.......     .+..|+||++.+..++.++.++ |+|.||..||.+|++.+.+||+||+++..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            34556677899999998887654     5678999999999888888899 99999999999999999999999998864

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

Probab=99.80  E-value=2.8e-20  Score=106.01  Aligned_cols=65  Identities=31%  Similarity=0.697  Sum_probs=54.8

Q ss_pred             HHcCCCceecCCC----CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           45 KIRGFPWFDCQRN----LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        45 ~~~~l~~~~~~~~----~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .++.+|...++..    .+..|+||++.+..++.++.++ |+|.||..||.+|++.+.+||+||+++...
T Consensus         5 ~i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            5 SSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hHhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3455666655443    6678999999999888888898 999999999999999999999999998764

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

Probab=99.76  E-value=3.8e-19  Score=95.47  Aligned_cols=51  Identities=43%  Similarity=0.906  Sum_probs=46.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ++..|+||++.+..++.+..++.|+|.||..||.+|++++.+||+||+++.
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            467899999999988888888679999999999999999999999999875

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

Probab=99.73  E-value=5.5e-19  Score=102.14  Aligned_cols=54  Identities=26%  Similarity=0.688  Sum_probs=43.7

Q ss_pred             CccccccccccccC-----------CCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHK-----------GERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~-----------~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      +++.|+||++.+..           ++.++.++.|+|.||..||.+|++++.+||+||+++..++
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQR   78 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhh
Confidence            46668888887743           4556666669999999999999999999999999987653

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

Probab=99.73  E-value=2.6e-18  Score=96.18  Aligned_cols=52  Identities=35%  Similarity=0.929  Sum_probs=47.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..++.++.++ |+|.||..||.+|++.+.+||+||+++...
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            5678999999998878888898 999999999999999999999999988654

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

Probab=99.73  E-value=2.2e-18  Score=98.66  Aligned_cols=53  Identities=34%  Similarity=0.809  Sum_probs=48.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.|..+..+..++ |+|.||..||.+|++.+.+||+||+++..+.
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN   66 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSC
T ss_pred             CCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcc
Confidence            5678999999998888888888 9999999999999999999999999987654

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

Probab=99.72  E-value=5.3e-18  Score=96.14  Aligned_cols=51  Identities=37%  Similarity=0.859  Sum_probs=46.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..+..+..++ |+|.||..||.+|++.+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             CCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            4678999999998888888888 99999999999999999999999998754

>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=99.68  E-value=2.4e-17  Score=88.25  Aligned_cols=50  Identities=26%  Similarity=0.716  Sum_probs=43.0

Q ss_pred             CccccccccccccCCC-ceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGE-RSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~-~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      .+..|+||++.+..++ .+..++ |+|.||..||.+|++.+.+||+||+++.
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            4678999999986544 466677 9999999999999998899999999875

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

Probab=99.67  E-value=1.9e-17  Score=92.95  Aligned_cols=53  Identities=32%  Similarity=0.687  Sum_probs=45.2

Q ss_pred             CccccccccccccC----CCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHK----GERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~----~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+..    ++.++.++ |||.||..||.+|++++.+||+||+++..+.
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            57789999999864    24446777 9999999999999999999999999987664

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=99.67  E-value=3.7e-17  Score=98.83  Aligned_cols=52  Identities=29%  Similarity=0.648  Sum_probs=43.7

Q ss_pred             CccccccccccccCC--------------C-ceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKG--------------E-RSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~--------------~-~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .++.|+||++.|...              + .++.++ |+|.||..||.+|+..+.+||+||+++..+
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~~  102 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQ  102 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcceee
Confidence            578899999998753              1 245566 999999999999999999999999997654

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

Probab=99.66  E-value=3e-17  Score=90.28  Aligned_cols=53  Identities=30%  Similarity=0.629  Sum_probs=44.7

Q ss_pred             CccccccccccccCC----CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKG----ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+...    +.+..++ |||.||..||.+|++++.+||+||+++..+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            356899999998642    3446677 9999999999999999999999999987654

>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=99.65  E-value=1.2e-16  Score=97.45  Aligned_cols=52  Identities=23%  Similarity=0.602  Sum_probs=41.5

Q ss_pred             CccccccccccccCCC---------------ceeecCCCcCcccHHhHHHHH-----hCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGE---------------RSRNFSICKHVFHARCIDLWL-----VRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~w~-----~~~~~CP~Cr~~~~~~  110 (112)
                      .++.|+||++.|..+.               .+..++ |+|.||..||.+|+     ..+.+||+||+.+..+
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4678999999996543               233566 99999999999999     4577999999987643

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

Probab=99.65  E-value=7.6e-17  Score=89.88  Aligned_cols=51  Identities=31%  Similarity=0.639  Sum_probs=43.6

Q ss_pred             CccccccccccccCC----CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKG----ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ....|+||++.+...    +.+..++ |||.||..||.+|++.+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            577899999998643    3346677 99999999999999999999999998864

>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=99.62  E-value=3.4e-17  Score=100.43  Aligned_cols=54  Identities=28%  Similarity=0.717  Sum_probs=1.3

Q ss_pred             CccccccccccccCC--------------CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKG--------------ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~--------------~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .++.|+||++.|...              +..+.+++|+|.||..||.+|++.+.+||+||+++..++
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~k  114 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQK  114 (117)
T ss_dssp             CC------------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeeeec
Confidence            678999999999642              122332339999999999999999999999999987654

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

Probab=99.61  E-value=5.2e-16  Score=89.35  Aligned_cols=51  Identities=25%  Similarity=0.615  Sum_probs=43.3

Q ss_pred             CccccccccccccCCCceeecCCCc-----CcccHHhHHHHHhCC--CCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICK-----HVFHARCIDLWLVRR--LTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~-----H~fh~~Ci~~w~~~~--~~CP~Cr~~~~~~  110 (112)
                      ++..|.||++++..++.+ .+| |+     |.||..||.+|+..+  .+||+||+++..+
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            567899999999876665 577 96     999999999999864  5899999998764

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

Probab=99.61  E-value=6.4e-16  Score=89.96  Aligned_cols=53  Identities=17%  Similarity=0.584  Sum_probs=44.9

Q ss_pred             CccccccccccccCCCc-eeecCCCcCcccHHhHHHHHhCC---CCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGER-SRNFSICKHVFHARCIDLWLVRR---LTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~-~~~~~~C~H~fh~~Ci~~w~~~~---~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.+..++. ++.++ |||.||..||.+|++.+   .+||+||+++..+.
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             CCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            56789999999976654 67777 99999999999999865   78999999876643

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

Probab=99.61  E-value=6.4e-16  Score=87.13  Aligned_cols=50  Identities=20%  Similarity=0.494  Sum_probs=43.0

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   ++.+ + |||.||..||.+|++.+.+||+||+++..+.
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           14 PYILCSICKGYLID---ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGGSCTTTSSCCSS---CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             CCCCCCCCChHHHC---cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            46789999999864   4555 6 9999999999999998999999999987654

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

Probab=99.60  E-value=5.1e-16  Score=87.31  Aligned_cols=48  Identities=27%  Similarity=0.529  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..   .+.++ |+|.||..||.+|+..+.+||+||.++..
T Consensus        14 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           14 TVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            56789999999854   56777 99999999999999999999999998864

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

Probab=99.59  E-value=1.6e-15  Score=85.46  Aligned_cols=51  Identities=27%  Similarity=0.675  Sum_probs=43.4

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh---CCCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV---RRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~---~~~~CP~Cr~~~~~~~~  112 (112)
                      .+..|+||++.+..   ++.++ |||.||..||..|++   .+..||+||+++..+.+
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            57789999999863   66677 999999999999997   45689999999987754

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

Probab=99.59  E-value=1.3e-15  Score=84.48  Aligned_cols=51  Identities=20%  Similarity=0.440  Sum_probs=42.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh-CCCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~~~~~~  112 (112)
                      .+..|+||++.+..   +..++ |||.||..||.+|++ .+.+||+||+++..+.|
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           14 DKYKCEKCHLVLCS---PKQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             CCEECTTTCCEESS---CCCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             cCCCCCCCChHhcC---eeECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            46789999999864   44467 999999999999995 56789999999987764

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

Probab=99.59  E-value=4.6e-16  Score=87.17  Aligned_cols=48  Identities=33%  Similarity=0.798  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..    +.++ |+|.||..||.+|+.++.+||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCC
T ss_pred             CCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCC
Confidence            46789999999864    6677 999999999999999999999999988654

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

Probab=99.59  E-value=7.7e-16  Score=85.73  Aligned_cols=48  Identities=33%  Similarity=0.845  Sum_probs=41.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      .+..|+||++.+..  .+..++ |||.||..|+.+|++++.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            36689999999853  346777 9999999999999999999999999875

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

Probab=99.57  E-value=7.4e-16  Score=97.01  Aligned_cols=48  Identities=29%  Similarity=0.803  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|+||++.+..   ++.++ |||.||..||..|+..+.+||+||+++..
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            35679999999854   67788 99999999999999999999999998864

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

Probab=99.56  E-value=1.5e-15  Score=90.84  Aligned_cols=50  Identities=26%  Similarity=0.758  Sum_probs=42.8

Q ss_pred             CccccccccccccCCCceee-cCCCcCcccHHhHHHHHhCC-CCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRN-FSICKHVFHARCIDLWLVRR-LTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~-~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+..   ++. ++ |||.||..||.+|+..+ .+||+||.++..+.
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           21 EVFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            46789999999853   666 66 99999999999999877 79999999987653

