Citrus Sinensis ID: 037842

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------
Protein Sequence
VCESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPPASS
Secondary Structure (PSIPRED)
ccccccccccccccEEEEcccccccccccEEccccHHHHHHHHHHHHccccccccccccccccEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccEEcccccccEEEcccccccHHHHHHHHHHccccccccccccHHHcHHEEcccccccccc
Coil and Loop (DISEMBL)
vcesrngavvVGEVRFTCGICldtmkeesstkcghvfcKSCIVDAIrlqgkcptcrtrmsVRSIRRiffpqlqppass
Flexible Loop (DISEMBL)
vcesrngavvvgevrfTCGICLDTMKeesstkcgHVFCKSCIVDairlqgkcptcrtrmsvrsirriffpqlqppass
Low Complexity Region (SEG)
VCESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPPASS
Disordered region (IsUnstruct)
******GAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP********
Disordered Region (DISOPRED)
*****************CGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR************
Disordered Region (DISEMBL)
********VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPPASS
Disordered Region (DISPRO)
******GAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQ*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
VCESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPPASS
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	78	2.2.26 [Sep-21-2011]
Q00940	295	Peroxisome biogenesis fac	N/A	no	0.602	0.159	0.446	3e-08
Q06554	1556	Uncharacterized ATP-depen	yes	no	0.692	0.034	0.388	5e-07
Q7YR34	539	Tripartite motif-containi	yes	no	0.717	0.103	0.372	1e-06
Q12899	539	Tripartite motif-containi	yes	no	0.717	0.103	0.372	1e-06
O77666	545	Tripartite motif-containi	no	no	0.717	0.102	0.372	2e-06
Q99496	336	E3 ubiquitin-protein liga	no	no	0.615	0.142	0.509	2e-06
Q9CQJ4	336	E3 ubiquitin-protein liga	no	no	0.615	0.142	0.509	2e-06
Q5R9J5	336	E3 ubiquitin-protein liga	no	no	0.615	0.142	0.509	2e-06
Q803I4	336	E3 ubiquitin-protein liga	no	no	0.615	0.142	0.509	2e-06
Q99PN3	545	Tripartite motif-containi	no	no	0.717	0.102	0.372	3e-06

>sp|Q00940|PEX10_PICAN Peroxisome biogenesis factor 10 OS=Pichia angusta GN=PEX10 PE=3 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 31/47 (65%)

Query: 13  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRM 59
           E   TC +CL  MK+ S  +CGHVFC  C++D ++ + +CP CR +M
Sbjct: 240 EASRTCMLCLSPMKDPSCGECGHVFCWKCVLDWVKERQECPLCRAKM 286

Somewhat implicated in the biogenesis of peroxisomes. It plays an important role in the regulation of peroxisome proliferation. May interact with PER1 (PEX8).
Pichia angusta (taxid: 870730)

>sp|Q06554|IRC20_YEAST Uncharacterized ATP-dependent helicase IRC20 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=IRC20 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 21/54 (38%), Positives = 30/54 (55%)

Query: 16   FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
             +C ICL  ++  +  KCGH FCKSCI+  +R   KCP C+   S+  +    F
Sbjct: 1237 LSCSICLGEVEIGAIIKCGHYFCKSCILTWLRAHSKCPICKGFCSISEVYNFKF 1290

Is probably involved in a pathway contributing to genomic integrity.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: -

>sp|Q7YR34|TRI26_PANTR Tripartite motif-containing protein 26 OS=Pan troglodytes GN=TRIM26 PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
          E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct: 11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

Pan troglodytes (taxid: 9598)

>sp|Q12899|TRI26_HUMAN Tripartite motif-containing protein 26 OS=Homo sapiens GN=TRIM26 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
          E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct: 11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

Homo sapiens (taxid: 9606)

>sp|O77666|TRI26_PIG Tripartite motif-containing protein 26 OS=Sus scrofa GN=TRIM26 PE=3 SV=2

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
          E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+   +  +IR ++
Sbjct: 11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDIHPVSGGRPVCPLCKKPFTKENIRPVW 69

Sus scrofa (taxid: 9823)

>sp|Q99496|RING2_HUMAN E3 ubiquitin-protein ligase RING2 OS=Homo sapiens GN=RNF2 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/51 (50%), Positives = 33/51 (64%), Gaps = 3/51 (5%)

Query: 18  CGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
           C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 51  CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 101

E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9CQJ4|RING2_MOUSE E3 ubiquitin-protein ligase RING2 OS=Mus musculus GN=Rnf2 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/51 (50%), Positives = 33/51 (64%), Gaps = 3/51 (5%)

Query: 18  CGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
           C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 51  CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 101

E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Association to the chromosomal DNA is cell-cycle dependent.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5R9J5|RING2_PONAB E3 ubiquitin-protein ligase RING2 OS=Pongo abelii GN=RNF2 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/51 (50%), Positives = 33/51 (64%), Gaps = 3/51 (5%)

Query: 18  CGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
           C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 51  CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 101

E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q803I4|RING2_DANRE E3 ubiquitin-protein ligase RING2 OS=Danio rerio GN=rnf2 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/51 (50%), Positives = 33/51 (64%), Gaps = 3/51 (5%)

Query: 18  CGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
           C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 51  CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 101

E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility.

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q99PN3|TRI26_MOUSE Tripartite motif-containing protein 26 OS=Mus musculus GN=Trim26 PE=2 SV=3

 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
          E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct: 11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTSDIRPISGNRPVCPLCKKPFKKENIRPVW 69

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	78
116784892	231	unknown [Picea sitchensis] gi|224284637|	0.858	0.290	0.597	7e-17
116781725	203	unknown [Picea sitchensis]	0.730	0.280	0.561	2e-13
224053707	252	predicted protein [Populus trichocarpa]	0.730	0.226	0.561	6e-13
294462707	205	unknown [Picea sitchensis]	0.756	0.287	0.525	9e-13
224075260	242	predicted protein [Populus trichocarpa]	0.705	0.227	0.636	2e-12
217075410	242	unknown [Medicago truncatula] gi|3884945	0.705	0.227	0.581	3e-12
217070974	247	unknown [Medicago truncatula]	0.705	0.222	0.581	3e-12
224132232	213	predicted protein [Populus trichocarpa]	0.743	0.272	0.568	4e-12
15231414	182	RING/U-box domain-containing protein [Ar	0.871	0.373	0.5	4e-12
226528685	197	ubiquitin-protein ligase/ zinc ion bindi	0.794	0.314	0.516	4e-12

>gi|116784892|gb|ABK23508.1| unknown [Picea sitchensis] gi|224284637|gb|ACN40051.1| unknown [Picea sitchensis] gi|224285742|gb|ACN40586.1| unknown [Picea sitchensis]

 Score = 91.3 bits (225), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 40/67 (59%), Positives = 52/67 (77%)

Query: 4   SRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS 63
           S N  V V EV+ TC IC+D+MKEE+ST CGH+FC+SCI+ AI+ Q KCPTCR ++S+ +
Sbjct: 161 SNNLPVEVKEVKLTCAICMDSMKEETSTICGHIFCRSCIMSAIQFQKKCPTCRRKLSMAN 220

Query: 64  IRRIFFP 70
           I RIF P
Sbjct: 221 IHRIFLP 227

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116781725|gb|ABK22217.1| unknown [Picea sitchensis]

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 44/57 (77%)

Query: 13  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
           EV+ TC IC+ TM+EE+ST CGH+FCK CI +AI L  +CPTCR ++++ SI RI+ 
Sbjct: 142 EVKLTCAICMSTMEEETSTVCGHIFCKKCITNAIHLWKRCPTCRKKLTISSIHRIYI 198

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053707|ref|XP_002297939.1| predicted protein [Populus trichocarpa] gi|222845197|gb|EEE82744.1| predicted protein [Populus trichocarpa]

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 32/57 (56%), Positives = 42/57 (73%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQL 72
           F C IC+D ++E +STKCGHVFCK+CI  A+ +Q KCPTCR +   +SI RIF P +
Sbjct: 195 FRCPICMDELQEATSTKCGHVFCKNCIKKALAVQKKCPTCRMKCRAKSIYRIFLPTV 251

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294462707|gb|ADE76898.1| unknown [Picea sitchensis]

 Score = 77.8 bits (190), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 46/59 (77%)

Query: 11  VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
           V E++ +C IC+D MKEE++T CGHVFCK CIV AI +  +CP+CR +++++SI RI+ 
Sbjct: 143 VKEIKLSCAICMDKMKEETTTICGHVFCKKCIVRAIEVYKQCPSCRKKLTMKSIHRIYI 201

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224075260|ref|XP_002304583.1| predicted protein [Populus trichocarpa] gi|222842015|gb|EEE79562.1| predicted protein [Populus trichocarpa]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/55 (63%), Positives = 41/55 (74%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP 70
           F C IC+D MKE +STKCGHVFCKSCI  A+ +Q KCPTCR +   +SI RIF P
Sbjct: 185 FCCPICMDEMKEATSTKCGHVFCKSCIEKALAVQKKCPTCRMKCIAKSIFRIFLP 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217075410|gb|ACJ86065.1| unknown [Medicago truncatula] gi|388494518|gb|AFK35325.1| unknown [Medicago truncatula]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 41/55 (74%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP 70
           FTC IC+  M EE ST+CGH+FCKSCI  AI  Q KCPTCR +++V+ + R+F P
Sbjct: 185 FTCPICMGPMVEEMSTRCGHIFCKSCIKAAISAQAKCPTCRKKITVKELIRVFLP 239

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217070974|gb|ACJ83847.1| unknown [Medicago truncatula]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 41/55 (74%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP 70
           FTC IC+  M EE ST+CGH+FCKSCI  AI  Q KCPTCR +++V+ + R+F P
Sbjct: 190 FTCPICMGPMVEEMSTRCGHIFCKSCIKAAISAQAKCPTCRKKITVKELIRVFLP 244

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132232|ref|XP_002321288.1| predicted protein [Populus trichocarpa] gi|222862061|gb|EEE99603.1| predicted protein [Populus trichocarpa]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/58 (56%), Positives = 42/58 (72%)

Query: 13  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP 70
           E  F C ICL  + EE STKCGH+FCK+CI DAI+ Q KCPTCR R++ + + R+F P
Sbjct: 153 EPTFNCPICLCPLVEEMSTKCGHIFCKTCIADAIKRQAKCPTCRKRVTNKELIRVFLP 210

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231414|ref|NP_187376.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|145331994|ref|NP_001078119.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|6642645|gb|AAF20226.1|AC012395_13 putative RING zinc finger protein [Arabidopsis thaliana] gi|332640992|gb|AEE74513.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|332640993|gb|AEE74514.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/68 (50%), Positives = 48/68 (70%)

Query: 3   ESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR 62
           +S+  A  V E +F+C ICL    +E STKCGH+FCK CI +A+ LQ KCPTCR +++V+
Sbjct: 112 KSKAVAPPVEEPKFSCPICLCPFTQEVSTKCGHIFCKKCIKNALSLQAKCPTCRKKITVK 171

Query: 63  SIRRIFFP 70
            + R+F P
Sbjct: 172 DLIRVFLP 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226528685|ref|NP_001148999.1| ubiquitin-protein ligase/ zinc ion binding protein [Zea mays] gi|195623858|gb|ACG33759.1| ubiquitin-protein ligase/ zinc ion binding protein [Zea mays] gi|223974557|gb|ACN31466.1| unknown [Zea mays]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/62 (51%), Positives = 42/62 (67%)

Query: 10  VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
           V  E  FTC IC + M+E S+T CGH+FC +CI  AI++Q KCPTCR  + + S+ RIF 
Sbjct: 133 VPKEPSFTCPICWNKMEEPSTTTCGHIFCDTCIKQAIKVQKKCPTCRKGLKMNSVHRIFL 192

Query: 70  PQ 71
           P 
Sbjct: 193 PN 194

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	78
TAIR|locus:2098505	182	AT3G07200 [Arabidopsis thalian	0.871	0.373	0.5	1.6e-15
TAIR|locus:505006682	203	AT5G48655 [Arabidopsis thalian	0.897	0.344	0.5	3.3e-15
FB|FBgn0037384	319	dgrn "degringolade" [Drosophil	0.717	0.175	0.465	3.2e-10
UNIPROTKB|F1ND52	190	RNF4 "Uncharacterized protein"	0.666	0.273	0.423	2e-08
UNIPROTKB|F1NLH3	196	RNF4 "Uncharacterized protein"	0.666	0.265	0.423	2e-08
UNIPROTKB|G4NE71	448	MGG_00145 "Uncharacterized pro	0.705	0.122	0.418	3.7e-08
MGI|MGI:106657	470	Trim21 "tripartite motif-conta	0.628	0.104	0.48	5.2e-08
UNIPROTKB|A2AE50	122	TRIM26 "Tripartite motif-conta	0.717	0.459	0.372	5.3e-08
UNIPROTKB|A2AE51	159	TRIM26 "Tripartite motif-conta	0.717	0.352	0.372	5.3e-08
UNIPROTKB|Q5SPU2	157	TRIM26 "Tripartite motif-conta	0.717	0.356	0.372	5.3e-08

TAIR|locus:2098505 AT3G07200 [Arabidopsis thaliana (taxid:3702)]

 Score = 195 (73.7 bits), Expect = 1.6e-15, P = 1.6e-15
 Identities = 34/68 (50%), Positives = 48/68 (70%)

Query:     3 ESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR 62
             +S+  A  V E +F+C ICL    +E STKCGH+FCK CI +A+ LQ KCPTCR +++V+
Sbjct:   112 KSKAVAPPVEEPKFSCPICLCPFTQEVSTKCGHIFCKKCIKNALSLQAKCPTCRKKITVK 171

Query:    63 SIRRIFFP 70
              + R+F P
Sbjct:   172 DLIRVFLP 179

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:505006682 AT5G48655 [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 35/70 (50%), Positives = 45/70 (64%)

Query:     1 VCESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS 60
             V  S+  A    E +FTC IC+    EE STKCGH+FCK CI  AI  QGKCPTCR +++
Sbjct:   131 VSRSKAPAPPPEEPKFTCPICMCPFTEEMSTKCGHIFCKGCIKMAISRQGKCPTCRKKVT 190

Query:    61 VRSIRRIFFP 70
              + + R+F P
Sbjct:   191 AKELIRVFLP 200

GO:0005634 "nucleus" evidence=ISM

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

GO:0010200 "response to chitin" evidence=IEP

FB|FBgn0037384 dgrn "degringolade" [Drosophila melanogaster (taxid:7227)]

 Score = 150 (57.9 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/58 (46%), Positives = 37/58 (63%)

Query:    13 EVRFTCGICLDTM--KEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF 68
             E  + C IC+D++  +E  STKCGHVFC+ CI  AIR   KCP C  +++ R   RI+
Sbjct:   261 EELYKCPICMDSVSKREPVSTKCGHVFCRECIETAIRATHKCPICNKKLTARQFFRIY 318

GO:0008270 "zinc ion binding" evidence=IEA

GO:0032183 "SUMO binding" evidence=IPI

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0001103 "RNA polymerase II repressing transcription factor binding" evidence=IPI

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

GO:0005634 "nucleus" evidence=IDA

GO:0033768 "SUMO-targeted ubiquitin ligase complex" evidence=IC

GO:0070201 "regulation of establishment of protein localization" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0043393 "regulation of protein binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007530 "sex determination" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0022008 "neurogenesis" evidence=IGI

UNIPROTKB|F1ND52 RNF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 128 (50.1 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query:    17 TCGICLDTMKE--ES-----STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF 68
             +C IC+D   E  +S     STKCGHVFC  C+ D++R    CPTCR +++ R    I+
Sbjct:   131 SCPICMDGYSEIVQSGRLIVSTKCGHVFCSQCLRDSLRNANSCPTCRKKLTHRQYHPIY 189

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1NLH3 RNF4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 128 (50.1 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query:    17 TCGICLDTMKE--ES-----STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF 68
             +C IC+D   E  +S     STKCGHVFC  C+ D++R    CPTCR +++ R    I+
Sbjct:   137 SCPICMDGYSEIVQSGRLIVSTKCGHVFCSQCLRDSLRNANSCPTCRKKLTHRQYHPIY 195

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0090169 "regulation of spindle assembly" evidence=IEA

GO:0090234 "regulation of kinetochore assembly" evidence=IEA

UNIPROTKB|G4NE71 MGG_00145 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 134 (52.2 bits), Expect = 3.7e-08, P = 3.7e-08
 Identities = 23/55 (41%), Positives = 36/55 (65%)

Query:    10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSI 64
             + G+ +  C +CL+ +++ S+T CGHVFC SCI D +R + +CP CR    V+ I
Sbjct:   385 IKGDQQRRCTLCLEGLRDPSATPCGHVFCWSCIGDWVREKPECPLCRREALVQHI 439

GO:0008150 "biological_process" evidence=ND

MGI|MGI:106657 Trim21 "tripartite motif-containing 21" [Mus musculus (taxid:10090)]

 Score = 133 (51.9 bits), Expect = 5.2e-08, P = 5.2e-08
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query:    17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMSVRSIR 65
             TC ICLD M E  S +CGH FCK CI +  +  G  CP CR +  +R++R
Sbjct:    19 TCSICLDPMVEPMSIECGHCFCKECIFEVGKNGGSSCPECRQQFLLRNLR 68

GO:0000209 "protein polyubiquitination" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0006513 "protein monoubiquitination" evidence=ISO

GO:0007049 "cell cycle" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016874 "ligase activity" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0031648 "protein destabilization" evidence=ISO

GO:0032088 "negative regulation of NF-kappaB transcription factor activity" evidence=ISO

GO:0045787 "positive regulation of cell cycle" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=ISO

GO:0070206 "protein trimerization" evidence=ISO

GO:0090086 "negative regulation of protein deubiquitination" evidence=ISO

UNIPROTKB|A2AE50 TRIM26 "Tripartite motif-containing protein 26" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%)

Query:    13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
             E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct:    11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|A2AE51 TRIM26 "Tripartite motif-containing protein 26" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%)

Query:    13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
             E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct:    11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q5SPU2 TRIM26 "Tripartite motif-containing protein 26" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%)

Query:    13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRRIF 68
             E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct:    11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" 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

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	78
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	2e-08
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	2e-07
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	5e-07
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	1e-06
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	3e-06
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-05
COG5152	259	COG5152, COG5152, Uncharacterized conserved protei	1e-05
PLN03208	193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	3e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	5e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	6e-04
smart00184	40	smart00184, RING, Ring finger	0.001

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 17/44 (38%), Positives = 19/44 (43%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCR 56
          +    C IC D       T C H FC  CI   +  Q KCP CR
Sbjct: 24 DTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 3   ESRNGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ--GKCPTCRTRMS 60
             +NG   +    + C +CL+  +  S T CGH+FC SC++ +   +    CP CR ++ 
Sbjct: 203 SKKNGLPFIPLADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262

Query: 61  VRSI 64
            + +
Sbjct: 263 PKKV 266

Length = 271

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

 Score = 41.6 bits (98), Expect = 5e-07
 Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 16 FTCGICLDTMKEESS---TKCGHVFCKSCIVDAIRLQGKCPTCRTR 58
            C ICLD  +         CGHVF K C+   +R    CP CR  
Sbjct: 1  DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 40.6 bits (95), Expect = 1e-06
 Identities = 20/44 (45%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 15 RFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRT 57
             C ICLD +++    T CGHVFC+ CI+  ++ + KCP CRT
Sbjct: 2  ELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 16/39 (41%), Positives = 18/39 (46%)

Query: 18 CGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCR 56
          C IC   +     T CGH FC  CI   +  Q  CP CR
Sbjct: 28 CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

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

 Score = 38.2 bits (89), Expect = 1e-05
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 17 TCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGKCPTCRT 57
           C ICL+  +E      CGHVFC+SCI   ++  +  CP CRT
Sbjct: 1  ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43

Length = 45

>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]

 Score = 40.4 bits (94), Expect = 1e-05
 Identities = 14/47 (29%), Positives = 21/47 (44%)

Query: 13  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRM 59
           ++ F CGIC    +    T+CGH FC  C +   +   +C  C    
Sbjct: 194 KIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240

Length = 259

>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2; Provisional

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 16/78 (20%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCI----------------VDAIRLQGKCPTCRTRM 59
          F C ICLD +++   T CGH+FC  CI                 D  R   KCP C++ +
Sbjct: 19 FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78

Query: 60 SVRSIRRIFFPQLQPPAS 77
          S  ++  I+    + P S
Sbjct: 79 SEATLVPIYGRGQKAPQS 96

Length = 193

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

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 11/63 (17%)

Query: 18  CGICLDTMKEESS--------TKCGHVFCKSCIVDAIRLQGKCPTCRTR-MSVRSIRRIF 68
           C IC++ + ++          + C HVFC  CI    + +  CP CRT  +SV   R  F
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVIKSR--F 234

Query: 69  FPQ 71
           F +
Sbjct: 235 FTK 237

Length = 238

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

 Score = 34.0 bits (78), Expect = 5e-04
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 18 CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQG-KCPTC 55
          C ICL+  K+      CGH+FC  CI+  +      CP C
Sbjct: 1  CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif

 Score = 33.8 bits (78), Expect = 6e-04
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 6/46 (13%)

Query: 15 RFTCGICLDTMKEES----STKCGHVFCKSCIVD--AIRLQGKCPT 54
           F C I  + M +E        CGHV+ +  +        + KCP 
Sbjct: 10 IFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCPY 55

This zinc-finger is the dimerisation motif for LisH proteins, and is also a typical RING-type of plant ubiquitin ligases. Length = 55

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

 Score = 32.9 bits (75), Expect = 0.001
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 18 CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQG-KCPTC 55
          C ICL+   ++     CGH FC+SCI   +      CP C
Sbjct: 1  CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	78
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.69
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.61
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.6
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.59
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.59
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.53
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.52
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.52
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.49
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.45
PHA02929	238	N1R/p28-like protein; Provisional	99.44
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	99.39
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.36
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.31
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.3
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.26
PF14634	44	zf-RING_5: zinc-RING finger domain	99.25
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.24
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.23
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	99.23
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.22
PHA02926	242	zinc finger-like protein; Provisional	99.19
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.16
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	99.16
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.14
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	99.13
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.97
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.97
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.95
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.9
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.85
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.81
COG5152	259	Uncharacterized conserved protein, contains RING a	98.76
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.67
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.64
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.61
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.58
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.55
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.5
KOG2660	331	consensus Locus-specific chromosome binding protei	98.44
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.38
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.37
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.36
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.34
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	98.29
KOG3039	303	consensus Uncharacterized conserved protein [Funct	98.26
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	98.21
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.18
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.05
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.04
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.01
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	98.01
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.96
PF04641	260	Rtf2: Rtf2 RING-finger	97.94
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.82
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.79
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.75
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.71
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.7
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.68
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.67
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.66
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.61
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.42
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	97.32
KOG4367	699	consensus Predicted Zn-finger protein [Function un	97.32
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.29
KOG4739	233	consensus Uncharacterized protein involved in syna	97.25
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	97.23
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.22
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.13
KOG1001	674	consensus Helicase-like transcription factor HLTF/	97.09
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	97.07
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	97.04
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	96.94
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.74
KOG4445	368	consensus Uncharacterized conserved protein, conta	96.71
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.69
KOG3002	299	consensus Zn finger protein [General function pred	96.63
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	96.25
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	96.25
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.21
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.17
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	96.17
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.01
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	95.87
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.8
KOG1940	276	consensus Zn-finger protein [General function pred	95.78
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.75
KOG0298	1394	consensus DEAD box-containing helicase-like transc	95.65
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	95.52
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.5
PHA03096	284	p28-like protein; Provisional	95.49
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.46
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.3
KOG3899	381	consensus Uncharacterized conserved protein [Funct	95.22
PHA02862	156	5L protein; Provisional	95.03
COG5109	396	Uncharacterized conserved protein, contains RING Z	94.95
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	94.93
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	94.91
KOG3113	293	consensus Uncharacterized conserved protein [Funct	94.8
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	94.41
KOG0289	506	consensus mRNA splicing factor [General function p	94.1
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	93.47
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.78
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	92.67
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	92.37
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	92.04
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	91.74
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	91.2
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.09
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	91.05
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	89.45
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.1
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	88.23
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	87.99
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	86.05
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	84.87
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	84.29
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	83.83
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	81.68
KOG2979	262	consensus Protein involved in DNA repair [General	81.26
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	81.25
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	80.4
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	80.27