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

Probab=99.55  E-value=5e-15  Score=84.51  Aligned_cols=50  Identities=18%  Similarity=0.329  Sum_probs=43.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   ++.++ |||.||+.||.+|+.+ +.+||+||+++..+.
T Consensus         7 ~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            7 EYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            46789999999854   66777 9999999999999987 789999999987653

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

Probab=99.54  E-value=4.7e-15  Score=85.30  Aligned_cols=47  Identities=19%  Similarity=0.465  Sum_probs=41.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ....|+||++.+..   ++.++ |||.||..||.+|++...+||+||+++.
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            46789999999854   56677 9999999999999999999999999875

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

Probab=99.54  E-value=7.8e-15  Score=81.01  Aligned_cols=53  Identities=25%  Similarity=0.530  Sum_probs=42.0

Q ss_pred             Cccccccccc-cccCCCce-eecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLD-GVHKGERS-RNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~-~~~~~~~~-~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++ .+...... ..++ |||.||..||.+|+.+ +.+||+||+++..+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   57 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccccc
Confidence            3568999999 77654433 3456 9999999999999765 578999999987664

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

Probab=99.53  E-value=3.1e-15  Score=92.81  Aligned_cols=53  Identities=30%  Similarity=0.617  Sum_probs=44.9

Q ss_pred             CccccccccccccCC----CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKG----ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+...    +.++.++ |||.||..||.+|++++.+||+||+.+..+.
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            467899999998642    4447777 9999999999999999999999999887654

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

Probab=99.53  E-value=6.6e-15  Score=83.39  Aligned_cols=49  Identities=24%  Similarity=0.520  Sum_probs=40.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC--CCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR--LTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~--~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..   ++.++.|||.||..||.+|++.+  .+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           14 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             GGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            57789999999864   55565599999999999999865  689999998643

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

Probab=99.52  E-value=1.1e-14  Score=83.95  Aligned_cols=50  Identities=28%  Similarity=0.715  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC------CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR------RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~------~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   ...++ |+|.||..||..|+..      ...||+||.++..+.
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           18 EEVTCPICLELLKE---PVSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             TTTSCTTTCSCCSS---CEECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             cCCCCcCCChhhCc---ceeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            46789999999854   45677 9999999999999986      678999999987654

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

Probab=99.52  E-value=6.2e-15  Score=87.76  Aligned_cols=50  Identities=22%  Similarity=0.527  Sum_probs=42.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..   ++.+++|||.||..||.+|+..+.+||+||.++..+
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            46789999999864   555523999999999999999999999999988653

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

Probab=99.50  E-value=1.2e-14  Score=83.77  Aligned_cols=50  Identities=24%  Similarity=0.664  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC------CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR------RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~------~~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.+..   +..++ |||.||..|+..|+..      ...||+||..+..+.
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           18 EEVTCPICLELLTQ---PLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCTTTCSCCSS---CBCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             CCCCCCCCCcccCC---ceeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            46789999999864   55667 9999999999999976      789999999887654

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

Probab=99.50  E-value=3e-15  Score=85.50  Aligned_cols=49  Identities=22%  Similarity=0.646  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-------CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-------RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-------~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|+..       ...||+||.++..+
T Consensus        11 ~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           11 EEVTCPICLELLTE---PLSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCEETTTTEECSS---CCCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             cCCCCcCCCcccCC---eeECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            46789999999864   55677 9999999999999986       67899999988754

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

Probab=99.49  E-value=2e-14  Score=81.39  Aligned_cols=50  Identities=22%  Similarity=0.621  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC--CCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR--LTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~--~~CP~Cr~~~~~~  110 (112)
                      ....|+||.+.+..++...  . |+|.||..||.+||+++  .+||+||+++..+
T Consensus        14 ~i~~C~IC~~~i~~g~~C~--~-C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSCE--T-CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSCBCSSSCCBCSSSEECS--S-SCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCcCcchhhHcccCCccC--C-CCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            4577999999997654332  4 99999999999999876  8999999998654

>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=99.48  E-value=3e-14  Score=86.03  Aligned_cols=49  Identities=22%  Similarity=0.512  Sum_probs=42.4

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..   ++.+ + |||.||..||..|+..+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID---ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC---cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            46789999999854   5565 6 999999999999999999999999988653

>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=99.47  E-value=3.5e-14  Score=87.72  Aligned_cols=48  Identities=23%  Similarity=0.550  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-CCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..   ++.++ |||.||..||..|+..+ ..||+||.++..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            46789999999864   67777 99999999999999854 599999999865

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

Probab=99.46  E-value=1.8e-14  Score=89.31  Aligned_cols=53  Identities=30%  Similarity=0.617  Sum_probs=44.8

Q ss_pred             CccccccccccccCC----CceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKG----ERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~----~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.+...    ...+.++ |||.||..||.+|++.+++||+||+++..+.
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            678899999998642    3346667 9999999999999999999999999987654

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

Probab=99.46  E-value=6.4e-14  Score=76.80  Aligned_cols=42  Identities=33%  Similarity=0.737  Sum_probs=36.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh---CCCCCccc
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV---RRLTCPTC  103 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~---~~~~CP~C  103 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|++   .+.+||+|
T Consensus        19 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            57789999999864   66677 999999999999998   45689998

>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=99.45  E-value=4.2e-14  Score=85.63  Aligned_cols=50  Identities=22%  Similarity=0.607  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC---CCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR---LTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~---~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.+..   +..++ |||.||..||..|+..+   .+||+||.++..+.
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCCcccChhhcC---eEECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            35679999999854   45567 99999999999999865   48999999887654

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

Probab=99.43  E-value=1.1e-13  Score=81.19  Aligned_cols=47  Identities=26%  Similarity=0.569  Sum_probs=39.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--~~~CP~Cr~~~  107 (112)
                      .+..|+||++.+..   ++.++.|||.||..||.+|+..  ...||+||.++
T Consensus        12 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           12 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             TTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             cCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            57789999999864   5566559999999999999974  36899999987

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

Probab=99.42  E-value=1.2e-13  Score=74.37  Aligned_cols=42  Identities=36%  Similarity=0.903  Sum_probs=35.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh---CCCCCccc
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV---RRLTCPTC  103 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~---~~~~CP~C  103 (112)
                      .+..|+||++.+..   .+.++ |||.||..||.+|+.   ++.+||+|
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKE---PVIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSS---CCCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCc---cEeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            46789999999865   45577 999999999999954   56789998

>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=99.41  E-value=8e-14  Score=85.46  Aligned_cols=49  Identities=20%  Similarity=0.380  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCC-CCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRL-TCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|+..+. +||+||.++..+
T Consensus        17 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           17 SKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCcCChhhcC---eEECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            56789999999864   56677 999999999999998754 999999988754

>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=99.41  E-value=8.5e-14  Score=85.01  Aligned_cols=49  Identities=31%  Similarity=0.551  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~  110 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|+.. +.+||+||.++..+
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            46789999999854   66677 9999999999999986 78999999988654

>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=99.41  E-value=1.6e-13  Score=87.52  Aligned_cols=49  Identities=20%  Similarity=0.539  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCC-CCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRL-TCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~-~CP~Cr~~~~~~  110 (112)
                      ....|+||++.+..   ++.++ |||.||..||..|+.... .||+||.++..+
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45689999999854   66677 999999999999998754 899999998765

>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=99.39  E-value=2.1e-13  Score=87.94  Aligned_cols=48  Identities=33%  Similarity=0.670  Sum_probs=40.9

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHHHHhC-CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDLWLVR-RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..   ++.+ + |||.||..||..|+.. +..||+||.++..
T Consensus        53 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKN---TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhC---cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            45689999999864   5555 6 9999999999999987 7889999998853

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

Probab=99.38  E-value=3.2e-13  Score=78.40  Aligned_cols=50  Identities=12%  Similarity=-0.065  Sum_probs=44.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   +++++ |||.|++.||.+|+.++.+||+||.++..+.
T Consensus        13 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   62 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTESM   62 (85)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             hheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChHh
Confidence            47889999999965   88888 9999999999999998899999999887543

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.38  E-value=4.5e-13  Score=80.04  Aligned_cols=50  Identities=10%  Similarity=-0.050  Sum_probs=45.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   ++.++ |||.|++.||.+|+..+.+||+||.++..+.
T Consensus        28 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~   77 (100)
T 2kre_A           28 DEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESM   77 (100)
T ss_dssp             TTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTS
T ss_pred             HhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhh
Confidence            57889999999965   88888 9999999999999998899999999987654

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

Probab=99.37  E-value=9.8e-13  Score=75.23  Aligned_cols=53  Identities=19%  Similarity=0.491  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCce-eecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERS-RNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~-~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+...+.. ..++ |||.||..|+..+... ...||.||+++..++
T Consensus        10 ~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            567899999988643322 2245 9999999999998753 678999999987654

>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=99.36  E-value=6.8e-14  Score=85.32  Aligned_cols=47  Identities=21%  Similarity=0.639  Sum_probs=40.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~  108 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|+.. +..||+||+++.
T Consensus        14 ~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           14 SECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            46789999999854   66777 9999999999999976 678999999875

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.36  E-value=7.4e-13  Score=78.83  Aligned_cols=50  Identities=16%  Similarity=0.114  Sum_probs=44.8

Q ss_pred             CccccccccccccCCCceeecCCCc-CcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICK-HVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   +++++ || |.|++.||.+|+..+.+||+||.++..+.
T Consensus        21 ~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~   71 (98)
T 1wgm_A           21 DEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQ   71 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTT
T ss_pred             HhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhh
Confidence            47889999999965   78888 99 99999999999998899999999987654

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=99.34  E-value=8.3e-13  Score=72.79  Aligned_cols=47  Identities=21%  Similarity=0.480  Sum_probs=39.7

Q ss_pred             CccccccccccccCCCceeec--CCCcCc-ccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF--SICKHV-FHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~--~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ++..|.||++...+   ...+  | |||. |+..|+..|.+.+..||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            46789999998643   4444  8 9999 899999999998899999999875

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

Probab=99.32  E-value=5.7e-13  Score=84.13  Aligned_cols=48  Identities=17%  Similarity=0.427  Sum_probs=40.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-CCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~  109 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|+... .+||+||.++..
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            57789999999864   56677 99999999999999865 489999997643

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

Probab=99.30  E-value=4.7e-13  Score=81.89  Aligned_cols=47  Identities=21%  Similarity=0.615  Sum_probs=40.2

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      ....|+||++.+..   ++.+ + |||.||..||..|+.  ..||+||.++...
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~   68 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQ   68 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCS
T ss_pred             hCCCCCCCChHhhC---ccEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCccc
Confidence            46789999999854   5666 6 999999999999987  8899999988654

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

Probab=99.29  E-value=2.3e-12  Score=92.80  Aligned_cols=48  Identities=23%  Similarity=0.648  Sum_probs=41.5

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHh-CCCCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~~~~  110 (112)
                      ...|+||++.+..   ++.+| |||.||..|+..|+. .+.+||+||+++...
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            3689999998843   77788 999999999999998 688999999987643

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.27  E-value=3.2e-12  Score=70.18  Aligned_cols=47  Identities=17%  Similarity=0.417  Sum_probs=38.9

Q ss_pred             CccccccccccccCCCceeec--CCCcCc-ccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF--SICKHV-FHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~--~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      .+..|.||++....   ...+  | |||. |+..|+..|.+++..||+||+++.
T Consensus         6 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRD---GNIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSC---EEEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCC---eEEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            46689999997532   3333  7 9998 999999999988899999999875

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

Probab=99.27  E-value=9.6e-13  Score=70.64  Aligned_cols=46  Identities=20%  Similarity=0.632  Sum_probs=38.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~  110 (112)
                      +...|+||++.+..   ++.++ |||.||..|+..|   ...||+||+++..+
T Consensus         5 ~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            5 QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             cCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            46789999999864   57788 9999999999874   67899999988754

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

Probab=99.23  E-value=2.3e-12  Score=72.91  Aligned_cols=44  Identities=20%  Similarity=0.551  Sum_probs=37.7

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|+||++.+..   ++.+| |||. ||..|+..|    ..||+||+++..
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            46789999998753   77788 9999 999999988    889999998753

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens}

Probab=99.21  E-value=5.5e-12  Score=81.61  Aligned_cols=49  Identities=20%  Similarity=0.397  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-CCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~~  110 (112)
                      +...|+||++.+..   ++.++ |||.||..||.+|+..+ .+||+||.++..+
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            57889999999864   56677 99999999999999764 5999999988754

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=99.17  E-value=1.3e-11  Score=84.84  Aligned_cols=50  Identities=16%  Similarity=0.137  Sum_probs=43.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ....|+||++.+..   +++++ |||+|++.||.+|+.. +.+||+||.++..+.
T Consensus       207 ~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~  257 (281)
T 2c2l_A          207 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ  257 (281)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             cccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchhc
Confidence            57889999999964   88888 9999999999999986 455999999987543

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

Probab=99.17  E-value=3.1e-12  Score=90.51  Aligned_cols=51  Identities=24%  Similarity=0.560  Sum_probs=39.3

Q ss_pred             CccccccccccccC-CCce---eecCCCcCcccHHhHHHHHhCC-----------CCCccccCCCC
Q 038517           58 LAAICAVCLDGVHK-GERS---RNFSICKHVFHARCIDLWLVRR-----------LTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~-~~~~---~~~~~C~H~fh~~Ci~~w~~~~-----------~~CP~Cr~~~~  108 (112)
                      ...+|+||++.+.. ++.+   ...+.|+|.||..||.+||++.           .+||+||++++
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            56789999999876 3322   2233599999999999999742           46999999875

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=1e-11  Score=73.22  Aligned_cols=49  Identities=18%  Similarity=0.472  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC------CCCcc--ccCC-CCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR------LTCPT--CRSP-FKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~------~~CP~--Cr~~-~~~  109 (112)
                      .+..|+||++.|..   ++.++.|||.|++.||.+|+..+      .+||+  |+.. +..
T Consensus         6 ~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~   63 (94)
T 2yu4_A            6 SGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRK   63 (94)
T ss_dssp             SCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCG
T ss_pred             cEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCH
Confidence            46789999999964   77774499999999999999753      48999  9865 543

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

Probab=99.11  E-value=6.6e-11  Score=64.31  Aligned_cols=48  Identities=21%  Similarity=0.625  Sum_probs=37.5

Q ss_pred             CccccccccccccCCCceeecCCCc--C---cccHHhHHHHHhC--CCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICK--H---VFHARCIDLWLVR--RLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~--H---~fh~~Ci~~w~~~--~~~CP~Cr~~~~~  109 (112)
                      ++..|.||+++.  ++.. .+| |.  +   .||..||.+|+..  +.+||+|+.++..
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            567899999973  2333 466 66  4   8999999999974  6789999998865

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

Probab=99.08  E-value=4e-11  Score=67.82  Aligned_cols=44  Identities=20%  Similarity=0.556  Sum_probs=36.3

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|+||++.+..   ++.+| |||. ||..|+..    ...||+||.++..
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            35679999998743   66778 9999 99999964    4789999998864

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

Probab=99.06  E-value=9.6e-11  Score=76.49  Aligned_cols=49  Identities=14%  Similarity=0.119  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC-CCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-LTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~-~~CP~Cr~~~~~~  110 (112)
                      ....|+||++.+..   +++++ |||.|++.||..|+..+ .+||+||.++..+
T Consensus       105 ~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~  154 (179)
T 2f42_A          105 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQD  154 (179)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             HhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChh
Confidence            57889999999964   77888 99999999999999863 5799999988754

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

Probab=99.01  E-value=3.6e-10  Score=62.83  Aligned_cols=44  Identities=25%  Similarity=0.611  Sum_probs=36.7

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|.||++...   .++.+| |+|. |+..|+..    ...||+||+++..
T Consensus        14 ~~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCcCcCCC---CEEEEC-CCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            5678999999764   377788 9999 99999974    5789999998753

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

Probab=99.00  E-value=1.4e-10  Score=68.18  Aligned_cols=48  Identities=19%  Similarity=0.555  Sum_probs=37.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC--------CCCCcc--ccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR--------RLTCPT--CRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~--------~~~CP~--Cr~~  106 (112)
                      ...+|+||++++...+.+...+ |||.||..|+.+++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            3567999999986544444456 9999999999999863        237999  9987

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

Probab=99.00  E-value=9.7e-11  Score=66.97  Aligned_cols=43  Identities=30%  Similarity=0.640  Sum_probs=36.0

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ++..|+||++.+.   .++.+| |||. |+..|+..|    ..||+||.++.
T Consensus        17 ~~~~C~IC~~~~~---~~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           17 EAMLCMVCCEEEI---NSTFCP-CGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             HHTBCTTTSSSBC---CEEEET-TCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CCCEeEEeCcccC---cEEEEC-CCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            3567999999874   377788 9999 999999876    48999999875

>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=98.92  E-value=5e-10  Score=60.99  Aligned_cols=50  Identities=12%  Similarity=0.250  Sum_probs=41.9

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ...|+|+++.+.+   ++..+.+||+|.+.||.+|++++.+||+.+.++..+.
T Consensus         3 ~~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~   52 (61)
T 2bay_A            3 HMLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE   52 (61)
T ss_dssp             -CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGG
T ss_pred             eEEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhh
Confidence            3579999999864   6666239999999999999998888999999987654

>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=98.86  E-value=7.8e-10  Score=75.81  Aligned_cols=49  Identities=22%  Similarity=0.462  Sum_probs=40.5

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHHHHhCC--CCCcc--ccCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDLWLVRR--LTCPT--CRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~w~~~~--~~CP~--Cr~~~~~~  110 (112)
                      .+..|+||++.|..   +++. . |||.|++.||.+|+..+  .+||+  ||..+..+
T Consensus       180 ~el~CPIcl~~f~D---PVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~  233 (267)
T 3htk_C          180 IELTCPITCKPYEA---PLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR  233 (267)
T ss_dssp             CCSBCTTTSSBCSS---EEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGG
T ss_pred             eeeECcCccCcccC---CeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCchh
Confidence            67899999999954   5554 6 99999999999999764  57999  99877553

>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=98.84  E-value=6.2e-10  Score=79.34  Aligned_cols=44  Identities=27%  Similarity=0.572  Sum_probs=37.9

Q ss_pred             CccccccccccccCCCceeecCCCcCc-ccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV-FHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~-fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ++..|+||++.+..   ++.+| |||. ||..|+..|    ..||+||.++..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            56789999998853   77788 9999 999999988    789999998753

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

Probab=98.64  E-value=2.7e-08  Score=58.58  Aligned_cols=45  Identities=31%  Similarity=0.651  Sum_probs=36.1

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFK  108 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~  108 (112)
                      .|.+|--.+.  ...+..| |+|+||.+|+..|.++ .++||.|+.++.
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            4777776654  3556677 9999999999999864 689999999874

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

Probab=98.52  E-value=1.2e-07  Score=64.45  Aligned_cols=49  Identities=22%  Similarity=0.628  Sum_probs=39.8

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC--CCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR--LTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~--~~CP~Cr~~~~~~  110 (112)
                      -..|.||.+....|.   ..+.|+|.||..|+..|++++  ..||.|+.+++.+
T Consensus       180 i~~C~iC~~iv~~g~---~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSCE---ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCCc---ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            568999999886542   223499999999999999864  4899999998765