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.69  E-value=6.1e-17  Score=96.25  Aligned_cols=66  Identities=32%  Similarity=0.671  Sum_probs=55.7

Q ss_pred             CcccCCCcccccccccccccCceecCCCChhhHHhHHHHhhC----------------CCCcccccccccccceeeeccC
Q 037842            7 GAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL----------------QGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus         7 ~~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~----------------~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      .......+++.|+||++.+.+|+.++|||.||+.|+..|+..                ...||.|+..+...++.+++..
T Consensus        10 ~~~~~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygr   89 (193)
T PLN03208         10 TTLVDSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGR   89 (193)
T ss_pred             ceeccCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeecc
Confidence            344455577999999999999999999999999999999742                2479999999999999998865


Q ss_pred             CC
Q 037842           71 QL   72 (78)
Q Consensus        71 ~~   72 (78)
                      +.
T Consensus        90 g~   91 (193)
T PLN03208         90 GQ   91 (193)
T ss_pred             CC
Confidence            54

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

Probab=99.61  E-value=6.3e-16  Score=96.04  Aligned_cols=62  Identities=31%  Similarity=0.742  Sum_probs=54.0

Q ss_pred             CCcccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842            6 NGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus         6 ~~~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      .......+....|.+|++...+|..++|||.||+.|+..|...+..||.||..+.+.+++-+
T Consensus       230 ~~~~~i~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi~L  291 (293)
T KOG0317|consen  230 NSLSSIPEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVICL  291 (293)
T ss_pred             cCCccCCCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcceeee
Confidence            33444455668999999999999999999999999999999999999999999998887654

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

Probab=99.60  E-value=1.9e-15  Score=91.54  Aligned_cols=62  Identities=29%  Similarity=0.729  Sum_probs=55.6

Q ss_pred             CCcccccccccccccCceecCCCChhhHHhHHHHhhC---CCCcccccccccccceeeeccCCCC
Q 037842           12 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL---QGKCPTCRTRMSVRSIRRIFFPQLQ   73 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~---~~~CP~C~~~~~~~~~~~~~~~~~~   73 (78)
                      ....+.|.||++.-++|+.+.|||.||+.||.+|+..   ...||+|+..+..+.+.++|-.+..
T Consensus        44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~  108 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSK  108 (230)
T ss_pred             CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCC
Confidence            4567999999999999999999999999999999985   3468999999999999999987763

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

Probab=99.59  E-value=8.3e-16  Score=71.74  Aligned_cols=38  Identities=45%  Similarity=1.050  Sum_probs=30.5

Q ss_pred             cccccccccCceecCCCChhhHHhHHHHhhCC----CCcccc
Q 037842           18 CGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ----GKCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~----~~CP~C   55 (78)
                      |+||++.+.+|++++|||+||..|+.++++..    ..||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999999999999999999999998853    358876

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

Probab=99.59  E-value=1.3e-15  Score=89.10  Aligned_cols=58  Identities=48%  Similarity=1.087  Sum_probs=51.3

Q ss_pred             CCcccccccccccccCc--eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           12 GEVRFTCGICLDTMKEE--SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~--~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      .+..+.||||++.+...  +.+.|||+||+.|+...++....||.|++.++.+.+.++|+
T Consensus       128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~rI~L  187 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFHRIYL  187 (187)
T ss_pred             cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhheeccC
Confidence            44558999999998864  56799999999999999999999999999999999988874

>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=99.53  E-value=4.3e-15  Score=68.28  Aligned_cols=38  Identities=47%  Similarity=1.161  Sum_probs=33.5

Q ss_pred             cccccccccCc-eecCCCChhhHHhHHHHhhCCCCcccc
Q 037842           18 CGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGKCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~~-~~~~CgH~fc~~C~~~~~~~~~~CP~C   55 (78)
                      |+||++.+.+| +.++|||.||+.|+.+|++.+..||.|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999999 578999999999999999998899987

>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=99.52  E-value=7.9e-15  Score=70.72  Aligned_cols=46  Identities=30%  Similarity=0.861  Sum_probs=41.2

Q ss_pred             ccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCccccccccc
Q 037842           15 RFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +..|.||++...+.+.++|||. ||..|+.+|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            5789999999999999999999 999999999998899999998875

...

>smart00504 Ubox Modified RING finger domain

Probab=99.52  E-value=1.5e-14  Score=72.51  Aligned_cols=53  Identities=19%  Similarity=0.329  Sum_probs=48.3

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ++.|+||.+.+.+|+.++|||+||+.|+..|+.....||.|+..+..+++.++
T Consensus         1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~   53 (63)
T smart00504        1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN   53 (63)
T ss_pred             CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence            36799999999999999999999999999999988899999999987777665

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

>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=99.49  E-value=7e-15  Score=69.15  Aligned_cols=40  Identities=40%  Similarity=1.028  Sum_probs=34.8

Q ss_pred             ccccccccccC---ceecCCCChhhHHhHHHHhhCCCCccccc
Q 037842           17 TCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCR   56 (78)
Q Consensus        17 ~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~   56 (78)
                      .|+||++.+..   .+.++|||.||..|+.+|++.+..||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            59999999863   35679999999999999999999999996

...

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.45  E-value=5.9e-14  Score=91.34  Aligned_cols=59  Identities=31%  Similarity=0.648  Sum_probs=51.2

Q ss_pred             cccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842            8 AVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      .....+..+.|+||.+.+.+|++++|||.||..|+..|+.....||.|+..+....+..
T Consensus        19 ~l~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~   77 (397)
T TIGR00599        19 SLYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRS   77 (397)
T ss_pred             cccccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCcc
Confidence            34566778999999999999999999999999999999998889999999887655544

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.44  E-value=1e-13  Score=85.23  Aligned_cols=49  Identities=31%  Similarity=0.737  Sum_probs=41.8

Q ss_pred             CcccccccccccccCc--------eecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           13 EVRFTCGICLDTMKEE--------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~--------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      .++..|+||++.+.++        +.++|+|.||..|+.+|+..+..||+||..+..
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~  228 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS  228 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence            4568999999987653        445899999999999999998999999998773

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

Probab=99.39  E-value=6.3e-14  Score=89.20  Aligned_cols=59  Identities=27%  Similarity=0.660  Sum_probs=52.7

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ....++.++|.||.++|..|++++|+|+||.-||..++..+..||.|+.++...+++.+
T Consensus        17 lk~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n   75 (442)
T KOG0287|consen   17 LKTLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNN   75 (442)
T ss_pred             hhhhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhh
Confidence            44566779999999999999999999999999999999999999999999887666654

>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=99.36  E-value=4.6e-13  Score=61.93  Aligned_cols=38  Identities=37%  Similarity=1.003  Sum_probs=34.3

Q ss_pred             cccccccccCce-ecCCCChhhHHhHHHHhh--CCCCcccc
Q 037842           18 CGICLDTMKEES-STKCGHVFCKSCIVDAIR--LQGKCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~~~-~~~CgH~fc~~C~~~~~~--~~~~CP~C   55 (78)
                      |+||++.+.++. .++|||.||..|+.+|+.  ....||.|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            799999999998 889999999999999998  45579987

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 ....

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

Probab=99.31  E-value=2.2e-12  Score=59.91  Aligned_cols=42  Identities=45%  Similarity=1.073  Sum_probs=36.2

Q ss_pred             ccccccccccCceecC-CCChhhHHhHHHHhhC-CCCccccccc
Q 037842           17 TCGICLDTMKEESSTK-CGHVFCKSCIVDAIRL-QGKCPTCRTR   58 (78)
Q Consensus        17 ~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~-~~~CP~C~~~   58 (78)
                      .|+||++.+.+++.+. |||.||..|+..|+.. ...||.|+..
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~   44 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTP   44 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence            4899999997776654 9999999999999987 6789999865

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

Probab=99.30  E-value=1.2e-12  Score=86.63  Aligned_cols=60  Identities=30%  Similarity=0.794  Sum_probs=53.4

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhCC-----CCcccccccccccceeeeccCCCCC
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-----GKCPTCRTRMSVRSIRRIFFPQLQP   74 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~-----~~CP~C~~~~~~~~~~~~~~~~~~~   74 (78)
                      +..||||++...-|+.+.|||.||..||.+++...     +.||+|+..+..+++...++...+.
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~~qk  250 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIEDDQK  250 (513)
T ss_pred             CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeeccccc
Confidence            78999999999999999999999999999998743     4799999999999999988877643

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

Probab=99.26  E-value=5.5e-12  Score=65.13  Aligned_cols=55  Identities=22%  Similarity=0.298  Sum_probs=44.9

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceeee
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~   67 (78)
                      .+.+.|+|+.+.+.+|+.+++||+|.+.++..|+.. ...||.++..+...++..+
T Consensus         2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn   57 (73)
T PF04564_consen    2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPN   57 (73)
T ss_dssp             SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-
T ss_pred             CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceEC
Confidence            357899999999999999999999999999999998 7799999999988777664

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 ....

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.25  E-value=7.9e-12  Score=58.72  Aligned_cols=41  Identities=37%  Similarity=0.980  Sum_probs=34.4

Q ss_pred             cccccccccc---CceecCCCChhhHHhHHHHhhCCCCcccccc
Q 037842           17 TCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQGKCPTCRT   57 (78)
Q Consensus        17 ~C~iC~~~~~---~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~   57 (78)
                      .|++|.+.+.   .+.+++|||+||..|+.........||+|++
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4899999982   3577899999999999998856678999974

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

Probab=99.24  E-value=5.8e-12  Score=77.78  Aligned_cols=52  Identities=31%  Similarity=0.788  Sum_probs=46.4

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHH-HhhCCCC-cccccccccccce
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVD-AIRLQGK-CPTCRTRMSVRSI   64 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~-~~~~~~~-CP~C~~~~~~~~~   64 (78)
                      ..++.|+||++....|..++|||+||..|+.. |-.++.. ||.||+.+..+++
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            45789999999999999999999999999999 7776665 9999999887776

>smart00184 RING Ring finger

Probab=99.23  E-value=1.3e-11  Score=55.50  Aligned_cols=38  Identities=42%  Similarity=1.108  Sum_probs=33.7

Q ss_pred             cccccccccCceecCCCChhhHHhHHHHhh-CCCCcccc
Q 037842           18 CGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGKCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~-~~~~CP~C   55 (78)
                      |+||++...+++.++|||.||..|+..|+. ....||.|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999988888999999999999999998 45579876

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)

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

Probab=99.23  E-value=4.5e-12  Score=79.54  Aligned_cols=56  Identities=29%  Similarity=0.559  Sum_probs=49.1

Q ss_pred             CCcccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842            6 NGAVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus         6 ~~~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      +......+..+.|-||.+.+..|..++|||.||+-||.+++..+..||+||.....
T Consensus        16 IPSL~~LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          16 IPSLKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             CcchhcchhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            33445566778999999999999999999999999999999999999999988653

>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=99.22  E-value=1.2e-11  Score=63.94  Aligned_cols=41  Identities=32%  Similarity=0.843  Sum_probs=33.8

Q ss_pred             cccccccccccCc------------e-ecCCCChhhHHhHHHHhhCCCCccccc
Q 037842           16 FTCGICLDTMKEE------------S-STKCGHVFCKSCIVDAIRLQGKCPTCR   56 (78)
Q Consensus        16 ~~C~iC~~~~~~~------------~-~~~CgH~fc~~C~~~~~~~~~~CP~C~   56 (78)
                      ..|+||++.+.++            + ..+|||.|+..||.+|+.....||+||
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            3499999998432            2 347999999999999999999999997

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 ....

>PHA02926 zinc finger-like protein; Provisional

Probab=99.19  E-value=6.7e-12  Score=76.11  Aligned_cols=51  Identities=33%  Similarity=0.724  Sum_probs=40.1

Q ss_pred             CCCcccccccccccccC---------ceecCCCChhhHHhHHHHhhCC------CCcccccccccc
Q 037842           11 VGEVRFTCGICLDTMKE---------ESSTKCGHVFCKSCIVDAIRLQ------GKCPTCRTRMSV   61 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~---------~~~~~CgH~fc~~C~~~~~~~~------~~CP~C~~~~~~   61 (78)
                      ....+..|+||++...+         ++..+|+|.||..|+..|...+      ..||+||..+..
T Consensus       166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            44567899999997532         2455899999999999999742      359999998763

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

Probab=99.16  E-value=1.5e-11  Score=57.45  Aligned_cols=30  Identities=37%  Similarity=0.926  Sum_probs=21.1

Q ss_pred             cccccccccC----ceecCCCChhhHHhHHHHhhC
Q 037842           18 CGICLDTMKE----ESSTKCGHVFCKSCIVDAIRL   48 (78)
Q Consensus        18 C~iC~~~~~~----~~~~~CgH~fc~~C~~~~~~~   48 (78)
                      |+||.+ +.+    |+.++|||+||..|++++...
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhc
Confidence            899999 777    889999999999999999874

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

Probab=99.16  E-value=1.1e-11  Score=84.97  Aligned_cols=56  Identities=34%  Similarity=0.831  Sum_probs=50.8

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhh-CCCCcccccccccccceeeecc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~-~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      .-+.|++|...+.+.+++.|||.||..|+...+. +++.||.|...|...++.++++
T Consensus       642 ~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l  698 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL  698 (698)
T ss_pred             hceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence            4588999999999999999999999999999877 4779999999999999998874

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

Probab=99.14  E-value=4.3e-11  Score=76.81  Aligned_cols=45  Identities=29%  Similarity=0.699  Sum_probs=39.5

Q ss_pred             cccccccccccCc---eecCCCChhhHHhHHHHhhCCCC-ccccccccc
Q 037842           16 FTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMS   60 (78)
Q Consensus        16 ~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~~~~~-CP~C~~~~~   60 (78)
                      ..|+||++.+...   ..|+|+|.||..|+..|+...+. ||+|+..+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            4899999999975   46899999999999999998764 999998764

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

Probab=99.13  E-value=5.2e-12  Score=63.06  Aligned_cols=53  Identities=40%  Similarity=0.872  Sum_probs=28.0

Q ss_pred             CcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           13 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ++.+.|++|.+.+.+|+.+ .|.|.||+.|+.+.+.  ..||+|+.+...++++-+
T Consensus         5 e~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~N   58 (65)
T PF14835_consen    5 EELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQIN   58 (65)
T ss_dssp             HHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----
T ss_pred             HHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhh
Confidence            4567899999999999865 7999999999977554  359999999887777643

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

Probab=98.97  E-value=2.9e-10  Score=73.48  Aligned_cols=48  Identities=31%  Similarity=0.750  Sum_probs=41.5

Q ss_pred             CCcccccccccccccC-c------------eecCCCChhhHHhHHHHhhCCCCcccccccc
Q 037842           12 GEVRFTCGICLDTMKE-E------------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRM   59 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~-~------------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~   59 (78)
                      ..++..|.||++.+.. +            ..++|||.++..|++.|++++..||+||.++
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcc
Confidence            4567899999998443 2            5689999999999999999999999999985

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.97  E-value=5.6e-10  Score=70.79  Aligned_cols=57  Identities=30%  Similarity=0.665  Sum_probs=44.4

Q ss_pred             cccccccccc-ccCce---ec-CCCChhhHHhHHHHhhC-CCCcccccccccccceeeeccCC
Q 037842           15 RFTCGICLDT-MKEES---ST-KCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIFFPQ   71 (78)
Q Consensus        15 ~~~C~iC~~~-~~~~~---~~-~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~~~~~   71 (78)
                      +..||+|... +.+|.   .+ +|||.||..|+...+.. ...||.|+..+..+++....|+.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr~q~F~D   65 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED   65 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhhcccccccc
Confidence            4689999994 33442   23 69999999999997654 45899999999988887776665

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).

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

Probab=98.95  E-value=3.1e-10  Score=70.00  Aligned_cols=48  Identities=35%  Similarity=0.836  Sum_probs=42.3

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCR   56 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~   56 (78)
                      .....+.+.|+||++.+..|..++|||.||..|+..++.....||.||
T Consensus         7 ~~~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen    7 LEVLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             hhhccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccC
Confidence            445567899999999999998889999999999999888555899999

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

Probab=98.90  E-value=6.6e-10  Score=75.23  Aligned_cols=48  Identities=35%  Similarity=0.735  Sum_probs=43.1

Q ss_pred             cccccccccccccC-----ceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           14 VRFTCGICLDTMKE-----ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~-----~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      .+..|+||.+.+..     +..++|||.||..|+..|++++..||.||..+..
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~  342 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYD  342 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhc
Confidence            46789999999998     6889999999999999999999999999985543

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

Probab=98.85  E-value=1.5e-09  Score=68.68  Aligned_cols=48  Identities=27%  Similarity=0.653  Sum_probs=40.2

Q ss_pred             cccccccccccccCc---eecCCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           14 VRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      ....|+||++.+...   +.+||.|.|+..|+..|+.. +..||+||.++.+
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            347899999988743   56799999999999999984 6689999988763

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

Probab=98.81  E-value=6.4e-09  Score=54.83  Aligned_cols=48  Identities=31%  Similarity=0.706  Sum_probs=37.1

Q ss_pred             ccccccccccccC------------ceec-CCCChhhHHhHHHHhhC---CCCccccccccccc
Q 037842           15 RFTCGICLDTMKE------------ESST-KCGHVFCKSCIVDAIRL---QGKCPTCRTRMSVR   62 (78)
Q Consensus        15 ~~~C~iC~~~~~~------------~~~~-~CgH~fc~~C~~~~~~~---~~~CP~C~~~~~~~   62 (78)
                      +..|.||...|..            |+.. .|+|.|+..||.+|+..   +..||+||+....+
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            5678888877762            2333 69999999999999985   45899999887543

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

Probab=98.76  E-value=5e-09  Score=62.94  Aligned_cols=52  Identities=27%  Similarity=0.663  Sum_probs=44.5

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .....-.+.|.||.+.+..|+.+.|||.||..|..+-+.....|-+|.+...
T Consensus       190 ~~~e~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         190 GPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             CCCCCCceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            3334445899999999999999999999999999998888889999987653

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

Probab=98.67  E-value=1.2e-08  Score=64.31  Aligned_cols=51  Identities=25%  Similarity=0.497  Sum_probs=43.5

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccce
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSI   64 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~   64 (78)
                      ....|+||+....-|+.+.|+|.||+-|+...... ++.|++||.+++..-+
T Consensus         6 ~~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    6 KKKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             cCCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            35679999999999999999999999999987765 4569999999975433

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

Probab=98.64  E-value=3e-08  Score=63.71  Aligned_cols=48  Identities=27%  Similarity=0.686  Sum_probs=42.8

Q ss_pred             CcccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +...+|.||+...++.+.+||.|. .|..|.+...-+..+||+||+++.
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            446789999999999999999997 799999887777889999999876

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

Probab=98.61  E-value=2.2e-08  Score=65.71  Aligned_cols=51  Identities=27%  Similarity=0.726  Sum_probs=45.8

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .....++.|.||...+..|+.++|||.||..|+.+.+.....||.||..+.
T Consensus        79 ~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~  129 (398)
T KOG4159|consen   79 EEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELV  129 (398)
T ss_pred             ccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCcccccccc
Confidence            344678999999999999999999999999999998888889999998875

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

Probab=98.58  E-value=1.5e-08  Score=49.10  Aligned_cols=45  Identities=31%  Similarity=0.809  Sum_probs=39.2

Q ss_pred             cccccccccccCceecCCCCh-hhHHhHHHHhh-CCCCccccccccc
Q 037842           16 FTCGICLDTMKEESSTKCGHV-FCKSCIVDAIR-LQGKCPTCRTRMS   60 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~-~~~~CP~C~~~~~   60 (78)
                      .+|.||.+...+.+.-.|||. +|+.|-.+.++ ..+.||+||+++.
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            679999999999888899997 79999888777 4678999999875

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

Probab=98.55  E-value=8.8e-09  Score=66.14  Aligned_cols=50  Identities=38%  Similarity=0.885  Sum_probs=42.3

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      ...++.|+||++.+...+++ .|+|.||..||...++. ...||.||+.+..
T Consensus        40 ~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            34568999999999988776 59999999999988876 4589999998754

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

Probab=98.50  E-value=5.3e-08  Score=60.88  Aligned_cols=59  Identities=19%  Similarity=0.466  Sum_probs=45.7

Q ss_pred             CcccccccccccccCc----------eecCCCChhhHHhHHHHhh--CCCCcccccccccccceeeeccCC
Q 037842           13 EVRFTCGICLDTMKEE----------SSTKCGHVFCKSCIVDAIR--LQGKCPTCRTRMSVRSIRRIFFPQ   71 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~----------~~~~CgH~fc~~C~~~~~~--~~~~CP~C~~~~~~~~~~~~~~~~   71 (78)
                      .++..|+||-+.+...          ..++|+|+|+..|+..|-.  ++..||.|+..++.+...++...+
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsnpWek  292 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSNPWEK  292 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccCcccc
Confidence            3567899999876533          4679999999999999965  456899999999877766654443

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

Probab=98.44  E-value=5.1e-08  Score=62.13  Aligned_cols=52  Identities=31%  Similarity=0.695  Sum_probs=45.1

Q ss_pred             ccCCCcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCccccccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .........|.+|..++.++.++ .|-|+||++||..++.....||.|...+.
T Consensus         9 ~~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen    9 LTELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             hhhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            34456678999999999999765 69999999999999999999999987764

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

Probab=98.38  E-value=4.1e-07  Score=56.97  Aligned_cols=52  Identities=25%  Similarity=0.618  Sum_probs=42.7

Q ss_pred             ccCCCcccccccccccccCceec-CCCChhhHHhHHHHhhC--CCCccccccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL--QGKCPTCRTRMS   60 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~--~~~CP~C~~~~~   60 (78)
                      ......+.+|++|.+....|.++ +|||+||+.|+......  ...||.|..+..
T Consensus       233 ss~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  233 SSTGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            33455678999999999999877 59999999999887664  358999988765

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

Probab=98.37  E-value=1.9e-07  Score=61.33  Aligned_cols=52  Identities=29%  Similarity=0.879  Sum_probs=45.9

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      .++++.|++|...+.+|+.. .|||.||..|+..|+.....||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            56779999999999999984 99999999999999999889999987765443

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

Probab=98.36  E-value=2.8e-07  Score=45.41  Aligned_cols=43  Identities=33%  Similarity=0.770  Sum_probs=30.1

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhC--CCCccc
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL--QGKCPT   54 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~--~~~CP~   54 (78)
                      ....+.|||.+..+.+|+.. .|||+|-+..+..|+..  ...||.
T Consensus         8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            44568999999999999875 89999999999999944  347998

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

Probab=98.34  E-value=4.9e-07  Score=46.99  Aligned_cols=46  Identities=26%  Similarity=0.556  Sum_probs=35.9

Q ss_pred             cccccccccccCc---------------eec-CCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           16 FTCGICLDTMKEE---------------SST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        16 ~~C~iC~~~~~~~---------------~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ..|+||...+.++               +.. -|.|.|+..|+.+|+..++.||+++++...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            4577777665532               222 599999999999999999999999987654

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

Probab=98.29  E-value=2.6e-07  Score=58.28  Aligned_cols=46  Identities=33%  Similarity=0.746  Sum_probs=41.4

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .+.|-||...+.+||.+.|||.||..|....+.....|.+|.+...
T Consensus       241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             CccccccccccccchhhcCCceeehhhhccccccCCcceecccccc
Confidence            4679999999999999999999999999988888889999987653

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.26  E-value=1.5e-06  Score=53.89  Aligned_cols=62  Identities=23%  Similarity=0.313  Sum_probs=54.3

Q ss_pred             cccccccccccccCce----ecCCCChhhHHhHHHHhhCCCCcccccccccccceeeeccCCCCCC
Q 037842           14 VRFTCGICLDTMKEES----STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPP   75 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~----~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~   75 (78)
                      ..+.||+|.+.+.|.+    .-+|||+++..|+...+.....||+|..++..++++.+.-.++-.+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~LqrGGTGfa  285 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQRGGTGFA  285 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeeeccccccc
Confidence            5689999999999863    3489999999999999999999999999999999999887766544