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

Probab=96.50  E-value=0.0027  Score=34.57  Aligned_cols=50  Identities=32%  Similarity=0.554  Sum_probs=35.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC----CCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR----LTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~----~~CP~Cr~~~~~~~  111 (112)
                      .+..|.||.+.    ..+..-..|...||..|+...+...    =.||.|+......+
T Consensus        11 ~~~~C~vC~~~----~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~p~P   64 (66)
T 2lri_C           11 PGARCGVCGDG----TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVTPAP   64 (66)
T ss_dssp             TTCCCTTTSCC----TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCCCCC
T ss_pred             CCCCcCCCCCC----CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCccCC
Confidence            45679999753    3344444599999999998887643    36999987665544

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

Probab=96.46  E-value=0.0022  Score=37.35  Aligned_cols=35  Identities=11%  Similarity=0.413  Sum_probs=25.2

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHH-HH
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDL-WL   94 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~-w~   94 (112)
                      +..|.||.+.+.......-+. |+|.|+..|+.. |.
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATHP   38 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHSC
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHhc
Confidence            567999998643322222366 999999999998 53

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

Probab=95.42  E-value=0.004  Score=33.40  Aligned_cols=49  Identities=20%  Similarity=0.591  Sum_probs=35.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh-----CCCCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-----RRLTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-----~~~~CP~Cr~~  106 (112)
                      ++..|+||...+..+...+.-..|...||..|+.--..     ....||.|+..
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            46679999998865555555555999999999754221     34579999754

>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=95.01  E-value=0.011  Score=38.40  Aligned_cols=49  Identities=20%  Similarity=0.500  Sum_probs=35.3

Q ss_pred             ccccccccccccCCCc---eeecCCCcCcccHHhHHH------HHh-----CCCCCccccCCC
Q 038517           59 AAICAVCLDGVHKGER---SRNFSICKHVFHARCIDL------WLV-----RRLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~---~~~~~~C~H~fh~~Ci~~------w~~-----~~~~CP~Cr~~~  107 (112)
                      +..|+||...|..++.   .+.-..|...||..|+.-      -+.     ....||.|+..-
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            4569999999987663   555556999999999632      111     157899998753

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

Probab=94.20  E-value=0.043  Score=29.13  Aligned_cols=46  Identities=24%  Similarity=0.665  Sum_probs=32.5

Q ss_pred             CCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCC
Q 038517           57 NLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSP  106 (112)
Q Consensus        57 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~  106 (112)
                      ..+..|.+|.+.    ..+..-..|...||..|+..-+.+    .-.||.|+..
T Consensus         9 ~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            357789999873    345455559999999999875432    2369999763

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=94.02  E-value=0.057  Score=43.16  Aligned_cols=50  Identities=16%  Similarity=0.124  Sum_probs=43.0

Q ss_pred             CccccccccccccCCCceeecCCCc-CcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICK-HVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~-H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ++..|||-++.+..   ++.+| -| +.|-+..|.+|+.++.+||.=|.++..+.
T Consensus       890 ~~F~cPIs~~lM~D---PVilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~  940 (968)
T 3m62_A          890 DEFLDPLMYTIMKD---PVILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLED  940 (968)
T ss_dssp             GGGBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGG
T ss_pred             HHhCCcchhhHHhC---CeEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCccc
Confidence            57889999998865   88888 76 68999999999999999999999887543

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=93.74  E-value=0.08  Score=30.05  Aligned_cols=34  Identities=24%  Similarity=0.398  Sum_probs=22.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLW   93 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w   93 (112)
                      .++.|.||--- ..++...--- |+-+||..|+.+.
T Consensus        14 ~D~~C~VC~~~-t~~~l~pCRv-C~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVCEVW-TAESLFPCRV-CTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTTCCC-CSSCCSSCSS-SSSCCCHHHHHHH
T ss_pred             CCcccCccccc-cccceecccc-ccccccHhhcccc
Confidence            57889999732 2222222222 9999999999996

>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=93.30  E-value=0.09  Score=28.30  Aligned_cols=34  Identities=21%  Similarity=0.507  Sum_probs=26.0

Q ss_pred             CccccccccccccCCCceeecC-CCcCcccHHhHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFS-ICKHVFHARCID   91 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~   91 (112)
                      ....|++|...+..++..+.-. .|.-.||..|+.
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            4567999999987766666655 699999999964

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=92.82  E-value=0.042  Score=30.23  Aligned_cols=50  Identities=22%  Similarity=0.494  Sum_probs=34.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~~  108 (112)
                      +...|.||..... ++..+.-..|.-.||..|+..-...    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            4567999988753 4445555559999999998754432    346999987554

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.70  E-value=0.07  Score=27.03  Aligned_cols=44  Identities=25%  Similarity=0.600  Sum_probs=29.1

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRS  105 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~  105 (112)
                      .|.||...-.. +.+..-..|...||..|+.+=+.+    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCC-CCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            58888875433 334444459999999999753432    235999975

>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=91.85  E-value=0.16  Score=28.20  Aligned_cols=48  Identities=21%  Similarity=0.584  Sum_probs=32.3

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHh-----CCCCCccccCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-----RRLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-----~~~~CP~Cr~~~  107 (112)
                      ...| ||...+..+...+.-..|...||..|+.--..     ....||.|+..-
T Consensus        12 ~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             ccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            4456 89888754455555555999999999852111     345799998754

>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=91.81  E-value=0.057  Score=27.63  Aligned_cols=44  Identities=16%  Similarity=0.326  Sum_probs=29.7

Q ss_pred             ccccccccccCCCceeecC-CCcCcccHHhHHHHH----hCCCCCcccc
Q 038517           61 ICAVCLDGVHKGERSRNFS-ICKHVFHARCIDLWL----VRRLTCPTCR  104 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w~----~~~~~CP~Cr  104 (112)
                      .|.+|...+..+...+.-. .|.-.||..|+.--.    .....||.|+
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            4778988886555555544 588899999964211    2466799885

>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=90.41  E-value=0.091  Score=33.81  Aligned_cols=46  Identities=35%  Similarity=0.608  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      ++..|.+|.+.   |+ +..-..|.-.||..|+.+-+..    .-.||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            46779999853   34 4444459999999998776543    23599998754

>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=90.07  E-value=0.084  Score=27.94  Aligned_cols=46  Identities=30%  Similarity=0.723  Sum_probs=31.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      .+..|.+|.+.   + .+..-..|...||..|+..-+..    .-.||.|+...
T Consensus         8 ~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG---G-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---S-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC---C-CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            56779999863   2 34444449999999999864432    23599998653

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=89.78  E-value=0.052  Score=31.02  Aligned_cols=52  Identities=19%  Similarity=0.508  Sum_probs=33.7

Q ss_pred             Cccccccccccc-cCCCceeecCCCcCcccHHhHHHHHh--CCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGV-HKGERSRNFSICKHVFHARCIDLWLV--RRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~--~~~~CP~Cr~~~~~  109 (112)
                      ++..|.||...- ..++.+..-..|.-.||..|+..-..  ..-.||.|......
T Consensus        24 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~   78 (88)
T 2l43_A           24 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR   78 (88)
T ss_dssp             CCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTS
T ss_pred             CCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccch
Confidence            567899999753 22234555555989999999974321  12359998765433

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=89.21  E-value=0.26  Score=28.94  Aligned_cols=49  Identities=18%  Similarity=0.407  Sum_probs=33.4

Q ss_pred             ccccccccccccCCCceeecC-CCcCcccHHhHHHHH----------hCCCCCccccCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFS-ICKHVFHARCIDLWL----------VRRLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~-~C~H~fh~~Ci~~w~----------~~~~~CP~Cr~~~  107 (112)
                      ...|+||...+..+...+.-. .|.-.||..|+.--.          .....||.|+..-
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            356999999986655555543 589999999974211          0245699998643

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.94  E-value=0.069  Score=29.75  Aligned_cols=47  Identities=21%  Similarity=0.505  Sum_probs=30.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~  105 (112)
                      .+..|.||...-.. ..+..-..|...||..|+.+=+..     .=.||.|+.
T Consensus        25 ~~c~C~vC~~~~~~-~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           25 HSCSCRVCGGKHEP-NMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSSSCSSSCCCCCS-TTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCCCcCcCCcCCC-CCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            34478899864322 345455559999999999854432     225888865

>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=88.92  E-value=0.11  Score=34.15  Aligned_cols=46  Identities=33%  Similarity=0.564  Sum_probs=32.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      .+..|.+|...   | .+.....|...||..|+.+-+..    .-.||.|+..-
T Consensus         6 ~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            6 NEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            56779999853   2 35455559999999999776543    23699998743

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=88.67  E-value=0.63  Score=26.13  Aligned_cols=39  Identities=15%  Similarity=0.230  Sum_probs=28.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR   96 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~   96 (112)
                      ....|.+|.+.++....+-.-..=+|.||..|-+..+++
T Consensus        14 a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           14 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            356799999999876655422224599999999988864

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=88.50  E-value=1.6  Score=24.90  Aligned_cols=51  Identities=20%  Similarity=0.480  Sum_probs=34.8

Q ss_pred             Ccccccccccccc---CCCceeecCCCcCcccHHhHHHHHh-CCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVH---KGERSRNFSICKHVFHARCIDLWLV-RRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~---~~~~~~~~~~C~H~fh~~Ci~~w~~-~~~~CP~Cr~~~~  108 (112)
                      ....|.||=++.-   .|+.-+-...|+--.|+.|+.-=.+ .++.||.|++.+.
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            4678999998854   2222222233777789999765443 4789999999875