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

Probab=98.21  E-value=1.5e-06  Score=56.41  Aligned_cols=52  Identities=21%  Similarity=0.418  Sum_probs=46.1

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      .+..++..|+||.-...+.+..||+|.-|+.|+.+.+.+.+.|-.|+..+..
T Consensus       417 lp~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  417 LPDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             CCCcccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            3445678999999998899999999999999999999999999999887764

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

Probab=98.20  E-value=7.7e-07  Score=59.69  Aligned_cols=49  Identities=24%  Similarity=0.634  Sum_probs=38.6

Q ss_pred             CcccccccccccccCc-----------------eecCCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           13 EVRFTCGICLDTMKEE-----------------SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~-----------------~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      +....|+||+..+.-.                 +.+||.|.|+..|+.+|+.. +-.||.||.++..
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3457899999875421                 23599999999999999995 5589999988753

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

Probab=98.18  E-value=2.6e-07  Score=47.27  Aligned_cols=47  Identities=28%  Similarity=0.705  Sum_probs=23.6

Q ss_pred             cccccccccccc-C---cee----cCCCChhhHHhHHHHhhC---C--------CCcccccccccc
Q 037842           15 RFTCGICLDTMK-E---ESS----TKCGHVFCKSCIVDAIRL---Q--------GKCPTCRTRMSV   61 (78)
Q Consensus        15 ~~~C~iC~~~~~-~---~~~----~~CgH~fc~~C~~~~~~~---~--------~~CP~C~~~~~~   61 (78)
                      +..|+||...+. +   |..    ..|+..|+..||.+|+..   .        +.||.|+.++.-
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            467999999765 2   222    269999999999999873   1        259999988753

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

Probab=98.05  E-value=5.8e-06  Score=39.51  Aligned_cols=40  Identities=23%  Similarity=0.579  Sum_probs=30.1

Q ss_pred             ccccccc--cccCceecCCC-----ChhhHHhHHHHhhCC--CCccccc
Q 037842           17 TCGICLD--TMKEESSTKCG-----HVFCKSCIVDAIRLQ--GKCPTCR   56 (78)
Q Consensus        17 ~C~iC~~--~~~~~~~~~Cg-----H~fc~~C~~~~~~~~--~~CP~C~   56 (78)
                      .|-||++  .-.++...||.     |.++..|+.+|+..+  ..||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3789987  33345667874     789999999999754  3799884

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

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

Probab=98.05  E-value=2.7e-06  Score=55.67  Aligned_cols=50  Identities=26%  Similarity=0.760  Sum_probs=37.1

Q ss_pred             cccccccccccCce---ec-CCCChhhHHhHHHHhhC---CCCccccccccccccee
Q 037842           16 FTCGICLDTMKEES---ST-KCGHVFCKSCIVDAIRL---QGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        16 ~~C~iC~~~~~~~~---~~-~CgH~fc~~C~~~~~~~---~~~CP~C~~~~~~~~~~   65 (78)
                      ..|.||.+.+.+..   .+ .|||+|+..|+..|+..   .+.||+|+..+..+.+.
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~   61 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA   61 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence            57999966544332   23 49999999999999985   35899999666655554

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

Probab=98.04  E-value=3e-06  Score=56.18  Aligned_cols=51  Identities=29%  Similarity=0.572  Sum_probs=40.0

Q ss_pred             cccCCCcccccccccccccCce----ecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842            8 AVVVGEVRFTCGICLDTMKEES----STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~----~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +.....+--+||||++.+...+    .+.|.|.|+-.|+..|..  ..||+||.-..
T Consensus       168 ~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  168 PPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             CCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence            3344556679999999998764    457999999999999965  46999987655

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

Probab=98.03  E-value=3.6e-06  Score=54.54  Aligned_cols=49  Identities=35%  Similarity=0.805  Sum_probs=39.3

Q ss_pred             CCcccccccccccccCce-----e---cCCCChhhHHhHHHHhh--C-----CCCccccccccc
Q 037842           12 GEVRFTCGICLDTMKEES-----S---TKCGHVFCKSCIVDAIR--L-----QGKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~-----~---~~CgH~fc~~C~~~~~~--~-----~~~CP~C~~~~~   60 (78)
                      ...+..|.||++...+..     .   .+|.|.||..|+..|..  +     .+.||.||....
T Consensus       158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            355789999999877654     2   46999999999999984  3     368999998765

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

Probab=98.01  E-value=1.7e-06  Score=56.86  Aligned_cols=54  Identities=35%  Similarity=0.752  Sum_probs=42.6

Q ss_pred             ccccccccccccCc-----eecCCCChhhHHhHHHHhhC--CCCcccccccccccceeeec
Q 037842           15 RFTCGICLDTMKEE-----SSTKCGHVFCKSCIVDAIRL--QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        15 ~~~C~iC~~~~~~~-----~~~~CgH~fc~~C~~~~~~~--~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ...||||++.+.-+     +.+.|||.|-.+|+++|+.+  +..||.|......+.++..+
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~   64 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEY   64 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHH
Confidence            46899999998865     45689999999999999974  34799998877666555443

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

Probab=98.01  E-value=1.9e-06  Score=55.18  Aligned_cols=57  Identities=30%  Similarity=0.587  Sum_probs=49.4

Q ss_pred             CcccccccccccccCceecC-CCChhhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           13 EVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      .+...||+|+....+|..+. -|-+||+.|+..++.+.+.||+-..+....++++++.
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~  355 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFN  355 (357)
T ss_pred             CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHhc
Confidence            34578999999999997765 6999999999999999999999998888888877764

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

Probab=97.96  E-value=6.4e-06  Score=54.33  Aligned_cols=47  Identities=30%  Similarity=0.705  Sum_probs=39.8

Q ss_pred             cccccccccccCceecCCCChhhHHhHHHHhhC--CCCccccccccccc
Q 037842           16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL--QGKCPTCRTRMSVR   62 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~--~~~CP~C~~~~~~~   62 (78)
                      ..|.||.+.-.+..+-+|||..|..|+..|...  ...||.||..++-.
T Consensus       370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt  418 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT  418 (563)
T ss_pred             HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence            468999998888777799999999999999864  34799999988643

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.94  E-value=1.7e-05  Score=49.65  Aligned_cols=58  Identities=24%  Similarity=0.479  Sum_probs=46.8

Q ss_pred             CCcccccccccccccCc----eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeeccC
Q 037842           12 GEVRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      ....+.|||....+...    ...+|||+|...++...- ....||+|..++...+++.+.-+
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp~  171 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNPP  171 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecCC
Confidence            45679999999998653    234899999999998874 34579999999999998887544

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

Probab=97.82  E-value=9.4e-06  Score=41.94  Aligned_cols=46  Identities=35%  Similarity=0.711  Sum_probs=35.0

Q ss_pred             cccccccccccC------------ceec-CCCChhhHHhHHHHhhC---CCCcccccccccc
Q 037842           16 FTCGICLDTMKE------------ESST-KCGHVFCKSCIVDAIRL---QGKCPTCRTRMSV   61 (78)
Q Consensus        16 ~~C~iC~~~~~~------------~~~~-~CgH~fc~~C~~~~~~~---~~~CP~C~~~~~~   61 (78)
                      ..|.||.-.|..            |..+ .|.|.|+..|+.+|+..   +..||+||+....
T Consensus        21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            377777776653            2333 59999999999999874   4589999987654

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

Probab=97.79  E-value=1.3e-05  Score=54.49  Aligned_cols=51  Identities=27%  Similarity=0.775  Sum_probs=42.7

Q ss_pred             CCcccccccccccccCceecCCCChhhHHhHHHHhhC-----CCCccccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-----QGKCPTCRTRMSVR   62 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-----~~~CP~C~~~~~~~   62 (78)
                      ......|.+|.+.-.+++..+|.|.||+.|+.+|...     ...||.|...+...
T Consensus       533 nk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             ccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            3456789999999999999999999999999888763     34799998877643

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

Probab=97.75  E-value=2.9e-05  Score=36.87  Aligned_cols=42  Identities=31%  Similarity=0.872  Sum_probs=21.7

Q ss_pred             cccccccccCc--eec--CCCChhhHHhHHHHhh-CCCCcccccccc
Q 037842           18 CGICLDTMKEE--SST--KCGHVFCKSCIVDAIR-LQGKCPTCRTRM   59 (78)
Q Consensus        18 C~iC~~~~~~~--~~~--~CgH~fc~~C~~~~~~-~~~~CP~C~~~~   59 (78)
                      ||+|.+.+...  ...  +||+..|..|+.+.+. ..+.||.||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            68888887433  233  6899999999999886 477999999864

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

Probab=97.71  E-value=4.1e-06  Score=53.10  Aligned_cols=43  Identities=33%  Similarity=0.832  Sum_probs=35.5

Q ss_pred             cccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ....|+||++...+-+.++|||. -|..|-.+.    ..||+||+.+.
T Consensus       299 ~~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  299 TRRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            36789999999999999999995 588885443    37999998764

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

Probab=97.70  E-value=1e-05  Score=57.05  Aligned_cols=51  Identities=24%  Similarity=0.525  Sum_probs=41.5

Q ss_pred             CcccccccccccccCcee---cCCCChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           13 EVRFTCGICLDTMKEESS---TKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~---~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      .....|++|+..+.+...   ..|+|.||..|+..|.+....||+||..|..-.
T Consensus       121 ~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  121 HVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            345678999888776532   479999999999999999899999999886433

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

Probab=97.68  E-value=2.8e-05  Score=49.75  Aligned_cols=43  Identities=35%  Similarity=0.869  Sum_probs=37.3

Q ss_pred             ccccccccccccCceecC-CCChhhHHhHHHHhh-CCCCcccccc
Q 037842           15 RFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIR-LQGKCPTCRT   57 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~-~~~~CP~C~~   57 (78)
                      .+.|++|..++.+|+.++ |+|.||..|+...+. ....||.|..
T Consensus       274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            389999999999999885 899999999987765 4568999965

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.67  E-value=1.5e-05  Score=38.79  Aligned_cols=47  Identities=23%  Similarity=0.585  Sum_probs=35.3

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      ...|-.|...-...+.++|||..|..|+..+  +-..||.|..++...+
T Consensus         7 ~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    7 EQPCVFCGFVGTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ceeEEEccccccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence            4456666666666788899999999998643  3457999999887654

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

Probab=97.66  E-value=1.7e-05  Score=57.03  Aligned_cols=49  Identities=22%  Similarity=0.621  Sum_probs=38.0

Q ss_pred             CCccccccccccccc--C---ce--ecCCCChhhHHhHHHHhhC--CCCccccccccc
Q 037842           12 GEVRFTCGICLDTMK--E---ES--STKCGHVFCKSCIVDAIRL--QGKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~--~---~~--~~~CgH~fc~~C~~~~~~~--~~~CP~C~~~~~   60 (78)
                      .+...+|+||...+.  +   |.  -..|.|.|+..|+..|+..  ..+||.||..++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            445678999999876  2   22  2359999999999999986  458999997664

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.61  E-value=8.3e-05  Score=48.35  Aligned_cols=53  Identities=25%  Similarity=0.693  Sum_probs=40.0

Q ss_pred             ccccccccccccCc----eecCCCChhhHHhHHHHhhC-CCCcccccccccccceeee
Q 037842           15 RFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        15 ~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~   67 (78)
                      +..||+|++.+...    .-.+||...|.-|+...... .+.||.||...+.++++..
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~   71 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV   71 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence            33499999987754    22479999999998765543 5789999999887777643

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

Probab=97.43  E-value=0.00011  Score=48.65  Aligned_cols=34  Identities=38%  Similarity=0.866  Sum_probs=28.9

Q ss_pred             cccccccccccccCc---eecCCCChhhHHhHHHHhh
Q 037842           14 VRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIR   47 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~   47 (78)
                      ..+.|.||++.....   +.++|+|+||+.|+..|+.
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT  219 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence            357899999987763   4679999999999999986

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

Probab=97.42  E-value=0.00012  Score=39.95  Aligned_cols=27  Identities=26%  Similarity=0.604  Sum_probs=24.7

Q ss_pred             CCCChhhHHhHHHHhhCCCCccccccc
Q 037842           32 KCGHVFCKSCIVDAIRLQGKCPTCRTR   58 (78)
Q Consensus        32 ~CgH~fc~~C~~~~~~~~~~CP~C~~~   58 (78)
                      .|.|.|+.-|+.+|++.+..||++.+.
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            599999999999999999999999654

>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=97.32  E-value=0.0002  Score=41.87  Aligned_cols=52  Identities=19%  Similarity=0.501  Sum_probs=36.4

Q ss_pred             cccccccccccccCceecCCC------------Chh-hHHhHHHHhhC-------------------------------C
Q 037842           14 VRFTCGICLDTMKEESSTKCG------------HVF-CKSCIVDAIRL-------------------------------Q   49 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~Cg------------H~f-c~~C~~~~~~~-------------------------------~   49 (78)
                      ++..||||++...+.|+|-|.            ..| +..|+.++.+.                               .
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE   80 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence            467899999999999887432            211 56788877541                               1


Q ss_pred             CCccccccccccccee
Q 037842           50 GKCPTCRTRMSVRSIR   65 (78)
Q Consensus        50 ~~CP~C~~~~~~~~~~   65 (78)
                      ..||+||..+....+.
T Consensus        81 L~CPLCRG~V~GWtvv   96 (162)
T PF07800_consen   81 LACPLCRGEVKGWTVV   96 (162)
T ss_pred             ccCccccCceeceEEc
Confidence            1399999998765554

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.

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

Probab=97.32  E-value=0.00017  Score=48.41  Aligned_cols=35  Identities=23%  Similarity=0.623  Sum_probs=31.6

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhh
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR   47 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~   47 (78)
                      ++++.|+||...+++|++++|+|..|..|....+.
T Consensus         2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhccCceEeecccHHHHHHHHhhcc
Confidence            56789999999999999999999999999986654

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

Probab=97.29  E-value=0.00017  Score=46.91  Aligned_cols=47  Identities=34%  Similarity=0.716  Sum_probs=36.0

Q ss_pred             CCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .......|.||.+...+.+.++|||+-|  |..-... ...||+||+.+.
T Consensus       301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~  347 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIR  347 (355)
T ss_pred             ccCCCCceEEecCCccceeeecCCcEEE--chHHHhh-CCCCchhHHHHH
Confidence            3445578999999999999999999977  6554433 345999998765

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

Probab=97.25  E-value=8.9e-05  Score=45.79  Aligned_cols=49  Identities=27%  Similarity=0.749  Sum_probs=33.2

Q ss_pred             ccccccccccc-Cc-eecCCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842           16 FTCGICLDTMK-EE-SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        16 ~~C~iC~~~~~-~~-~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      ..|..|...-. ++ .++.|+|+||..|....  ....||.|++++....+..
T Consensus         4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i~l~~   54 (233)
T KOG4739|consen    4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRIIQLNR   54 (233)
T ss_pred             EEeccccccCCCCceeeeechhhhhhhhcccC--Cccccccccceeeeeeccc
Confidence            45777766444 33 35689999999997533  2338999999876544443

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

Probab=97.23  E-value=0.00028  Score=46.43  Aligned_cols=56  Identities=21%  Similarity=0.469  Sum_probs=43.2

Q ss_pred             ccccccccccccc---CceecCCCChhhHHhHHHHhhCC---CCcccccccccccceeeecc
Q 037842           14 VRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        14 ~~~~C~iC~~~~~---~~~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~~~~~~~~~~~~~   69 (78)
                      ..+.|||=.+--.   .|+.+.|||+.++.-+.+...+.   .+||.|-......+.++++|
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~~~~~kql~F  394 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQLASDTKQLYF  394 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccCHHhcccccC
Confidence            4578998666433   36889999999999998877653   47999988877777777664

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

Probab=97.22  E-value=0.00015  Score=47.84  Aligned_cols=44  Identities=25%  Similarity=0.810  Sum_probs=35.6

Q ss_pred             cccccccccccccCc----eecCCCChhhHHhHHHHhhCC--CCcccccc
Q 037842           14 VRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQ--GKCPTCRT   57 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~~--~~CP~C~~   57 (78)
                      ..+.|..|-+.+...    -.++|.|+|+..|+..++.++  +.||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            457899999876532    357999999999999998764  48999983

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

Probab=97.13  E-value=0.00061  Score=44.57  Aligned_cols=51  Identities=31%  Similarity=0.720  Sum_probs=41.6

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHH--hhCCCCcccccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDA--IRLQGKCPTCRTRM   59 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~--~~~~~~CP~C~~~~   59 (78)
                      ....++...|.||.+.+.-...+||+|..|--|..+.  +..++.|+.||..-
T Consensus        55 ddtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          55 DDTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            4456677899999999888888999999999998654  44678899998754

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

Probab=97.09  E-value=0.00018  Score=50.47  Aligned_cols=50  Identities=32%  Similarity=0.790  Sum_probs=41.7

Q ss_pred             cccccccccccCceecCCCChhhHHhHHHHhhCC--CCcccccccccccceee
Q 037842           16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ--GKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~--~~CP~C~~~~~~~~~~~   66 (78)
                      ..|.+|.+ ...++.+.|||.||..|+...+...  ..||.|+..+..+.+..
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhh
Confidence            78999999 7778889999999999999887753  37999998887665544

>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=97.07  E-value=0.00076  Score=31.29  Aligned_cols=38  Identities=24%  Similarity=0.722  Sum_probs=24.0

Q ss_pred             cccccccccCceecC---CCChhhHHhHHHHhhCCC--Ccccc
Q 037842           18 CGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQG--KCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~~~~~~---CgH~fc~~C~~~~~~~~~--~CP~C   55 (78)
                      |.+|.+.....+.-+   |+-.++..|+..++....  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            678888888776654   888999999999998755  69987

; PDB: 3NW0_A 2CT0_A.

>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=97.04  E-value=0.0006  Score=43.31  Aligned_cols=54  Identities=26%  Similarity=0.659  Sum_probs=40.5

Q ss_pred             cccccccc-ccCce--e--cCCCChhhHHhHHHHhhC-CCCcccccccccccceeeeccC
Q 037842           17 TCGICLDT-MKEES--S--TKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        17 ~C~iC~~~-~~~~~--~--~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      .||+|... +.+|.  +  -+|||..|.+|+...+.. ...||.|...+....++...|.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~fE   61 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTFE   61 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhcc
Confidence            58888863 55552  1  279999999999998775 5689999988877776665554

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

Probab=96.94  E-value=0.00092  Score=38.10  Aligned_cols=50  Identities=32%  Similarity=0.755  Sum_probs=40.9

Q ss_pred             cccccccccccccCceecC----CCChhhHHhHHHHhhC---CCCcccccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTK----CGHVFCKSCIVDAIRL---QGKCPTCRTRMSVRS   63 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~----CgH~fc~~C~~~~~~~---~~~CP~C~~~~~~~~   63 (78)
                      .-++|.||.+...+...+.    ||-..|..|....|+.   ...||+|+.++....
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            5689999999988887762    9999999999887775   357999999887543

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

Probab=96.74  E-value=0.00083  Score=42.56  Aligned_cols=44  Identities=30%  Similarity=0.745  Sum_probs=35.4

Q ss_pred             cccccccccccC------ceecCCCChhhHHhHHHHhhCCC-Ccccccccc
Q 037842           16 FTCGICLDTMKE------ESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRM   59 (78)
Q Consensus        16 ~~C~iC~~~~~~------~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~   59 (78)
                      ..|-||.+.+..      |..+.|||.+|..|+...+.... .||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            568899888774      45678999999999988777643 689999884

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

Probab=96.71  E-value=0.0007  Score=43.43  Aligned_cols=49  Identities=27%  Similarity=0.640  Sum_probs=37.8

Q ss_pred             cccccccccccccCc---eecCCCChhhHHhHHHHhhC-----------------------CCCccccccccccc
Q 037842           14 VRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRL-----------------------QGKCPTCRTRMSVR   62 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~~-----------------------~~~CP~C~~~~~~~   62 (78)
                      ....|.||+.-|.+.   ..++|.|.|+..|+.+++..                       ...||+||..+..+
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            356799999988764   35689999999999998751                       11499999988643

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

Probab=96.69  E-value=0.0004  Score=37.58  Aligned_cols=32  Identities=28%  Similarity=0.543  Sum_probs=26.2

Q ss_pred             CCcccccccccccccCce--ecCCCChhhHHhHH
Q 037842           12 GEVRFTCGICLDTMKEES--STKCGHVFCKSCIV   43 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~--~~~CgH~fc~~C~~   43 (78)
                      .+++..|++|...+.+..  ..||||.||..|+.
T Consensus        75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            455678999999999874  35999999999975

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 [].

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

Probab=96.63  E-value=0.0013  Score=42.16  Aligned_cols=46  Identities=28%  Similarity=0.748  Sum_probs=37.3

Q ss_pred             CCcccccccccccccCce-ecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           12 GEVRFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~-~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ..+-+.||||.+.+..|+ +-.=||..|..|-.   +....||.|+.++.
T Consensus        45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            445689999999999885 45789999999965   33457999999886

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

Probab=96.25  E-value=0.0066  Score=40.81  Aligned_cols=58  Identities=24%  Similarity=0.660  Sum_probs=42.4

Q ss_pred             CcccccccccccccC-ceecCCCChhhHHhHHHHhhCC--------CCccc--ccccccccceeeeccC
Q 037842           13 EVRFTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQ--------GKCPT--CRTRMSVRSIRRIFFP   70 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~-~~~~~CgH~fc~~C~~~~~~~~--------~~CP~--C~~~~~~~~~~~~~~~   70 (78)
                      .....|.||.+.+.. .+.+.|||.||..|+..++..+        ..||.  |...+....+..+.-+
T Consensus        68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~  136 (444)
T KOG1815|consen   68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSD  136 (444)
T ss_pred             CccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCC
Confidence            445789999999886 5567899999999999998742        24655  7766666665555433

>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=96.25  E-value=0.0017  Score=40.61  Aligned_cols=60  Identities=18%  Similarity=0.451  Sum_probs=42.9

Q ss_pred             ccccccccccc-ccCc-e-e-c-C-CCChhhHHhHHHHhhCC-CCcc--cccccccccceeeeccCCCC
Q 037842           14 VRFTCGICLDT-MKEE-S-S-T-K-CGHVFCKSCIVDAIRLQ-GKCP--TCRTRMSVRSIRRIFFPQLQ   73 (78)
Q Consensus        14 ~~~~C~iC~~~-~~~~-~-~-~-~-CgH~fc~~C~~~~~~~~-~~CP--~C~~~~~~~~~~~~~~~~~~   73 (78)
                      .+..||+|... +-+| + . + | |-|.+|.+|+.+.+... ..||  -|.+-+....++...|....
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~   77 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDIT   77 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhh
Confidence            45689999874 4455 2 2 2 4 99999999999998864 4899  58877766666666555443

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.21  E-value=0.0083  Score=35.24  Aligned_cols=51  Identities=22%  Similarity=0.514  Sum_probs=36.4

Q ss_pred             CCCcccccccccccccCceecCC--CC---hhhHHhHHHHhhCC--CCccccccccccc
Q 037842           11 VGEVRFTCGICLDTMKEESSTKC--GH---VFCKSCIVDAIRLQ--GKCPTCRTRMSVR   62 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~C--gH---~fc~~C~~~~~~~~--~~CP~C~~~~~~~   62 (78)
                      .+..+..|-||.+...+ ..-+|  ..   ..+..|+++|+..+  ..|+.|+.++...
T Consensus         4 ~s~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          4 VSLMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             cCCCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            34556789999987542 23354  33   34999999999864  4799999887644

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

Probab=96.17  E-value=0.0035  Score=44.98  Aligned_cols=41  Identities=27%  Similarity=0.672  Sum_probs=34.2

Q ss_pred             ccccccccccccCce-ecCCCChhhHHhHHHHhhCCCCccccccc
Q 037842           15 RFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRTR   58 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~-~~~CgH~fc~~C~~~~~~~~~~CP~C~~~   58 (78)
                      .-.|..|...+.-|+ ...|||.|+..|+.   .+...||.|+..
T Consensus       840 ~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eeeecccCCccccceeeeecccHHHHHhhc---cCcccCCccchh
Confidence            357999999999884 57999999999997   445689999763

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

Probab=96.17  E-value=0.0026  Score=41.04  Aligned_cols=43  Identities=28%  Similarity=0.605  Sum_probs=30.4

Q ss_pred             cccccccccccCc-eecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           16 FTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        16 ~~C~iC~~~~~~~-~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ..|.-|-..+... .+++|.|+||.+|..  ....+.||.|...+.
T Consensus        91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr--~~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIAIYGRMIPCKHVFCLECAR--SDSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcceeeecccccchhhhhhhhh--cCccccCcCcccHHH
Confidence            4566666655443 567999999999975  344668999976653

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

Probab=96.01  E-value=0.0069  Score=36.37  Aligned_cols=49  Identities=29%  Similarity=0.725  Sum_probs=34.2

Q ss_pred             cccccccccccccCce-------ecCCCChhhHHhHHHHhhC-----------CCCccccccccccc
Q 037842           14 VRFTCGICLDTMKEES-------STKCGHVFCKSCIVDAIRL-----------QGKCPTCRTRMSVR   62 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~-------~~~CgH~fc~~C~~~~~~~-----------~~~CP~C~~~~~~~   62 (78)
                      .-..|.||..+--+..       -..||..|+.-|+..|++.           -+.||.|..++..+
T Consensus       164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            3345677766543321       2479999999999999973           13699998887643

>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=95.87  E-value=0.0033  Score=29.72  Aligned_cols=35  Identities=23%  Similarity=0.729  Sum_probs=23.5

Q ss_pred             CceecCCC-ChhhHHhHHHHhhCCCCcccccccccc
Q 037842           27 EESSTKCG-HVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        27 ~~~~~~Cg-H~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      +.-.+.|. |-.|..|+...+.....||+|..+++.
T Consensus        12 ~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   12 NKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             CCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            33456675 778999999988888899999988764

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.

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

Probab=95.80  E-value=0.0038  Score=41.33  Aligned_cols=53  Identities=40%  Similarity=0.928  Sum_probs=35.2

Q ss_pred             cccccccccccccCc----eecCCCChhhHHhHHHHhhCC------CCccc--ccccccccceee
Q 037842           14 VRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQ------GKCPT--CRTRMSVRSIRR   66 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~~------~~CP~--C~~~~~~~~~~~   66 (78)
                      ....|.||.......    ....|+|.||..|+.+++..+      ..||.  |...+.......
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~~c~~  209 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLESCRK  209 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHHHHhh
Confidence            467899999433322    235799999999999988742      25765  655555444333

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

Probab=95.78  E-value=0.0066  Score=38.58  Aligned_cols=43  Identities=30%  Similarity=0.696  Sum_probs=35.4

Q ss_pred             ccccccccccccC----ceecCCCChhhHHhHHHHhhCCCCcccccc
Q 037842           15 RFTCGICLDTMKE----ESSTKCGHVFCKSCIVDAIRLQGKCPTCRT   57 (78)
Q Consensus        15 ~~~C~iC~~~~~~----~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~   57 (78)
                      ...||||.+.+..    +..++|||..+..|+.........||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            3459999997654    356799999999999998877789999988

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

Probab=95.75  E-value=0.0099  Score=36.96  Aligned_cols=45  Identities=20%  Similarity=0.561  Sum_probs=35.9

Q ss_pred             ccccccccccccCc--eecCCCChhhHHhHHHHhhC--------CCCcccccccc
Q 037842           15 RFTCGICLDTMKEE--SSTKCGHVFCKSCIVDAIRL--------QGKCPTCRTRM   59 (78)
Q Consensus        15 ~~~C~iC~~~~~~~--~~~~CgH~fc~~C~~~~~~~--------~~~CP~C~~~~   59 (78)
                      .-.|.+|...+...  +.+.|-|.|+++|+..|..+        ...||.|...+
T Consensus        50 ~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei  104 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI  104 (299)
T ss_pred             CCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence            45688999888754  66789999999999998763        23699998775

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

Probab=95.65  E-value=0.0019  Score=47.99  Aligned_cols=45  Identities=31%  Similarity=0.777  Sum_probs=39.1

Q ss_pred             CcccccccccccccC-ceecCCCChhhHHhHHHHhhCCCCcccccc
Q 037842           13 EVRFTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGKCPTCRT   57 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~-~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~   57 (78)
                      .....|.||.+.+.+ .....|||.+|..|...|+..+..||.|..
T Consensus      1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             hcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            355689999999994 566789999999999999999999999963

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

Probab=95.52  E-value=0.0038  Score=43.89  Aligned_cols=50  Identities=34%  Similarity=0.750  Sum_probs=40.5

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhhCC---CCcccccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRS   63 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~~~~~~~   63 (78)
                      ..+.|+||...+..|+.+.|.|.||..|+...+...   ..||+|+..+....
T Consensus        20 k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s   72 (684)
T KOG4362|consen   20 KILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRS   72 (684)
T ss_pred             hhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhh
Confidence            457899999999999999999999999998766543   47999986655433

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

Probab=95.50  E-value=0.0088  Score=43.04  Aligned_cols=47  Identities=30%  Similarity=0.740  Sum_probs=35.6

Q ss_pred             CCcccccccccccccCcee----cCCCChhhHHhHHHHhhCC-------CCccccccc
Q 037842           12 GEVRFTCGICLDTMKEESS----TKCGHVFCKSCIVDAIRLQ-------GKCPTCRTR   58 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~----~~CgH~fc~~C~~~~~~~~-------~~CP~C~~~   58 (78)
                      ....+.|.||.+.+.....    ..|-|+|+..||..|-.+.       -.||.|...
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            3456899999998875422    2689999999999997741       169999843

>PHA03096 p28-like protein; Provisional

Probab=95.49  E-value=0.011  Score=37.86  Aligned_cols=42  Identities=29%  Similarity=0.457  Sum_probs=29.5

Q ss_pred             cccccccccccCc--------eecCCCChhhHHhHHHHhhCC---CCcccccc
Q 037842           16 FTCGICLDTMKEE--------SSTKCGHVFCKSCIVDAIRLQ---GKCPTCRT   57 (78)
Q Consensus        16 ~~C~iC~~~~~~~--------~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~   57 (78)
                      ..|.||++.....        ....|.|.||..|+..|....   ..||.|+.
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            5799999975532        233699999999999998742   24444443

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

Probab=95.46  E-value=0.0061  Score=46.68  Aligned_cols=49  Identities=20%  Similarity=0.588  Sum_probs=36.8

Q ss_pred             CCcccccccccccccC---ceecCCCChhhHHhHHHHhhCC----------CCccccccccc
Q 037842           12 GEVRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQ----------GKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~----------~~CP~C~~~~~   60 (78)
                      -+.+..|.||+..--.   .+.+.|+|.|+..|..+.+.+.          ..||+|..++.
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3456689999875332   2678999999999998876642          15999988875

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

Probab=95.30  E-value=0.015  Score=38.24  Aligned_cols=33  Identities=24%  Similarity=0.748  Sum_probs=25.6

Q ss_pred             CCChhhHHhHHHHhhC-------------CCCccccccccccccee
Q 037842           33 CGHVFCKSCIVDAIRL-------------QGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        33 CgH~fc~~C~~~~~~~-------------~~~CP~C~~~~~~~~~~   65 (78)
                      |....|..|+.+|+..             +..||.||+.+-..|+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV~  356 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDVC  356 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeeee
Confidence            5667799999998863             23699999998877654

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

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.22  E-value=0.022  Score=36.72  Aligned_cols=41  Identities=27%  Similarity=0.778  Sum_probs=31.3

Q ss_pred             CCCChhhHHhHHHHhhC-------------CCCcccccccccccceeeeccCCC
Q 037842           32 KCGHVFCKSCIVDAIRL-------------QGKCPTCRTRMSVRSIRRIFFPQL   72 (78)
Q Consensus        32 ~CgH~fc~~C~~~~~~~-------------~~~CP~C~~~~~~~~~~~~~~~~~   72 (78)
                      -|....|.+|+.+|+..             +..||.||+.+-..++.-+-+.-.
T Consensus       324 ~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~~~~~  377 (381)
T KOG3899|consen  324 ICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVDFDYI  377 (381)
T ss_pred             ccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEEeeee
Confidence            36778899999998752             336999999998888876655443

>PHA02862 5L protein; Provisional

Probab=95.03  E-value=0.026  Score=32.75  Aligned_cols=46  Identities=28%  Similarity=0.611  Sum_probs=33.2

Q ss_pred             cccccccccccCceecCCCC-----hhhHHhHHHHhhC--CCCccccccccccc
Q 037842           16 FTCGICLDTMKEESSTKCGH-----VFCKSCIVDAIRL--QGKCPTCRTRMSVR   62 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~~CgH-----~fc~~C~~~~~~~--~~~CP~C~~~~~~~   62 (78)
                      ..|=||.+.-.+. .-||.-     .-|..|+.+|+..  +..|+.|+.++..+
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            4688999876544 345433     3589999999975  44799999887543

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

Probab=94.95  E-value=0.02  Score=37.25  Aligned_cols=55  Identities=24%  Similarity=0.394  Sum_probs=39.0

Q ss_pred             ccccccccccccc---CceecCCCChhhHHhHHHHhhCC---CCcccccccccccceeeec
Q 037842           14 VRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        14 ~~~~C~iC~~~~~---~~~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~~~~~~~~~~~~   68 (78)
                      .-+.||+=.+.-.   .|+++.|||+.-..-+.+..++.   ..||.|-......++.+.+
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvr  395 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVR  395 (396)
T ss_pred             ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhccc
Confidence            3478888666433   36899999999988887765542   3799997766666665544

>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=94.93  E-value=0.028  Score=26.78  Aligned_cols=43  Identities=19%  Similarity=0.560  Sum_probs=21.4

Q ss_pred             ccccccccccccCceec-CCCChhhHHhHHHHhh---C--CCCccccccc
Q 037842           15 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIR---L--QGKCPTCRTR   58 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~---~--~~~CP~C~~~   58 (78)
                      .+.||+-...+..|+.. .|.|.-|.+ +..|+.   .  .-.||+|.++
T Consensus         2 sL~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    2 SLRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             ESB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            36799999999999865 799986643 223333   2  2269999753

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.

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

Probab=94.91  E-value=0.01  Score=41.75  Aligned_cols=42  Identities=31%  Similarity=0.728  Sum_probs=32.1

Q ss_pred             cCCCccccccccccccc----CceecCCCChhhHHhHHHHhhCCCCcc
Q 037842           10 VVGEVRFTCGICLDTMK----EESSTKCGHVFCKSCIVDAIRLQGKCP   53 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~----~~~~~~CgH~fc~~C~~~~~~~~~~CP   53 (78)
                      ....+-+.|+||+..+.    .|+.+.|||+.|..|+......  .||
T Consensus         6 ~~w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn~--scp   51 (861)
T KOG3161|consen    6 LKWVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYNA--SCP   51 (861)
T ss_pred             hhhHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhhc--cCC
Confidence            34456678999988766    4688899999999999876554  455

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.80  E-value=0.061  Score=34.00  Aligned_cols=54  Identities=19%  Similarity=0.389  Sum_probs=41.2

Q ss_pred             CcccccccccccccCc----eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeec
Q 037842           13 EVRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ...+.|||-.-.+...    ....|||+|-..-+.+.-  ...|+.|.+.+...+++.+-
T Consensus       109 ~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvlN  166 (293)
T KOG3113|consen  109 RARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVLN  166 (293)
T ss_pred             cceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEeeC
Confidence            4558899987777765    334899999988776643  56899999999888877653

>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=94.41  E-value=0.026  Score=32.28  Aligned_cols=33  Identities=27%  Similarity=0.619  Sum_probs=25.8

Q ss_pred             ccccccccccccC--ce-ecCCC------ChhhHHhHHHHhh
Q 037842           15 RFTCGICLDTMKE--ES-STKCG------HVFCKSCIVDAIR   47 (78)
Q Consensus        15 ~~~C~iC~~~~~~--~~-~~~Cg------H~fc~~C~~~~~~   47 (78)
                      ..+|.||++.+.+  .+ .+++|      |.||..|+.+|..
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            5789999999887  43 34554      6699999999954

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.

>KOG0289 consensus mRNA splicing factor [General function prediction only]

Probab=94.10  E-value=0.1  Score=35.35  Aligned_cols=60  Identities=28%  Similarity=0.401  Sum_probs=52.2

Q ss_pred             ccccccccccCceecC-CCChhhHHhHHHHhhCCCCcccccccccccceeeeccCCCCCCC
Q 037842           17 TCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQPPA   76 (78)
Q Consensus        17 ~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~   76 (78)
                      .|+|--+..+.|+.-+ -||+|=++-+++++...+++|+-..++..+++.++..+....|.
T Consensus         2 ~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~e~G~DPIt~~pLs~eelV~Ik~~~~v~pk   62 (506)
T KOG0289|consen    2 VCAISGEVPEEPVVSPVSGHVFEKRLIEQYIAETGKDPITNEPLSIEELVEIKVPAQVRPK   62 (506)
T ss_pred             eecccCCCCCCccccccccchHHHHHHHHHHHHcCCCCCCCCcCCHHHeeeccccccccCC
Confidence            5888889999998764 99999999999999999999999999999999998777665443

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

Probab=93.47  E-value=0.032  Score=35.83  Aligned_cols=36  Identities=25%  Similarity=0.761  Sum_probs=30.2

Q ss_pred             cccccccccccccCceecCC----CChhhHHhHHHHhhCC
Q 037842           14 VRFTCGICLDTMKEESSTKC----GHVFCKSCIVDAIRLQ   49 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~C----gH~fc~~C~~~~~~~~   49 (78)
                      ..+.|.+|.+.+++...+.|    .|.||..|-.+.++.+
T Consensus       267 apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q  306 (352)
T KOG3579|consen  267 APLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ  306 (352)
T ss_pred             CceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence            34889999999999876655    7999999999988854

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.78  E-value=0.072  Score=33.64  Aligned_cols=36  Identities=19%  Similarity=0.254  Sum_probs=31.1

Q ss_pred             CCcccccccccccccCceecCCCChhhHHhHHHHhh
Q 037842           12 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR   47 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~   47 (78)
                      ..+-.-|.+|+....+|+..+=||.|++.||.+++.
T Consensus        40 iK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il   75 (303)
T KOG3039|consen   40 IKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL   75 (303)
T ss_pred             cCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence            334456789999999999999999999999988875

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

Probab=92.67  E-value=0.035  Score=34.00  Aligned_cols=39  Identities=26%  Similarity=0.628  Sum_probs=29.7

Q ss_pred             cccccccccCceecCCCCh-hhHHhHHHHhhCCCCccccccccc
Q 037842           18 CGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        18 C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      |-.|.+.-.....+||.|. +|..|-..    ...||+|+....
T Consensus       161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            8888887777677899985 78888543    346999987654

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

Probab=92.37  E-value=0.09  Score=37.97  Aligned_cols=39  Identities=36%  Similarity=0.808  Sum_probs=30.8

Q ss_pred             cccccccccccCce--ecCCCChhhHHhHHHHhhCCCCccc
Q 037842           16 FTCGICLDTMKEES--STKCGHVFCKSCIVDAIRLQGKCPT   54 (78)
Q Consensus        16 ~~C~iC~~~~~~~~--~~~CgH~fc~~C~~~~~~~~~~CP~   54 (78)
                      +.|++|.-.+....  -..|+|+.+.+|...|+.....||.
T Consensus      1029 ~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            55777766555442  2479999999999999999889987

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

Probab=92.04  E-value=0.075  Score=35.34  Aligned_cols=40  Identities=28%  Similarity=0.548  Sum_probs=30.8

Q ss_pred             ccccccccccccCc-----eecCCCChhhHHhHHHHhhCCCCccc
Q 037842           15 RFTCGICLDTMKEE-----SSTKCGHVFCKSCIVDAIRLQGKCPT   54 (78)
Q Consensus        15 ~~~C~iC~~~~~~~-----~~~~CgH~fc~~C~~~~~~~~~~CP~   54 (78)
                      -..|+.|...+...     ++-.|||-||+.|...|...+..|..
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~  350 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYE  350 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccC
Confidence            46799999876532     44569999999999999887776644

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

Probab=91.74  E-value=0.12  Score=37.56  Aligned_cols=36  Identities=22%  Similarity=0.503  Sum_probs=27.4

Q ss_pred             CCcccccccccccccC-c-eecCCCChhhHHhHHHHhh
Q 037842           12 GEVRFTCGICLDTMKE-E-SSTKCGHVFCKSCIVDAIR   47 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~-~-~~~~CgH~fc~~C~~~~~~   47 (78)
                      .+....|.+|...+.. | +..+|||.|++.|+.+...
T Consensus       814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             ecCccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence            3455689999987654 4 3459999999999987654

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

Probab=91.20  E-value=0.13  Score=31.67  Aligned_cols=45  Identities=18%  Similarity=0.491  Sum_probs=37.0

Q ss_pred             cccccccccccccCceec-CCCChhhHHhHHHHhhCCCCccccccc
Q 037842           14 VRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTR   58 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~   58 (78)
                      .-..|.+|.......+.. +|+-.++..|+..++.....||.|.--
T Consensus       180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d~  225 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGDL  225 (235)
T ss_pred             HHHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhcc
Confidence            346799999988776654 688889999999999998899999543

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

Probab=91.09  E-value=0.22  Score=24.37  Aligned_cols=45  Identities=27%  Similarity=0.745  Sum_probs=29.2

Q ss_pred             ccccccccccCce--ecCC--CChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           17 TCGICLDTMKEES--STKC--GHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        17 ~C~iC~~~~~~~~--~~~C--gH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      .|-.|-..+....  ..-|  ..+||..|....+  ...||.|...+..+-
T Consensus         7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~RP   55 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRRP   55 (57)
T ss_pred             CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccCC
Confidence            3555666554322  2223  3479999998876  457999998876543

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

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

Probab=91.05  E-value=0.46  Score=34.84  Aligned_cols=57  Identities=18%  Similarity=0.399  Sum_probs=40.6

Q ss_pred             CCccccccccccccc--CceecCCCCh-----hhHHhHHHHhhC--CCCcccccccccccceeeec
Q 037842           12 GEVRFTCGICLDTMK--EESSTKCGHV-----FCKSCIVDAIRL--QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~--~~~~~~CgH~-----fc~~C~~~~~~~--~~~CP~C~~~~~~~~~~~~~   68 (78)
                      .+++..|-||...-.  +|..-||..+     .+..|+.+|+..  ..+|-+|+.++.-+++-..-
T Consensus         9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~   74 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKED   74 (1175)
T ss_pred             CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccC
Confidence            445689999987533  4555566543     689999999985  45899999988766654433

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

Probab=89.45  E-value=0.15  Score=23.85  Aligned_cols=38  Identities=34%  Similarity=0.718  Sum_probs=22.3

Q ss_pred             cccccccccC--ceecCCCC-----hhhHHhHHHHhhC--CCCcccc
Q 037842           18 CGICLDTMKE--ESSTKCGH-----VFCKSCIVDAIRL--QGKCPTC   55 (78)
Q Consensus        18 C~iC~~~~~~--~~~~~CgH-----~fc~~C~~~~~~~--~~~CP~C   55 (78)
                      |-||++...+  +...+|+-     ..+..|+.+|+..  ...|++|
T Consensus         1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            5677776553  34556542     3588999999984  3467766

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.10  E-value=0.48  Score=23.00  Aligned_cols=31  Identities=19%  Similarity=0.603  Sum_probs=23.4

Q ss_pred             ccccccccccccc--Ccee-c-CCCChhhHHhHHH
Q 037842           14 VRFTCGICLDTMK--EESS-T-KCGHVFCKSCIVD   44 (78)
Q Consensus        14 ~~~~C~iC~~~~~--~~~~-~-~CgH~fc~~C~~~   44 (78)
                      ....|++|.+.|.  +.+. - .||-.+++.|+..
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            3467999999994  4433 3 5999999999754

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=88.23  E-value=0.017  Score=29.54  Aligned_cols=40  Identities=28%  Similarity=0.701  Sum_probs=20.8

Q ss_pred             cccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +.||.|...+.-.    =++.+|..|-..+ .....||.|..++.
T Consensus         2 ~~CP~C~~~L~~~----~~~~~C~~C~~~~-~~~a~CPdC~~~Le   41 (70)
T PF07191_consen    2 NTCPKCQQELEWQ----GGHYHCEACQKDY-KKEAFCPDCGQPLE   41 (70)
T ss_dssp             -B-SSS-SBEEEE----TTEEEETTT--EE-EEEEE-TTT-SB-E
T ss_pred             CcCCCCCCccEEe----CCEEECccccccc-eecccCCCcccHHH
Confidence            5799998876532    1677777776543 33457899887764

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=87.99  E-value=0.24  Score=20.38  Aligned_cols=9  Identities=22%  Similarity=0.552  Sum_probs=4.6

Q ss_pred             ccccccccc
Q 037842           18 CGICLDTMK   26 (78)
Q Consensus        18 C~iC~~~~~   26 (78)
                      ||-|...+.
T Consensus         3 CP~C~~~V~   11 (26)
T PF10571_consen    3 CPECGAEVP   11 (26)
T ss_pred             CCCCcCCch
Confidence            555555443

Several members are annotated as putative helicases.