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=88.41  E-value=0.15  Score=30.31  Aligned_cols=47  Identities=28%  Similarity=0.566  Sum_probs=30.9

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRS  105 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~  105 (112)
                      -..|.||.+.-..++.+..-..|...||..|+.+-+..    .=.||.|+.
T Consensus        61 C~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           61 CKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             TCCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CCccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            34688888643233344444559999999999765543    236999974

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.24  E-value=0.3  Score=27.91  Aligned_cols=48  Identities=27%  Similarity=0.512  Sum_probs=33.4

Q ss_pred             CCCccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCC
Q 038517           56 RNLAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        56 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      ...+..|.+|.+.   ++ +..-..|.-.||..|+.+=+..    .-.||.|+..-
T Consensus        22 d~n~~~C~vC~~~---g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           22 DDSATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            3367889999964   33 4444458899999999775543    23599998643

>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=87.91  E-value=0.14  Score=30.21  Aligned_cols=37  Identities=24%  Similarity=0.438  Sum_probs=25.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV   95 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~   95 (112)
                      ++..|.||.+.-+..+ +..-..|+..||..|+...+.
T Consensus         6 ~~~~C~~C~~~g~~~~-ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLD-QFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCSCBTTTCCCCCTTT-SEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCcCCCCCCCCcC-CeECCCCCCCcChHHhCCccc
Confidence            5778999987632212 233344999999999987664

>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=87.51  E-value=0.14  Score=32.51  Aligned_cols=47  Identities=21%  Similarity=0.645  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHH-----hCCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL-----VRRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~-----~~~~~CP~Cr~  105 (112)
                      ....| +|......+...+.-..|...||..|+.--.     ...-.||.|+.
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~   58 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS   58 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcc
Confidence            45678 9998765445555555599999999984211     12457999975

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.42  E-value=0.97  Score=28.06  Aligned_cols=44  Identities=25%  Similarity=0.585  Sum_probs=32.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh-----------CCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-----------RRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-----------~~~~CP~Cr~  105 (112)
                      .+..|.+|-+.   | .+..-..|...||..||.+-+.           ..=.||.|+.
T Consensus        62 ~~d~C~vC~~G---G-~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           62 MDEQCRWCAEG---G-NLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCC---S-SEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCC---C-cEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            67889999974   2 3444445999999999997652           1236999974

>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=87.30  E-value=0.076  Score=28.99  Aligned_cols=45  Identities=27%  Similarity=0.610  Sum_probs=28.3

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSP  106 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~  106 (112)
                      .|.||...-. +..+..-..|...||..|+.+=+.+     .=.||.|+.+
T Consensus        20 ~C~~C~~~~~-~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~~   69 (70)
T 3asl_A           20 ACHLCGGRQD-PDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   69 (70)
T ss_dssp             SBTTTCCCSC-GGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSCC
T ss_pred             CCcCCCCcCC-CCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccCc
Confidence            5667775422 2344444458899999999854432     2259998753

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.20  E-value=0.057  Score=28.06  Aligned_cols=44  Identities=30%  Similarity=0.713  Sum_probs=30.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~  105 (112)
                      .+..|.+|.+.   + .+..-..|...||..|+.+-+..    .-.||.|+.
T Consensus         8 ~~~~C~vC~~~---g-~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---S-CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---C-eEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            56789999874   2 34444459999999999864432    225888864

>4fo9_A E3 SUMO-protein ligase PIAS2; E3 ligase, pinit domain, SP-ring domain, structural GE consortium, SGC; 2.39A {Homo sapiens} PDB: 2asq_B

Probab=87.04  E-value=0.55  Score=33.58  Aligned_cols=51  Identities=18%  Similarity=0.333  Sum_probs=32.9

Q ss_pred             CccccccccccccCCCceeecCCCcCc--ccHHhHHHHHhC--CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV--FHARCIDLWLVR--RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~--fh~~Ci~~w~~~--~~~CP~Cr~~~~~~~  111 (112)
                      ....|+|-...+..   +.....|.|.  |-..-+.....+  .-.||+|.+.+..+.
T Consensus       214 vSL~CPlS~~ri~~---P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~d  268 (360)
T 4fo9_A          214 VSLMCPLGKMRLTI---PCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYES  268 (360)
T ss_dssp             EESBCTTTCSBCSS---EEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGG
T ss_pred             EeeeCCCccceecc---CCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHH
Confidence            35578887776642   4444349998  665554444433  347999999887654

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=86.68  E-value=0.59  Score=33.55  Aligned_cols=51  Identities=22%  Similarity=0.518  Sum_probs=32.3

Q ss_pred             CccccccccccccCCCceeecCCCcCc--ccHHhHHHHHhC--CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHV--FHARCIDLWLVR--RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~--fh~~Ci~~w~~~--~~~CP~Cr~~~~~~~  111 (112)
                      ....|+|-...+..  -++... |.|.  |-..-+.....+  .-.||+|.+.+..+.
T Consensus       248 vSL~CPlS~~ri~~--PvRg~~-C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~d  302 (371)
T 3i2d_A          248 MSLQCPISYTRMKY--PSKSIN-CKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALEN  302 (371)
T ss_dssp             EESBCTTTSSBCSS--EEEETT-CCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGG
T ss_pred             EeecCCCccccccc--cCcCCc-CCCcceECHHHHHHHhhcCCceeCCCCCcccCHHH
Confidence            35678887777642  334444 9998  555444444333  357999999886654

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.89  E-value=1.7  Score=25.52  Aligned_cols=33  Identities=27%  Similarity=0.548  Sum_probs=22.4

Q ss_pred             cccccccccccc-----CCCceeecCCCcCcccHHhHH
Q 038517           59 AAICAVCLDGVH-----KGERSRNFSICKHVFHARCID   91 (112)
Q Consensus        59 ~~~C~IC~~~~~-----~~~~~~~~~~C~H~fh~~Ci~   91 (112)
                      ...|.+|+..-.     .++.+..-..|+..||..|+.
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            456999987521     223444444599999999995

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=85.86  E-value=0.12  Score=27.08  Aligned_cols=45  Identities=29%  Similarity=0.696  Sum_probs=30.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~  106 (112)
                      .+..|.+|...   + .+..-..|.-.||..|+.+=+..    .-.||.|+..
T Consensus         4 ~~~~C~vC~~~---g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   52 (60)
T 2puy_A            4 HEDFCSVCRKS---G-QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQ   52 (60)
T ss_dssp             CCSSCTTTCCC---S-SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHH
T ss_pred             CCCCCcCCCCC---C-cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccCh
Confidence            46779999874   2 34444459999999999864432    2358888653

>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=85.75  E-value=0.45  Score=26.05  Aligned_cols=47  Identities=21%  Similarity=0.480  Sum_probs=31.3

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHH---------hCCCCCccccCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL---------VRRLTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~---------~~~~~CP~Cr~~~  107 (112)
                      ...| ||..... +...+.-..|...||..|+.--.         .....||.|+..-
T Consensus        16 ~~~C-~C~~~~~-~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           16 ALYC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCEE-ECCCccC-CCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            4557 8988764 33444544599999999984211         2467899998643

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=85.43  E-value=0.13  Score=27.63  Aligned_cols=45  Identities=31%  Similarity=0.612  Sum_probs=31.1

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~  106 (112)
                      .+..|.||.+.   + .+..-..|...||..|+.+-+..    .-.||.|...
T Consensus         7 ~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            7 NEDECAVCRDG---G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCCSBSSSSCC---S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCccCCCC---C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            57789999864   2 34444459999999999854432    2359999753

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=84.38  E-value=0.23  Score=29.27  Aligned_cols=26  Identities=35%  Similarity=0.726  Sum_probs=18.0

Q ss_pred             CcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           81 CKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        81 C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ||+.|.     .-+.+...||.|+++...+|
T Consensus        73 CG~~F~-----~~~~kPsrCP~CkSe~Ie~P   98 (105)
T 2gmg_A           73 CGFVFK-----AEINIPSRCPKCKSEWIEEP   98 (105)
T ss_dssp             TCCBCC-----CCSSCCSSCSSSCCCCBCCC
T ss_pred             CcCeec-----ccCCCCCCCcCCCCCccCCc
Confidence            999981     11234578999999776554

>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=83.69  E-value=2.2  Score=26.01  Aligned_cols=44  Identities=23%  Similarity=0.554  Sum_probs=30.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHH------h-----CCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL------V-----RRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~------~-----~~~~CP~Cr~  105 (112)
                      .+..|.+|-+.    ..+..-..|-..||..||.+-+      +     ..=.|+.|+-
T Consensus        56 ~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           56 MDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             CBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            67789999964    2344444589999999999752      1     1236999964

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=82.96  E-value=0.25  Score=26.70  Aligned_cols=46  Identities=20%  Similarity=0.517  Sum_probs=30.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh---CCCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV---RRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~---~~~~CP~Cr~  105 (112)
                      +...| ||-.... +...+.-..|...||..|+.---.   ....||.|+.
T Consensus        18 ~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           18 GLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            45567 9987664 444555555999999999853221   2456998864

>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=82.71  E-value=0.65  Score=24.56  Aligned_cols=51  Identities=14%  Similarity=0.385  Sum_probs=34.4

Q ss_pred             Ccccccccccccc-CCCceeecCCCcCcccHHhHHHHHh-------CCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVH-KGERSRNFSICKHVFHARCIDLWLV-------RRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~-~~~~~~~~~~C~H~fh~~Ci~~w~~-------~~~~CP~Cr~~~~  108 (112)
                      ++..|.||..... .+..+..-..|.-.||..|+..=+.       ..-.||.|+....
T Consensus         5 ~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            5678999997643 2344555556999999999875331       2346999876544

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.57  E-value=0.68  Score=24.55  Aligned_cols=40  Identities=25%  Similarity=0.623  Sum_probs=21.6

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ..|+-|-+.+..++.+.. . -+..||..|+.        |-.|++++..
T Consensus         6 ~~C~~C~~~I~~~~~~~~-a-~~~~~H~~CF~--------C~~C~~~L~~   45 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLE-Y-GGQTWHEHCFL--------CSGCEQPLGS   45 (72)
T ss_dssp             CBCSSSCCBCCSSSCEEC-S-TTCCEETTTCB--------CTTTCCBTTT
T ss_pred             CCCccCCCccccCccEEE-E-CccccCcccCe--------ECCCCCcCCC
Confidence            456777766654322221 1 45667766643        6666665543

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=82.33  E-value=1  Score=25.08  Aligned_cols=35  Identities=23%  Similarity=0.469  Sum_probs=24.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDL   92 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~   92 (112)
                      +...|.+|...|..-..--.--.||.+|+..|...
T Consensus        18 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   52 (82)
T 2yw8_A           18 EATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSN   52 (82)
T ss_dssp             CCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCE
T ss_pred             cCCcccCcCCcccCccccccCCCCCCEEChHHhCC
Confidence            45679999999864332222334999999999754

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=82.29  E-value=0.28  Score=32.87  Aligned_cols=47  Identities=26%  Similarity=0.595  Sum_probs=26.9

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----CCCCccccCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSP  106 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~  106 (112)
                      +..|.+|...-.. ..+.....|...||..|+.+=+..     .=.||.|+..
T Consensus       174 ~c~C~vC~~~~~~-~~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~~  225 (226)
T 3ask_A          174 VCACHLCGGRQDP-DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND  225 (226)
T ss_dssp             TTSCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC--
T ss_pred             CCCCcCCCCCCCC-CCeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcCc
Confidence            3468888764322 334444459999999999854432     2259999753

>2o35_A Hypothetical protein DUF1244; helix bundle, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.12A {Sinorhizobium meliloti} SCOP: a.293.1.1

Probab=82.01  E-value=0.57  Score=27.30  Aligned_cols=12  Identities=25%  Similarity=0.725  Sum_probs=10.7

Q ss_pred             cccHHhHHHHHh
Q 038517           84 VFHARCIDLWLV   95 (112)
Q Consensus        84 ~fh~~Ci~~w~~   95 (112)
                      -||+.|+..|+.
T Consensus        42 GFCRNCLskWy~   53 (105)
T 2o35_A           42 GFCRNCLSNWYR   53 (105)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999995

>3fyb_A Protein of unknown function (DUF1244); hydrocar degrading, structural genomics, PSI-2; HET: PEG; 1.80A {Alcanivorax borkumensis SK2}

Probab=81.96  E-value=0.58  Score=27.24  Aligned_cols=12  Identities=33%  Similarity=0.949  Sum_probs=10.8

Q ss_pred             cccHHhHHHHHh
Q 038517           84 VFHARCIDLWLV   95 (112)
Q Consensus        84 ~fh~~Ci~~w~~   95 (112)
                      -||+.|+..|+.
T Consensus        41 GFCRNCLskWy~   52 (104)
T 3fyb_A           41 DFCRNCLAKWLM   52 (104)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999995

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=81.87  E-value=1.6  Score=24.94  Aligned_cols=46  Identities=24%  Similarity=0.573  Sum_probs=29.5

Q ss_pred             CccccccccccccCCCceeecCC--Cc-CcccHHhHHHHHhC----CCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSI--CK-HVFHARCIDLWLVR----RLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~----~~~CP~Cr~~~~  108 (112)
                      +...| ||..... + ..+.-..  |. ..||..|+.  +..    .-.||.|+..-.
T Consensus        35 e~~yC-iC~~~~~-g-~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           35 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCBCS-TTCCBCC-S-CCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCcEE-ECCCCCC-C-CEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            55667 9988642 3 3443334  54 579999987  332    346999987543

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=81.58  E-value=1.8  Score=23.45  Aligned_cols=46  Identities=24%  Similarity=0.573  Sum_probs=29.6

Q ss_pred             CccccccccccccCCCceeecCC--Cc-CcccHHhHHHHHhC----CCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSI--CK-HVFHARCIDLWLVR----RLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~--C~-H~fh~~Ci~~w~~~----~~~CP~Cr~~~~  108 (112)
                      +...| ||..... + ..+.-..  |. ..||..|+.  +..    .-.||.|+..-.
T Consensus        15 ~~~~C-~C~~~~~-g-~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           15 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             SCCCS-TTCCCSC-S-SEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCEE-ECCCCCC-C-CEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            45667 8987642 3 3444444  55 689999997  432    346999987543

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.07  E-value=1.1  Score=24.59  Aligned_cols=41  Identities=29%  Similarity=0.587  Sum_probs=27.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKM  109 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~  109 (112)
                      ....|+.|-+.+..++.+.  . -+..||..|+.        |-.|++.+..
T Consensus        14 ~~~~C~~C~~~I~~~e~v~--a-~~~~wH~~CF~--------C~~C~~~L~~   54 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLC--V-NGHFFHRSCFR--------CHTCEATLWP   54 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCC--B-TTBCCBTTTCB--------CSSSCCBCCT
T ss_pred             CCCCCcccCCCcccceEEE--E-CCCeeCCCcCE--------EcCCCCCcCC
Confidence            4567999998876555443  2 56778888864        7777766543

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=80.89  E-value=2  Score=23.26  Aligned_cols=48  Identities=21%  Similarity=0.585  Sum_probs=32.1

Q ss_pred             Cccccccccccc-cCCCceeecCCCcCcccHHhHHHHHh--CCCCCccccC
Q 038517           58 LAAICAVCLDGV-HKGERSRNFSICKHVFHARCIDLWLV--RRLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~-~~~~~~~~~~~C~H~fh~~Ci~~w~~--~~~~CP~Cr~  105 (112)
                      .+..|.||.+.- ..++.+..-..|.-.||..|+..-..  ..=.||.|+.
T Consensus        15 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           15 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             SSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            678899998753 23345555556999999999874221  1235888864

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.80  E-value=0.91  Score=24.02  Aligned_cols=39  Identities=23%  Similarity=0.646  Sum_probs=20.9

Q ss_pred             cccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           60 AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        60 ~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ..|+.|-+.+..++.+...  -+..||..|+.        |-.|++++.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a--~~~~~H~~CF~--------C~~C~~~L~   44 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEY--KGSSWHETCFI--------CHRCQQPIG   44 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEE--TTEEEETTTTC--------CSSSCCCCC
T ss_pred             CCCccCCCcccCCceEEEE--CcCeecccCCc--------ccccCCccC
Confidence            3566676666543333222  34566666643        666666554

>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=80.14  E-value=0.12  Score=29.64  Aligned_cols=47  Identities=26%  Similarity=0.471  Sum_probs=31.4

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~  105 (112)
                      +...|.||...-.. +.+..-..|...||..|+.+=+..    .=.||.|+.
T Consensus        15 ~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           15 DSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            56679999976432 334444459999999999743332    224999865

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=80.06  E-value=0.23  Score=27.62  Aligned_cols=44  Identities=27%  Similarity=0.631  Sum_probs=28.0

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC----C-CCCccccC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----R-LTCPTCRS  105 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~-~~CP~Cr~  105 (112)
                      .|.+|...-.. +.+..-..|...||..|+.+-+..    . =.||.|+.
T Consensus        28 ~C~vC~~~~d~-~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQDP-DKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCSCG-GGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCCCC-cceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            56777665322 334444458899999999865543    1 35999875

---

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	112
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-12
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-09
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-06
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-06
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-06
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-06
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-05
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-04
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.001

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 55.6 bits (134), Expect = 1e-12
 Identities = 22/45 (48%), Positives = 26/45 (57%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSP 106
           CAVCL  +  GE +R    C H FHA C+D+WL    TCP CR  
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLT 52

>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 = 49.6 bits (118), Expect = 5e-10
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           C +CL+       +     C H F   CI  W+ +  TCP C+ P +
Sbjct: 8   CPICLEDPSNYSMALP---CLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 3e-09
 Identities = 13/47 (27%), Positives = 18/47 (38%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK 108
           C          E +  + +C H FH  CI  WL  R  CP     ++
Sbjct: 38  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE 84

>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 = 40.6 bits (94), Expect = 1e-06
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 3/52 (5%)

Query: 60  AICAVCLDGVHKG-ERSRNFSICKHVFHARCIDLWL--VRRLTCPTCRSPFK 108
            +C +C + +     R+   +      H  C+  WL   R   C  C   + 
Sbjct: 7   PVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>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 = 41.1 bits (96), Expect = 1e-06
 Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 5/50 (10%)

Query: 60  AICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRL-TCPTCRSPFK 108
            +C +C +     ++      C H+    C+  W       CP CR   K
Sbjct: 24  QLCKICAEN----DKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 69

>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 = 40.2 bits (94), Expect = 1e-06
 Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 7/51 (13%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP 111
            C  C               C H   + C++      + CP C++P+ +  
Sbjct: 8   RCQQCQAEAKCP----KLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA 51

>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 = 40.1 bits (93), Expect = 2e-06
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWL-VRRLTCPTCRSPFK 108
           C +C++ +   + +     C +     C           CP CR P+ 
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 50

>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 = 40.0 bits (92), Expect = 6e-06
 Identities = 9/51 (17%), Positives = 16/51 (31%), Gaps = 5/51 (9%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR-----LTCPTCRSPF 107
             +              + C H FH  C+            L CP+C++ +
Sbjct: 42  SDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIY 92