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=86.05  E-value=0.089  Score=33.52  Aligned_cols=47  Identities=21%  Similarity=0.311  Sum_probs=23.6

Q ss_pred             CCcccccccccccccCceecC-----CCChhhHHhHHHHhhCCCCccccccc
Q 037842           12 GEVRFTCGICLDTMKEESSTK-----CGHVFCKSCIVDAIRLQGKCPTCRTR   58 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~-----CgH~fc~~C~~~~~~~~~~CP~C~~~   58 (78)
                      .+....||||-....-.+...     =.+.+|..|-..|......||.|...
T Consensus       169 ~w~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~  220 (290)
T PF04216_consen  169 GWQRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT  220 (290)
T ss_dssp             -TT-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred             CccCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence            445679999999766544432     24567889999998888899999654

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.87  E-value=0.66  Score=23.92  Aligned_cols=32  Identities=31%  Similarity=0.825  Sum_probs=23.2

Q ss_pred             CCCChhhHHhHHHHhhCCCCccccccccccccee
Q 037842           32 KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        32 ~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~   65 (78)
                      .-.++||..|....+.  +.||.|...+..+.++
T Consensus        26 tfEcTFCadCae~~l~--g~CPnCGGelv~RP~R   57 (84)
T COG3813          26 TFECTFCADCAENRLH--GLCPNCGGELVARPIR   57 (84)
T ss_pred             EEeeehhHhHHHHhhc--CcCCCCCchhhcCcCC
Confidence            3457899999986554  5799998887654443

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

Probab=84.29  E-value=0.069  Score=35.67  Aligned_cols=49  Identities=22%  Similarity=0.567  Sum_probs=39.8

Q ss_pred             ccccccccccccCc----eecCCCChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           15 RFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        15 ~~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      ...+.||...+..-    ..+.|||.+...++..|+.....+|.|+..+....
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~  248 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNG  248 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhh
Confidence            35688988877643    35689999999999999999889999998886543

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

Probab=83.83  E-value=0.76  Score=23.22  Aligned_cols=12  Identities=33%  Similarity=0.916  Sum_probs=8.8

Q ss_pred             hhhHHhHHHHhh
Q 037842           36 VFCKSCIVDAIR   47 (78)
Q Consensus        36 ~fc~~C~~~~~~   47 (78)
                      .||+.|+.+|..
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999987

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

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=81.68  E-value=0.78  Score=29.87  Aligned_cols=45  Identities=20%  Similarity=0.389  Sum_probs=32.7

Q ss_pred             CcccccccccccccCcee-c--CC--CChhhHHhHHHHhhCCCCcccccc
Q 037842           13 EVRFTCGICLDTMKEESS-T--KC--GHVFCKSCIVDAIRLQGKCPTCRT   57 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~-~--~C--gH~fc~~C~~~~~~~~~~CP~C~~   57 (78)
                      +....||+|-....-.+. .  .=  .+.+|..|-..|......||.|..
T Consensus       185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~  234 (309)
T PRK03564        185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ  234 (309)
T ss_pred             cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence            356899999997654432 1  22  345688898899888889999975

>KOG2979 consensus Protein involved in DNA repair [General function prediction only]

Probab=81.26  E-value=0.84  Score=28.98  Aligned_cols=40  Identities=23%  Similarity=0.404  Sum_probs=33.0

Q ss_pred             ccccccccccccCcee-cCCCChhhHHhHHHHhhC--CCCccc
Q 037842           15 RFTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRL--QGKCPT   54 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~-~~CgH~fc~~C~~~~~~~--~~~CP~   54 (78)
                      .++||+=...+.+|+. ..|||+|=+.-+..++..  ...||+
T Consensus       176 s~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv  218 (262)
T KOG2979|consen  176 SNRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPV  218 (262)
T ss_pred             cccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeeccc
Confidence            4789998889999965 479999999999888876  346887

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.25  E-value=0.3  Score=24.30  Aligned_cols=32  Identities=28%  Similarity=0.583  Sum_probs=16.1

Q ss_pred             CcccccccccccccCce---e-cCCCChhhHHhHHH
Q 037842           13 EVRFTCGICLDTMKEES---S-TKCGHVFCKSCIVD   44 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~---~-~~CgH~fc~~C~~~   44 (78)
                      .+...|.+|...|.--.   . -.||++||..|...
T Consensus         7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~   42 (69)
T PF01363_consen    7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQ   42 (69)
T ss_dssp             GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-E
T ss_pred             CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCC
Confidence            44578999999885321   1 26999999888754

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=80.40  E-value=2.1  Score=22.94  Aligned_cols=37  Identities=24%  Similarity=0.779  Sum_probs=27.1

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ...|-||...+..+     ||.||..|..    .++.|.+|...+.
T Consensus        44 ~~~C~~CK~~v~q~-----g~~YCq~CAY----kkGiCamCGKki~   80 (90)
T PF10235_consen   44 SSKCKICKTKVHQP-----GAKYCQTCAY----KKGICAMCGKKIL   80 (90)
T ss_pred             CccccccccccccC-----CCccChhhhc----ccCcccccCCeec
Confidence            34688887766543     7889999953    3568999998874

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=80.27  E-value=1.3  Score=21.04  Aligned_cols=40  Identities=25%  Similarity=0.557  Sum_probs=21.6

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhhC--CCCccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL--QGKCPTCRTRMS   60 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~--~~~CP~C~~~~~   60 (78)
                      +.+.||.|.+.+...       .+..-+.......  ...||+|...+.
T Consensus         1 ~~f~CP~C~~~~~~~-------~L~~H~~~~H~~~~~~v~CPiC~~~~~   42 (54)
T PF05605_consen    1 DSFTCPYCGKGFSES-------SLVEHCEDEHRSESKNVVCPICSSRVT   42 (54)
T ss_pred             CCcCCCCCCCccCHH-------HHHHHHHhHCcCCCCCccCCCchhhhh
Confidence            357899999854432       1222233222222  346999986544

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	78
4ap4_A	133	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		2e-06
1jm7_A	112	Solution Structure Of The Brca1/bard1 Ring-domain H		6e-06
2ckl_B	165	Ring1b-Bmi1 E3 Catalytic Domain Structure Length =		8e-06
3rpg_C	121	Bmi1RING1B-Ubch5c Complex Structure Length = 121		8e-06
2h0d_B	100	Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquiti		1e-05
2eci_A	86	Solution Structure Of The Ring Domain Of The Human		1e-05
3hcs_A	170	Crystal Structure Of The N-Terminal Domain Of Traf6		1e-05
3hct_A	118	Crystal Structure Of Traf6 In Complex With Ubc13 In		1e-05
3ng2_A	71	Crystal Structure Of The Rnf4 Ring Domain Dimer Len		1e-05
2xeu_A	64	Ring Domain Length = 64		1e-05
2jmd_A	63	Solution Structure Of The Ring Domain Of Human Traf		3e-05
2ea6_A	69	Solution Structure Of The Ring Domain Of The Human		8e-05
2ecw_A	85	Solution Structure Of The Zinc Finger, C3hc4 Type (		6e-04

>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Length = 133

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 3   ESRNGAVVVGEVRFTCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGKCPTC 55
             R   + +G    +C IC+D   E         ST+CGHVFC  C+ D+++    CPTC
Sbjct: 60  HKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTC 119
Query: 56  RTRMSVRSIRRIFF 69
           R +++ +    I+ 
Sbjct: 120 RKKINHKRYHPIYI 133

>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain Heterodimer Length = 112

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRSIRR 66
            C ICL+ +KE  STKC H+FCK C++  +  +    +CP C+  ++ RS++ 
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 75

>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure Length = 165

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 16  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
             C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 55  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 107

>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure Length = 121

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 33/54 (61%), Gaps = 3/54 (5%)
Query: 15  RFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
              C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 53  ELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 106

>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin Ligase Complex Length = 100

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 16 FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTRM-SVRSIR 65
            C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR ++ S RS+R
Sbjct: 35 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 87

>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf Receptor-Associated Factor 6 Protein Length = 86

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPT 54
          E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP 
Sbjct: 23 ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 65

>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6 Length = 170

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPT 54
          E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP 
Sbjct: 16 ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58

>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1 Space Group Length = 118

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/43 (48%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPT 54
          E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP 
Sbjct: 16 ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58

>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer Length = 71

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 17 TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
          +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I+ 
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 71

>pdb|2XEU|A Chain A, Ring Domain Length = 64

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 17 TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF 69
          +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I+ 
Sbjct: 5  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 64

>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6 Length = 63

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPT 54
          ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP 
Sbjct: 6  KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 46

>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 4 Length = 69

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 17 TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS 60
          +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 67

>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Tripartite Motif Protein 30 Length = 85

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGKCPTCRTRMSVRSIR 65
          TC ICL+ +KE  S  C H FC++CI            +G CP CR      +++
Sbjct: 21 TCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLK 75

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	78
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	7e-15
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-15
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-13
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	8e-13
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	4e-12
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-12
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-11
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-11
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-10
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-10
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-10
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	2e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-10
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	6e-10
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	6e-10
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-09
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	3e-09
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	3e-09
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	6e-09
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	6e-09
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-08
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	2e-08
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-08
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	5e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-06
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-07
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	1e-07
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-07
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	1e-07
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-07
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	3e-07
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	3e-07
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-07
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	5e-07
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	6e-07
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-06
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	2e-06
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	1e-05
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-05
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-05
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-04
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-04
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-04

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

 Score = 61.3 bits (149), Expect = 7e-15
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 15 RFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI 67
            +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I
Sbjct: 3  MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 62

Query: 68 F 68
          +
Sbjct: 63 Y 63

>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 = 61.4 bits (149), Expect = 9e-15
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)

Query: 16 FTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF 68
           +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I+
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 70

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

 Score = 57.9 bits (140), Expect = 2e-13
 Identities = 16/45 (35%), Positives = 22/45 (48%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRT 57
          E+ F C IC    +    TKC H FC+SC ++  R   +C  C  
Sbjct: 13 EIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQ 57

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

 Score = 56.4 bits (136), Expect = 8e-13
 Identities = 17/50 (34%), Positives = 21/50 (42%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIR 65
            C ICL T     S  C HVFC  C+  A  L  +C  CR  +    + 
Sbjct: 16 PECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD 65

>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 = 58.6 bits (141), Expect = 4e-12
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 13  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMS 60
                C IC +  K+     CGH+ C SC+      +G+ CP CR  + 
Sbjct: 330 STFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 378

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

 Score = 56.2 bits (135), Expect = 5e-12
 Identities = 14/48 (29%), Positives = 24/48 (50%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS 63
             C IC +   E  +  C H FC  CI + ++ + +CP CR  +  ++
Sbjct: 65  LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT 112

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

 Score = 54.0 bits (130), Expect = 1e-11
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 16 FTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR 66
            CGIC +         +C H +C  CI   +  + +CPTC   ++   ++ 
Sbjct: 23 LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKN 74

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

 Score = 53.0 bits (127), Expect = 2e-11
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 7/54 (12%)

Query: 16 FTCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR 62
           +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +
Sbjct: 16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

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

 Score = 50.9 bits (122), Expect = 1e-10
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 16 FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGKCPTCRT 57
            C IC   + + ++ T+C H FCKSCIV       +CP C  
Sbjct: 16 ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNI 58

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

 Score = 52.7 bits (126), Expect = 1e-10
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMSVR 62
           F C  C + + +  +T+C H  CK C+  + + Q   CP CR  +   
Sbjct: 79  FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 126

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

 Score = 51.5 bits (123), Expect = 2e-10
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVR 62
           F C  C + +    +T C H  CK C+  + R Q   CP CR  +   
Sbjct: 53  FQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

>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 = 51.0 bits (122), Expect = 2e-10
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 16 FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQ-GKCPTCRTRMSVRSIRRIFF 69
          F C IC++ +++      C  + C SCI   +  Q  +CP CR  + +R +    +
Sbjct: 23 FRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRW 78

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 112

 Score = 51.3 bits (123), Expect = 2e-10
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIRR 66
            C ICL+ +KE  STKC H+FCK C++  +  +     CP C+  ++ RS++ 
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 75

>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 = 50.2 bits (120), Expect = 4e-10
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 16 FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGKCPTCRT 57
            C +C     + ++  +C H FCK+CIV  +     CP C  
Sbjct: 16 LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDV 58

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

 Score = 49.0 bits (117), Expect = 6e-10
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSI 64
          E ++ C  C   +     T+CGH FC+SC+   +     KC  C+  +    +
Sbjct: 13 EDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV 65

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

 Score = 51.1 bits (122), Expect = 6e-10
 Identities = 26/53 (49%), Positives = 33/53 (62%), Gaps = 3/53 (5%)

Query: 16  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK-CPTCRTR-MSVRSIR 65
             C ICLD +K   +TK C H FC  CI+ A+R   K CPTCR + +S RS+R
Sbjct: 55  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 107

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

 Score = 49.1 bits (117), Expect = 2e-09
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 16 FTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR 66
            C  C + ++E      C H+FC +C+ D I     CP C T   ++ ++ 
Sbjct: 23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQDLKI 72

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

 Score = 47.4 bits (113), Expect = 3e-09
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTCRTRMSVRSIR 65
            C ICLD +++  +  CGH FC  CI            CP C+T +   +IR
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAIR 73

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

 Score = 47.0 bits (112), Expect = 3e-09
 Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 17 TCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS 60
           C ICL+     S +  C H FC  CI   IR    CP C+  + 
Sbjct: 7  RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

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

 Score = 47.6 bits (113), Expect = 6e-09
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMSVRSIRR 66
            CGIC++ + E  +  C H  CK C    +      CP CR R+S  +   
Sbjct: 16 CQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYH 67

>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} Length = 267

 Score = 49.6 bits (117), Expect = 6e-09
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 8   AVVVGEVRFTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGK--CPT--CRTRMSVR 62
            +  G++  TC I     +    S KC HVF +  I + ++      CP   C   +S+R
Sbjct: 174 QIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR 233

Query: 63  SIR 65
              
Sbjct: 234 DFV 236

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

 Score = 45.7 bits (109), Expect = 1e-08
 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 7/58 (12%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-------CPTCRTRMSVRSIRR 66
           TC ICL+ + E  S  CGH  C++CI  + +           CP C    S   ++ 
Sbjct: 13 VTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQA 70

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

 Score = 46.7 bits (111), Expect = 2e-08
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSIRR 66
          ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP     +    +  
Sbjct: 18 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP 70

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

 Score = 45.8 bits (109), Expect = 2e-08
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 6/57 (10%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK------CPTCRTRMSVRSIRR 66
           TC ICL+ +KE  S  C H FC++CI               CP CR      +++ 
Sbjct: 20 VTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP 76

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

 Score = 44.6 bits (106), Expect = 5e-08
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVD------AIRLQGKCPTCRTRMSVRSIRR 66
           TC ICL+ + +  S  CGH FC++C+          + +  CP CR      +IR 
Sbjct: 20 VTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRP 76

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

 Score = 45.5 bits (107), Expect = 6e-08
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 16 FTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF 68
           +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I+
Sbjct: 8  VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 67

Query: 69 FPQ 71
             
Sbjct: 68 IGS 70

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

 Score = 41.3 bits (96), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 7/75 (9%)

Query: 1   VCESRNGAVVVGEVRFTCGICLDTMKEESS-------TKCGHVFCKSCIVDAIRLQGKCP 53
           +   R   + +G    +C IC+D   E          T+CGHVFC  C+ D+++    CP
Sbjct: 58  INHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCP 117

Query: 54  TCRTRMSVRSIRRIF 68
           TCR +++ +    I+
Sbjct: 118 TCRKKINHKRYHPIY 132

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

 Score = 43.1 bits (102), Expect = 1e-07
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS 60
           C IC+D  + +    C H FC+ CI         CP CR +M+
Sbjct: 17 ECCICMD-GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59

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

 Score = 43.5 bits (103), Expect = 1e-07
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 7/58 (12%)

Query: 15 RFTCGICLDTMKEESST----KCGHVFCKSCIVDAIRLQG---KCPTCRTRMSVRSIR 65
             C IC+++  EE        CGH  C+ C+   +       +CP C     + S+ 
Sbjct: 15 VLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLT 72

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

 Score = 44.1 bits (104), Expect = 1e-07
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMSVRSIRR 66
           +C IC   + +   T C H+FC+ CI+  +++ G  CP+CR       +  
Sbjct: 24 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES 75

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

 Score = 44.7 bits (105), Expect = 1e-07
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 1/65 (1%)

Query: 13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK-CPTCRTRMSVRSIRRIFFPQ 71
          E ++ C  C + ++     +CGH +C  C+   +    + C  C           I    
Sbjct: 29 EAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESS 88

Query: 72 LQPPA 76
             P 
Sbjct: 89 SAFPD 93

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

 Score = 42.8 bits (101), Expect = 2e-07
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 16 FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK--CPTCRTRMSVR 62
            C IC D M +      CG+ +C  CI  A+    +  CPTC       
Sbjct: 16 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP 65

>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 Length = 281

 Score = 44.5 bits (105), Expect = 3e-07
 Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 16  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKC-PTCRTRMSVRSIR 65
               I  + M+E   T  G  + +  I + ++  G   P  R+ ++   + 
Sbjct: 209 LCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLI 259

>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 Length = 61

 Score = 42.0 bits (99), Expect = 3e-07
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 1/53 (1%)

Query: 16 FTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI 67
            C I     +    S K   +F KS +   ++  G  P     +S+  I  I
Sbjct: 4  MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI 56

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

 Score = 42.4 bits (100), Expect = 4e-07
 Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 16 FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGK--CPTCRTR 58
            C IC D M +      CG+ +C  CI  A+    +  CPTC   
Sbjct: 14 LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 63

 Score = 41.6 bits (98), Expect = 5e-07
 Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 3/43 (6%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGK---CPTC 55
            C ICLD +++  +  CGH FC  CI            CP C
Sbjct: 21 VICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 56

 Score = 41.2 bits (97), Expect = 6e-07
 Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 3/45 (6%)

Query: 17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV 61
           C  C    K      C H  C  C+        +CP C+    +
Sbjct: 8  RCQQCQAEAKCPKLLPCLHTLCSGCLE---ASGMQCPICQAPWPL 49

>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} Length = 170

 Score = 42.0 bits (98), Expect = 2e-06
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSIRRIFF 69
          ++ C ICL  ++E   T CGH FCK+CI+ +IR  G KCP     +    +    F
Sbjct: 18 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNF 73

>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 58

 Score = 39.6 bits (93), Expect = 2e-06
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTC 55
           +C +CL+ +KE    +CGH FCK+CI        +   C
Sbjct: 16 ASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPC 55

>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 = 37.6 bits (88), Expect = 1e-05
 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 18 CGICLDTMKEESST----KCGHVFCKSCIVDAIRLQGKCPTCR 56
          C ICL+ +           CGH+  ++C  + ++   +CP C 
Sbjct: 8  CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 38.5 bits (90), Expect = 2e-05
 Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 3/45 (6%)

Query: 18 CGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGKCPTCRTRM 59
          C IC     +        C H F K C+   ++  G CP CR   
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

>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 = 37.0 bits (86), Expect = 3e-05
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 17 TCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS 63
           C +C +      S +   C H+F  SCIV  +     CP CR  ++ ++
Sbjct: 17 ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN 66

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

 Score = 35.1 bits (81), Expect = 2e-04
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 17 TCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGKCPTCRTRM 59
           C +CL+  K         C H F + C++  + ++  CP C   +
Sbjct: 17 LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

 Score = 35.2 bits (81), Expect = 2e-04
 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 3/37 (8%)

Query: 16 FTCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQ 49
            C +CL     E  T    C  +FC  C+   + L 
Sbjct: 6  SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELL 42

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

 Score = 34.1 bits (78), Expect = 5e-04
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 4/44 (9%)

Query: 17 TCGICLDTMKEESST----KCGHVFCKSCIVDAIRLQGKCPTCR 56
           C  C    K+E       +C H F   C+   ++   +CP C+
Sbjct: 28 ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 35.6 bits (81), Expect = 5e-04
 Identities = 11/69 (15%), Positives = 19/69 (27%), Gaps = 19/69 (27%)

Query: 13  EVRFTCGICLDTMKEESS--------TKCGHVFCKSCIVDAIR-----------LQGKCP 53
                C IC     +            KC       C+ +  +             G+CP
Sbjct: 306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCP 365

Query: 54  TCRTRMSVR 62
            C+ ++S  
Sbjct: 366 FCKAKLSTS 374

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	78
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.76
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.76
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.74
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.74
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.73
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.73
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.72
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.71
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.7
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.7
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.7
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.7
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.7
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.7
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.7
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.69
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.68
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.68
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.68
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.67
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.67
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.66
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.66
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.66
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.66
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.65
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.65
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.63
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.63
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.63
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.62
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.61
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.61
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.6
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.6
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.6
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.6
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.59
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.59
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.59
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.59
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.58
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.56
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.55
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.55
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.55
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.54
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.54
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.54
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.54
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.53
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.52
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.51
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.49
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.48
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.46
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.44
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.42
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.41
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.38
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.36
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.36
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.33
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.26
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.23
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.22
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	99.11
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.06
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.71
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.62
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.61
3nw0_A	238	Non-structural maintenance of chromosomes element	97.87
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.58
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	97.42
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	96.11
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.89
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	93.93
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	93.72
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	92.12
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	90.7
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	90.48
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	88.53
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	87.97
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	87.62
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	87.08
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	86.84
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	86.15
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	86.05
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	85.48
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	85.15
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	84.99
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	84.62
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	84.34
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	82.5
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	82.38
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	82.05
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	81.55

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

Probab=99.76  E-value=1.9e-19  Score=91.33  Aligned_cols=59  Identities=36%  Similarity=0.864  Sum_probs=53.0

Q ss_pred             CCCcccccccccccccCc-------eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           11 VGEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~-------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      ..+++..|+||++.+.++       +.++|||.||..|+.+|+..+..||.||..+..+++.++|+
T Consensus         6 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~l   71 (71)
T 3ng2_A            6 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI   71 (71)
T ss_dssp             CCTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCCCCC
T ss_pred             CCCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhheeeccC
Confidence            445678999999999887       78899999999999999998899999999999988888764

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

Probab=99.76  E-value=9.4e-19  Score=89.26  Aligned_cols=62  Identities=26%  Similarity=0.536  Sum_probs=53.4

Q ss_pred             CcccCCCcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceeeec
Q 037842            7 GAVVVGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus         7 ~~~~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ......++.+.|+||++.+.+|+.+ +|||.||..|+..|+.....||+||..+...++....
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A            7 GNLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CCCCCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCCC
T ss_pred             hhHhhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccccccC
Confidence            3445567789999999999999987 9999999999999999888999999999877666543

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

Probab=99.74  E-value=8.1e-19  Score=87.28  Aligned_cols=56  Identities=38%  Similarity=0.942  Sum_probs=51.0

Q ss_pred             cccccccccccccCc-------eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           14 VRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~-------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      ++..|+||++.+.++       +.++|||.||..|+.+|+..+..||.||..+..+++.++++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~l   64 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI   64 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEEECCC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccceeeeeC
Confidence            467899999999876       77899999999999999998889999999999999988874

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

Probab=99.74  E-value=3.4e-18  Score=85.83  Aligned_cols=56  Identities=27%  Similarity=0.663  Sum_probs=48.8

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhh-CCCCcccccccccccce
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGKCPTCRTRMSVRSI   64 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~-~~~~CP~C~~~~~~~~~   64 (78)
                      .....+.+.|+||++.+.+|+.++|||.||..|+.+|+. ....||+||..+..+++
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A            9 VKTVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             CCSCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             hhcCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            445567899999999999999999999999999999995 45689999999887654

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

Probab=99.73  E-value=1.3e-18  Score=88.58  Aligned_cols=58  Identities=29%  Similarity=0.572  Sum_probs=50.8

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      .....+.+.|+||++.+.+++.++|||.||..|+..|+.....||+||..+..+++.+
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   66 (71)
T 2d8t_A            9 TAPSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLDS   66 (71)
T ss_dssp             CCSSSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHSC
T ss_pred             cccCCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhccC
Confidence            3445667899999999999999999999999999999998889999999988765544

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

Probab=99.73  E-value=3.4e-18  Score=88.24  Aligned_cols=57  Identities=19%  Similarity=0.324  Sum_probs=50.4

Q ss_pred             CCCcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~   67 (78)
                      ...+++.|+||++.+.+|+.++|||+||..|+.+|+.. ...||.|+..+...++..+
T Consensus         4 ~~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n   61 (78)
T 1t1h_A            4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             CCcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccC
Confidence            35668999999999999999999999999999999987 6789999999987766554

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

Probab=99.72  E-value=8e-18  Score=85.74  Aligned_cols=55  Identities=33%  Similarity=0.670  Sum_probs=47.9

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhh---CCCCcccccccccccce
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGKCPTCRTRMSVRSI   64 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~---~~~~CP~C~~~~~~~~~   64 (78)
                      ....+.+.|+||++.+.+|+.++|||.||..|+..|+.   ....||+||..+..+++
T Consensus        15 ~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             HhCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            34567789999999999999999999999999999997   35589999999887654

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

Probab=99.71  E-value=1.8e-17  Score=86.29  Aligned_cols=59  Identities=32%  Similarity=0.763  Sum_probs=51.6

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhC------CCCcccccccccccceeeec
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~------~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ....+.+.|+||++.+.+|+.++|||.||..|+..|+..      ...||.||..+..+++..++
T Consensus        14 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~   78 (85)
T 2ecw_A           14 EMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNL   78 (85)
T ss_dssp             CCCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECS
T ss_pred             HhCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCH
Confidence            345677899999999999999999999999999999987      56899999999887776654

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

Probab=99.70  E-value=7.1e-18  Score=86.44  Aligned_cols=55  Identities=29%  Similarity=0.594  Sum_probs=47.3

Q ss_pred             CcccCCCcccccccccccccCceecC-CCChhhHHhHHHHhhCC--CCcccccccccc
Q 037842            7 GAVVVGEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ--GKCPTCRTRMSV   61 (78)
Q Consensus         7 ~~~~~~~~~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~--~~CP~C~~~~~~   61 (78)
                      .......+++.|+||++.+.+|+.++ |||.||..|+..|+...  ..||+||..+..
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            7 GEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             SCCCCSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cccccCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            34555677899999999999999999 99999999999999864  589999997543

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

Probab=99.70  E-value=3e-18  Score=88.49  Aligned_cols=60  Identities=28%  Similarity=0.621  Sum_probs=51.2

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhC-------CCCcccccccccccceeeec
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-------QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-------~~~CP~C~~~~~~~~~~~~~   68 (78)
                      .....+.+.|+||++.+.+|+.++|||.||..|+..|+..       ...||.||..+...++..++
T Consensus         6 ~~~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~   72 (79)
T 2egp_A            6 SGNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQ   72 (79)
T ss_dssp             SCCCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCS
T ss_pred             HhhcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCH
Confidence            3445678999999999999999999999999999999886       55899999999877665544