>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 = 38.2 bits (88), Expect = 1e-05
 Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 2/49 (4%)

Query: 62  CAVCLDGVHKGERSRNFSI-CKHVFHARCIDLWL-VRRLTCPTCRSPFK 108
           C  C    ++    +     C H     C+DL        CP C +P +
Sbjct: 6   CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR 54

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.7 bits (82), Expect = 1e-04
 Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 5/53 (9%)

Query: 61  ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWL-VRRLTCPTCRSPFKMEPV 112
            C +C   +     +     CKH+F   CI   L V    CP+CR P     +
Sbjct: 25  SCQICEHILADPVETS----CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 73

>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 = 33.5 bits (76), Expect = 0.001
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 62  CAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR---LTCPTCRSPFKME 110
           C +CL+ + +   ++    C H+F   C+   L ++     CP C++     
Sbjct: 24  CPICLELIKEPVSTK----CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	112
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.84
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.72
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.72
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.72
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.68
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.65
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.63
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.63
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.55
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.53
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.49
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.47
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.4
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.39
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.37
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.32
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.94
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.63
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.29
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.27
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.82
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	92.61
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	92.33
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	90.49
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.01
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	88.0
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	85.96
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	85.75
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	84.71
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	84.4
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	83.66
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	83.52
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	83.48
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	82.65
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	81.06

>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=99.84  E-value=3.5e-22  Score=106.35  Aligned_cols=51  Identities=43%  Similarity=0.906  Sum_probs=46.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      ++.+|+||+++|..++.+..++.|+|.||..||.+|++++++||+||+++.
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            456799999999999998888679999999999999999999999999874

>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=99.72  E-value=9.3e-19  Score=91.91  Aligned_cols=49  Identities=18%  Similarity=0.503  Sum_probs=41.0

Q ss_pred             ccccccccccCCCce-eecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCC
Q 038517           61 ICAVCLDGVHKGERS-RNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKME  110 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~-~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~  110 (112)
                      +|+||+++|..++.. ..++ |||.||..|+.+|++. +.+||+||+++..+
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            699999999876654 4455 9999999999999986 55799999998754

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.72  E-value=1.2e-18  Score=96.23  Aligned_cols=48  Identities=33%  Similarity=0.845  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~  108 (112)
                      .++.|+||++.+..  .++.++ |||.||..||.+|++++.+||+||+++.
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            46779999999853  455677 9999999999999999999999999874

>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=99.72  E-value=2.2e-18  Score=99.71  Aligned_cols=53  Identities=26%  Similarity=0.590  Sum_probs=43.7

Q ss_pred             CccccccccccccCCC---------------ceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGE---------------RSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~---------------~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      .++.|+||++.+....               .+..++ |||.||..||.+|++.+++||+||+++..++
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   87 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEFQK   87 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCEEE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccccc
Confidence            4667999998886432               245566 9999999999999999999999999998764

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.6e-17  Score=90.06  Aligned_cols=53  Identities=25%  Similarity=0.550  Sum_probs=41.3

Q ss_pred             CccccccccccccCC-C-ceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKG-E-RSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~-~-~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+..+ + .+...+ |||.||..||.+|+++ +.+||+||+++....
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            467899999976433 2 334456 9999999999999965 568999999886543

>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=99.65  E-value=5.2e-17  Score=97.80  Aligned_cols=52  Identities=23%  Similarity=0.615  Sum_probs=40.5

Q ss_pred             CccccccccccccCC---------------CceeecCCCcCcccHHhHHHHHhC-----CCCCccccCCCCCC
Q 038517           58 LAAICAVCLDGVHKG---------------ERSRNFSICKHVFHARCIDLWLVR-----RLTCPTCRSPFKME  110 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~---------------~~~~~~~~C~H~fh~~Ci~~w~~~-----~~~CP~Cr~~~~~~  110 (112)
                      .++.|+||++++...               ..+..++ |+|.||..||..|++.     +.+||+||+.+..+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            567899999988532               2345566 9999999999999974     34799999977554

>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=99.63  E-value=1.9e-16  Score=89.67  Aligned_cols=48  Identities=23%  Similarity=0.639  Sum_probs=40.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKME  110 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~  110 (112)
                      ...|+||++.+.   .++.++ |||.||..||..|+.. +++||+||+++...
T Consensus        23 ~~~C~IC~~~~~---~~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDK---DVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBC---CEECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCC---CeEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            356999999875   377788 9999999999999974 57899999998653

>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=99.63  E-value=5.2e-17  Score=86.32  Aligned_cols=49  Identities=12%  Similarity=0.287  Sum_probs=42.6

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCCC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~~  112 (112)
                      .|+||++.+.+   ++.++.|||+||++||.+|++++++||+||+++..+.|
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            59999999853   66665599999999999999999999999999987653

>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=99.55  E-value=1e-15  Score=87.70  Aligned_cols=50  Identities=30%  Similarity=0.535  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      .+..|+||++.+..   ++.++ |||.||..||.+|++. +.+||+||.++....
T Consensus        22 ~~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            45679999999854   77888 9999999999999974 568999999886543

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=2.5e-15  Score=88.84  Aligned_cols=49  Identities=22%  Similarity=0.634  Sum_probs=41.0

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC---CCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR---LTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~---~~CP~Cr~~~~~~~  111 (112)
                      ...|+||++.+..   ++.++ |||.||..||.+|++.+   ..||+||.++..+.
T Consensus        21 ~l~CpIC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          21 ILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CcCCCccCchhCC---eEEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            4579999999864   66677 99999999999999764   47999999887654

>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=99.49  E-value=1.2e-14  Score=77.97  Aligned_cols=54  Identities=17%  Similarity=0.456  Sum_probs=38.9

Q ss_pred             CCccccccccccccCCCcee-ecCCCcCcccHHhHHHHHh--CCCCCccccCCCCCC
Q 038517           57 NLAAICAVCLDGVHKGERSR-NFSICKHVFHARCIDLWLV--RRLTCPTCRSPFKME  110 (112)
Q Consensus        57 ~~~~~C~IC~~~~~~~~~~~-~~~~C~H~fh~~Ci~~w~~--~~~~CP~Cr~~~~~~  110 (112)
                      .+...|.||++++....... ....|+|.||..||.+|+.  ++.+||+||+++..+
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~k   60 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR   60 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeecC
Confidence            35678999999875432111 1111569999999999995  456899999988653

>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=99.47  E-value=2.5e-15  Score=79.59  Aligned_cols=46  Identities=20%  Similarity=0.646  Sum_probs=38.5

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ...|+||++.+..   ++.++ |||.||..||.+|   +.+||+||+++...+
T Consensus         6 ~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            3589999999864   66788 9999999999765   678999999987653

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.40  E-value=2.6e-14  Score=83.55  Aligned_cols=48  Identities=21%  Similarity=0.580  Sum_probs=38.5

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ...|+||++.|..   ++.++.|||.||..||.+|+.  +.||.||.++..++
T Consensus        22 ~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          22 LLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (97)
T ss_dssp             TTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             cCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcCchhh
Confidence            5679999999964   444433999999999999984  45999999886654

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.39  E-value=1.3e-13  Score=77.80  Aligned_cols=50  Identities=16%  Similarity=0.137  Sum_probs=42.8

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+..   ++.++ |||.|++.||.+|+.+ +.+||.||.++..+.
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGG
T ss_pred             ccccCcCcCchhhh---hcccC-CcCeecHHHHHHHHhcCCccCCCccccccccc
Confidence            57889999999964   77788 9999999999999975 568999999887543

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.37  E-value=3.1e-13  Score=75.87  Aligned_cols=50  Identities=18%  Similarity=0.329  Sum_probs=43.2

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-CCCCccccCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-RLTCPTCRSPFKMEP  111 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-~~~CP~Cr~~~~~~~  111 (112)
                      ++..|+||++.+.+   +++++ |||.|++.||.+|+.. ...||.|+.++..+.
T Consensus         7 ~~l~CpIc~~~m~d---PV~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~   57 (78)
T d1t1ha_           7 EYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCcCcCchhhC---ceEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCccc
Confidence            47889999999965   67788 9999999999999976 567999999987664

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.4e-12  Score=76.22  Aligned_cols=52  Identities=15%  Similarity=0.135  Sum_probs=44.7

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccccCCCCCCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCRSPFKMEPV  112 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~~  112 (112)
                      ++..|+||.+.+..   +++++.|+|.|++.||.+|++++.+||+||.++..+.|
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L   72 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQI   72 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTS
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccchhh
Confidence            57899999999965   88888345689999999999999999999999987653

>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=98.94  E-value=1.5e-10  Score=66.67  Aligned_cols=47  Identities=17%  Similarity=0.482  Sum_probs=36.3

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC-----C---CCCccccC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR-----R---LTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~-----~---~~CP~Cr~  105 (112)
                      ....|+||++++...+.+..++ |+|.||.+|+..|++.     .   -+||.|+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            3567999999997655566566 9999999999999952     1   25998653

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.0031  Score=31.06  Aligned_cols=44  Identities=25%  Similarity=0.600  Sum_probs=30.8

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccC
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRS  105 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~  105 (112)
                      .|.||...-.. +.++.-..|...||..|+..-+..    .-.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            58888765433 344445559999999999886643    235999975

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.29  E-value=0.0066  Score=32.94  Aligned_cols=34  Identities=24%  Similarity=0.462  Sum_probs=25.0

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHH
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLW   93 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w   93 (112)
                      .+..|.|| +.+...+..---- |+-+||..|+.+.
T Consensus        14 ~D~mC~vC-~v~t~~~l~pCRv-CtRv~H~~CL~r~   47 (89)
T d1wila_          14 NDEMCDVC-EVWTAESLFPCRV-CTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTT-CCCCSSCCSSCSS-SSSCCCHHHHHHH
T ss_pred             cCcccccc-Ccccccceeccee-ecchhhHHHHHHh
Confidence            68889999 6665444332222 9999999999997

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.27  E-value=0.012  Score=30.22  Aligned_cols=49  Identities=20%  Similarity=0.591  Sum_probs=35.5

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHh-----CCCCCccccCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLV-----RRLTCPTCRSP  106 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~-----~~~~CP~Cr~~  106 (112)
                      ....|.+|.+....++..+.-..|+..||..|+..-..     ....||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            45679999988777666565556999999999853111     24579999864

>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=92.82  E-value=0.025  Score=29.56  Aligned_cols=45  Identities=29%  Similarity=0.530  Sum_probs=30.0

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCC----CCCccccCCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRR----LTCPTCRSPF  107 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~----~~CP~Cr~~~  107 (112)
                      ...|.+|.+.   ++ +..-..|...||..|+.+.+...    -.||.|+..-
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            3456667542   33 44444599999999999876532    3599997643

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.61  E-value=0.018  Score=29.24  Aligned_cols=46  Identities=28%  Similarity=0.670  Sum_probs=31.6

Q ss_pred             CccccccccccccCCCceeecCCCcCcccHHhHHHHHhC----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      .++.|.+|.+.    ..++.-..|.-.||..|+...+..    .-.||.|+...
T Consensus         8 ~~~~C~~C~~~----g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC----CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            45679999853    234444459999999998765543    33699997643

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.33  E-value=0.16  Score=26.81  Aligned_cols=46  Identities=22%  Similarity=0.525  Sum_probs=31.8

Q ss_pred             cccccccccCCCceeecCCCcCcccHHhHH--HHH-h--CCCCCccccCCC
Q 038517           62 CAVCLDGVHKGERSRNFSICKHVFHARCID--LWL-V--RRLTCPTCRSPF  107 (112)
Q Consensus        62 C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~--~w~-~--~~~~CP~Cr~~~  107 (112)
                      +-||...+..+...+.-..|+-.||..|+.  ..- .  .+..||.|+...
T Consensus        14 ~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          14 YCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             EeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            449998776555555566699999999984  222 1  236799998754

>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=90.49  E-value=0.013  Score=31.93  Aligned_cols=48  Identities=19%  Similarity=0.494  Sum_probs=31.3

Q ss_pred             CccccccccccccC-CCceeecCCCcCcccHHhHHHHH-----hC---CCCCccccC
Q 038517           58 LAAICAVCLDGVHK-GERSRNFSICKHVFHARCIDLWL-----VR---RLTCPTCRS  105 (112)
Q Consensus        58 ~~~~C~IC~~~~~~-~~~~~~~~~C~H~fh~~Ci~~w~-----~~---~~~CP~Cr~  105 (112)
                      ....|.||...... +..++.-..|...||..|+...+     ..   .-.||.|..
T Consensus        15 ~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~   71 (88)
T d1weva_          15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTR   71 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHH
T ss_pred             CcCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCc
Confidence            34569999875433 23455455599999999976432     11   346999964

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.01  E-value=0.4  Score=24.93  Aligned_cols=38  Identities=16%  Similarity=0.274  Sum_probs=28.0

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVR   96 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~   96 (112)
                      ...|.+|.|.++....+..-..=+|.||..|-+..+++
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            45799999999776555322224599999999998864

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.00  E-value=0.024  Score=27.89  Aligned_cols=44  Identities=20%  Similarity=0.347  Sum_probs=27.0

Q ss_pred             ccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCcccc
Q 038517           61 ICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTCR  104 (112)
Q Consensus        61 ~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~Cr  104 (112)
                      .|.+|...|..-..-..-..||.+|+..|....-+....|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            47888888764333223334999999999765444455677764

>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=85.96  E-value=0.37  Score=24.90  Aligned_cols=46  Identities=24%  Similarity=0.545  Sum_probs=29.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHH------HHH---hCCCCCccccCC
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCID------LWL---VRRLTCPTCRSP  106 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~------~w~---~~~~~CP~Cr~~  106 (112)
                      ...| ||...... ...+.-..|.-.||..|+.      ...   ...-.||.|+..
T Consensus        16 ~~~C-iC~~~~~~-~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          16 ALYC-ICRQPHNN-RFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCCS-SCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             cCEE-ECCCccCC-CeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            4457 88776543 4455555599999999982      111   234689999653

>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=85.75  E-value=0.25  Score=24.77  Aligned_cols=44  Identities=20%  Similarity=0.519  Sum_probs=29.8

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHHHhCCCCCccc
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLWLVRRLTCPTC  103 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w~~~~~~CP~C  103 (112)
                      ...|--|...+.. .....-+.|++.|+.+|=.--=..-..||.|
T Consensus        15 ~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            4568888888753 3445566799999999943211234579987

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=84.71  E-value=0.19  Score=26.59  Aligned_cols=12  Identities=25%  Similarity=0.725  Sum_probs=10.7

Q ss_pred             cccHHhHHHHHh
Q 038517           84 VFHARCIDLWLV   95 (112)
Q Consensus        84 ~fh~~Ci~~w~~   95 (112)
                      -||+.|+.+|..
T Consensus        39 GFCRNCLskWy~   50 (79)
T d2o35a1          39 GFCRNCLSNWYR   50 (79)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999995

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.40  E-value=1.9  Score=23.11  Aligned_cols=51  Identities=20%  Similarity=0.459  Sum_probs=34.3

Q ss_pred             CccccccccccccC---CCceeecCCCcCcccHHhHHHHH-hCCCCCccccCCCC
Q 038517           58 LAAICAVCLDGVHK---GERSRNFSICKHVFHARCIDLWL-VRRLTCPTCRSPFK  108 (112)
Q Consensus        58 ~~~~C~IC~~~~~~---~~~~~~~~~C~H~fh~~Ci~~w~-~~~~~CP~Cr~~~~  108 (112)
                      ....|.||-+....   ++..+-...|+--.|+.|..-=. ..++.||.|++.+.
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Yk   69 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhh
Confidence            57789999987642   22222223377778999975333 34788999998764

>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=83.66  E-value=0.37  Score=24.92  Aligned_cols=46  Identities=28%  Similarity=0.582  Sum_probs=26.3

Q ss_pred             CccccccccccccCCCceeec-CCCc-CcccHHhHHHHHhC----CCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICK-HVFHARCIDLWLVR----RLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~-H~fh~~Ci~~w~~~----~~~CP~Cr~~~  107 (112)
                      +...| ||.+... ++.+... ..|. ..||..|+.  +..    .-.||.|+..-
T Consensus        15 e~~~C-iC~~~~~-~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~~   66 (71)
T d1wesa_          15 EPTYC-LCNQVSY-GEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGDS   66 (71)
T ss_dssp             SCCCS-TTCCCCC-SSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSCC
T ss_pred             CCCEE-EeCCCCC-CCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCcccc
Confidence            34456 9987642 2322221 1244 469999984  332    34699998643

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=83.52  E-value=0.5  Score=24.67  Aligned_cols=49  Identities=20%  Similarity=0.384  Sum_probs=29.9

Q ss_pred             CccccccccccccCCCceeec-CCCcCcccHHhHHH----HHh-----CCCCCccccCCC
Q 038517           58 LAAICAVCLDGVHKGERSRNF-SICKHVFHARCIDL----WLV-----RRLTCPTCRSPF  107 (112)
Q Consensus        58 ~~~~C~IC~~~~~~~~~~~~~-~~C~H~fh~~Ci~~----w~~-----~~~~CP~Cr~~~  107 (112)
                      ....| ||......+..+... ..|...||..|+.-    .-.     ....||.|+..-
T Consensus        15 ~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            34567 898876544333222 24999999999831    100     135799997644

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=83.48  E-value=0.13  Score=28.98  Aligned_cols=26  Identities=38%  Similarity=0.772  Sum_probs=18.9

Q ss_pred             CcCcccHHhHHHHHhCCCCCccccCCCCCCC
Q 038517           81 CKHVFHARCIDLWLVRRLTCPTCRSPFKMEP  111 (112)
Q Consensus        81 C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~  111 (112)
                      ||-+|-.     -+++-..||.|+.++-.+|
T Consensus        73 CGfvFr~-----~~kkPSRCP~CKSE~Ie~P   98 (105)
T d2gmga1          73 CGFVFKA-----EINIPSRCPKCKSEWIEEP   98 (105)
T ss_dssp             TCCBCCC-----CSSCCSSCSSSCCCCBCCC
T ss_pred             cCCeecc-----cCCCCCCCCCCCCccccCC
Confidence            8888731     2455678999999887665

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.65  E-value=0.37  Score=24.97  Aligned_cols=35  Identities=20%  Similarity=0.429  Sum_probs=24.6

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHH
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLW   93 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w   93 (112)
                      +..|.+|-..|..-..-..-..||++|+..|....
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~~   47 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ   47 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCCc
Confidence            45699999988654433333449999999997543

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.06  E-value=0.61  Score=23.67  Aligned_cols=35  Identities=17%  Similarity=0.289  Sum_probs=23.7

Q ss_pred             ccccccccccccCCCceeecCCCcCcccHHhHHHH
Q 038517           59 AAICAVCLDGVHKGERSRNFSICKHVFHARCIDLW   93 (112)
Q Consensus        59 ~~~C~IC~~~~~~~~~~~~~~~C~H~fh~~Ci~~w   93 (112)
                      +..|.+|-..|..-..--.--.||.+|+..|...+
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCCc
Confidence            35699999988643332222349999999996543