>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=99.70  E-value=7.1e-18  Score=90.90  Aligned_cols=57  Identities=26%  Similarity=0.653  Sum_probs=50.7

Q ss_pred             CCcccccccccccccCcee-cCCCChhhHHhHHHHhhCC-CCcccccccccccceeeec
Q 037842           12 GEVRFTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQ-GKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~-~~CgH~fc~~C~~~~~~~~-~~CP~C~~~~~~~~~~~~~   68 (78)
                      ..+.+.|+||++.+.+|+. ++|||.||..|+..|+... ..||.||..+...++....
T Consensus        19 l~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~~   77 (100)
T 3lrq_A           19 IAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCR   77 (100)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECT
T ss_pred             CCCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhhH
Confidence            4467899999999999999 8999999999999999987 6999999999887776653

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

Probab=99.70  E-value=1.3e-17  Score=83.41  Aligned_cols=57  Identities=26%  Similarity=0.608  Sum_probs=49.4

Q ss_pred             cccccccccc-cccCc----eecCCCChhhHHhHHHHhhC-CCCcccccccccccceeeeccC
Q 037842           14 VRFTCGICLD-TMKEE----SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        14 ~~~~C~iC~~-~~~~~----~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      ++..|+||++ .+.++    +.++|||+||..|+.+|+.. ...||.||..+..+++...+++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~   64 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE   64 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEECCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccceeeccc
Confidence            4578999999 88888    46799999999999999765 4579999999999999888775

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

Probab=99.70  E-value=9.6e-18  Score=84.45  Aligned_cols=55  Identities=38%  Similarity=0.891  Sum_probs=47.7

Q ss_pred             CcccCCCcccccccccccccCc-------eecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842            7 GAVVVGEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus         7 ~~~~~~~~~~~C~iC~~~~~~~-------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      .......+...|+||++.+.++       +.++|||.||..|+..|+.....||+||..+..
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A            7 GTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             ccccCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3445566788999999999887       788999999999999999988899999988764

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

Probab=99.70  E-value=2.5e-17  Score=85.57  Aligned_cols=51  Identities=31%  Similarity=0.729  Sum_probs=46.4

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ....+.+.|+||++.+.+|+.++|||+||..|+..|+.....||+||..+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           10 EEEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SCCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             ccCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            445567899999999999999999999999999999998889999999975

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

Probab=99.70  E-value=2.4e-17  Score=86.65  Aligned_cols=59  Identities=14%  Similarity=0.099  Sum_probs=52.6

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      .....+.+.|+||++.+.+|+.++|||+||+.||..|+.....||.|+..+...++..+
T Consensus         8 ~~~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn   66 (85)
T 2kr4_A            8 YSDAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPV   66 (85)
T ss_dssp             CTTCCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             hhcCchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchH
Confidence            34456789999999999999999999999999999999988899999999988777654

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

Probab=99.69  E-value=2.9e-17  Score=87.02  Aligned_cols=58  Identities=28%  Similarity=0.546  Sum_probs=47.9

Q ss_pred             cccCCCcccccccccccccCceecC-CCChhhHHhHHHHhhCC--CCcccccccc-ccccee
Q 037842            8 AVVVGEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ--GKCPTCRTRM-SVRSIR   65 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~--~~CP~C~~~~-~~~~~~   65 (78)
                      ......+++.|+||++.+.+|+.++ |||+||..|+..|+...  ..||.||..+ ....+.
T Consensus         6 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~   67 (92)
T 3ztg_A            6 EDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALI   67 (92)
T ss_dssp             SCCCCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCE
T ss_pred             ccccCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccC
Confidence            3445667899999999999999999 99999999999998743  5899999987 333443

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

Probab=99.68  E-value=1.6e-17  Score=84.14  Aligned_cols=58  Identities=28%  Similarity=0.533  Sum_probs=49.6

Q ss_pred             cccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842            8 AVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      ......+...|+||++.+.+ +.++|||.||..|+.+|+.....||+||..+...+...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A            8 RVKQLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCC
T ss_pred             hhhcCCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCccc
Confidence            34456677899999999999 88999999999999999998889999999988655443

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

Probab=99.68  E-value=2.6e-17  Score=85.65  Aligned_cols=59  Identities=32%  Similarity=0.727  Sum_probs=51.1

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhC------CCCcccccccccccceeeec
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~------~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ....+.+.|+||++.+.+|+.++|||.||..|+..|+..      ...||.||..+...++..++
T Consensus        14 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~   78 (85)
T 2ecv_A           14 VNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNR   78 (85)
T ss_dssp             CCCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSC
T ss_pred             HHccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccH
Confidence            345567899999999999999999999999999999876      67899999999887766554

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

Probab=99.68  E-value=2.9e-17  Score=86.21  Aligned_cols=57  Identities=23%  Similarity=0.650  Sum_probs=49.0

Q ss_pred             cccCCCcccccccccccccC----ceecCCCChhhHHhHHHHhhCC---CCcccccccccccce
Q 037842            8 AVVVGEVRFTCGICLDTMKE----ESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRSI   64 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~----~~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~~~~~~~~   64 (78)
                      ......+.+.|+||++.+.+    ++.++|||.||..|+..|+...   ..||.||..+...++
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A            8 NLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             SCCCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSST
T ss_pred             ChhhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhH
Confidence            44556678899999999998    8899999999999999999875   689999999876544

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

Probab=99.67  E-value=5.7e-17  Score=83.58  Aligned_cols=60  Identities=22%  Similarity=0.499  Sum_probs=50.3

Q ss_pred             cccCCCcccccccccccccCc---eecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842            8 AVVVGEVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ......+...|+||++.+.++   ..++|||.||..|+.+|+.....||+||..+...++...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A            8 TEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             CCTTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CcccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            444556678999999999865   456999999999999999988899999999987766554

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

Probab=99.67  E-value=1.7e-17  Score=93.84  Aligned_cols=50  Identities=30%  Similarity=0.761  Sum_probs=45.5

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      ++++.|+||++.+.+|+.++|||.||..|+..|+.....||.||..+...
T Consensus        51 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBCSSEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCcccCCceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            34578999999999999999999999999999999989999999988643

>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=99.66  E-value=1.1e-16  Score=86.16  Aligned_cols=57  Identities=16%  Similarity=0.062  Sum_probs=51.4

Q ss_pred             CCCcccccccccccccCceecCCC-ChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCG-HVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~Cg-H~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ...+++.||||++.+.+|+.++|| |+||+.||.+|+.....||.|+.++...++.++
T Consensus        18 ~~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn   75 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             cCcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEc
Confidence            345689999999999999999999 999999999999988899999999987777654

>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=99.66  E-value=8.2e-17  Score=86.90  Aligned_cols=57  Identities=12%  Similarity=0.122  Sum_probs=51.5

Q ss_pred             CCCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ...+.+.||||++.+.+|+.++|||+||+.||..|+.....||.|+.++...++.++
T Consensus        25 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn   81 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPV   81 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEEC
T ss_pred             cCcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceEC
Confidence            445689999999999999999999999999999999988899999999987777654

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

Probab=99.66  E-value=5e-17  Score=87.23  Aligned_cols=55  Identities=24%  Similarity=0.692  Sum_probs=48.8

Q ss_pred             CcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           13 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      .+.+.|+||++.+.+|+.+ +|||.||..|+..|+..+..||.||..+...++..+
T Consensus        20 ~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n   75 (99)
T 2y43_A           20 DDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNN   75 (99)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcC
Confidence            3568999999999999887 899999999999999988899999999987666553

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

Probab=99.66  E-value=1.5e-16  Score=79.06  Aligned_cols=46  Identities=35%  Similarity=0.728  Sum_probs=40.7

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhh---CCCCcccc
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGKCPTC   55 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~---~~~~CP~C   55 (78)
                      ...++++.|+||++.+.+|+.++|||+||..|+.+|+.   ....||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            44567899999999999999999999999999999998   35589987

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

Probab=99.65  E-value=7.4e-17  Score=89.86  Aligned_cols=59  Identities=36%  Similarity=0.876  Sum_probs=53.4

Q ss_pred             CcccccccccccccCc-------eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeeccCC
Q 037842           13 EVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQ   71 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~-------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~~   71 (78)
                      .+.+.|+||++.+.++       +.++|||+||..|+.+|+..+..||.||..+..+.+..+++.+
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~i~~   70 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYIGS   70 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECBCSS
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccccCC
Confidence            4578999999999988       8899999999999999999989999999999998888877653

>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=99.65  E-value=2e-16  Score=79.81  Aligned_cols=56  Identities=25%  Similarity=0.573  Sum_probs=46.3

Q ss_pred             CCcccCCCcccccccccccccC---ceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842            6 NGAVVVGEVRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus         6 ~~~~~~~~~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ............|+||++.+..   ++.++|||.||..|+..|+.....||+||..+..
T Consensus         5 ~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A            5 GEEGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             STTCCSTTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             ccCcCcCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            3344556667899999998853   4678999999999999999988899999988764

>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=99.63  E-value=7e-17  Score=87.89  Aligned_cols=53  Identities=25%  Similarity=0.618  Sum_probs=47.8

Q ss_pred             cCCCcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      ....+++.|+||++.+.+|+.+ +|||+||..|+..|+.....||.||..+...
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           10 TELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HHHGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             hccCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            3456789999999999999987 9999999999999999889999999998754

>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=99.63  E-value=1e-16  Score=89.06  Aligned_cols=49  Identities=33%  Similarity=0.715  Sum_probs=44.4

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhCCC-Ccccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~~~   61 (78)
                      .+.+.|+||++.+.+|+.++|||+||..|+..|+.... .||.||..+..
T Consensus        50 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           50 EETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             ccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45688999999999999999999999999999998544 89999999876

>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=99.63  E-value=1.7e-16  Score=87.67  Aligned_cols=58  Identities=36%  Similarity=0.734  Sum_probs=50.3

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCC-Ccccccccccccceee
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSIRR   66 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~~~~~~~~   66 (78)
                      .....+.+.|+||++.+.+|+.++|||+||..|+..|+.... .||.||..+...++.+
T Consensus        12 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (118)
T 3hct_A           12 DPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (118)
T ss_dssp             SSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             ccCCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhccc
Confidence            345667899999999999999999999999999999998755 8999999998766544

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

Probab=99.62  E-value=5.2e-16  Score=75.71  Aligned_cols=48  Identities=38%  Similarity=0.812  Sum_probs=40.8

Q ss_pred             cccCCCcccccccccccccCceecCCCChhhHHhHHHHhh---CCCCcccc
Q 037842            8 AVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGKCPTC   55 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~---~~~~CP~C   55 (78)
                      ......+.+.|+||++.+.+|+.++|||.||..|+.+|+.   ....||+|
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A            8 ALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CSSCSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             HhhccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            3445567789999999999999999999999999999954   45689987

>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=99.61  E-value=2.9e-16  Score=85.62  Aligned_cols=55  Identities=36%  Similarity=0.899  Sum_probs=48.1

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhCCC---Ccccccccccccceeee
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---KCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~---~CP~C~~~~~~~~~~~~   67 (78)
                      .+.+.|+||++.+.+|+.++|||.||..|+..|+....   .||.||..+...++...
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~   76 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             cCCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCcc
Confidence            35678999999999999999999999999999998653   89999999987776554

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

Probab=99.61  E-value=2.9e-16  Score=87.46  Aligned_cols=60  Identities=37%  Similarity=0.917  Sum_probs=53.7

Q ss_pred             cCCCcccccccccccccCc-------eecCCCChhhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           10 VVGEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~-------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      ...++...|+||++.+.++       +.++|||.||..|+.+|+...+.||+||..+..+++.++|+
T Consensus        67 ~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  133 (133)
T 4ap4_A           67 YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI  133 (133)
T ss_dssp             BCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEEECC
T ss_pred             ccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcceeeeC
Confidence            3456778999999999876       77899999999999999999999999999999999998874

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

Probab=99.60  E-value=3.1e-16  Score=75.88  Aligned_cols=48  Identities=25%  Similarity=0.672  Sum_probs=42.1

Q ss_pred             CcccccccccccccC---ceecC-CCChhhHHhHHHHhhCCCCccccccccc
Q 037842           13 EVRFTCGICLDTMKE---ESSTK-CGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~---~~~~~-CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +++..|+||++.+.+   ++.++ |||.||..|+.+|+..+..||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            456789999999987   56676 9999999999999999899999998764

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

Probab=99.60  E-value=5.2e-16  Score=79.21  Aligned_cols=54  Identities=22%  Similarity=0.616  Sum_probs=45.2

Q ss_pred             cccCCCcccccccccccccCcee---cCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842            8 AVVVGEVRFTCGICLDTMKEESS---TKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~---~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ......++..|+||++.+.++..   ++|||.||..|+.+|+.....||+||..+..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A            8 KVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCCCCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             ccccCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            34455667899999999987643   4999999999999999988899999988763

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

Probab=99.60  E-value=2.9e-16  Score=80.47  Aligned_cols=50  Identities=20%  Similarity=0.563  Sum_probs=44.1

Q ss_pred             CCcccccccccccccCc---eecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~---~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ..+...|+||++.+.++   +.++|||.||..|+..|+.....||+||..+..
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            44668899999999877   667999999999999999988899999988764

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

Probab=99.60  E-value=7.6e-16  Score=81.65  Aligned_cols=50  Identities=26%  Similarity=0.615  Sum_probs=43.8

Q ss_pred             CCcccccccccccccC---ceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ..++..|+||++.+.+   ++.++|||.||..|+..|+.....||+||..+..
T Consensus        37 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            4466789999999887   5678999999999999999998999999988764

>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=99.59  E-value=1.5e-16  Score=87.35  Aligned_cols=53  Identities=30%  Similarity=0.760  Sum_probs=46.7

Q ss_pred             ccCCCcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842            9 VVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus         9 ~~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      .....+++.|+||++.+.+|+.++|||+||..|+..|+.. ...||.||..+..
T Consensus         9 ~~~~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A            9 AIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCCCHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             ccCCCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            4456678999999999999999999999999999999876 5689999998763

>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=99.59  E-value=3.8e-16  Score=75.51  Aligned_cols=48  Identities=25%  Similarity=0.659  Sum_probs=41.9

Q ss_pred             CcccccccccccccC----ceecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           13 EVRFTCGICLDTMKE----ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~----~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      .++..|+||++.+.+    ++.++|||.||..|+.+|+.....||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            356789999999865    567899999999999999998899999998764

>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=99.59  E-value=4.6e-16  Score=85.53  Aligned_cols=54  Identities=26%  Similarity=0.738  Sum_probs=47.9

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceee
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~   66 (78)
                      .+.+.|+||++.+.+|+.++|||.||..|+.+|+.. ...||.||..+...++..
T Consensus        21 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            456899999999999999999999999999999986 678999999988766543

>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=99.59  E-value=6.2e-16  Score=88.64  Aligned_cols=50  Identities=30%  Similarity=0.733  Sum_probs=45.3

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhCCC-Cccccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVR   62 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~~~~   62 (78)
                      .+.+.|+||++.+.+|+.++|||+||..|+..|+.... .||+||..+...
T Consensus        76 ~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           76 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             ccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            35689999999999999999999999999999998754 899999998865

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

Probab=99.58  E-value=5.3e-16  Score=77.99  Aligned_cols=48  Identities=33%  Similarity=0.721  Sum_probs=43.2

Q ss_pred             CcccccccccccccCc-eecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           13 EVRFTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~-~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      +....|+||++.+.++ +.++|||.||..|+.+|+.....||.||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            3 TVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            3456899999999987 67899999999999999998889999999876

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

Probab=99.56  E-value=4.4e-15  Score=77.23  Aligned_cols=51  Identities=25%  Similarity=0.570  Sum_probs=43.0

Q ss_pred             cccccccccccccC--------------ceec-CCCChhhHHhHHHHhhCCCCcccccccccccce
Q 037842           14 VRFTCGICLDTMKE--------------ESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSI   64 (78)
Q Consensus        14 ~~~~C~iC~~~~~~--------------~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~   64 (78)
                      ++..|+||++.+.+              ++.+ +|||.||..|+.+|+..+..||+||+.+..+++
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~   79 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRI   79 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhhc
Confidence            56779999999876              3344 599999999999999999999999999876554

>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=99.55  E-value=1.4e-15  Score=86.41  Aligned_cols=51  Identities=20%  Similarity=0.635  Sum_probs=45.2

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCCC-Cccccccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMS   60 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~~   60 (78)
                      ...++.+.|+||++.+.+|+.++|||+||..|+..|+.... .||.||..+.
T Consensus        26 ~~l~~~~~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           26 TKLEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GGCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             ccCCcCcCCCCCChhhcCcEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            34567899999999999999999999999999999998654 8999999753

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

Probab=99.55  E-value=8.7e-15  Score=75.77  Aligned_cols=57  Identities=21%  Similarity=0.503  Sum_probs=44.9

Q ss_pred             cCCCccccccccccccc--CceecC--CCChhhHHhHHHHhhC-CCCcccccccccccceee
Q 037842           10 VVGEVRFTCGICLDTMK--EESSTK--CGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~--~~~~~~--CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~   66 (78)
                      ...++++.|+||++.+.  ++..++  |||.||..|+..++.. ...||.||+.+....+..
T Consensus         6 ~~~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~~   67 (78)
T 1e4u_A            6 DAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVY   67 (78)
T ss_dssp             CCCCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSCC
T ss_pred             cccccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchhh
Confidence            34567789999999885  344544  9999999999998754 568999999998766543

>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=99.55  E-value=3e-15  Score=86.95  Aligned_cols=57  Identities=35%  Similarity=0.717  Sum_probs=49.6

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCC-CCcccccccccccceee
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~-~~CP~C~~~~~~~~~~~   66 (78)
                      ...++.+.|+||++.+.+|+.++|||+||..|+.+|+..+ ..||.||..+...++.+
T Consensus        13 ~~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (170)
T 3hcs_A           13 PPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (170)
T ss_dssp             SCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             cCCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhh
Confidence            4566789999999999999999999999999999999764 48999999988765543

>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=99.54  E-value=3.4e-15  Score=74.63  Aligned_cols=56  Identities=27%  Similarity=0.529  Sum_probs=48.1

Q ss_pred             CCcccccccccccccCceec--CCCCh-hhHHhHHHHhhCCCCcccccccccccceeeecc
Q 037842           12 GEVRFTCGICLDTMKEESST--KCGHV-FCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFF   69 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~--~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~   69 (78)
                      ..++..|+||++...+++.+  +|||. ||..|+..|......||+||.++.  .+.++|+
T Consensus         5 ~~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~~   63 (64)
T 2vje_A            5 LNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ--MIVLTYF   63 (64)
T ss_dssp             CGGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC--EEEEEEC
T ss_pred             CCCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh--ceEeeec
Confidence            44667899999999999877  99999 899999999988889999999875  5666664

>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=99.54  E-value=2.7e-15  Score=86.82  Aligned_cols=50  Identities=40%  Similarity=0.927  Sum_probs=44.4

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      ..+.+.|+||++.+.+|+.+ +|||.||..|+..|+.. ...||.||..+..
T Consensus        51 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           51 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             CHHHHBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCCcccChHhhCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34567999999999999887 99999999999999997 6789999999853

>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=99.54  E-value=6.6e-16  Score=85.12  Aligned_cols=53  Identities=28%  Similarity=0.737  Sum_probs=46.2

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      ..+.+.|+||++.+.+|+.+ +|||+||..|+..|+.  ..||.||..+...++..
T Consensus        19 l~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~   72 (117)
T 1jm7_B           19 LEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKI   72 (117)
T ss_dssp             HHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCC
T ss_pred             chhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccccc
Confidence            34678999999999999999 9999999999999987  78999999987655544

>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=99.54  E-value=3.2e-15  Score=79.74  Aligned_cols=56  Identities=30%  Similarity=0.626  Sum_probs=47.1

Q ss_pred             CCcccccccccccccCceecC-CCChhhHHhHHHHhhCC------CCccc--cccc-ccccceeee
Q 037842           12 GEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ------GKCPT--CRTR-MSVRSIRRI   67 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~------~~CP~--C~~~-~~~~~~~~~   67 (78)
                      ..+.+.||||++.|.+|+.++ |||+||+.||..|+...      ..||.  |+.. +...++.++
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn   69 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQD   69 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEEC
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCC
Confidence            456789999999999999995 99999999999999753      48999  8866 766666654

>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=99.53  E-value=5.9e-15  Score=80.74  Aligned_cols=49  Identities=29%  Similarity=0.610  Sum_probs=40.6

Q ss_pred             cccccccccccccCce------------------ecCCCChhhHHhHHHHhh-----CCCCccccccccccc
Q 037842           14 VRFTCGICLDTMKEES------------------STKCGHVFCKSCIVDAIR-----LQGKCPTCRTRMSVR   62 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~------------------~~~CgH~fc~~C~~~~~~-----~~~~CP~C~~~~~~~   62 (78)
                      .+..|+||++.+.++.                  .++|||.||..||..|+.     ....||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4568999999987653                  678999999999999994     456899999987643

>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=99.52  E-value=5.6e-15  Score=90.64  Aligned_cols=57  Identities=16%  Similarity=0.167  Sum_probs=49.6

Q ss_pred             CCCcccccccccccccCceecCCCChhhHHhHHHHhhCCC-Ccccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~-~CP~C~~~~~~~~~~~~   67 (78)
                      ...+.+.|+||++.+.+|++++|||+||..|+.+|+.... .||.|+.++...++.++
T Consensus       204 ~~~~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n  261 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN  261 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CCCcccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCccc
Confidence            4456799999999999999999999999999999998644 59999999987776654

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

Probab=99.51  E-value=1.7e-15  Score=73.88  Aligned_cols=47  Identities=21%  Similarity=0.512  Sum_probs=40.8

Q ss_pred             CCcccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ..+.+.|+||++.+.+|+.++|||+||..|+..   ....||.||..+..
T Consensus         3 e~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~~   49 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPWPL   49 (56)
T ss_dssp             SCCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSS---SSSSCSSCCSSSSC
T ss_pred             cccCCCceEeCCccCCeEEcCCCCcccHHHHcc---CCCCCCcCCcEeec
Confidence            356788999999999999999999999999876   35689999998764

>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=99.49  E-value=1.5e-14  Score=72.02  Aligned_cols=55  Identities=18%  Similarity=0.586  Sum_probs=46.4

Q ss_pred             CCcccccccccccccCceec--CCCCh-hhHHhHHHHhhCCCCcccccccccccceeeec
Q 037842           12 GEVRFTCGICLDTMKEESST--KCGHV-FCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~--~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~   68 (78)
                      .+....|+||++...+++.+  +|||. ||..|+..+......||+||.++.  .+.++|
T Consensus         4 ~~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~   61 (63)
T 2vje_B            4 QNLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ--LVIKVF   61 (63)
T ss_dssp             GGGGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC--EEEEEE
T ss_pred             CCcCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh--ceEEEe
Confidence            34567899999999998777  99998 999999999888889999999875  455554

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.48  E-value=2.6e-14  Score=83.97  Aligned_cols=59  Identities=14%  Similarity=0.110  Sum_probs=51.2

Q ss_pred             cCCCcccccccccccccCceecCCCChhhHHhHHHHhhCC-CCcccccccccccceeeec
Q 037842           10 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~-~~CP~C~~~~~~~~~~~~~   68 (78)
                      ....+.+.||||++.+.+|+.++|||+||..|+..|+... ..||.|+.++...++.++.
T Consensus       101 ~~ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~  160 (179)
T 2f42_A          101 REIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNL  160 (179)
T ss_dssp             CCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECH
T ss_pred             cCCcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchH
Confidence            3456789999999999999999999999999999999864 3699999999887777653

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

Probab=99.46  E-value=1.3e-14  Score=74.25  Aligned_cols=45  Identities=33%  Similarity=0.746  Sum_probs=40.4

Q ss_pred             CcccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCcccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      .++..|+||++.+.+++.++|||. ||..|+..|    ..||+||..+..
T Consensus        22 ~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           22 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             ccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            456889999999999999999999 999999877    789999998763

>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=99.44  E-value=7.4e-14  Score=75.98  Aligned_cols=48  Identities=23%  Similarity=0.479  Sum_probs=41.2

Q ss_pred             cccccccccccccCc------------------eecCCCChhhHHhHHHHhhCCCCcccccccccc
Q 037842           14 VRFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~------------------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ++..|+||++.+.++                  +.++|+|.||..|+..|+..+..||+||+.+..
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  101 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCccee
Confidence            456799999998865                  346899999999999999999999999998654

>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=99.42  E-value=1.7e-13  Score=84.36  Aligned_cols=60  Identities=27%  Similarity=0.516  Sum_probs=50.7

Q ss_pred             cccCCCcccccccccccccCceec-CCCChhhHHhHHHHhhCC--CCccc--ccccccccceeee
Q 037842            8 AVVVGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQ--GKCPT--CRTRMSVRSIRRI   67 (78)
Q Consensus         8 ~~~~~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~--~~CP~--C~~~~~~~~~~~~   67 (78)
                      ........+.||||++.|.+|+.. .|||+||+.||..|+...  ..||+  |+..+...++...
T Consensus       174 ~v~~~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN  238 (267)
T 3htk_C          174 QIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRD  238 (267)
T ss_dssp             CCCSSBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEEC
T ss_pred             eecCCceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcC
Confidence            334456789999999999999985 999999999999999864  47999  9999988777654

>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=99.41  E-value=1.2e-13  Score=89.03  Aligned_cols=51  Identities=27%  Similarity=0.600  Sum_probs=45.5

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhh-CCCCccccccccccccee
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~-~~~~CP~C~~~~~~~~~~   65 (78)
                      ...|+||++.+.+++.++|||.||..|+..|+. ....||.||..+....+.
T Consensus       332 ~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~i  383 (389)
T 2y1n_A          332 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI  383 (389)
T ss_dssp             SSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEEC
T ss_pred             CCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCceeE
Confidence            368999999999999999999999999999998 677999999998865443

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

Probab=99.38  E-value=9e-14  Score=71.22  Aligned_cols=45  Identities=33%  Similarity=0.734  Sum_probs=39.1

Q ss_pred             CcccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCcccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ++...|+||++.+.+++.++|||. ||..|+..    ...||+||..+..
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhC----CCCCccCCceecC
Confidence            345789999999999999999999 99999964    3689999998864

>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=99.36  E-value=2.6e-13  Score=67.16  Aligned_cols=56  Identities=20%  Similarity=0.287  Sum_probs=51.0

Q ss_pred             ccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceeeeccC
Q 037842           15 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      .+.|+|+++.+.+|+.+ ++||+|++.++.+|+...+.||+.+.++..+++.++.+.
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~~~   59 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVPS   59 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECCCC
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECccC
Confidence            47899999999999999 899999999999999887789999999999999887654

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

Probab=99.36  E-value=5.9e-13  Score=67.14  Aligned_cols=54  Identities=22%  Similarity=0.476  Sum_probs=43.8

Q ss_pred             CCCcccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCcccccccccccceeeeccC
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      ...+...|.||++...+++.++|||. ||..|+..    ...||+||..+.  ...+++.+
T Consensus        11 ~~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~--~~~~i~~~   65 (68)
T 2ea5_A           11 SEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQ--ESFALSGP   65 (68)
T ss_dssp             SCCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCC--CEECCCSS
T ss_pred             cCCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc----CCCCCCCCcchh--ceEEeecC
Confidence            34457889999999999999999999 99999974    368999999876  35555543

>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=99.33  E-value=3.9e-13  Score=69.60  Aligned_cols=53  Identities=26%  Similarity=0.814  Sum_probs=44.0

Q ss_pred             CcccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCcccccccccccceeeeccCC
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQ   71 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~~~~   71 (78)
                      .+...|+||++.+.+++.++|||. ||..|+..+    ..||+||..+..  ..+++++.
T Consensus        16 ~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~--~~~i~~p~   69 (79)
T 2yho_A           16 KEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEH--VQHVYLPT   69 (79)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE--EEECBCTT
T ss_pred             CCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhC--eEEEEeCc
Confidence            456789999999999999999999 999999765    389999998774  45666554

>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=99.26  E-value=5.8e-13  Score=73.55  Aligned_cols=48  Identities=21%  Similarity=0.451  Sum_probs=0.4

Q ss_pred             ccccccccccccCc-----------------e-ecCCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           15 RFTCGICLDTMKEE-----------------S-STKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        15 ~~~C~iC~~~~~~~-----------------~-~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      +..|+||++.+.++                 + .++|+|.||..|+.+|+..+..||+||..+...
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~~  113 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ  113 (117)
T ss_dssp             C-----------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeeee
Confidence            46899999998763                 1 248999999999999999988999999986543

>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=99.23  E-value=1.3e-12  Score=69.36  Aligned_cols=55  Identities=25%  Similarity=0.642  Sum_probs=43.0

Q ss_pred             CcccccccccccccCceec---CCCChhhHHhHHHHhhC--------CCCccc--cccc--ccccceeee
Q 037842           13 EVRFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRL--------QGKCPT--CRTR--MSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~--------~~~CP~--C~~~--~~~~~~~~~   67 (78)
                      .+.+.|+||++.+..+..+   +|||.||..||..++..        ...||.  |+..  +....+..+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~~l   72 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECM   72 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHH
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHHHH
Confidence            4567899999999877543   69999999999999863        137999  9998  766555443

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

Probab=99.22  E-value=7e-12  Score=65.04  Aligned_cols=51  Identities=20%  Similarity=0.409  Sum_probs=41.4

Q ss_pred             CCccccccccccccc--CceecCCC-----ChhhHHhHHHHhhCC--CCccccccccccc
Q 037842           12 GEVRFTCGICLDTMK--EESSTKCG-----HVFCKSCIVDAIRLQ--GKCPTCRTRMSVR   62 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~--~~~~~~Cg-----H~fc~~C~~~~~~~~--~~CP~C~~~~~~~   62 (78)
                      ..+...|.||++.+.  +++.++|+     |.||..||.+|+..+  ..||+||..+..+
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            345578999998774  46777896     999999999999864  4899999988654

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=99.11  E-value=8.7e-12  Score=79.45  Aligned_cols=44  Identities=32%  Similarity=0.758  Sum_probs=39.8

Q ss_pred             cccccccccccccCceecCCCCh-hhHHhHHHHhhCCCCcccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGKCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~-fc~~C~~~~~~~~~~CP~C~~~~~~   61 (78)
                      ++..|+||++.+.+++.++|||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            56889999999999999999999 999999876    689999998763

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

Probab=99.06  E-value=3.7e-10  Score=57.73  Aligned_cols=49  Identities=20%  Similarity=0.541  Sum_probs=40.7

Q ss_pred             CCcccccccccccccCceec-CCCChhhHHhHHHHhhCC--CCccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQ--GKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~--~~CP~C~~~~~   60 (78)
                      .+....|+||.+.+...... .|+|.|+..|+.+|++..  ..||+|+....
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             cCCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            33457899999999865544 799999999999999876  78999997655

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

Probab=98.71  E-value=1.3e-08  Score=49.99  Aligned_cols=49  Identities=22%  Similarity=0.494  Sum_probs=39.0

Q ss_pred             CcccccccccccccCceecCCC--C---hhhHHhHHHHhhC--CCCcccccccccc
Q 037842           13 EVRFTCGICLDTMKEESSTKCG--H---VFCKSCIVDAIRL--QGKCPTCRTRMSV   61 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~Cg--H---~fc~~C~~~~~~~--~~~CP~C~~~~~~   61 (78)
                      ++...|.||++...++..+||.  +   .|+..|+.+|+..  +..||+|+..+..
T Consensus         4 ~~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            4567899999987777667754  4   7999999999974  5689999988753

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.62  E-value=3.2e-08  Score=52.86  Aligned_cols=45  Identities=27%  Similarity=0.586  Sum_probs=37.4

Q ss_pred             ccccccccccCc-eecCCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           17 TCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        17 ~C~iC~~~~~~~-~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      .|++|.-.+... .+++|+|+||++|+..|.++ .+.||.|+.++..
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            588888877765 56799999999999998754 6789999998863

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

Probab=98.61  E-value=6.3e-09  Score=66.40  Aligned_cols=49  Identities=22%  Similarity=0.615  Sum_probs=38.6

Q ss_pred             CCcccccccccccccC----ce----ecCCCChhhHHhHHHHhhCC-----------CCccccccccc
Q 037842           12 GEVRFTCGICLDTMKE----ES----STKCGHVFCKSCIVDAIRLQ-----------GKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~----~~----~~~CgH~fc~~C~~~~~~~~-----------~~CP~C~~~~~   60 (78)
                      .+....|+||++.+.+    |.    ...|||.|+..|+.+|+...           +.||.|+.++.
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            3456789999998776    21    13799999999999999741           46999999876

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

Probab=97.87  E-value=1.5e-05  Score=48.53  Aligned_cols=48  Identities=21%  Similarity=0.553  Sum_probs=39.4

Q ss_pred             cccccccccccccCceecC-CCChhhHHhHHHHhhCCC--Ccccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQG--KCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~-CgH~fc~~C~~~~~~~~~--~CP~C~~~~~~   61 (78)
                      ....|.+|.+.+......+ |+|.|+..|+..|++...  .||.|+.....
T Consensus       179 ~i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             TCCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            3568999999988776654 999999999999997644  89999886543

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=97.58  E-value=3.5e-05  Score=40.77  Aligned_cols=32  Identities=16%  Similarity=0.626  Sum_probs=26.8

Q ss_pred             ccccccccccc-ccCcee--cCCCChhhHHhHHHH
Q 037842           14 VRFTCGICLDT-MKEESS--TKCGHVFCKSCIVDA   45 (78)
Q Consensus        14 ~~~~C~iC~~~-~~~~~~--~~CgH~fc~~C~~~~   45 (78)
                      +++.|+||.+. +.+++.  +.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            35789999975 667777  899999999999983

>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=97.42  E-value=0.00017  Score=51.19  Aligned_cols=57  Identities=12%  Similarity=0.044  Sum_probs=51.0

Q ss_pred             CCCcccccccccccccCceecCCC-ChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCG-HVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~Cg-H~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ...+++.|||-.+.+.+||.++-| ++|=+..+.+|+.....||.-|.++...++.++
T Consensus       887 ~iP~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN  944 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPN  944 (968)
T ss_dssp             CSCGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CCcHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCccccccc
Confidence            455789999999999999999998 689999999999988899999999988777765

>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=96.11  E-value=0.01  Score=30.49  Aligned_cols=38  Identities=21%  Similarity=0.560  Sum_probs=30.4

Q ss_pred             CCCcccccccccccccCceecC----CCChhhHHhHHHHhhC
Q 037842           11 VGEVRFTCGICLDTMKEESSTK----CGHVFCKSCIVDAIRL   48 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~----CgH~fc~~C~~~~~~~   48 (78)
                      .....+.|.+|.+.+++...+.    =+|.||..|-..+++.
T Consensus        11 ~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           11 ANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            3456689999999999985443    3799999999988874

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=93.93  E-value=0.046  Score=35.33  Aligned_cols=53  Identities=21%  Similarity=0.493  Sum_probs=36.9

Q ss_pred             CcccccccccccccCcee-cCCCChhhH--HhHHHHhhC--CCCccccccccccccee
Q 037842           13 EVRFTCGICLDTMKEESS-TKCGHVFCK--SCIVDAIRL--QGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~-~~CgH~fc~--~C~~~~~~~--~~~CP~C~~~~~~~~~~   65 (78)
                      .-.+.||+-...+..|+. ..|.|.-|.  .-+.....+  .-.||+|.+.+...++.
T Consensus       247 ~vSL~CPlS~~ri~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~dL~  304 (371)
T 3i2d_A          247 IMSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLA  304 (371)
T ss_dssp             EEESBCTTTSSBCSSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGGEE
T ss_pred             EEeecCCCccccccccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHHee
Confidence            345889999999999976 479998443  333333322  33799999988766654

>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=93.72  E-value=0.06  Score=34.64  Aligned_cols=53  Identities=17%  Similarity=0.394  Sum_probs=37.0

Q ss_pred             CcccccccccccccCcee-cCCCChhh--HHhHHHHhhC--CCCccccccccccccee
Q 037842           13 EVRFTCGICLDTMKEESS-TKCGHVFC--KSCIVDAIRL--QGKCPTCRTRMSVRSIR   65 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~-~~CgH~fc--~~C~~~~~~~--~~~CP~C~~~~~~~~~~   65 (78)
                      .-.+.||+-...+..|+. ..|.|.-|  ..-+.....+  .-.||+|.+.+..+++.
T Consensus       213 ~vSL~CPlS~~ri~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~dL~  270 (360)
T 4fo9_A          213 RVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLI  270 (360)
T ss_dssp             EEESBCTTTCSBCSSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGGEE
T ss_pred             EEeeeCCCccceeccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHHeE
Confidence            345789999999999976 47999844  3333333332  33799999998766654

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=92.12  E-value=0.082  Score=28.52  Aligned_cols=49  Identities=18%  Similarity=0.341  Sum_probs=37.6

Q ss_pred             cccccccccccC---ceecCCCChhhHHhHHHHhhCCCCcccccccccccce
Q 037842           16 FTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSI   64 (78)
Q Consensus        16 ~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~   64 (78)
                      +.|..|...+.+   .....=|..||..|..+.+..+..|-.|..++....+
T Consensus        33 F~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~   84 (122)
T 1m3v_A           33 LKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDV   84 (122)
T ss_dssp             HCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEES
T ss_pred             CCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchhe
Confidence            788899888863   3444567789999998877766689999988876544

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=90.70  E-value=0.23  Score=24.22  Aligned_cols=44  Identities=23%  Similarity=0.517  Sum_probs=30.2

Q ss_pred             CcccccccccccccCceec--CCCChhhHHhHHHHhhCCC----Cccccccc
Q 037842           13 EVRFTCGICLDTMKEESST--KCGHVFCKSCIVDAIRLQG----KCPTCRTR   58 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~--~CgH~fc~~C~~~~~~~~~----~CP~C~~~   58 (78)
                      .....|.||.+.-  .+++  .|...|+..|+...+....    .|+.|...
T Consensus        10 ~~~~~C~vC~~~~--~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           10 APGARCGVCGDGT--DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CTTCCCTTTSCCT--TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCCCcCCCCCCC--eEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            3456799998642  2222  6999999999976665432    69999654

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}

Probab=90.48  E-value=0.039  Score=23.67  Aligned_cols=16  Identities=19%  Similarity=0.623  Sum_probs=11.9

Q ss_pred             CcccccccccccccCc
Q 037842           13 EVRFTCGICLDTMKEE   28 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~   28 (78)
                      .+.+.||+|+..+.++
T Consensus         3 ~EGFiCP~C~~~l~s~   18 (34)
T 3mjh_B            3 SEGFICPQCMKSLGSA   18 (34)
T ss_dssp             SEEEECTTTCCEESSH
T ss_pred             CcccCCcHHHHHcCCH
Confidence            3458888888887765

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=88.53  E-value=0.48  Score=22.56  Aligned_cols=46  Identities=17%  Similarity=0.458  Sum_probs=30.7

Q ss_pred             cCCCcccccccccccccCceec--CCCChhhHHhHHHHhhCC----CCcccccc
Q 037842           10 VVGEVRFTCGICLDTMKEESST--KCGHVFCKSCIVDAIRLQ----GKCPTCRT   57 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~~~~~--~CgH~fc~~C~~~~~~~~----~~CP~C~~   57 (78)
                      .....+..|.+|.+.  ..+++  .|...|+..|+..-+...    -.||.|..
T Consensus         6 ~~~~~~~~C~vC~~~--g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            6 YETDHQDYCEVCQQG--GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CSSCCCSSCTTTSCC--SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             ccCCCCCCCccCCCC--CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            345556789999874  22222  688899999998654332    25999964

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=87.97  E-value=0.2  Score=24.76  Aligned_cols=29  Identities=28%  Similarity=0.572  Sum_probs=21.5

Q ss_pred             ccccccccccccCc---ee-cCCCChhhHHhHH
Q 037842           15 RFTCGICLDTMKEE---SS-TKCGHVFCKSCIV   43 (78)
Q Consensus        15 ~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~   43 (78)
                      +..|.+|...|.--   .. -.||.+||..|..
T Consensus        11 ~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~   43 (73)
T 1vfy_A           11 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSS   43 (73)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSC
T ss_pred             CCcccCCCCccCCccccccCCCCCEEEcccccC
Confidence            45899999987642   12 3799999999864

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=87.62  E-value=0.19  Score=24.83  Aligned_cols=49  Identities=18%  Similarity=0.419  Sum_probs=32.4

Q ss_pred             CCcccccccccccccCceec---CCCChhhHHhHHHHhhC----CCCccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRL----QGKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~----~~~CP~C~~~~~   60 (78)
                      ..+...|.+|........++   .|..-|+..|+......    .-.||.|...+.
T Consensus        15 ~~~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           15 GNQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             SCEEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            34556799998876543333   57778999998643332    236999977654

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=87.08  E-value=0.55  Score=25.25  Aligned_cols=49  Identities=20%  Similarity=0.474  Sum_probs=35.9

Q ss_pred             cccccccccccccC---ceecCCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           14 VRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        14 ~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      +-+.|..|...+..   .....=|..||..|..+.+.....|..|...+...
T Consensus        28 ~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~   79 (131)
T 2xjy_A           28 DCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAY   79 (131)
T ss_dssp             TTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTT
T ss_pred             HHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCcc
Confidence            34788889888853   34455677899999987765544799998888653

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=86.84  E-value=0.3  Score=25.14  Aligned_cols=54  Identities=15%  Similarity=0.282  Sum_probs=33.5

Q ss_pred             cCCCcccccccccccc--cCceec---CCCChhhHHhHHHHhhCC--CCcccccccccccc
Q 037842           10 VVGEVRFTCGICLDTM--KEESST---KCGHVFCKSCIVDAIRLQ--GKCPTCRTRMSVRS   63 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~--~~~~~~---~CgH~fc~~C~~~~~~~~--~~CP~C~~~~~~~~   63 (78)
                      ...+++..|.||...-  ....++   .|.-.|+..|+..-....  -.||.|........
T Consensus        20 ~~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~~~   80 (88)
T 2l43_A           20 SLIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPA   80 (88)
T ss_dssp             CCCCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTSCC
T ss_pred             CcCCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccchhh
Confidence            3445678999999764  111222   688889999986433222  25999976554433

>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=86.15  E-value=2.4  Score=22.05  Aligned_cols=48  Identities=29%  Similarity=0.590  Sum_probs=34.2

Q ss_pred             cccccccccccccCc----eec---CCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           14 VRFTCGICLDTMKEE----SST---KCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~----~~~---~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      ....|.||-+.+-..    +..   .|+--.|+.|+.--.+. ...||.|+..+..
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr   70 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccc
Confidence            456899999975522    222   57878899999755443 4579999988763

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=86.05  E-value=0.44  Score=24.52  Aligned_cols=32  Identities=25%  Similarity=0.513  Sum_probs=23.0

Q ss_pred             cccccccccccccCc---ee-cCCCChhhHHhHHHH
Q 037842           14 VRFTCGICLDTMKEE---SS-TKCGHVFCKSCIVDA   45 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~~~   45 (78)
                      +...|.+|...|.--   .. -.||.+||..|....
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~   54 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRK   54 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCe
Confidence            346799999887632   12 379999999997543

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=85.48  E-value=0.37  Score=27.82  Aligned_cols=49  Identities=20%  Similarity=0.548  Sum_probs=35.4

Q ss_pred             cccccccccccccC---ceecCCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           14 VRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        14 ~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      +-+.|..|...+..   .....=|..||..|..+.+..+..|..|...+...
T Consensus        31 ~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~   82 (188)
T 1rut_X           31 RCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS   82 (188)
T ss_dssp             GGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTT
T ss_pred             cCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccC
Confidence            34788888888764   34445678899999887665444799998888643

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=85.15  E-value=0.29  Score=24.72  Aligned_cols=31  Identities=26%  Similarity=0.763  Sum_probs=22.5

Q ss_pred             cccccccccccccCce---e-cCCCChhhHHhHHH
Q 037842           14 VRFTCGICLDTMKEES---S-TKCGHVFCKSCIVD   44 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~---~-~~CgH~fc~~C~~~   44 (78)
                      +...|.+|...|.--.   . -.||.+||..|...
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            3457999999876331   2 37999999999754

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=84.99  E-value=0.31  Score=24.74  Aligned_cols=31  Identities=23%  Similarity=0.502  Sum_probs=22.9

Q ss_pred             cccccccccccccCc---ee-cCCCChhhHHhHHH
Q 037842           14 VRFTCGICLDTMKEE---SS-TKCGHVFCKSCIVD   44 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~~   44 (78)
                      +...|.+|...|.--   .. -.||.+||..|...
T Consensus        20 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   54 (84)
T 1z2q_A           20 DAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRH   54 (84)
T ss_dssp             TCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCC
T ss_pred             CCCCCcCcCCccccchhcccccCCCcEEChHHhCC
Confidence            456899999987642   12 37999999999654

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=84.62  E-value=0.29  Score=26.78  Aligned_cols=30  Identities=23%  Similarity=0.680  Sum_probs=21.9

Q ss_pred             ccccccccccccCc---ee-cCCCChhhHHhHHH
Q 037842           15 RFTCGICLDTMKEE---SS-TKCGHVFCKSCIVD   44 (78)
Q Consensus        15 ~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~~   44 (78)
                      ...|.+|...|.--   .. -.||++||..|...
T Consensus        69 ~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~  102 (125)
T 1joc_A           69 VQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAK  102 (125)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCE
T ss_pred             CCCCcCcCCccccccccccCCCCCeEEChHHhCC
Confidence            45799999987632   12 37999999998643

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.34  E-value=0.31  Score=24.70  Aligned_cols=32  Identities=28%  Similarity=0.569  Sum_probs=22.7

Q ss_pred             CCcccccccccccccCc---ee-cCCCChhhHHhHH
Q 037842           12 GEVRFTCGICLDTMKEE---SS-TKCGHVFCKSCIV   43 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~   43 (78)
                      +.+...|.+|...|..-   .. -.||.+||..|..
T Consensus        11 d~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~   46 (84)
T 1x4u_A           11 TNNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCS   46 (84)
T ss_dssp             CCCCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSC
T ss_pred             CCCCCcCcCcCCccccchhhhhhcCCCcEEChhhcC
Confidence            33446799999987532   12 3799999999864

>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=82.50  E-value=0.12  Score=26.93  Aligned_cols=54  Identities=13%  Similarity=0.377  Sum_probs=33.4

Q ss_pred             CCCcccCCCcccccccccccccCceec---CCCChhhHHhHHHHhhCCC----Cccccccc
Q 037842            5 RNGAVVVGEVRFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRLQG----KCPTCRTR   58 (78)
Q Consensus         5 ~~~~~~~~~~~~~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~~~----~CP~C~~~   58 (78)
                      +........+...|.||...-....++   .|...|+..|+..-+....    .||.|...
T Consensus         6 ~~~s~~~~~~~~~C~vC~~~~~~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A            6 SGHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCCCCCCCCSSSCCSGGGGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             CCCchhhccCCCCCccCCCcCCCCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            344445555667899999865422222   5887888888864443321    59998654

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=82.38  E-value=0.066  Score=29.32  Aligned_cols=45  Identities=18%  Similarity=0.461  Sum_probs=26.9

Q ss_pred             CCcccccccccccccCc---ee-cCCCChhhHHhHHHHhhCCCCccccc
Q 037842           12 GEVRFTCGICLDTMKEE---SS-TKCGHVFCKSCIVDAIRLQGKCPTCR   56 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~~~~~~~~~CP~C~   56 (78)
                      ..+...|..|...|..-   .. -.||.+||..|........+.|-.|-
T Consensus        16 d~~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~   64 (120)
T 1y02_A           16 TGLEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   64 (120)
T ss_dssp             ----CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             ccccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHH
Confidence            44456899999987642   12 37999999999765444455666663

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=82.05  E-value=0.52  Score=24.21  Aligned_cols=49  Identities=22%  Similarity=0.522  Sum_probs=30.4

Q ss_pred             CCcccccccccccccCce---e-cCCCChhhHHhHHHHhh-------CCCCccccccccc
Q 037842           12 GEVRFTCGICLDTMKEES---S-TKCGHVFCKSCIVDAIR-------LQGKCPTCRTRMS   60 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~---~-~~CgH~fc~~C~~~~~~-------~~~~CP~C~~~~~   60 (78)
                      ..+...|.+|...|.--.   . -.||.+||..|......       ..+.|-.|-..+.
T Consensus         6 ~~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~   65 (88)
T 1wfk_A            6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILT   65 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHH
T ss_pred             CCcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHH
Confidence            334557999999876431   2 37999999999754221       1234666655443

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=81.55  E-value=0.55  Score=21.33  Aligned_cols=41  Identities=22%  Similarity=0.645  Sum_probs=25.4

Q ss_pred             ccccccccccCceec---CCCChhhHHhHHHHhhCC----CCcccccc
Q 037842           17 TCGICLDTMKEESST---KCGHVFCKSCIVDAIRLQ----GKCPTCRT   57 (78)
Q Consensus        17 ~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~~----~~CP~C~~   57 (78)
                      .|.+|...-....++   .|...|+..|+..-+...    -.||.|..
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            477887654322222   688889999996544432    15888854

---

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	78
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-10
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	2e-09
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-07
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-07
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	4e-05
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	9e-05
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	9e-04
d2c2la2	80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	0.002
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	0.003

>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 = 49.9 bits (119), Expect = 1e-10
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMSVRSIR 65
           +C IC   + +   T C H+FC+ CI+  +++ G  CP+CR       + 
Sbjct: 24 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

>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 = 47.8 bits (113), Expect = 2e-09
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---KCPTCRTRMSVRSIRR 66
            C ICL+ +KE  STKC H+FCK C++  +  +    +CP C+  ++ RS++ 
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 75

>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 = 43.0 bits (101), Expect = 5e-08
 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 18 CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS 60
          C ICL+     S +  C H FC  CI   IR    CP C+  + 
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 42.2 bits (99), Expect = 1e-07
 Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 3/46 (6%)

Query: 17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR 62
           C  C    K      C H  C  C+        +CP C+    + 
Sbjct: 8  RCQQCQAEAKCPKLLPCLHTLCSGCL---EASGMQCPICQAPWPLG 50

>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 = 42.3 bits (99), Expect = 1e-07
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 17 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-KCPTCRTRMS 60
           C IC +  K+     CGH+ C SC+      +G  CP CR  + 
Sbjct: 25 LCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 69

>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 = 38.7 bits (90), Expect = 2e-06
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 17 TCGICLDTMKEESS----TKCGHVFCKSCIVDAIRLQGKCPTCRTRMSV 61
           C +CL  +++        +CGH F   C+   +     CP CR  + V
Sbjct: 7  ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 4e-05
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 16 FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR 66
            C  C + ++E      C H+FC +C+ D   +   CP C T   ++ ++ 
Sbjct: 23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDC--IGTGCPVCYTPAWIQDLKI 72

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

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]

 Score = 35.1 bits (80), Expect = 9e-05
 Identities = 10/41 (24%), Positives = 15/41 (36%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCR 56
          F C I L+ MK+      G  + +S I   +    K     
Sbjct: 9  FRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKS 49

>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 = 34.8 bits (79), Expect = 1e-04
 Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 17 TCGICLDTMKEESS-----TKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIFFP 70
           C  C  T     S       CGH  C+SC+        G CP C T +   + R   F 
Sbjct: 5  GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE 64

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.0 bits (72), Expect = 9e-04
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 1/52 (1%)

Query: 17 TCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI 67
           C I     +    +     +F KS +   ++  G  P     +S+  I  I
Sbjct: 2  LCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI 53

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

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]

 Score = 31.7 bits (71), Expect = 0.002
 Identities = 9/58 (15%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 16 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIFFPQLQ 73
              I  + M+E   T  G  + +  I + ++ +       TR  +   + I    ++
Sbjct: 8  LCGKISFELMREPCITPSGITYDRKDIEEHLQ-RVGHFNPVTRSPLTQEQLIPNLAMK 64

>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 = 31.3 bits (70), Expect = 0.003
 Identities = 10/59 (16%), Positives = 16/59 (27%), Gaps = 18/59 (30%)

Query: 17 TCGICLDTMKEES------------------STKCGHVFCKSCIVDAIRLQGKCPTCRT 57
           C IC + + +                       C H F   CI   ++ +  CP    
Sbjct: 23 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	78
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.72
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.7
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.69
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.69
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.68
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.67
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.63
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.61
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.58
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.57
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.56
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.55
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.45
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.43
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.3
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.78
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.26
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	94.57
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	93.52
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	91.45
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	88.53
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	86.72
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	85.63
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	84.52
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	83.19
d1wfha_	64	Zinc finger A20 and AN1 domains containing protein	82.94
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	82.6
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	81.76
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	80.73

>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=99.72  E-value=1.1e-18  Score=90.74  Aligned_cols=53  Identities=26%  Similarity=0.764  Sum_probs=46.7

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceee
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~   66 (78)
                      +.+.|+||++.+.+|+.++|||+||+.|+.+|++. ...||.||.++...++..
T Consensus        22 ~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhccC
Confidence            45789999999999999999999999999999974 458999999988776543

>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=99.70  E-value=1.6e-18  Score=83.68  Aligned_cols=53  Identities=21%  Similarity=0.320  Sum_probs=48.6

Q ss_pred             cccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceeeec
Q 037842           16 FTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        16 ~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~~   68 (78)
                      +.|+||++.+.+|+.+ .|||+||+.|+.+|+...+.||.||.++..+++.++.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipik   54 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV   54 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECC
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeCC
Confidence            4699999999999987 5999999999999999989999999999999987764

>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=99.69  E-value=2.3e-18  Score=92.05  Aligned_cols=55  Identities=36%  Similarity=0.908  Sum_probs=47.5

Q ss_pred             CcccccccccccccCceecCCCChhhHHhHHHHhhCC---CCcccccccccccceeee
Q 037842           13 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~---~~CP~C~~~~~~~~~~~~   67 (78)
                      ++.+.|+||++.+.+|+.++|||+||..|+.+|+...   ..||.||..+...++...
T Consensus        19 ~~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n   76 (103)
T d1jm7a_          19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (103)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             ccCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcC
Confidence            3558899999999999999999999999999998764   379999999987776544

>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=99.69  E-value=1.1e-17  Score=85.38  Aligned_cols=58  Identities=19%  Similarity=0.347  Sum_probs=50.9

Q ss_pred             CCCcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceeeec
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIF   68 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~~   68 (78)
                      ...+++.|+||++.+.+|+.++|||+||+.|+.+|+.. ...||.|+.++...++..++
T Consensus         4 eiP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~   62 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CCCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccchH
Confidence            35578999999999999999999999999999999976 45799999999887776653

>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=99.69  E-value=1.1e-17  Score=85.66  Aligned_cols=49  Identities=29%  Similarity=0.664  Sum_probs=43.4

Q ss_pred             ccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccc
Q 037842           15 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRS   63 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~   63 (78)
                      ...|+||++.+.+++.++|||.||..|+..|+.. ...||+||..+...+
T Consensus        23 ~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            3569999999999999999999999999999975 467999999987544

>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=1e-17  Score=82.94  Aligned_cols=57  Identities=28%  Similarity=0.584  Sum_probs=46.1

Q ss_pred             cccccccccccccC-c----eecCCCChhhHHhHHHHhhC-CCCcccccccccccceeeeccC
Q 037842           14 VRFTCGICLDTMKE-E----SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRIFFP   70 (78)
Q Consensus        14 ~~~~C~iC~~~~~~-~----~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~~~~   70 (78)
                      ++..|+||++.+.. +    +.++|||.||..|+..|+.. ...||.||+.+..++++...|.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~~~~~~fd   64 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE   64 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEEECCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccccccccCCC
Confidence            46789999987532 2    44589999999999999865 4579999999998888777664

>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=99.67  E-value=1.3e-17  Score=85.57  Aligned_cols=56  Identities=14%  Similarity=0.142  Sum_probs=49.2

Q ss_pred             CCcccccccccccccCceecCCCChhhHHhHHHHhhC-CCCcccccccccccceeee
Q 037842           12 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~~~~~~   67 (78)
                      ..+++.|+||++.+.+|+.++|||+||..|+.+|+.. ...||.|+.++...++..+
T Consensus         4 iP~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN   60 (80)
T d2c2la2           4 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPN   60 (80)
T ss_dssp             CCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEEC
T ss_pred             CCccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccccH
Confidence            4578999999999999999999999999999999975 4579999999987776654

>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=99.63  E-value=1.1e-16  Score=79.79  Aligned_cols=45  Identities=36%  Similarity=0.775  Sum_probs=40.4

Q ss_pred             cccccccccccCce-ecCCCChhhHHhHHHHhhCCCCccccccccc
Q 037842           16 FTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGKCPTCRTRMS   60 (78)
Q Consensus        16 ~~C~iC~~~~~~~~-~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~   60 (78)
                      ..|+||++.+.+++ .++|||.||..|+.+|+..+..||+||.++.
T Consensus         6 d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           6 ERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            46999999998875 4799999999999999999999999998875

>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=99.61  E-value=9.7e-17  Score=77.01  Aligned_cols=47  Identities=26%  Similarity=0.711  Sum_probs=40.3

Q ss_pred             CcccccccccccccCc---eec-CCCChhhHHhHHHHhhCCCCcccccccc
Q 037842           13 EVRFTCGICLDTMKEE---SST-KCGHVFCKSCIVDAIRLQGKCPTCRTRM   59 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~---~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~   59 (78)
                      +++..|+||++.+.+.   ..+ .|||.||..|+.+|++.+..||+||.++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEe
Confidence            4567899999999753   344 6999999999999999999999999875

>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=99.58  E-value=6.9e-17  Score=77.76  Aligned_cols=47  Identities=21%  Similarity=0.569  Sum_probs=40.3

Q ss_pred             cccccccccccccCceecCCCChhhHHhHHHHhhCCCCcccccccccccc
Q 037842           14 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRS   63 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~   63 (78)
                      +.+.|+||++.+.+|+.++|||+||..|+.+|   +..||+||..+....
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            45789999999999999999999999998643   568999999887543

>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=99.57  E-value=6.5e-16  Score=73.27  Aligned_cols=46  Identities=24%  Similarity=0.699  Sum_probs=38.1

Q ss_pred             cccccccccccCc----eecCCCChhhHHhHHHHhhC-CCCcccccccccc
Q 037842           16 FTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRL-QGKCPTCRTRMSV   61 (78)
Q Consensus        16 ~~C~iC~~~~~~~----~~~~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~   61 (78)
                      +.|+||++.+...    ..++|||.||..|+.+|+.. +..||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            4699999988643    33589999999999999986 4579999998864

>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=99.56  E-value=1.5e-16  Score=84.07  Aligned_cols=52  Identities=29%  Similarity=0.779  Sum_probs=44.3

Q ss_pred             CcccccccccccccCceec-CCCChhhHHhHHHHhhCCCCcccccccccccceee
Q 037842           13 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRR   66 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~~~~-~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~   66 (78)
                      .+.+.|+||++.+.+|+.+ +|||+||..|+.+|+.  ..||.||..+...++..
T Consensus        20 ~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~   72 (97)
T d1jm7b_          20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKI   72 (97)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCC
T ss_pred             hhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCcc
Confidence            4568999999999999875 7999999999999985  35999999887666544

>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=99.55  E-value=3.1e-15  Score=79.17  Aligned_cols=57  Identities=16%  Similarity=0.062  Sum_probs=50.1

Q ss_pred             CCCcccccccccccccCceecCCC-ChhhHHhHHHHhhCCCCcccccccccccceeee
Q 037842           11 VGEVRFTCGICLDTMKEESSTKCG-HVFCKSCIVDAIRLQGKCPTCRTRMSVRSIRRI   67 (78)
Q Consensus        11 ~~~~~~~C~iC~~~~~~~~~~~Cg-H~fc~~C~~~~~~~~~~CP~C~~~~~~~~~~~~   67 (78)
                      ...+++.||||.++|.+||+++|| |+||+.||.+|+..+..||.|+.++...++..+
T Consensus        18 ~~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN   75 (98)
T d1wgma_          18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             CCcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcch
Confidence            344689999999999999999876 589999999999988899999999988777654

>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=99.45  E-value=2.8e-14  Score=74.01  Aligned_cols=48  Identities=21%  Similarity=0.465  Sum_probs=39.6

Q ss_pred             ccccccccccccCc------------------eecCCCChhhHHhHHHHhhCCCCccccccccccc
Q 037842           15 RFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQGKCPTCRTRMSVR   62 (78)
Q Consensus        15 ~~~C~iC~~~~~~~------------------~~~~CgH~fc~~C~~~~~~~~~~CP~C~~~~~~~   62 (78)
                      +..|+||++.+.++                  +.++|||.||..||.+|+..+..||+||+++..+
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            34599998876542                  3458999999999999999999999999987654

>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=99.43  E-value=4.1e-14  Score=76.31  Aligned_cols=50  Identities=26%  Similarity=0.583  Sum_probs=39.2

Q ss_pred             CcccccccccccccCc------------------eecCCCChhhHHhHHHHhhCC-----CCccccccccccc
Q 037842           13 EVRFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQ-----GKCPTCRTRMSVR   62 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~------------------~~~~CgH~fc~~C~~~~~~~~-----~~CP~C~~~~~~~   62 (78)
                      ..+..|+||++.+.++                  ..++|||.||..||..|+..+     ..||+||..+..+
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            3456799999987542                  346899999999999999743     3799999887544

>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=99.30  E-value=9.1e-13  Score=63.75  Aligned_cols=50  Identities=18%  Similarity=0.327  Sum_probs=40.3

Q ss_pred             CCcccccccccccccCceecC-----CCChhhHHhHHHHhhC--CCCcccccccccc
Q 037842           12 GEVRFTCGICLDTMKEESSTK-----CGHVFCKSCIVDAIRL--QGKCPTCRTRMSV   61 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~~-----CgH~fc~~C~~~~~~~--~~~CP~C~~~~~~   61 (78)
                      .++...|.||++.+.++...+     |+|.||..|+.+|+..  +..||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            456678999999888776554     4599999999999864  4589999998764

>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=98.78  E-value=1.2e-09  Score=56.56  Aligned_cols=43  Identities=23%  Similarity=0.627  Sum_probs=32.7

Q ss_pred             cccccccccccccC---ceecCCCChhhHHhHHHHhhCC--------CCccccc
Q 037842           14 VRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQ--------GKCPTCR   56 (78)
Q Consensus        14 ~~~~C~iC~~~~~~---~~~~~CgH~fc~~C~~~~~~~~--------~~CP~C~   56 (78)
                      ....|+||++.+..   +..++|||.||..||..|+..+        ..||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            45689999998754   2345899999999999998631        2599854

>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=96.26  E-value=0.003  Score=30.39  Aligned_cols=35  Identities=26%  Similarity=0.740  Sum_probs=28.6

Q ss_pred             cccccccccccccCceecCC----CChhhHHhHHHHhhC
Q 037842           14 VRFTCGICLDTMKEESSTKC----GHVFCKSCIVDAIRL   48 (78)
Q Consensus        14 ~~~~C~iC~~~~~~~~~~~C----gH~fc~~C~~~~~~~   48 (78)
                      ..+.|.+|.+.+++...+.|    +|.||..|-..+++.
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            45789999999999854433    799999999988874

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.57  E-value=0.03  Score=27.55  Aligned_cols=38  Identities=24%  Similarity=0.441  Sum_probs=28.7

Q ss_pred             CcccCCCcccccccccccccCceecC---CCChhhHHhHHHH
Q 037842            7 GAVVVGEVRFTCGICLDTMKEESSTK---CGHVFCKSCIVDA   45 (78)
Q Consensus         7 ~~~~~~~~~~~C~iC~~~~~~~~~~~---CgH~fc~~C~~~~   45 (78)
                      .+.++...+..|.|| +.+.....++   |+.+|+..|+.+.
T Consensus         7 ~~re~v~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_           7 GPREPVVNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCCCCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CcccCCCcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            344456678899999 6666555555   7889999999987

>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=93.52  E-value=0.015  Score=27.77  Aligned_cols=41  Identities=20%  Similarity=0.442  Sum_probs=28.1

Q ss_pred             CCCCCCCcccCCCcccccccccccccCc---ee-cCCCChhhHHhHH
Q 037842            1 VCESRNGAVVVGEVRFTCGICLDTMKEE---SS-TKCGHVFCKSCIV   43 (78)
Q Consensus         1 ~~es~~~~~~~~~~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~   43 (78)
                      |++++..+...  ++..|.+|...|..-   .. -.||++||..|..
T Consensus         1 m~~~~~~p~W~--~~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~   45 (72)
T d1dvpa2           1 MFTADTAPNWA--DGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTA   45 (72)
T ss_dssp             CCCCSCCCCCC--CCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSC
T ss_pred             CCcCCCCCCCC--cCCccccCCCcccCccccccccccCCeeChhhhC
Confidence            45666665443  445799999987642   22 3699999999864

>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=91.45  E-value=0.03  Score=24.63  Aligned_cols=41  Identities=22%  Similarity=0.664  Sum_probs=27.1

Q ss_pred             ccccccccccCceec---CCCChhhHHhHHHHhhCCC----Ccccccc
Q 037842           17 TCGICLDTMKEESST---KCGHVFCKSCIVDAIRLQG----KCPTCRT   57 (78)
Q Consensus        17 ~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~~~----~CP~C~~   57 (78)
                      .|.||...-....++   .|...|+..|+..-+....    .|+.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            578887654433222   6889999999976554322    5888864

>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=88.53  E-value=0.18  Score=23.04  Aligned_cols=41  Identities=29%  Similarity=0.607  Sum_probs=27.9

Q ss_pred             ccccccccccccCceec---CCCChhhHHhHHHHhhCCCCcccc
Q 037842           15 RFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRLQGKCPTC   55 (78)
Q Consensus        15 ~~~C~iC~~~~~~~~~~---~CgH~fc~~C~~~~~~~~~~CP~C   55 (78)
                      ...|--|...+.+....   .|++.||..|=.=.-..--+||-|
T Consensus        15 ~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            45688898888776432   699999999954222223478876

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.72  E-value=0.099  Score=24.15  Aligned_cols=31  Identities=23%  Similarity=0.642  Sum_probs=21.8

Q ss_pred             CcccccccccccccCc---ee-cCCCChhhHHhHH
Q 037842           13 EVRFTCGICLDTMKEE---SS-TKCGHVFCKSCIV   43 (78)
Q Consensus        13 ~~~~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~   43 (78)
                      ++...|.+|...|..-   .. -.||.+||..|..
T Consensus         6 ~~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~   40 (64)
T d1joca1           6 NEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSA   40 (64)
T ss_dssp             GGCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSC
T ss_pred             ccCCcCcCcCCcccCCccccchhhhCCeecccccC
Confidence            3445699998877643   12 3699999999864

>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=85.63  E-value=0.015  Score=26.07  Aligned_cols=40  Identities=20%  Similarity=0.547  Sum_probs=23.4

Q ss_pred             ccccccccccCc---ee-cCCCChhhHHhHHHHhhCCCCccccc
Q 037842           17 TCGICLDTMKEE---SS-TKCGHVFCKSCIVDAIRLQGKCPTCR   56 (78)
Q Consensus        17 ~C~iC~~~~~~~---~~-~~CgH~fc~~C~~~~~~~~~~CP~C~   56 (78)
                      .|.+|...|..-   .. -.||..||..|........+.|..|.
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            367777766532   12 36999999999654333344566663

>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=84.52  E-value=0.85  Score=21.13  Aligned_cols=46  Identities=20%  Similarity=0.456  Sum_probs=29.0

Q ss_pred             CCcccccccccccccCceec---CCCChhhHHhHH----HH-----hhCCCCccccccc
Q 037842           12 GEVRFTCGICLDTMKEESST---KCGHVFCKSCIV----DA-----IRLQGKCPTCRTR   58 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~~~~---~CgH~fc~~C~~----~~-----~~~~~~CP~C~~~   58 (78)
                      ..+...| ||.....+..++   .|.--||..|+.    ..     ....-.||.|+..
T Consensus        13 d~~~~~C-iC~~~~~~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          13 DPNALYC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CTTCCCS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCCcCEE-ECCCccCCCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            4455678 898766554444   577789999972    11     1123579999654

>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=83.19  E-value=1.6  Score=21.33  Aligned_cols=51  Identities=27%  Similarity=0.526  Sum_probs=35.3

Q ss_pred             CCcccccccccccccCc----eec---CCCChhhHHhHHHHhhC-CCCccccccccccc
Q 037842           12 GEVRFTCGICLDTMKEE----SST---KCGHVFCKSCIVDAIRL-QGKCPTCRTRMSVR   62 (78)
Q Consensus        12 ~~~~~~C~iC~~~~~~~----~~~---~CgH~fc~~C~~~~~~~-~~~CP~C~~~~~~~   62 (78)
                      ......|.||-+.+...    ..+   .|+--.|+.|+.--.+. ...||.|+..+...
T Consensus        13 ~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          13 NLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             CCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             hcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhh
Confidence            33456899999976532    223   47777899999754443 55799999887643

>d1wfha_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At2g36320 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At2g36320
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=82.94  E-value=0.68  Score=21.38  Aligned_cols=31  Identities=23%  Similarity=0.501  Sum_probs=22.7

Q ss_pred             cCCCcccccccccccccC-ceecCCCChhhHH
Q 037842           10 VVGEVRFTCGICLDTMKE-ESSTKCGHVFCKS   40 (78)
Q Consensus        10 ~~~~~~~~C~iC~~~~~~-~~~~~CgH~fc~~   40 (78)
                      .......+|..|..-+.. .+.-.||+.||..
T Consensus        10 ~~~~k~~RC~~C~KKl~l~~~~CrCg~~FC~~   41 (64)
T d1wfha_          10 SPPQRPNRCTVCRKRVGLTGFMCRCGTTFCGS   41 (64)
T ss_dssp             CCCSSCCCCTTTCCCCCTTCEECSSSCEECTT
T ss_pred             CCCCCCCcChhhCCCccceeeeccCCCEehhh
Confidence            334556799999987654 4566899999964

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.60  E-value=0.25  Score=22.88  Aligned_cols=28  Identities=29%  Similarity=0.595  Sum_probs=20.3

Q ss_pred             cccccccccccCc---ee-cCCCChhhHHhHH
Q 037842           16 FTCGICLDTMKEE---SS-TKCGHVFCKSCIV   43 (78)
Q Consensus        16 ~~C~iC~~~~~~~---~~-~~CgH~fc~~C~~   43 (78)
                      ..|.+|...|.--   .. -.||.+||..|..
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~   37 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSS   37 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSC
T ss_pred             cccccCCCcccCcccccccccCCCEecccccC
Confidence            4699999877532   12 2699999999863

>d2epqa1 g.37.1.1 (A:380-411) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.76  E-value=0.23  Score=19.38  Aligned_cols=12  Identities=25%  Similarity=0.733  Sum_probs=7.0

Q ss_pred             cccccccccccc
Q 037842           15 RFTCGICLDTMK   26 (78)
Q Consensus        15 ~~~C~iC~~~~~   26 (78)
                      .+.|+||...|.
T Consensus         3 p~~cpic~qrfk   14 (32)
T d2epqa1           3 PYSCPVCGLRFK   14 (32)
T ss_dssp             SSEETTTTEECS
T ss_pred             CcccchHHHHhh
Confidence            355666666554

>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=80.73  E-value=0.33  Score=23.33  Aligned_cols=11  Identities=36%  Similarity=1.150  Sum_probs=10.3

Q ss_pred             hhHHhHHHHhh
Q 037842           37 FCKSCIVDAIR   47 (78)
Q Consensus        37 fc~~C~~~~~~   47 (78)
                      ||+.|+.+|+.
T Consensus        40 FCRNCLskWy~   50 (79)
T d2o35a1          40 FCRNCLSNWYR   50 (79)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999986